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López-Martínez A, Santos-Álvarez JC, Velázquez-Enríquez JM, Ramírez-Hernández AA, Vásquez-Garzón VR, Baltierrez-Hoyos R. lncRNA-mRNA Co-Expression and Regulation Analysis in Lung Fibroblasts from Idiopathic Pulmonary Fibrosis. Noncoding RNA 2024; 10:26. [PMID: 38668384 PMCID: PMC11054336 DOI: 10.3390/ncrna10020026] [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: 03/12/2024] [Revised: 04/05/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease marked by abnormal accumulation of extracellular matrix (ECM) due to dysregulated expression of various RNAs in pulmonary fibroblasts. This study utilized RNA-seq data meta-analysis to explore the regulatory network of hub long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) in IPF fibroblasts. The meta-analysis unveiled 584 differentially expressed mRNAs (DEmRNA) and 75 differentially expressed lncRNAs (DElncRNA) in lung fibroblasts from IPF. Among these, BCL6, EFNB1, EPHB2, FOXO1, FOXO3, GNAI1, IRF4, PIK3R1, and RXRA were identified as hub mRNAs, while AC008708.1, AC091806.1, AL442071.1, FAM111A-DT, and LINC01989 were designated as hub lncRNAs. Functional characterization revealed involvement in TGF-β, PI3K, FOXO, and MAPK signaling pathways. Additionally, this study identified regulatory interactions between sequences of hub mRNAs and lncRNAs. In summary, the findings suggest that AC008708.1, AC091806.1, FAM111A-DT, LINC01989, and AL442071.1 lncRNAs can regulate BCL6, EFNB1, EPHB2, FOXO1, FOXO3, GNAI1, IRF4, PIK3R1, and RXRA mRNAs in fibroblasts bearing IPF and contribute to fibrosis by modulating crucial signaling pathways such as FoxO signaling, chemical carcinogenesis, longevity regulatory pathways, non-small cell lung cancer, and AMPK signaling pathways.
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Affiliation(s)
- Armando López-Martínez
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico; (A.L.-M.); (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (V.R.V.-G.)
| | - Jovito Cesar Santos-Álvarez
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico; (A.L.-M.); (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (V.R.V.-G.)
| | - Juan Manuel Velázquez-Enríquez
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico; (A.L.-M.); (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (V.R.V.-G.)
| | - Alma Aurora Ramírez-Hernández
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico; (A.L.-M.); (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (V.R.V.-G.)
| | - Verónica Rocío Vásquez-Garzón
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico; (A.L.-M.); (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (V.R.V.-G.)
- CONACYT-Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico
| | - Rafael Baltierrez-Hoyos
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico; (A.L.-M.); (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (V.R.V.-G.)
- CONACYT-Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico
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Singh J, Narayan G, Dixit VK. The long intergenic non-coding RNA LINC01140 modulates gastric cancer phenotypes and cancer cell lines aggressiveness. Dig Liver Dis 2024:S1590-8658(24)00307-4. [PMID: 38556409 DOI: 10.1016/j.dld.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/06/2024] [Accepted: 03/09/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND Long-intergenic non-protein coding gene 01140 (LINC01140) a long non-coding RNA is highly expressed in various cancers. However, its biological functions in gastric cancer progression is still unknown. METHOD To elucidate LINC01140 function, 70 GC tumor samples and 30 normal gastric tissues were collected. LINC01140 expression level were determined by qRT-PCR analysis and correlated with different clinico-pathological parameters. Then we tried to see the impact of LINC01140 on gastric cell line aggressiveness by knocking down the target gene and performing cell viability assay, migration assay and invasive capacity of the cell lines along with immunoblotting to check several protein levels. RESULT LINC01140 RNA is found to be positively correlated with FGF9 and significantly up regulated in GC tissues. LINC01140 knockdown inhibited the viability, migratory capacity and invasive capacity of AGS cells. LINC01140 targets miR-140-5p, while miR-140-5p targeted FGF9 to form lncRNA-miRNA-mRNA axis. The affect of miR-140-5p inhibition on gastric cancer cell aggressiveness were opposite to those of LINC01140 or FGF9 knockdown. Additionally, inhibition partially reversed the effects of LINC01140 knockdown on FGF9 protein levels, gastric cancer cell phenotypes. CONCLUSION LINC01140, miR-140-5p and FGF9 form a lncRNA-miRNA-mRNA axis that modulates the gastric cancer phenotypes and in turn affects gastric cancer cell aggressiveness.
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Affiliation(s)
- Juhi Singh
- Department of Gastroenterology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Gopeshwar Narayan
- Department of Molecular and Human Genetics, Banaras Hindu University, Varanasi, 221005, India
| | - Vinod Kumar Dixit
- Department of Gastroenterology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India.
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Donato A, Di Stefano A, Freato N, Bertocchi L, Brun P. Inhibition of Pro-Fibrotic Molecules Expression in Idiopathic Pulmonary Fibrosis-Derived Lung Fibroblasts by Lactose-Modified Hyaluronic Acid Compounds. Polymers (Basel) 2023; 16:138. [PMID: 38201803 PMCID: PMC10780654 DOI: 10.3390/polym16010138] [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: 11/30/2023] [Revised: 12/21/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic inflammatory and fibrotic pathological condition with undefined effective therapies and a poor prognosis, partly due to the lack of specific and effective therapies. Galectin 3 (Gal-3), a pro-fibrotic ß-galactoside binding lectin, was upregulated in the early stages of the pathology, suggesting that it may be considered a marker of active fibrosis. In the present in vitro study, we use Hylach®, a lactose-modified hyaluronic acid able to bind Gal-3, to prevent the activation of lung myofibroblast and the consequent excessive ECM protein cell expression. Primary human pulmonary fibroblasts obtained from normal and IPF subjects activated with TGF-β were used, and changes in cell viability, fibrotic components, and pro-inflammatory mediator expression at both gene and protein levels were analyzed. Hylach compounds with a lactosylation degree of about 10% and 30% (Hylach1 and Hylach 2), administrated to TGF-β-stimulated lung fibroblast cultures, significantly downregulated α-smooth muscle actin (α-SMA) gene expression and decreased collagen type I, collagen type III, elastin, fibronectin gene and protein expression to near baseline values. This anti-fibrotic activity is accompanied by a strong anti-inflammatory effect and by a downregulation of the gene expression of Smad2 for both Hylachs in comparison to the native HA. In conclusion, the Gal-3 binding molecules Hylachs attenuated inflammation and TGF-β-induced over-expression of α-SMA and ECM protein expression by primary human lung fibroblasts, providing a new direction for the treatment of pulmonary fibrotic diseases.
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Affiliation(s)
- Alice Donato
- Histology Unit, Department of Molecular Medicine, University of Padova, 35121 Padova, Italy;
| | - Antonino Di Stefano
- Divisione di Pneumologia e Laboratorio di Citoimmunopatologia Dell’apparato Cardio Respiratorio, Istituti Clinici Scientifici Maugeri, IRCCS, 28010 Veruno, Italy;
| | | | | | - Paola Brun
- Histology Unit, Department of Molecular Medicine, University of Padova, 35121 Padova, Italy;
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Ge Z, Liu H, Ji T, Liu Q, Zhang L, Zhu P, Li L, Zhu L. Long non-coding RNA 00960 promoted the aggressiveness of lung adenocarcinoma via the miR-124a/SphK1 axis. Bioengineered 2022; 13:1276-1287. [PMID: 34738865 PMCID: PMC8805815 DOI: 10.1080/21655979.2021.1996507] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/16/2021] [Indexed: 11/02/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are closely associated with the development of lung adenocarcinoma (LADC). The present study focused on the role of LINC00960 in LADC. miRNA and mRNA expression levels were detected using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Cellular functions were evaluated by MTT, colony formation, and Transwell assays, respectively. LINC00960 Luciferase and RNA pull-down assays were performed to clarify the interaction between miR-124a and LINC00960 or Recombinant Sphingosine Kinase 1 (SphK1). We observed that LINC00960 was overexpressed in LADC tumor tissues and cell lines. LINC00960 knockdown suppressed the proliferation, migration, and invasion of LADC cells. Moreover, LINC00960 sponged miR-124a to inhibit the SphK1/S1P pathway in LADC cells. LINC00960 knockdown markedly reduced the rate of tumor growth. The luciferase reporter assay results demonstrated an interaction between miR-124a and LINC00960 or SphK1. This interaction was confirmed using the RNA pull-down assay. In addition, miR-124a downregulation or SphK1 upregulation reversed the inhibitory effects of LINC00960 knockdown on cellular functions of LADC cells, suggesting that LINC00960 may be a potential therapeutic biomarker for LADC via the miR-124a/SphK1 axis. Accordingly, LINC00960 may be a potential therapeutic biomarker for LADC.
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Affiliation(s)
- Zhipeng Ge
- Weifang Medical University, Weifang, People’s Republic of China
| | - Haibo Liu
- Department of Thoracic Surgery, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong Province, P.R. China
| | - Tao Ji
- Chest Endoscopy Minimally Invasive Area, Shandong Provincial Chest Hospital, Jinan, Shandong Province, China
| | - Qiaoling Liu
- Department of Thoracic Surgery, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong Province, P.R. China
| | - Lulu Zhang
- Research Center of Basic Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Pengchong Zhu
- Department of Orthopaedics, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Liang Li
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Liangming Zhu
- Department of Thoracic Surgery, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong Province, P.R. China
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Huang Y, Yan Q, Yu D, Sun X, Jiang S, Li W, Jia L. Long intergenic non-protein coding RNA 960 regulates cancer cell viability, migration and invasion through modulating miR-146a-5p/interleukin 1 receptor associated kinase 1 axis in pancreatic ductal adenocarcinoma. Bioengineered 2021; 12:369-381. [PMID: 33380238 PMCID: PMC8806237 DOI: 10.1080/21655979.2020.1868742] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 01/18/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are considered as crucial regulatory factors in cancer biology. However, the biological function of long intergenic non-protein coding RNA 960 (LINC00960) in the tumorigenesis of pancreatic ductal adenocarcinoma (PDAC) is still unknown. The goal of this study is to investigate the role of LINC00960 in PDAC. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to examine the expression levels of LINC00960 in PDAC tissues and cell lines. After transfection, the loss-of-function models of LINC00960 or interleukin 1 receptor-associated kinase 1 (IRAK1) were established with BxPC-3 cells and Colo357 cells, and the malignant phenotypes of BxPC-3 cells and Colo357 cells were detected by CCK-8 assay, BrdU assay and Transwell assay, respectively. The interactions among LINC00960, miR-146a-5p and IRAK1 were predicted by bioinformatics analysis, and verified by luciferase reporter assay, RNA immunoprecipitation assay and RNA pull-down assay. The regulatory functions of LINC00960 and miR-146a-5p on IRAK1 were detected by Western blot. We demonstrated that the LINC00960 expression was increased in PDAC tissues and cell lines. Knocking down LINC00960 or IRAK1 could repress the viability, migration, and invasion of BxPC-3 and Colo357 cells. LINC00960 functioned as a molecular sponge for miR-146a-5p, and IRAK1 was verified as a target gene of miR-146a-5p. Additionally, LINC00960 could up-regulate IRAK1 expression via repressing miR-146a-5p, and the oncogenic properties of LINC00960 were partly reversed by miR-146a-5p. Our findings reveal that LINC00960 is a promoter of PDAC progression through regulating miR-146a-5p/IRAK1axis.
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Affiliation(s)
- Yaoxing Huang
- Department of Gastroenterology, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Qingqing Yan
- Department of Gastroenterology, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Danchun Yu
- Department of Gastroenterology, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Xiaojuan Sun
- Department of Gastroenterology, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Shuman Jiang
- Department of Gastroenterology, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Weidong Li
- Department of Gastroenterology, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Lin Jia
- Department of Gastroenterology, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
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Xia R, Geng G, Yu X, Xu Z, Guo J, Liu H, Li N, Li Z, Li Y, Dai X, Luo Q, Jiang J, Mi Y. LINC01140 promotes the progression and tumor immune escape in lung cancer by sponging multiple microRNAs. J Immunother Cancer 2021; 9:jitc-2021-002746. [PMID: 34446576 PMCID: PMC8395365 DOI: 10.1136/jitc-2021-002746] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Long intergenic non-protein coding RNA 1140 (LINC01140), a long non-coding RNA, is highly expressed in various cancers; however, its biological functions in lung cancer (LC) progression and immune escape are still unclear. METHODS Here, to elucidate LINC01140 function, 79 paired LC and paracancerous tissues were collected. LINC01140 expression levels were determined using fluorescence in situ hybridization and qPCR analysis. Cell counting kit-8 (CCK-8) assay and transwell assays were performed. The interaction between microRNAs (miRNAs) and LINC01140 was confirmed using an RNA immunoprecipitation assay. Cytokine-induced killer (CIK) cell phenotypes were analyzed by flow cytometry. Cytokine secretion levels were determined by ELISA. CIK cytotoxicity was assessed by measuring lactate dehydrogenase release. Besides, xenograft tumor mouse models were used to unveil the in vivo function of LINC01140. RESULTS We found that LINC01140 was highly expressed in human LC tissues and cell lines. High LINC01140 levels were associated with poor survival in patients with LC. LINC01140 upregulation promoted the proliferation, migration, and invasion of LC cells through direct interaction with miR-33a-5p and miR-33b-5p, thereby contributing to c-Myc expression and also inhibited cisplatin-induced cell apoptosis. In subcutaneous tumor xenograft mice, LINC01140 knockdown markedly reduced tumor growth and lung metastasis. Additionally, LINC01140 directly repressed miR-377-3 p and miR-155-5 p expression levels, resulting in the upregulation of their common downstream target programmed death-ligand 1 (PD-L1), a crucial target in LC immunotherapy. Notably, we proved that LINC01140 knockdown, along with CIK administration, suppressed the growth of subcutaneous LC xenografts by decreasing PD-L1 expression in severe combined immunodeficient mice. CONCLUSIONS Taken together, LINC01140 overexpression protects c-Myc and PD-L1 mRNA from miRNA-mediated inhibition and contributes to the proliferation, migration, invasion, and immune escape of LC cells. These results provide a theoretical basis that LINC01140 is a promising target for LC treatment.
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Affiliation(s)
- Rongmu Xia
- Department of Medical Oncology, Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University; School of Clinical Medicine, Fujian Medical University, Xiamen 361003, Fujian Province, China.,School of Medicine, Xiamen University, Xiamen 361102, Fujian Province, China
| | - Guojun Geng
- Department of Thoracic Surgery, Xiamen Key Laboratory of Thoracic tumor diagnosis and treatment, Institute of lung cancer, The First Affiliated Hospital of Xiamen University; School of clinical Medicine, Fujian Medical University, Xiamen 361003, Fujian Province, China
| | - Xiuyi Yu
- Department of Thoracic Surgery, Xiamen Key Laboratory of Thoracic tumor diagnosis and treatment, Institute of lung cancer, The First Affiliated Hospital of Xiamen University; School of clinical Medicine, Fujian Medical University, Xiamen 361003, Fujian Province, China
| | - Zhong Xu
- Department of Thoracic Surgery, Xiamen Key Laboratory of Thoracic tumor diagnosis and treatment, Institute of lung cancer, The First Affiliated Hospital of Xiamen University; School of clinical Medicine, Fujian Medical University, Xiamen 361003, Fujian Province, China
| | - Jing Guo
- Department of Medical Oncology, Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University; School of Clinical Medicine, Fujian Medical University, Xiamen 361003, Fujian Province, China
| | - Hongming Liu
- Department of Thoracic Surgery, Xiamen Key Laboratory of Thoracic tumor diagnosis and treatment, Institute of lung cancer, The First Affiliated Hospital of Xiamen University; School of clinical Medicine, Fujian Medical University, Xiamen 361003, Fujian Province, China
| | - Ning Li
- Department of Thoracic Surgery, Xiamen Key Laboratory of Thoracic tumor diagnosis and treatment, Institute of lung cancer, The First Affiliated Hospital of Xiamen University; School of clinical Medicine, Fujian Medical University, Xiamen 361003, Fujian Province, China
| | - Ziyan Li
- Department of Medical Oncology, Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University; School of Clinical Medicine, Fujian Medical University, Xiamen 361003, Fujian Province, China
| | - Yingli Li
- Department of Medical Oncology, Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University; School of Clinical Medicine, Fujian Medical University, Xiamen 361003, Fujian Province, China
| | - Xiaofang Dai
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Qicong Luo
- Department of Medical Oncology, Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University; School of Clinical Medicine, Fujian Medical University, Xiamen 361003, Fujian Province, China
| | - Jie Jiang
- Department of Thoracic Surgery, Xiamen Key Laboratory of Thoracic tumor diagnosis and treatment, Institute of lung cancer, The First Affiliated Hospital of Xiamen University; School of clinical Medicine, Fujian Medical University, Xiamen 361003, Fujian Province, China
| | - Yanjun Mi
- Department of Medical Oncology, Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University; School of Clinical Medicine, Fujian Medical University, Xiamen 361003, Fujian Province, China
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Zhan H, Sun X, Wang X, Gao Q, Yang M, Liu H, Zheng J, Gong X, Feng S, Chang X, Sun Y. LncRNA MEG3 Involved in NiO NPs-Induced Pulmonary Fibrosis via Regulating TGF-β1-Mediated PI3K/AKT Pathway. Toxicol Sci 2021; 182:120-131. [PMID: 33895847 DOI: 10.1093/toxsci/kfab047] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Long noncoding RNA maternally expressed gene 3 (MEG3) involves in fibrotic diseases, but its role in nickel oxide nanoparticles (NiO NPs)-induced pulmonary fibrosis remains unclear. The present study aimed to explore the relationships among MEG3, transforming growth factor-β1 (TGF-β1) and phosphoinositide 3-kinase (PI3K)/AKT pathway in NiO NPs-induced pulmonary fibrosis. Wistar rats were intratracheally instilled with NiO NPs twice a week for 9 weeks, and human lung adenocarcinoma epithelial cells (A549 cells) were exposed to NiO NPs for 24 h. The pathological alterations and increased hydroxyproline indicated that NiO NPs caused pulmonary fibrosis in rats. The up-regulated type I collagen (Col-I) suggested that NiO NPs-induced collagen deposition in A549 cells. Meanwhile, NiO NPs could significantly down-regulate MEG3, up-regulate TGF-β1 and activate PI3K/AKT signaling pathway both in vivo and in vitro. However, we found that the PI3K/AKT pathway activated by NiO NPs could be suppressed by 10 μM TGF-β1 inhibitor (SB431542) in A549 cells. The protein markers (Col-I, Fibronectin, and alpha-smooth muscle actin) of collagen deposition up-regulated by NiO NPs were reduced by 10 μM PI3K inhibitor (LY294002). Furthermore, we further found that overexpressed MEG3 inhibited the expression of TGF-β1, resulting in the inactivation of PI3K/AKT pathway and the reduction of collagen formation. In summary, our results validated that MEG3 could arrest NiO NPs-induced pulmonary fibrosis via inhibiting TGF-β1-mediated PI3K/AKT pathway.
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Affiliation(s)
- Haibing Zhan
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xingchang Sun
- Institute of Occupational Diseases, Gansu Baoshihua Hospital, Lanzhou 730000, China
| | - Xiaoxia Wang
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qing Gao
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Mengmeng Yang
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Han Liu
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Jinfa Zheng
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xuefeng Gong
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Sanwei Feng
- Institute of Occupational Diseases, Gansu Baoshihua Hospital, Lanzhou 730000, China
| | - Xuhong Chang
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Yingbiao Sun
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
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Sun S, Huang C, Leng D, Chen C, Zhang T, Lei KC, Zhang XD. Gene fusion of IL7 involved in the regulation of idiopathic pulmonary fibrosis. Ther Adv Respir Dis 2021; 15:1753466621995045. [PMID: 33878985 PMCID: PMC8064517 DOI: 10.1177/1753466621995045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Idiopathic pulmonary fibrosis (IPF) is a rare form of immune-mediated interstitial lung disease characterized by progressive pulmonary fibrosis and scarring. The pathogenesis of IPF is still unclear. Gene fusion events exist universally during transcription and show alternated patterns in a variety of lung diseases. Therefore, the comprehension of the function of gene fusion in IPF might shed light on IPF pathogenesis research and facilitate treatment development. Methods: In this study, we included 91 transcriptome datasets from the National Center for Biotechnology Information (NCBI), including 52 IPF patients and 39 healthy controls. We detected fusion events in these datasets and probed gene fusion-associated differential gene expression and functional pathways. To obtain robust results, we corrected the batch bias across different projects. Results: We identified 1550 gene fusion events in all transcriptomes and studied the possible impacts of IL7 = AC083837.1 gene fusion. The two genes locate adjacently in chromosome 8 and share the same promoters. Their fusion is associated with differential expression of 282 genes enriched in six Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and 35 functional gene sets. Gene ontology (GO) enrichment analysis shows that IL7 = AC083837.1 gene fusion is associated with the enrichment of 187 gene sets. The co-expression network of interleukin-7 (IL7) indicates that decreased IL7 expression is associated with many pathways that regulate IPF progress. Conclusion: Based on the results, we conclude that IL7 = AC083837.1 gene fusion might exacerbate fibrosis in IPF via enhancing activities of natural killer cell-mediated cytotoxicity, skin cell apoptosis, and vessel angiogenesis, the interaction of which contributes to the development of fibrosis and the deterioration of respiratory function of IPF patients. Our work unveils the possible roles of gene fusion in regulating IPF and demonstrates that gene fusion investigation is a valid approach in probing immunologic mechanisms and searching potential therapeutic targets for treating IPF. The reviews of this paper are available via the supplemental material section.
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Affiliation(s)
- Shixue Sun
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Chen Huang
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Dongliang Leng
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Chang Chen
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Teng Zhang
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Kuan Cheok Lei
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Xiaohua Douglas Zhang
- CRDA, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau SAR, China
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Mu L, Ding K, Tu R, Yang W. Identification of 4 immune cells and a 5-lncRNA risk signature with prognosis for early-stage lung adenocarcinoma. J Transl Med 2021; 19:127. [PMID: 33771173 PMCID: PMC8004399 DOI: 10.1186/s12967-021-02800-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/19/2021] [Indexed: 12/27/2022] Open
Abstract
Background Lung cancer is the most common cancer and cause of cancer‐related mortality worldwide, increasing evidence indicated that there was a significant correlation between tumors and the long non‐coding RNAs (lncRNAs), as well as tumor immune infiltration, but their role in early lung adenocarcinoma (LUAD) are still unclear. Methods Gene expression data and corresponding clinical data of early-stage LUAD patients were downloaded from GEO and TCGA databases. 24 kinds of tumor-infiltrating immune cells were analyzed by quantity analysis and univariate cox regression analysis, we divided patients into two subgroups using consensus clustering, recognized the differentially expressed genes (DEGs) in the subgroups, then, established lncRNA risk signature by least absolute shrinkage and selection operator (LASSO) regression. Results A total of 718 patients were enrolled in this study, including 246 from GSE31210 dataset, 127 from GSE50081 dataset and 345 from TCGA-LUAD. We identified that Th2 cells, TFH, NK CD56dim cells and Mast cells were prognosis-related(p < 0.05), then established a 5-lncRNA risk signature (risk score = 0.374600616* LINC00857 + 0.173825706* LINC01116 + (− 0.021398903)* DRAIC + (− 0.113658256)* LINC01140 + (− 0.008403702)* XIST), and draw a nomogram showed that the signature had a well prediction accuracy and discrimination. Conclusions We identified 4 immune infiltrating cells related to the prognosis of early-stage LUAD, and established a novel 5 immune-related lncRNA signature for predicting patients’ prognosis.
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Affiliation(s)
- Lan Mu
- Department of Thyroid Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410000, Hunan, China
| | - Ke Ding
- Department of Urology, Xiangya Hospital, Central South University, Changsha, 410000, Hunan, China
| | - Ranran Tu
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, 410000, Hunan, China
| | - Wei Yang
- Department of Respiratory Medicine, National Key Clinical Specialty, Xiangya Hospital, Central South University, Changsha, 410000, Hunan, China.
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10
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El-Desoky MM, Hewidy AA, Fouda AM, Hisham FA. Telomeric repeat-containing ribonucleic acid (TERRA) expression in patients with idiopathic pulmonary fibrosis. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-021-00141-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Idiopathic pulmonary fibrosis (IPF) represents a chronic disease with a progressive course. It is characterized by excessive lung scarring that ultimately contributes to irreversible lung function reduction. Interestingly, a type of long non-coding RNA termed as telomeric repeat-containing RNA (TERRA) is linked to fibrosis pathophysiology, including IPF. In this study, the expression profile of TERRA was investigated in IPF patients on radiological diagnosis [unusual interstitial pattern (UIP) in high-resolution computed tomography (HRCT)] to evaluate whether it could be employed as a reliable diagnostic biomarker.
Results
TERRA expression level was significantly higher in IPF patients over healthy controls. The expression level was significantly inversely correlated with the percentage of forced vital capacity predicted (FVC% predicted). By contrast, it was significantly directly correlated with HRCT reticular extent score.
Conclusion
TERRA expression is an essential biomarker in peripheral blood of IPF patients, providing a valuable non-invasive tool for IPF diagnosis. Moreover, TERRA expression is strongly correlated with UIP in HRCT reticular extent score.
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11
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Mao X, Chen S, Li G. Identification of a ten-long noncoding RNA signature for predicting the survival and immune status of patients with bladder urothelial carcinoma based on the GEO database: a superior machine learning model. Aging (Albany NY) 2021; 13:6957-6981. [PMID: 33621953 PMCID: PMC7993680 DOI: 10.18632/aging.202553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 12/18/2020] [Indexed: 02/05/2023]
Abstract
Bladder urothelial carcinoma (BLCA) is recognized to be immunogenic and tumorigenic. This study identified a novel long noncoding RNA (lncRNA) signature for predicting survival for patients with BLCA. A univariate Cox regression model and the random survival forest-variable hunting (RSF-VH) algorithm were employed to achieve variable selection. Ten lncRNAs (LOC105375787, CYTOR, URB1-AS1, C21orf91-OT1, CASC15, LOC101928433, FLJ45139, LINC00960, HOTAIR and TTTY19) with the highest prognostic values were identified to establish the prognostic model. The nomogram integrating the signature and clinical factors showed high concordance index values of 0.94, 0.7 and 0.90 in the three datasets, and the calibration curves showed concordance between the predicted and observed 3- and 5-year survival rates. The risk score based on the 10-lncRNA signature accurately distinguished high- and low-risk BLCA patients with different disease-specific survival(DSS) or overall survival(OS) outcomes, which were stratified according to clinical factors, including T stage and tumour grade. Gene set enrichment analysis identified BLCA-specific biological pathways and enriched functional categories, such as the cell cycle, DNA repair and immune system. Furthermore, the increased infiltration of immune cells in the high-risk group indicated that lncRNA-related inflammation may reduce the survival of BLCA patients.
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Affiliation(s)
- XuDong Mao
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - ShiHan Chen
- Department of Endocrinology and Metabolism, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - GongHui Li
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
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12
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Role of various imbalances centered on alveolar epithelial cell/fibroblast apoptosis imbalance in the pathogenesis of idiopathic pulmonary fibrosis. Chin Med J (Engl) 2021; 134:261-274. [PMID: 33522725 PMCID: PMC7846426 DOI: 10.1097/cm9.0000000000001288] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
There have been recent extensive studies and rapid advancement on the pathogenesis underlying idiopathic pulmonary fibrosis (IPF), and intricate pathogenesis of IPF has been suggested. The purpose of this study was to clarify the logical relationship between these mechanisms. An extensive search was undertaken of the PubMed using the following keywords: “etiology,” “pathogenesis,” “alveolar epithelial cell (AEC),” “fibroblast,” “lymphocyte,” “macrophage,” “epigenomics,” “histone,” acetylation,” “methylation,” “endoplasmic reticulum stress,” “mitochondrial dysfunction,” “telomerase,” “proteases,” “plasminogen,” “epithelial-mesenchymal transition,” “oxidative stress,” “inflammation,” “apoptosis,” and “idiopathic pulmonary fibrosis.” This search covered relevant research articles published up to April 30, 2020. Original articles, reviews, and other articles were searched and reviewed for content; 240 highly relevant studies were obtained after screening. IPF is likely the result of complex interactions between environmental, genetic, and epigenetic factors: environmental exposures affect epigenetic marks; epigenetic processes translate environmental exposures into the regulation of chromatin; epigenetic processes shape gene expression profiles; in turn, an individual's genetic background determines epigenetic marks; finally, these genetic and epigenetic factors act in concert to dysregulate gene expression in IPF lung tissue. The pathogenesis of IPF involves various imbalances including endoplasmic reticulum, telomere length homeostasis, mitochondrial dysfunction, oxidant/antioxidant imbalance, Th1/Th2 imbalance, M1–M2 polarization of macrophages, protease/antiprotease imbalance, and plasminogen activation/inhibition imbalance. These affect each other, promote each other, and ultimately promote AEC/fibroblast apoptosis imbalance directly or indirectly. Excessive AEC apoptosis and impaired apoptosis of fibroblasts contribute to fibrosis. IPF is likely the result of complex interactions between environmental, genetic, and epigenetic factors. The pathogenesis of IPF involves various imbalances centered on AEC/fibroblast apoptosis imbalance.
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13
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Bartczak K, Białas AJ, Kotecki MJ, Górski P, Piotrowski WJ. More than a Genetic Code: Epigenetics of Lung Fibrosis. Mol Diagn Ther 2020; 24:665-681. [PMID: 32926347 PMCID: PMC7677145 DOI: 10.1007/s40291-020-00490-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
At the end of the last century, genetic studies reported that genetic information is not transmitted solely by DNA, but is also transmitted by other mechanisms, named as epigenetics. The well-described epigenetic mechanisms include DNA methylation, biochemical modifications of histones, and microRNAs. The role of altered epigenetics in the biology of various fibrotic diseases is well-established, and recent advances demonstrate its importance in the pathogenesis of pulmonary fibrosis-predominantly referring to idiopathic pulmonary fibrosis, the most lethal of the interstitial lung diseases. The deficiency in effective medications suggests an urgent need to better understand the underlying pathobiology. This review summarizes the current knowledge concerning epigenetic changes in pulmonary fibrosis and associations of these changes with several cellular pathways of known significance in its pathogenesis. It also designates the most promising substances for further research that may bring us closer to new therapeutic options.
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Affiliation(s)
- Krystian Bartczak
- Department of Pneumology and Allergology, The Medical University of Lodz, Kopcińskiego 22, 90-153, Lodz, Poland.
| | - Adam J Białas
- Department of Pathobiology of Respiratory Diseases, The Medical University of Lodz, Lodz, Poland
| | - Mateusz J Kotecki
- Department of Pneumology and Allergology, The Medical University of Lodz, Kopcińskiego 22, 90-153, Lodz, Poland
| | - Paweł Górski
- Department of Pneumology and Allergology, The Medical University of Lodz, Kopcińskiego 22, 90-153, Lodz, Poland
| | - Wojciech J Piotrowski
- Department of Pneumology and Allergology, The Medical University of Lodz, Kopcińskiego 22, 90-153, Lodz, Poland
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14
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He L, Zhao X, He L. LINC01140 Alleviates the Oxidized Low-Density Lipoprotein-Induced Inflammatory Response in Macrophages via Suppressing miR-23b. Inflammation 2020; 43:66-73. [PMID: 31748847 DOI: 10.1007/s10753-019-01094-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Our previous study has demonstrated that miR-23b enhances oxidized low-density lipoprotein (oxLDL)-induced inflammatory response of macrophages through the A20/NF-κB signaling pathway, thus contributing to atherosclerosis. This study aims to further investigate the upstream regulators of miR-23b in mediating oxLDL-induced inflammatory response. Human monocyte cell line THP1 was induced to differentiate into macrophages followed by the oxLDL stimulation of inflammatory response. The expression of miR-23b, LINC01140, and p53 mRNA was detected by quantitative PCR. The combination of miR-23b and LINC01140 was confirmed by luciferase reporter assay and RNA immunoprecipitation. The binding of p53 and LINC01140 promoter was determined by luciferase reporter assay. The level of inflammatory cytokines, including MCP-1, TNF-α, and IL-1β, was assessed by enzyme-linked immunosorbent assay. LINC01140 was downregulated, while p53 and miR-23b were upregulated in oxLDL-induced inflammatory response of macrophages. Overexpression of LINC01140 reduced NF-κB activity by reducing miR-23b and increasing A20. The transcription of LINC01140 was inhibited by binding of p53 and the LINC01140 promoter region. Knockdown of p53 significantly reduced NF-κB activity and level of inflammatory cytokines by promoting LINC01140 expression. Our findings demonstrated that LINC01140 acts as an anti-inflammatory factor through negatively regulating miR-23/A20 axis. In addition, p53 is identified as a transcriptional repressor of LINC01140.
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Affiliation(s)
- Liping He
- Department of Cardiology, People's Hospital of Inner Mongolia Autonomous region, No. 20 of Zhaowuda Road, Hohhot city, 010020, Inner Mongolia, China
| | - Xingsheng Zhao
- Department of Cardiology, People's Hospital of Inner Mongolia Autonomous region, No. 20 of Zhaowuda Road, Hohhot city, 010020, Inner Mongolia, China.
| | - Leping He
- The Center of Computer Information, People's Hospital of Inner Mongolia Autonomous region, Hohhot, 010020, Inner Mongolia, China
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15
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Effect of Total Flavonoids of Oxytropis falcata Bunge on the Expression of p-JAK1-and p-STAT1-Related Proteins in Idiopathic Pulmonary Fibrosis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2020; 2020:2407239. [PMID: 32908556 PMCID: PMC7474768 DOI: 10.1155/2020/2407239] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/07/2020] [Indexed: 12/11/2022]
Abstract
Objective The study aimed to explore the effect of total flavonoids of Oxytropis falcata Bunge (FOFB) on the expression of p-JAK1/p-STAT1 and SOCS3 proteins in idiopathic pulmonary fibrosis (IPF). Methods Rats model with IPF was established by one-off intratracheal injection of bleomycin (BLM, 5 mg/kg). After 14 days, the same volume of low dose (100 mg/kg), medium dose (200 mg/kg), and high dose (400 mg/kg) of FOFB and prednisolone acetate (20 mg/kg) as positive control drugs, as well as normal saline, were orally administered to rats once a day for 28 consecutive days. Subsequently, the degree of fibrosis and alveolitis in rat lung tissue was observed, respectively, by HE and Masson staining. Further more, observing the ultrastructure of lung tissue by transmission electron microscopy (TEM), the detection of JAK/STAT pathway related indicators including p-JAK1, p-STAT1, and SOCS3 with immunohistochemistry and SOCS3 with real-time PCR (RT-PCR) was performed. Results Compared with the BLM group, the degree of alveolitis and fibrosis improved significantly, and the expression of p-JAK1 and p-STAT1 decreased; conversely, the expression of SOCS3 increased in the treatment group. Conclusion IPF causes high expression of p-JAK1 and p-STAT1 and low expression of SOCS3. FOFB can play a role in the treatment of IPF via upregulating SOCS3 and downregulating p-JAK1 and p-STAT1.
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16
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Ugai K, Matsuda S, Mikami H, Shimada A, Misawa T, Nakamura H, Tatsumi K, Hatano M, Murayama T, Kasuya Y. Inhibition of the SET8 Pathway Ameliorates Lung Fibrosis Even Through Fibroblast Dedifferentiation. Front Mol Biosci 2020; 7:192. [PMID: 32850975 PMCID: PMC7419601 DOI: 10.3389/fmolb.2020.00192] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/20/2020] [Indexed: 12/11/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal lung disease of unknown etiopathogenesis. The activation of extracellular matrix (ECM)-producing myofibroblasts plays a key role in fibrotic tissue remodeling. The dedifferentiation of myofibroblasts has attracted considerable attention as a promising target for the development of effective therapeutic interventions against IPF. Here, we screened a small library of epigenetics-related inhibitors using dedifferentiation assay of lung myofibroblasts prepared from a patient at the terminal stages of IPF and chose UNC0379. The inhibition of SET8, a histone H4 lysine 20 (H4K20) monomethyltransferase, by UNC0379 markedly suppressed the expression of α-smooth muscle actin (SMA) and ED-A-fibronectin in myofibroblasts. In IPF myofibroblasts, SET8 expression and H4K20 monomethylation (H4K20me1) levels, which were significantly higher than those in normal human lung fibroblasts, were reduced upon treatment with UNC0379. Hence, the changes in the expression of the two fibrotic markers clearly correlated with those in SET8 expression and H4K20me1 level. Furthermore, in a mouse model of bleomycin (BLM)-induced lung fibrosis, the intratracheal administration of UNC0379 at an early fibrotic stage markedly ameliorated the histopathological changes associated with collagen deposition in the lungs. However, treatment with UNC0379 did not significantly affect the number of proinflammatory cells or cytokine production in the bronchoalveolar lavage fluids from mice treated with BLM. In the BLM-injured lung, SET8 was predominantly localized to the nuclei of α-SMA-positive cells, which colocalized with H4K20me1. Taken together, our results indicate that the inhibition of SET8 resulting in myofibroblast dedifferentiation may partly mitigate lung fibrosis without affecting the inflammatory responses.
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Affiliation(s)
- Keita Ugai
- Department of Biomedical Science, Graduate School of Medicine, Chiba University, Chiba, Japan.,Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba, Japan
| | - Shuichi Matsuda
- Department of Biomedical Science, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hideki Mikami
- Department of Biomedical Science, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ayako Shimada
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomoko Misawa
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroyuki Nakamura
- Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba, Japan
| | - Koichiro Tatsumi
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masahiko Hatano
- Department of Biomedical Science, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Toshihiko Murayama
- Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba, Japan
| | - Yoshitoshi Kasuya
- Department of Biomedical Science, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Biochemistry and Molecular Pharmacology, Graduate School of Medicine, Chiba University, Chiba, Japan
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17
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Tait S, Baldassarre A, Masotti A, Calura E, Martini P, Varì R, Scazzocchio B, Gessani S, Del Cornò M. Integrated Transcriptome Analysis of Human Visceral Adipocytes Unravels Dysregulated microRNA-Long Non-coding RNA-mRNA Networks in Obesity and Colorectal Cancer. Front Oncol 2020; 10:1089. [PMID: 32714872 PMCID: PMC7351520 DOI: 10.3389/fonc.2020.01089] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/01/2020] [Indexed: 12/13/2022] Open
Abstract
Obesity, and the obesity-associated inflammation, represents a major risk factor for the development of chronic diseases, including colorectal cancer (CRC). Dysfunctional visceral adipose tissue (AT) is now recognized as key player in obesity-associated morbidities, although the biological processes underpinning the increased CRC risk in obese subjects are still a matter of debate. Recent findings have pointed to specific alterations in the expression pattern of non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), and long non-coding RNAs (lncRNAs), as mechanisms underlying dysfunctional adipocyte phenotype in obesity. Nevertheless, the regulatory networks and interrelated processes relevant for adipocyte functions, that may contribute to a tumor-promoting microenvironment, are poorly known yet. To this end, based on RNA sequencing data, we identified lncRNAs and miRNAs, which are aberrantly expressed in visceral adipocytes from obese and CRC subjects, as compared to healthy lean control, and validated a panel of modulated ncRNAs by real-time qPCR. Furthermore, by combining the differentially expressed lncRNA and miRNA profiles with the transcriptome analysis dataset of adipocytes from lean and obese subjects affected or not by CRC, lncRNA-miRNA-mRNA adipocyte networks were defined for obese and CRC subjects. This analysis highlighted several ncRNAs modulation that are common to both obesity and CRC or unique of each disorder. Functional enrichment analysis of network-related mRNA targets, revealed dysregulated pathways associated with metabolic processes, lipid and energy metabolism, inflammation, and cancer. Moreover, adipocytes from obese subjects affected by CRC exhibited a higher complexity, in terms of number of genes, lncRNAs, miRNAs, and biological processes found to be dysregulated, providing evidence that the transcriptional and post-transcriptional program of adipocytes from CRC patients is deeply affected by obesity. Overall, this study adds further evidence for a central role of visceral adipocyte dysfunctions in the obesity-cancer relationship.
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Affiliation(s)
- Sabrina Tait
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
| | | | - Andrea Masotti
- Bambino Gesù Children's Hospital-IRCCS, Research Laboratories, Rome, Italy
| | - Enrica Calura
- Department of Biology, University of Padua, Padua, Italy
| | - Paolo Martini
- Department of Biology, University of Padua, Padua, Italy
| | - Rosaria Varì
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
| | | | - Sandra Gessani
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Manuela Del Cornò
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
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18
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Wang Y, Xiao H, Zhao F, Li H, Gao R, Yan B, Ren J, Yang J. Decrypting the crosstalk of noncoding RNAs in the progression of IPF. Mol Biol Rep 2020; 47:3169-3179. [PMID: 32180083 DOI: 10.1007/s11033-020-05368-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 02/29/2020] [Indexed: 12/16/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is an agnogenic, rare, and lethal disease, with high mortality and poor prognosis and a median survival time as short as 3 to 5 years after diagnosis. No effective therapeutic drugs are still not available not only in clinical practice, but also in preclinical phases. To better and deeper understand pulmonary fibrosis will provide more effective strategies for therapy. Mounting evidence suggests that noncoding RNAs (ncRNAs) and their interactions may contribute to lung fibrosis; however, the mechanisms underlying their roles are largely unknown. In this review, we systematically summarized the recent advances regarding the crucial roles of long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) and crosstalk among them in the development of IPF. The perspective for related genes was well highlighted. In summary, ncRNA and their interactions play a key regulatory part in the progression of IPF and are bound to provide us with new diagnostic and therapeutic targets.
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Affiliation(s)
- Yujuan Wang
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Han Xiao
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Fenglian Zhao
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Han Li
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Rong Gao
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Bingdi Yan
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Jin Ren
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Junling Yang
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China.
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19
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Xin Y, Zhang W, Mao C, Li J, Liu X, Zhao J, Xue J, Li J, Ren Y. LncRNA LINC01140 Inhibits Glioma Cell Migration and Invasion via Modulation of miR-199a-3p/ZHX1 Axis. Onco Targets Ther 2020; 13:1833-1844. [PMID: 32184618 PMCID: PMC7053821 DOI: 10.2147/ott.s230895] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/23/2020] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Glioma is an aggressive tumor from the nervous system, which causes more than 70% of primary malignant brain tumors. Considering its severe malignancy, there is an urgent need to investigate more practical markers to understand the pathogenesis of glioma, and potential treatment methods for glioma patients. In the paper, we are focused on examining the roles of LINC01140, miR-199a-3p, and ZHX1 in the progression of gliomas, as well as their inner associations and modulation mechanisms. METHODS qRT-PCR was employed to examine the expression levels of LINC01140 and miR-199a-3p. We measured the expressions of ZHX1 via qRT-PCR and Western blotting. CCK8 assays, migration assays, and invasion assays were carried out to determine the cell viabilities and abilities of migration and invasion. We also conducted in vivo tumor growth experiments to investigate the roles of LINC01140 in glioma developments. RESULTS The expressions of LINC01140 were promoted in glioma. Silencing LINC01140 could inhibit glioma cell viabilities, migration, and invasion. In our experiments, miR-199a-3p was inhibited in glioma. LINC01140 negatively regulated the expressions of miR-199a-3p in glioma. MiR-199a-3p could target ZHX1 to inhibit its expression in glioma cells. CONCLUSION LINC01140 could promote glioma developments by modulating the miR-199a-3p/ZHX1 axis.
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Affiliation(s)
- Yanchao Xin
- Department of Neurosurgery, People’s Hospital of Jiaozuo City, Jiaozuo City, Henan Province454002, People’s Republic of China
| | - Wuzhong Zhang
- Department of Neurosurgery, People’s Hospital of Jiaozuo City, Jiaozuo City, Henan Province454002, People’s Republic of China
| | - Chongchong Mao
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University in Henan Province, Zhengzhou City, Henan Province450052, People’s Republic of China
| | - Jianxin Li
- Department of Neurosurgery, People’s Hospital of Jiaozuo City, Jiaozuo City, Henan Province454002, People’s Republic of China
| | - Xianzhi Liu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University in Henan Province, Zhengzhou City, Henan Province450052, People’s Republic of China
| | - Junbo Zhao
- Department of Neurosurgery, People’s Hospital of Jiaozuo City, Jiaozuo City, Henan Province454002, People’s Republic of China
| | - Junfeng Xue
- Department of Neurosurgery, People’s Hospital of Jiaozuo City, Jiaozuo City, Henan Province454002, People’s Republic of China
| | - Junqing Li
- Department of Neurosurgery, People’s Hospital of Jiaozuo City, Jiaozuo City, Henan Province454002, People’s Republic of China
| | - Yonglu Ren
- Department of Neurosurgery, People’s Hospital of Jiaozuo City, Jiaozuo City, Henan Province454002, People’s Republic of China
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Idiopathic Pulmonary Fibrosis: Pathogenesis and the Emerging Role of Long Non-Coding RNAs. Int J Mol Sci 2020; 21:ijms21020524. [PMID: 31947693 PMCID: PMC7013390 DOI: 10.3390/ijms21020524] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 12/16/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive chronic disease characterized by excessing scarring of the lungs leading to irreversible decline in lung function. The aetiology and pathogenesis of the disease are still unclear, although lung fibroblast and epithelial cell activation, as well as the secretion of fibrotic and inflammatory mediators, have been strongly associated with the development and progression of IPF. Significantly, long non-coding RNAs (lncRNAs) are emerging as modulators of multiple biological processes, although their function and mechanism of action in IPF is poorly understood. LncRNAs have been shown to be important regulators of several diseases and their aberrant expression has been linked to the pathophysiology of fibrosis including IPF. This review will provide an overview of this emerging role of lncRNAs in the development of IPF.
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21
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Hadjicharalambous MR, Lindsay MA. Long Non-Coding RNAs and the Innate Immune Response. Noncoding RNA 2019; 5:ncrna5020034. [PMID: 31010202 PMCID: PMC6630897 DOI: 10.3390/ncrna5020034] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/15/2019] [Accepted: 04/17/2019] [Indexed: 12/12/2022] Open
Abstract
Innate immunity provides the initial defence against infection and it is now clear that long non-coding RNAs (lncRNAs) are important regulators of this response. Following activation of the innate response, we commonly see rapid induction of these lncRNAs and this is often mediated via the pro-inflammatory transcription factor, nuclear factor-κB (NF-κB). Knockdown studies have shown that lncRNAs tend to act in trans to regulate the expression of multiple inflammatory mediators and other responses. Mechanistically, many lncRNAs have demonstrated acting through heterogeneous nuclear ribonucleoproteins, complexes that are implicated chromatin re-modelling, transcription process and translation. In addition, these lncRNAs have also been shown to interact with multiple other proteins involved in the regulation of chromatin re-modelling, as well as those proteins involved in intracellular immune signalling, which include NF-κB. In this review, we will describe the evidence that supports this emerging role of lncRNA in the innate immune response.
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Affiliation(s)
| | - Mark A Lindsay
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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