151
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Zhang H, Zhao J, Shao P. Long noncoding RNA MIAT2 alleviates lipopolysaccharide-induced inflammatory damage in WI-38 cells by sponging microRNA-15. J Cell Physiol 2019; 235:3690-3697. [PMID: 31566734 DOI: 10.1002/jcp.29263] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/03/2019] [Indexed: 12/19/2022]
Abstract
Neonatal pneumonia is a high neonatal mortality disease. We studied the function and mechanism of long noncoding RNA myocardial infarction-associated transcript 2 (lncRNA MIAT2) on lipopolysaccharide (LPS)-induced inflammation in WI-38 cells. Cell Counting Kit-8 and apoptosis assay were respectively used to detect the functions of LPS, MIAT2, and microRNA-15 (miR-15) on viability and apoptosis. MIAT2 and miR-15 expressions were changed by cell transfection. Moreover, reverse transcription-quantitative polymerase chain reaction (RT-qPCR), western blot, and enzyme-linked immunosorbent assay were used to detect the expressions of interleukin (IL)-6 and monocyte chemoattractant protein-1 (MCP-1). The levels of Bax, cleaved-caspase-3, and cell pathways-related proteins were tested by western blot. Besides, the levels of miR-15 and MIAT2 were tested by RT-qPCR. We found that LPS declined cell viability and heightened apoptosis and levels of Bax, cleaved-caspase-3, IL-6, and MCP-1. MIAT2 was negatively regulated by LPS and it alleviated LPS-induced damage. Furthermore, MIAT2 reversely regulated miR-15 and miR-15 mimic could reverse the effects of MIAT2. Finally, MIAT2 restrained the p38MAPK and NF-κB pathways by downregulating miR-15. In conclusion, MIAT2 alleviated LPS-induced inflammation damage in WI-38 cells by sponging miR-15 via p38MAPK and NF-κB pathways.
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Affiliation(s)
- Hong Zhang
- Department of Pediatrics, Liaocheng People's Hospital, Liaocheng, Shandong, China
| | - Jing Zhao
- Department of Pediatrics, Liaocheng People's Hospital, Liaocheng, Shandong, China
| | - Peng Shao
- Department of Pediatrics, Liaocheng People's Hospital, Liaocheng, Shandong, China
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152
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Wu H, Lai CF, Chang-Panesso M, Humphreys BD. Proximal Tubule Translational Profiling during Kidney Fibrosis Reveals Proinflammatory and Long Noncoding RNA Expression Patterns with Sexual Dimorphism. J Am Soc Nephrol 2019; 31:23-38. [PMID: 31537650 DOI: 10.1681/asn.2019040337] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/01/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Proximal tubule injury can initiate CKD, with progression rates that are approximately 50% faster in males versus females. The precise transcriptional changes in this nephron segment during fibrosis and potential differences between sexes remain undefined. METHODS We generated mice with proximal tubule-specific expression of an L10a ribosomal subunit protein fused with enhanced green fluorescent protein. We performed unilateral ureteral obstruction surgery on four male and three female mice to induce inflammation and fibrosis, collected proximal tubule-specific and bulk cortex mRNA at day 5 or 10, and sequenced samples to a depth of 30 million reads. We applied computational methods to identify sex-biased and shared molecular responses to fibrotic injury, including up- and downregulated long noncoding RNAs (lncRNAs) and transcriptional regulators, and used in situ hybridization to validate critical genes and pathways. RESULTS We identified >17,000 genes in each proximal tubule group, including 145 G-protein-coupled receptors. More than 700 transcripts were differentially expressed in the proximal tubule of males versus females. The >4000 genes displaying altered expression during fibrosis were enriched for proinflammatory and profibrotic pathways. Our identification of nearly 150 differentially expressed proximal tubule lncRNAs during fibrosis suggests they may have unanticipated regulatory roles. Network analysis prioritized proinflammatory and profibrotic transcription factors such as Irf1, Nfkb1, and Stat3 as drivers of fibrosis progression. CONCLUSIONS This comprehensive transcriptomic map of the proximal tubule revealed sexually dimorphic gene expression that may reflect sex-related disparities in CKD, proinflammatory gene modules, and previously unappreciated proximal tubule-specific bidirectional lncRNA regulation.
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Affiliation(s)
- Haojia Wu
- Division of Nephrology.,Departments of Medicine and
| | - Chun-Fu Lai
- Division of Nephrology.,Departments of Medicine and.,Renal Division, Department of Internal Medicine, National Taiwan University Hospital, Taipai, Taiwan
| | | | - Benjamin D Humphreys
- Division of Nephrology, .,Departments of Medicine and.,Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, Missouri; and
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153
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Targeting the TR4 nuclear receptor-mediated lncTASR/AXL signaling with tretinoin increases the sunitinib sensitivity to better suppress the RCC progression. Oncogene 2019; 39:530-545. [PMID: 31501521 PMCID: PMC6962095 DOI: 10.1038/s41388-019-0962-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 05/13/2019] [Indexed: 12/16/2022]
Abstract
Renal cell carcinoma (RCC) is one of the most lethal urological tumors. Using sunitinib to improve the survival has become the first-line therapy for metastatic RCC patients. However, the occurrence of sunitinib resistance in the clinical application has curtailed its efficacy. Here we found TR4 nuclear receptor might alter the sunitinib resistance to RCC via altering the TR4/lncTASR/AXL signaling. Mechanism dissection revealed that TR4 could modulate lncTASR (ENST00000600671.1) expression via transcriptional regulation, which might then increase AXL protein expression via enhancing the stability of AXL mRNA to increase the sunitinib resistance in RCC. Human clinical surveys also linked the expression of TR4, lncTASR, and AXL to the RCC survival, and results from multiple RCC cell lines revealed that targeting this newly identified TR4-mediated signaling with small molecules, including tretinoin, metformin, or TR4-shRNAs, all led to increase the sunitinib sensitivity to better suppress the RCC progression, and our preclinical study using the in vivo mouse model further proved tretinoin had a better synergistic effect to increase sunitinib sensitivity to suppress RCC progression. Future successful clinical trials may help in the development of a novel therapy to better suppress the RCC progression.
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154
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Fukuda M, Nishida S, Kakei Y, Shimada Y, Fujiwara T. Genome-Wide Analysis of Long Intergenic Noncoding RNAs Responding to Low-Nutrient Conditions in Arabidopsis thaliana: Possible Involvement of Trans-Acting siRNA3 in Response to Low Nitrogen. PLANT & CELL PHYSIOLOGY 2019; 60:1961-1973. [PMID: 30892644 DOI: 10.1093/pcp/pcz048] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/07/2019] [Indexed: 05/07/2023]
Abstract
Long intergenic noncoding RNAs (lincRNAs) play critical roles in transcriptional and post-transcriptional regulation of gene expression in a wide variety of organisms. Thousands of lincRNAs have been identified in plant genomes, although their functions remain mostly uncharacterized. Here, we report a genome-wide survey of lincRNAs involved in the response to low-nutrient conditions in Arabidopsis thaliana. We used RNA sequencing data derived from A. thaliana roots exposed to low levels of 12 different nutrients. Using bioinformatics approaches, 60 differentially expressed lincRNAs were identified that were significantly upregulated or downregulated under deficiency of at least one nutrient. To clarify their roles in nutrient response, correlations of expression patterns between lincRNAs and reference genes were examined across the 13 conditions (12 low-nutrient conditions and control). This analysis allowed us to identify lincRNA-RNA pairs with highly positive or negative correlations. In addition, calculating interaction energies of those pairs showed lincRNAs that may act as regulatory interactors; e.g. small interfering RNAs (siRNAs). Among them, trans-acting siRNA3 (TAS3), which is known to promote lateral root development by producing siRNA against Auxin response factor 2, 3, and 4, was revealed as a nitrogen (N)-responsive lincRNA. Furthermore, nitrate transporter 2 was identified as a potential target of TAS3-derived siRNA, suggesting that TAS3 participates in multiple pathways by regulating N transport and root development under low-N conditions. This study provides the first resource for candidate lincRNAs involved in multiple nutrient responses in plants.
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Affiliation(s)
- Makiha Fukuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Japan
| | - Sho Nishida
- Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-hiroshima, Japan
| | - Yusuke Kakei
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Institute of Vegetable and Floriculture Science, NARO, Tsu, Japan
| | - Yukihisa Shimada
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Toru Fujiwara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Japan
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155
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Huang D, Wei Y, Zhu J, Wang F. Long non-coding RNA SNHG1 functions as a competitive endogenous RNA to regulate PDCD4 expression by sponging miR-195-5p in hepatocellular carcinoma. Gene 2019; 714:143994. [DOI: 10.1016/j.gene.2019.143994] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 02/06/2023]
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156
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Xu J, Hu J, Xu H, Zhou H, Liu Z, Zhou Y, Liu R, Zhang W. Long Non-coding RNA Expression Profiling in Biopsy to Identify Renal Allograft at Risk of Chronic Damage and Future Graft Loss. Appl Biochem Biotechnol 2019; 190:660-673. [PMID: 31422559 DOI: 10.1007/s12010-019-03082-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/05/2019] [Indexed: 02/05/2023]
Abstract
The loss of allograft from chronic damage is still the major risk that renal transplant recipients face today. Biomarkers for early detection of chronic damage are needed to improve the long-term graft survival. This study aimed to identify long non-coding RNA (lncRNA) biomarkers associated with chronic damage and graft loss after renal transplantation. Gene Expression Omnibus (GEO) datasets including GSE57387 (n = 101), GSE21374 (n = 282), and GSE25902 (n = 24) from three high-quality studies were analyzed. By repurposing the publicly available array-based data coupled with Affymetrix Human Exon 1.0 ST and Human U133 Plus 2.0 arrays, we obtained expression profiles of 11323 and 3383 lncRNAs in biopsies after renal transplantation, respectively. The logistic regression model and Cox regression model were applied to identify lncRNAs associated with chronic damage and graft survival. High AC093673.5 expression was identified as significantly associated with the three endpoints including chronic damage, progressive chronic histological damage, and graft failure across these three datasets. A six-lncRNA signature was created to predict renal allograft at risk of chronic damage with a high predictive ability (AUC = 0.94). Gene set enrichment analysis (GSEA) indicated that our lncRNA signature was related with allograft rejection and immunity. Our study highlights the importance of lncRNAs in chronic graft damage and allograft loss, supporting their potential role as prognosis biomarkers.
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Affiliation(s)
- Jing Xu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Jinglei Hu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Heng Xu
- Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Zhaoqian Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, Changsha, 410078, People's Republic of China
| | - Yong Zhou
- Department of Orthopaedics, The Third Xiangya Hospital, Central South University, 138 Tongzipo Road, Changsha, Hunan, People's Republic of China.
| | - Rong Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China. .,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, Changsha, 410078, People's Republic of China. .,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China.
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China. .,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, Changsha, 410078, People's Republic of China. .,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China.
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157
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Lin Y, Lu Y, Li X. Biological characteristics of exosomes and genetically engineered exosomes for the targeted delivery of therapeutic agents. J Drug Target 2019; 28:129-141. [PMID: 31280623 DOI: 10.1080/1061186x.2019.1641508] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A primary focus of pharmacology is the accurate transport of drugs from the peripheral veins and their delivery to specific tissues and organs. Exosomes are nanoscale extracellular vesicles with comparatively enhanced circulation stability, biocompatibility, physicochemical stability and bio-barrier permeation ability, as well as reduced toxicity. Therefore, they are considered a superior drug delivery platform. Core ligands and homing peptides fuse with transmembrane proteins on the exosome surface. Genetically engineered exosomes target specific tissues or organs and agents such as siRNA, miRNA and chemotherapeutics can be loaded into exosomes to improve the regulation of target tissues and organs. Here, we review exosome biogenesis, release, uptake and isolation. We also summarise the current applications of genetically engineered exosomes for tumours, and neurological, cardiovascular and liver diseases.
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Affiliation(s)
- Yan Lin
- The First Clinical Medical College, Lanzhou University, Lanzhou, People's Republic of China
| | - Yaqiong Lu
- Gansu Provincial Cancer Hospital, Gansu Provincial Academic Institute for Medical Research, Lanzhou, People's Republic of China
| | - Xun Li
- The First Clinical Medical College, Lanzhou University, Lanzhou, People's Republic of China.,The Fifth Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, People's Republic of China.,Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, Lanzhou, People's Republic of China.,Hepatopancreatobiliary Surgery Institute of Gansu Province, Medical College Cancer Center of Lanzhou, Lanzhou, People's Republic of China
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158
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Kölling M, Haddad G, Wegmann U, Kistler A, Bosakova A, Seeger H, Hübel K, Haller H, Mueller T, Wüthrich RP, Lorenzen JM. Circular RNAs in Urine of Kidney Transplant Patients with Acute T Cell-Mediated Allograft Rejection. Clin Chem 2019; 65:1287-1294. [PMID: 31371281 DOI: 10.1373/clinchem.2019.305854] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/01/2019] [Indexed: 01/01/2023]
Abstract
BACKGROUND Circular RNAs (circRNAs) have recently been described as novel noncoding regulators of gene expression. They are detectable in the blood of patients with acute kidney injury. We tested whether circRNAs were present in urine and could serve as new predictors of outcome in renal transplant patients with acute rejection. METHODS A global circRNA expression analysis using RNA from urine of patients with acute T cell-mediated renal allograft rejection and control transplant patients was performed. Dysregulated circRNAs were confirmed in a cohort of 62 patients with acute rejection, 10 patients after successful antirejection therapy, 18 control transplant patients without rejection, and 13 stable transplant patients with urinary tract infection. RESULTS A global screen revealed several circRNAs to be altered in urine of patients with acute rejection. Concentrations of 2 circRNAs including hsa_circ_0001334 and hsa_circ_0071475 were significantly increased. These were validated in the whole cohort of patients. hsa_circ_0001334 was upregulated in patients with acute rejection compared with controls. Concentrations of hsa_circ_0001334 normalized in patients with acute rejection following successful antirejection therapy. hsa_circ_0001334 was associated with higher decline in glomerular filtration rate 1 year after transplantation. CONCLUSIONS CircRNA concentrations are significantly dysregulated in patients with acute rejection at subclinical time points. Urinary hsa_circ_0001334 is a novel biomarker of acute kidney rejection, identifying patients with acute rejection and predicting loss of kidney function.
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Affiliation(s)
- Malte Kölling
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland;
| | - George Haddad
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - Urs Wegmann
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | | | - Andrea Bosakova
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - Harald Seeger
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - Kerstin Hübel
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - Hermann Haller
- Division of Nephrology and Hypertension, Hanover Medical School, Hanover, Germany
| | - Thomas Mueller
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - Rudolf P Wüthrich
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - Johan M Lorenzen
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland;
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159
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Si Y, Yang Z, Ge Q, Yu L, Yao M, Sun X, Ren Z, Ding C. Long non-coding RNA Malat1 activated autophagy, hence promoting cell proliferation and inhibiting apoptosis by sponging miR-101 in colorectal cancer. Cell Mol Biol Lett 2019; 24:50. [PMID: 31372165 PMCID: PMC6660674 DOI: 10.1186/s11658-019-0175-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 07/16/2019] [Indexed: 01/17/2023] Open
Abstract
Background Long non-coding RNA Malat1 has been widely identified as an oncogene which shows a significant relationship with tumorigenesis in colorectal cancer (CRC). Nonetheless, whether Malat1 participates in the autophagy of colorectal cancer remains unclear. Materials and methods First, the expression level of Malat1 in 96 pairs of colorectal cancer tissues and four cell lines was detected by qRT-PCR. Subsequently, the autophagy activity in colorectal cancer tissues and cell lines was detected by western blot. Furthermore, the CCK-8 assay and flow cytometry (FCM) were performed to detect the role of autophagy activated by Malat1 in colorectal cancer cell lines. Results In this study, significantly increased Malat1 expression and autophagy activity were found in colorectal cancer tissues compared with the adjacent normal tissues. Also, the Malat1 level was positively correlated with the expression of LC3-II mRNA in vivo. Moreover, autophagy activation and cell proliferation were significantly facilitated by Malat1 in colorectal cancer cells, while apoptosis decreased. Above all, the inhibition of autophagy by 3-MA not only relieved the Malat1-induced cell proliferation but also promoted the Malat1-induced cell apoptosis. In addition, Malat1 was found to act as an endogenous sponge by directly binding to miR-101 to reduce miR-101. Furthermore, the suppressive effects of miR-101 on the autophagy, proliferation, and apoptosis of CRC were abolished by Malat1. Conclusion Long non-coding RNA Malat1 activated autophagy and promoted cell proliferation, yet inhibited apoptosis by sponging miR-101 in colorectal cancer cells.
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Affiliation(s)
- Yaoran Si
- 1Department of Gastroenterology, Huaihe Hospital, Henan University, Kaifeng, 475000 Henan China
| | - Zhaoguo Yang
- Department of General Surgery, Kaifeng Central Hospital, Kaifeng, Henan China
| | - Quanxing Ge
- 1Department of Gastroenterology, Huaihe Hospital, Henan University, Kaifeng, 475000 Henan China
| | - Lingbing Yu
- 1Department of Gastroenterology, Huaihe Hospital, Henan University, Kaifeng, 475000 Henan China
| | - Meiying Yao
- 1Department of Gastroenterology, Huaihe Hospital, Henan University, Kaifeng, 475000 Henan China
| | - Xinfang Sun
- 1Department of Gastroenterology, Huaihe Hospital, Henan University, Kaifeng, 475000 Henan China
| | - Zheng Ren
- 1Department of Gastroenterology, Huaihe Hospital, Henan University, Kaifeng, 475000 Henan China
| | - Chunsheng Ding
- 1Department of Gastroenterology, Huaihe Hospital, Henan University, Kaifeng, 475000 Henan China
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160
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Li CM, Li M, Ye ZC, Huang JY, Li Y, Yao ZY, Peng H, Lou TQ. Circular RNA expression profiles in cisplatin-induced acute kidney injury in mice. Epigenomics 2019; 11:1191-1207. [PMID: 31339054 DOI: 10.2217/epi-2018-0167] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Aim: This study was carried out to identify the expression profile and role of circRNAs in cisplatin-induced acute kidney injury (AKI). Materials & methods: In this study, an AKI model was established in cisplatin-treated mice, and the expression of circRNAs was profiled by next-generation sequencing. The differential expression levels of selected circRNAs were determined by quantitative real-time polymerase chain reaction. Bioinformatics analysis was conducted to predict the functions. Results: In total, 368 circRNAs were detected to be differentially expressed in response to cisplatin treatment. Bioinformatics analysis indicated that the parental genes of the differentially expressed circRNAs were predominantly implicated in the cell and cell part, cellular process and cancer pathways. Conclusion: CircRNAs might be differentially expressed in AKI, which are potentially involved in pathophysiology of cisplatin-induced nephrotoxicity.
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Affiliation(s)
- Can-Ming Li
- Department of Nephrology, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, PR China
| | - Ming Li
- Department of Nephrology, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, PR China
| | - Zeng-Chun Ye
- Department of Nephrology, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, PR China
| | - Jia-Yan Huang
- Department of Nephrology, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, PR China
| | - Yin Li
- Department of Nephrology, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, PR China
| | - Zi-Ying Yao
- Department of Nephrology, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, PR China
| | - Hui Peng
- Department of Nephrology, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, PR China
| | - Tan-Qi Lou
- Department of Nephrology, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, PR China
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161
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Rong J, Xu J, Liu Q, Wu Y, Guo H, Mu T, Zhou H, Chi H. Upregulation of long noncoding RNA RP4 exacerbates hypoxia injury in cardiomyocytes through regulating miR-939/Bnip3/Wnt/β-catenin pathway. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:3013-3020. [PMID: 31321998 DOI: 10.1080/21691401.2019.1640232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jingfeng Rong
- Department of Medicine Cardiovascular, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan, China
| | - Jijie Xu
- Institute of Cardiovascular Research, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qian Liu
- Department of Cardiovascular, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yaoyao Wu
- Department of Cardio-Thoracic Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Honglin Guo
- Department of Cardiovascular, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ting Mu
- Department of Cardiovascular, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hua Zhou
- Department of Cardiovascular, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hao Chi
- Department of Cardio-Thoracic Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
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162
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Brandenburger T, Salgado Somoza A, Devaux Y, Lorenzen JM. Noncoding RNAs in acute kidney injury. Kidney Int 2019; 94:870-881. [PMID: 30348304 DOI: 10.1016/j.kint.2018.06.033] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/30/2018] [Accepted: 06/11/2018] [Indexed: 02/09/2023]
Abstract
Acute kidney injury (AKI) is an important health issue concerning ∼50% of patients treated in intensive care units. AKI mainly occurs after sepsis, acute ischemia, nephrotoxicity, or hypoxia and leads to severe damage of the kidney and to an increased risk of mortality. The diagnosis of AKI is currently based on creatinine urea levels and diuresis. Yet, novel markers may improve the accuracy of this diagnosis at an early stage of the disease, thereby allowing early prevention and therapy, ultimately leading to a reduction in the need for renal replacement therapy and decreased mortality. Non-protein-coding RNAs or noncoding RNAs are central players in development and disease. They are important regulatory molecules that allow a fine-tuning of gene expression and protein synthesis. This regulation is necessary to maintain homeostasis, and its dysregulation is often associated with disease development. Noncoding RNAs are present in the kidney and in body fluids and their expression is modulated during AKI. This review article assembles the current knowledge of the role of noncoding RNAs, including microRNAs, long noncoding RNAs and circular RNAs, in the pathogenesis of AKI. Their potential as biomarkers and therapeutic targets as well as the challenges to translate research findings to clinical application are discussed. Although microRNAs have entered clinical testing, preclinical and clinical trials are needed before long noncoding RNAs and circular RNAs may be considered as useful biomarkers or therapeutic targets of AKI.
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Affiliation(s)
- Timo Brandenburger
- Department of Anesthesiology, University Hospital Duesseldorf, Duesseldorf, Germany.
| | - Antonio Salgado Somoza
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Johan M Lorenzen
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
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163
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Yang Z, Jiang S, Shang J, Jiang Y, Dai Y, Xu B, Yu Y, Liang Z, Yang Y. LncRNA: Shedding light on mechanisms and opportunities in fibrosis and aging. Ageing Res Rev 2019; 52:17-31. [PMID: 30954650 DOI: 10.1016/j.arr.2019.04.001] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/24/2019] [Accepted: 04/01/2019] [Indexed: 02/07/2023]
Abstract
Fibrosis is universally observed in multiple aging-related diseases and progressions and is characterized by excess accumulation of the extracellular matrix. Fibrosis occurs in various human organs and eventually results in organ failure. Noncoding RNAs (ncRNAs) have emerged as essential regulators of cellular signaling and relevant human diseases. In particular, the enigmatic class of long noncoding RNAs (lncRNAs) is a kind of noncoding RNA that is longer than 200 nucleotides and does not possess protein coding ability. LncRNAs have been identified to exert both promotive and inhibitory effects on the multifaceted processes of fibrosis. A growing body of studies has revealed that lncRNAs are involved in fibrosis in various organs, including the liver, heart, lung, and kidney. As lncRNAs have been increasingly identified, they have become promising targets for anti-fibrosis therapies. This review systematically highlights the recent advances regarding the roles of lncRNAs in fibrosis and sheds light on the use of lncRNAs as a potential treatment for fibrosis.
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164
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Zaiou M. Circular RNAs in hypertension: challenges and clinical promise. Hypertens Res 2019; 42:1653-1663. [PMID: 31239534 DOI: 10.1038/s41440-019-0294-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/03/2019] [Accepted: 05/29/2019] [Indexed: 12/14/2022]
Abstract
Hypertension (HT), or high blood pressure (BP), is a chronic disease that is common among populations worldwide. The occurrence of HT is one of the leading causes of cardiovascular morbidity and mortality in adults. Although multiple studies have stressed the multifactorial and multigenic nature of HT, uncertainties about its etiology persist, and current diagnostic biomarkers can explain only a small part of the phenotypic variance of BP. Hence, the search for novel biomarkers that enable early disease prevention and guided therapy is warranted. Regulatory circRNAs have emerged as the newest player in HT-related gene networks and hold promise for improving the accuracy of diagnosis. These RNAs are genome products that are formed through back-splicing of specific regions of pre-mRNAs. Evidence suggests that these RNA species are involved in various metabolic diseases. Recent studies have revealed that aberrant expression of circRNAs is relevant to the occurrence and development of HT. Accordingly, circRNAs are proposed as a new generation of predictive biomarkers and potential therapeutic targets for different forms of HT, including pulmonary hypertension and preeclampsia. This paper presents an overview of the findings from current research focusing on the emerging role of circRNAs in the pathogenesis of hypertension. Furthermore, some of the challenges encountered by circRNA studies are highlighted, and perspectives are provided on the future of research in this area.
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Affiliation(s)
- Mohamed Zaiou
- University of Lorraine, Department of Biochemistry and Molecular Biology, 7 Avenue de la Foret de Haye, BP 90170, 54505, Vandoeuvre les Nancy Cedex, France.
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165
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Saghafi T, Taheri RA, Parkkila S, Emameh RZ. Phytochemicals as Modulators of Long Non-Coding RNAs and Inhibitors of Cancer-Related Carbonic Anhydrases. Int J Mol Sci 2019; 20:E2939. [PMID: 31208095 PMCID: PMC6627131 DOI: 10.3390/ijms20122939] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 05/29/2019] [Accepted: 05/30/2019] [Indexed: 01/17/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are classified as a group of transcripts which regulate various biological processes, such as RNA processing, epigenetic control, and signaling pathways. According to recent studies, lncRNAs are dysregulated in cancer and play an important role in cancer incidence and spreading. There is also an association between lncRNAs and the overexpression of some tumor-associated proteins, including carbonic anhydrases II, IX, and XII (CA II, CA IX, and CA XII). Therefore, not only CA inhibition, but also lncRNA modulation, could represent an attractive strategy for cancer prevention and therapy. Experimental studies have suggested that herbal compounds regulate the expression of many lncRNAs involved in cancer, such as HOTAIR (HOX transcript antisense RNA), H19, MALAT1 (metastasis-associated lung adenocarcinoma transcript 1), PCGEM1 (Prostate cancer gene expression marker 1), PVT1, etc. These plant-derived drugs or phytochemicals include resveratrol, curcumin, genistein, quercetin, epigallocatechin-3-galate, camptothcin, and 3,3'-diindolylmethane. More comprehensive information about lncRNA modulation via phytochemicals would be helpful for the administration of new herbal derivatives in cancer therapy. In this review, we describe the state-of-the-art and potential of phytochemicals as modulators of lncRNAs in different types of cancers.
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Affiliation(s)
- Tayebeh Saghafi
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), 14965/161, Tehran, Iran.
| | - Ramezan Ali Taheri
- Nanobiotechnology Research Center, Baqiyatallah University of Medical Sciences, P.O.Box 14965/161 Tehran, Iran.
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland.
- Fimlab Laboratories Ltd. and Tampere University Hospital, FI-33520 Tampere, Finland.
| | - Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), 14965/161, Tehran, Iran.
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166
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Kong Y, Lu Z, Liu P, Liu Y, Wang F, Liang EY, Hou FF, Liang M. Long Noncoding RNA: Genomics and Relevance to Physiology. Compr Physiol 2019; 9:933-946. [PMID: 31187897 DOI: 10.1002/cphy.c180032] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The mammalian cell expresses thousands of long noncoding RNAs (lncRNAs) that are longer than 200 nucleotides but do not encode any protein. lncRNAs can change the expression of protein-coding genes through both cis and trans mechanisms, including imprinting and other types of transcriptional regulation, and posttranscriptional regulation including serving as molecular sponges. Deep sequencing, coupled with analysis of sequence characteristics, is the primary method used to identify lncRNAs. Physiological roles of specific lncRNAs can be examined using genetic targeting or knockdown with modified oligonucleotides. Identification of nucleic acids or proteins with which an lncRNA interacts is essential for understanding the molecular mechanism underlying its physiological role. lncRNAs have been reported to contribute to the regulation of physiological functions and disease development in several organ systems, including the cardiovascular, renal, muscular, endocrine, digestive, nervous, respiratory, and reproductive systems. The physiological role of the majority of lncRNAs, many of which are species and tissue specific, remains to be determined. © 2019 American Physiological Society. Compr Physiol 9:933-946, 2019.
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Affiliation(s)
- Yiwei Kong
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Zeyuan Lu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Pengyuan Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Sir Run Run Shaw Hospital, Institute of Translational Medicine, Zhejiang University, Zhejiang, China
| | - Yong Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Feng Wang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Eugene Y Liang
- Center for Advancing Population Science, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Fan Fan Hou
- National Clinical Research Center for Kidney Disease, State Key Laboratory of Organ Failure Research, Guangzhou Regenerative Medicine and Health - Guangdong Laboratory, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mingyu Liang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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167
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Thompson RD, Baisden JT, Zhang Q. NMR characterization of RNA small molecule interactions. Methods 2019; 167:66-77. [PMID: 31128236 DOI: 10.1016/j.ymeth.2019.05.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 05/17/2019] [Accepted: 05/17/2019] [Indexed: 01/25/2023] Open
Abstract
Exciting discoveries of naturally occurring ligand-sensing and disease-linked noncoding RNAs have promoted significant interests in understanding RNA-small molecule interactions. NMR spectroscopy is a powerful tool for characterizing intermolecular interactions. In this review, we describe protocols and approaches for applying NMR spectroscopy to investigate interactions between RNA and small molecules. We review protocols for RNA sample preparation, methods for identifying RNA-binding small molecules, approaches for mapping RNA-small molecule interactions, determining complex structures, and characterizing binding kinetics. We hope this review will provide a guideline to streamline NMR applications in studying RNA-small molecule interactions, facilitating both basic mechanistic understandings of RNA functions and translational efforts in developing RNA-targeted therapeutics.
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Affiliation(s)
- Rhese D Thompson
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jared T Baisden
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Qi Zhang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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168
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Zhou J, Li Y, Liu X, Long Y, Chen J. LncRNA-Regulated Autophagy and its Potential Role in Drug-Induced Liver Injury. Ann Hepatol 2019; 17:355-363. [PMID: 29735795 DOI: 10.5604/01.3001.0011.7381] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
INTRODUCTION AND AIM Autophagy and its regulated pathways participate in many important cellular physiology and pathological processes involving protein aggregates, damaged mitochondria, excessive peroxisomes, ribosomes, and invading pathogens. This study aimed to review recently published studies and further describe the long noncoding RNA (lncRNA)-regulated autophagy during drug-induced liver injury (DILI). MATERIAL AND METHODS DILI, autophagy, autophagy-related genes (ATGs), and lncRNA were used as key words to search published studies from PubMed, Google Scholar, and Web of Science. All related studies were reviewed and analyzed. RESULTS Many studies explicitly indicated that DILI and its progression to acute liver failure were causatively linked to endoplasmic reticulum stress and subsequently induced autophagy, which protect hepatocytes during DILI. LncRNA, as a noncoding RNA, influences the regulation of the expression of ATGs to manipulate autophagy. CONCLUSIONS This review described the recent findings on autophagy and its possible lncRNA-miRNA-associated pathways, thereby providing new insights for further studies on the pathogenesis of DILI.
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Affiliation(s)
- Juan Zhou
- Liver Diseases Center, Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - Yi Li
- Department of Infectious Diseases, The affiliated Zhuzhou hospital Xiangya medical college, Central South University, Zhuzhou, Hunan, P.R. China
| | - XinYu Liu
- Liver Diseases Center, Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - Yunzhu Long
- Department of Infectious Diseases, The affiliated Zhuzhou hospital Xiangya medical college, Central South University, Zhuzhou, Hunan, P.R. China
| | - Jun Chen
- Liver Diseases Center, Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
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169
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Wen L, Zhang Z, Peng R, Zhang L, Liu H, Peng H, Sun Y. Whole transcriptome analysis of diabetic nephropathy in the db/db mouse model of type 2 diabetes. J Cell Biochem 2019; 120:17520-17533. [PMID: 31106482 DOI: 10.1002/jcb.29016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 04/15/2019] [Accepted: 04/18/2019] [Indexed: 12/13/2022]
Abstract
Whole-transcriptome analysis using RNA sequencing (RNA-seq) affords broader insights about gene expression regulatory networks in diabetic nephropathy (DN). To better explore the molecular basis of DN, kidney tissue from db/db DN model mice and control mice were submitted to RNA-seq analysis. Thousands of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) were found to be significantly differentially expressed in the DN group relative to the control group. To research the regulatory mechanism of these lncRNAs and mRNAs, the integrated co-expression networks were constructed for 322 mRNAs and 27 lncRNAs that revealed significantly correlated expression patterns in DN. The potential roles of these co-expressed mRNAs were classified by Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses. The co-expression networks involved 27 lncRNAs interacting with 38 key mRNAs related to metabolic processes, including ND4/4L, Ndufa2/5, Ndufb4/7, Ndufs3, Uqcrc1, Aco2, Alad, Alas1, Alpl, Atp5j2, Coq5, Coq6, Cth, and CytB, all of which are highly related to encoding subunits of the mitochondrial complexes. Thus, mitochondrial dysfunction could result in renal function decline in DN. Seven dysregulated lncRNAs and nine dysregulated mRNAs in the DN model were confirmed by quantitative real-time polymerase chain reaction. The lncRNA-mRNA co-expression network provides novel evidence to support the contention that metabolic changes are associated with metabolic reprogramming in the kidneys, and that these changes play a critical role during the progression of DN.
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Affiliation(s)
- Li Wen
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China.,Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zheng Zhang
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China
| | - Rui Peng
- Department of Bioinformatics, Chongqing Medical University, Chongqing, China
| | - Luyu Zhang
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China
| | - Handeng Liu
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China
| | - Huimin Peng
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China
| | - Yan Sun
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China
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170
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Takata M, Pachera E, Frank-Bertoncelj M, Kozlova A, Jüngel A, Whitfield ML, Assassi S, Calcagni M, de Vries-Bouwstra J, Huizinga TW, Kurreeman F, Kania G, Distler O. OTUD6B-AS1 Might Be a Novel Regulator of Apoptosis in Systemic Sclerosis. Front Immunol 2019; 10:1100. [PMID: 31156645 PMCID: PMC6533854 DOI: 10.3389/fimmu.2019.01100] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/30/2019] [Indexed: 12/19/2022] Open
Abstract
Antisense long non-coding RNAs (AS lncRNAs) have increasingly been recognized as important regulators of gene expression and they have been found to play key roles in several diseases. However, very little is known about the role of AS lncRNAs in fibrotic diseases such as systemic sclerosis (SSc). Our recent screening experiments by RNA sequencing showed that ovarian tumor domain containing 6B antisense RNA1 (OTUD6B-AS1) and its sense gene OTUD6B were significantly downregulated in SSc skin biopsies. Therefore, we aimed to identify key regulators of OTUD6B-AS1 and to analyze the functional relevance of OTUD6B-AS1 in SSc. OTUD6B-AS1 and OTUD6B expression in SSc and healthy control (HC) dermal fibroblasts (Fb) after stimulation with transforming growth factor-β (TGFβ), Interleukin (IL)-4, IL-13, and platelet-derived growth factor (PDGF) was analyzed by qPCR. To identify the functional role of OTUD6B-AS1, dermal Fb or human pulmonary artery smooth muscle cells (HPASMC) were transfected with a locked nucleic acid antisense oligonucleotide (ASO) targeting OTUD6B-AS1. Proliferation was measured by BrdU and real-time proliferation assay. Apoptosis was measured by Caspase 3/7 assay and Western blot for cleaved caspase 3. While no difference was recorded at the basal level between HC and SSc dermal Fb, the expression of OTUD6B-AS1 and OTUD6B was significantly downregulated in both SSc and HC dermal Fb after PDGF stimulation in a time-dependent manner. Only mild and inconsistent effects were observed with TGFβ, IL-4, and IL-13. OTUD6B-AS1 knockdown in Fb and HPASMC did not affect extracellular matrix or pro-fibrotic/proinflammatory cytokine production. However, OTUD6B-AS1 knockdown significantly increased Cyclin D1 expression at the mRNA and protein level. Moreover, silencing of OTUD6B-AS1 significantly reduced proliferation and suppressed apoptosis in both dermal Fb and HPASMC. OTUD6B-AS1 knockdown did not affect OTUD6B expression at the mRNA level and protein level. Our data suggest that OTUD6B-AS1 regulates proliferation and apoptosis via cyclin D1 expression in a sense gene independent manner. This is the first report investigating the function of OTUD6B-AS1. Our data shed light on a novel apoptosis resistance mechanism in Fb and vascular smooth muscle cells that might be relevant for pathogenesis of SSc.
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Affiliation(s)
- Miki Takata
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
| | - Elena Pachera
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
| | - Mojca Frank-Bertoncelj
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
| | - Anastasiia Kozlova
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
| | - Astrid Jüngel
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
| | - Michael L Whitfield
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Shervin Assassi
- Department of Internal Medicine, Division of Rheumatology, The University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, United States
| | - Maurizio Calcagni
- Department of Plastic Surgery and Hand Surgery, University Hospital Zürich, Zurich, Switzerland
| | | | - Tom W Huizinga
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | - Fina Kurreeman
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | - Gabriela Kania
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
| | - Oliver Distler
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
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171
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Jiao J, Shi B, Wang T, Fang Y, Cao T, Zhou Y, Wang X, Li D. Characterization of long non-coding RNA and messenger RNA profiles in follicular fluid from mature and immature ovarian follicles of healthy women and women with polycystic ovary syndrome. Hum Reprod 2019; 33:1735-1748. [PMID: 30052945 DOI: 10.1093/humrep/dey255] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/03/2018] [Indexed: 12/31/2022] Open
Abstract
STUDY QUESTION Do long non-coding RNA (lncRNA) and messenger RNA (mRNA) profiles in follicular fluid from mature and immature ovarian follicles differ between healthy women and women with polycystic ovary syndrome (PCOS)? SUMMARY ANSWER lncRNA and mRNA profiles in follicular fluid from both mature and immature ovarian follicles differed significantly between healthy women and PCOS patients. WHAT IS KNOWN ALREADY Unlike microRNAs, which have been extensively studied, lncRNAs present in follicular fluid have never been sequenced and the biological associations of lncRNAs in healthy follicles and follicles in women who develop PCOS remain largely unknown. STUDY DESIGN, SIZE, DURATION A total of 18 subjects (8 controls and 10 PCOS patients) were recruited to participate in this study. Recruitment took place from May 2016 to September 2016. PARTICIPANTS/MATERIALS, SETTING, METHODS The follicular fluid donors underwent their first round of in-vitro fertilization treatment. Follicle size was determined based on the average follicular diameter, and follicular fluid samples were collected from mature follicles (17-22 mm) and matched-immature follicles (8-13 mm). RNA sequencing was performed on follicular fluids from mature and immature follicles of healthy women and PCOS patients. MAIN RESULTS AND THE ROLE OF CHANCE A total of 1583 novel lncRNAs were identified in 36 human follicular fluid samples and some were expressed differently in healthy and PCOS women. lncRNAs associated with the metabolic process were highly enriched in the follicular fluid of mature follicles from the PCOS group versus the healthy group. In the PCOS group, nervous system process lncRNAs were highly enriched in the follicular fluid of mature versus immature follicles, whereas in the healthy group, lncRNAs associated with junction adhesion and communication-related processes were highly enriched in the follicular fluid of mature versus immature follicles. In addition, differentially expressed mRNAs were principally linked to olfactory transduction pathways. Consistent results from Gene Set Enrichment Analysis (GSEA) and Gene Ontology (GO) indicated that telomere maintenance and MAPK and Wnt pathways may be conserved processes, active in follicular development, and monosaccharide biosynthesis might provide possible pathway markers to distinguish between normal and PCOS follicles. We constructed gene co-expression networks that identified many co-regulatory relationships among follicular fluid lncRNAs, mRNAs, and PCOS phenotypes. Weighted Gene Co-expression Network Analysis (WGCNA) revealed lncRNAs and mRNAs that were core and others associated with the PCOS phenotype. LIMITATIONS, REASONS FOR CAUTION It remains unclear whether these differential transcripts contribute directly to follicular development or the pathogenesis of PCOS, or are merely biomarkers. WIDER IMPLICATIONS OF THE FINDINGS It will be important in the future for investigators to ascertain the biologic mechanisms underlying the development of both normal and PCOS follicles. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the National Natural Science Foundation of China (No. 81671423, No. 81402130 and No. 81501247), the Fok Ying Tung Education Foundation (No. 151039), and Distinguished Talent Program of Shengjing Hospital (No. ME76). No competing interests declared.
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Affiliation(s)
- Jiao Jiao
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Bei Shi
- Department of Physiology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Tianren Wang
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Yuanyuan Fang
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Tiefeng Cao
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Yiming Zhou
- Department of Medicine, Brigham and Women's Hospital, Harvard Institutes of Medicine, Harvard Medical School, Boston, MA, USA
| | - Xiuxia Wang
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Da Li
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China
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172
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Ji S, Wang S, Zhao X, Lv L. Long noncoding RNA NEAT1 regulates the development of osteosarcoma through sponging miR-34a-5p to mediate HOXA13 expression as a competitive endogenous RNA. Mol Genet Genomic Med 2019; 7:e673. [PMID: 31044561 PMCID: PMC6565592 DOI: 10.1002/mgg3.673] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/09/2019] [Accepted: 03/13/2019] [Indexed: 12/27/2022] Open
Abstract
Background Long noncoding RNA (lncRNA) exerts a potential regulatory role in tumorigenesis. LncRNA NEAT1 expression remains high in osteosarcoma tissues. However, its biological mechanism in osteosarcoma remains unknown. Methods In this study, NEAT1 expression in osteosarcoma cells was detected by qRT‐PCR. Proliferative and apoptosis potentials of osteosarcoma cells were determined by CCK‐8 assay and Flow Cytometry, respectively. We identified the potential target of NEAT1 through bioinformatics and dual‐luciferase reporter gene assay. Furthermore, their interaction and functions in regulating the development of osteosarcoma were clarified by Western blot and RIP assay. Results Our results demonstrated a high expression of NEAT1 in osteosarcoma tissues and cells. Overexpression of NEAT1 markedly accelerated proliferative and reduced apoptosis potentials of osteosarcoma cells. Besides, NEAT1 could positively regulate the expression of HOXA13 by competing with miR‐34a‐5p. Conclusion These results indicated that NEAT1 participated in the development of osteosarcoma as a ceRNA to competitively bind to miR‐34a‐5p and thus mediate HOXA13 expression.
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Affiliation(s)
- Shaolin Ji
- Hand Foot Surgery, Yidu Central Hospital of Weifang City, Qingzhou, China
| | - Shunsheng Wang
- Anorectal Surgery, Yidu Central Hospital of Weifang City, Qingzhou, China
| | - Xiaodan Zhao
- Thoracic Surgery, The First Hospital of Xingtai City, Xingtai, China
| | - Li Lv
- Hand Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, China
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173
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Tao Q, Tianyu W, Jiangqiao Z, Zhongbao C, Xiaoxiong M, Long Z, Jilin Z. Expression analysis of long non-coding RNAs in a renal ischemia-reperfusion injury model. Acta Cir Bras 2019; 34:e201900403. [PMID: 31038583 PMCID: PMC6583919 DOI: 10.1590/s0102-865020190040000003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/13/2019] [Indexed: 01/24/2023] Open
Abstract
PURPOSE To investigate the long non-coding RNAs (lncRNAs) profile on renal ischemia reperfusion in a mouse model. METHODS Microarray analysis was used to study the expression of misregulated lncRNA in a mouse model of renal ischemia reperfusion(I/R) with long ischemia time. Quantitative real-time PCR (qPCR) was used to verify the expression of selected lncRNAs and mRNAs.The potential functions of the lncRNA was analyzed by bioinformatics tools and databases. RESULTS Kidney function was impaired in I/R group compared to the normal group. Analysis showed that a total of 2267 lncRNAs and 2341 messenger RNAs (mRNAs) were significantly expressed in I/R group (≥2.0-fold, p < 0.05).The qPCR result showed that lncRNAs and mRNAs expression were consistent with the microarray analysis. The co-expression network profile analysis based on five validated lncRNAs and 203 interacted mRNAs showed it existed a total of 208 nodes and 333 connections. The GO and KEEG pathway analysis results showed that multiple lncRNAs are involved the mechanism of I/R. CONCLUSION Multiple lncRNAs are involved in the mechanism of I/R.These analysis results will help us to further understand the mechanism of I/R and promote the new methods targeted at lncRNA to improve I/R injury.
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Affiliation(s)
- Qiu Tao
- PhD, Department of Organ Transplantation, Renmin Hospital, Wuhan University, Hubei, China. Conception and design of the study, acquisition and analysis of data, manuscript writing
| | - Wang Tianyu
- PhD, Department of Organ Transplantation, Renmin Hospital, Wuhan University, Hubei, China. Conception and design of the study, acquisition and analysis of data, manuscript writing
| | - Zhou Jiangqiao
- PhD, Department of Organ Transplantation, Renmin Hospital, Wuhan University, Hubei, China. Design and supervised all phases of the study
| | - Chen Zhongbao
- Physician, Department of Organ Transplantation, Renmin Hospital, Wuhan University, Hubei, China. Technical procedures, acquisition of data
| | - Ma Xiaoxiong
- Physician, Department of Organ Transplantation, Renmin Hospital, Wuhan University, Hubei, China. Technical procedures, acquisition of data
| | - Zhang Long
- Physician, Department of Organ Transplantation, Renmin Hospital, Wuhan University, Hubei, China. Manuscript preparation
| | - Zou Jilin
- Physician, Department of Organ Transplantation, Renmin Hospital, Wuhan University, Hubei, China. Manuscript preparation
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174
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Haddad G, Lorenzen JM. Biogenesis and Function of Circular RNAs in Health and in Disease. Front Pharmacol 2019; 10:428. [PMID: 31080413 PMCID: PMC6497739 DOI: 10.3389/fphar.2019.00428] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 04/04/2019] [Indexed: 12/15/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNA that were previously thought to be insignificant byproducts of splicing errors. However, recent advances in RNA sequencing confirmed the presence of circRNAs in multiple cell lines and across different species suggesting a functional role of this RNA species. CircRNAs arise from back-splicing events resulting in a circular RNA that is stable, specific and conserved. They can be generated from exons, exon-introns, or introns. CircRNAs have multifaceted functions. They are likely part of the competing endogenous RNA class. They can regulate gene expression by sponging microRNAs, binding proteins or they can be translated into a protein themselves. CircRNAs have been associated with health and disease, some with disease protective effects, some with disease promoting functions. The widespread expression and disease regulatory mechanisms endow circRNAs to be used as functional biomarkers and therapeutic targets for a variety of different disorders. In this concise article we provide an overview of the association of circRNAs with various diseases including cancer, cardiovascular and kidney disease as well as cellular senescence. We conclude with an assessment of the current status and future outlook of this new field of research that carries immense potential with respect to diagnostic and therapeutic approaches of a variety of diseases.
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Affiliation(s)
- George Haddad
- Division of Nephrology, University Hospital Zürich, Zurich, Switzerland
| | - Johan M. Lorenzen
- Division of Nephrology, University Hospital Zürich, Zurich, Switzerland
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175
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Plasma miR-22-5p, miR-132-5p, and miR-150-3p Are Associated with Acute Myocardial Infarction. BIOMED RESEARCH INTERNATIONAL 2019; 2019:5012648. [PMID: 31179325 PMCID: PMC6507259 DOI: 10.1155/2019/5012648] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 03/31/2019] [Indexed: 12/26/2022]
Abstract
Circulating microRNAs (miRNAs) are potential biomarkers for cardiovascular diseases. Our study aimed to determine whether miR-22-5p, miR-132-5p, and miR-150-3p represent novel biomarkers for acute myocardial infarction (AMI). Plasma samples were isolated from 35 AMI patients and 55 matched controls. Total RNA was extracted, and quantitative real-time PCR and ELISA were performed to investigate the expressions of miRNAs and cardiac troponin I (cTnI), respectively. We found that plasma levels of miR-22-5p and miR-150-3p were significantly higher during the early stage of AMI and their expression levels peaked earlier than cTnI. Conversely, circulating miR-132-5p was sustained at a low level during the early phase of AMI. All three circulating miRNAs were correlated with plasma cTnI levels. A receiver operating characteristic (ROC) analysis suggested that each single miRNA had considerable diagnostic efficacy for AMI. Moreover, combining the three miRNAs improved their diagnostic efficacy. Furthermore, neither heparin nor medications for coronary heart disease (CHD) affected plasma levels of miR-22-5p and miR-132-5p, but circulating miR-150-3p was downregulated by medications for CHD. We concluded that plasma miR-22-5p, miR-132-5p, and miR-150-3p may serve as candidate diagnostic biomarkers for early diagnosis of AMI. Moreover, a panel consisting of these three miRNAs may achieve a higher diagnostic value.
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176
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Liu S, Liu LH, Hu WW, Wang M. Long noncoding RNA TUG1 regulates the development of oral squamous cell carcinoma through sponging miR-524-5p to mediate DLX1 expression as a competitive endogenous RNA. J Cell Physiol 2019; 234:20206-20216. [PMID: 30980391 DOI: 10.1002/jcp.28620] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/27/2019] [Accepted: 03/06/2019] [Indexed: 12/12/2022]
Abstract
Long noncoding RNA (lncRNA) exerts a potential regulatory role in tumorigenesis. LncRNA TUG1 expression remains high in oral squamous cell carcinoma (OSCC) tissues. However, its biological mechanism in OSCC remains unknown. In this study, TUG1 expression in OSCC cells was detected by quantitative real-time polymerase chain reaction. Proliferative and migratory potentials of OSCC cells were determined by Cell Counting Kit 8, 5-Ethynyl-2'- deoxyuridine (EdU), and Transwell assay, respectively. We identified the potential target of TUG1 through bioinformatics and dual-luciferase reporter gene assay. Furthermore, their interaction and functions in regulating the development of OSCC were clarified by western blot and RNA immunoprecipitation assay. Our results demonstrated a high expression of TUG1 in OSCC cells. Overexpression of TUG1 markedly accelerated proliferative and migratory potentials of OSCC cells. Besides, TUG1 could positively regulate the expression of distal-less homeobox 1 (DLX1) by competing with miR-524-5p. These results indicated that TUG1 participated in the development of OSCC as a competing endogenous RNA to competitively bind to miR-524-5p and thus mediate DLX1 expression.
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Affiliation(s)
- Shuyan Liu
- Department of Stomatology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Li-Hong Liu
- Department of Pathology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei-Wei Hu
- Department of Stomatology, Huai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Meng Wang
- Department of Rehabilitation, Huai'an Second People's Hospital, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
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177
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Fico A, Fiorenzano A, Pascale E, Patriarca EJ, Minchiotti G. Long non-coding RNA in stem cell pluripotency and lineage commitment: functions and evolutionary conservation. Cell Mol Life Sci 2019; 76:1459-1471. [PMID: 30607432 PMCID: PMC6439142 DOI: 10.1007/s00018-018-3000-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/13/2018] [Accepted: 12/17/2018] [Indexed: 02/07/2023]
Abstract
LncRNAs have recently emerged as new and fundamental transcriptional and post-transcriptional regulators acting at multiple levels of gene expression. Indeed, lncRNAs participate in a wide variety of stem cell and developmental processes, acting in cis and/or in trans in the nuclear and/or in the cytoplasmic compartments, and generating an intricate network of interactions with RNAs, enhancers, and chromatin-modifier complexes. Given the versatility of these molecules to operate in different subcellular compartments, via different modes of action and with different target specificity, the interest in this research field is rapidly growing. Here, we review recent progress in defining the functional role of lncRNAs in stem cell biology with a specific focus on the underlying mechanisms. We also discuss recent findings on a new family of evolutionary conserved lncRNAs transcribed from ultraconserved elements, which show perfect conservation between human, mouse, and rat genomes, and that are emerging as new player in this complex scenario.
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Affiliation(s)
- Annalisa Fico
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131, Naples, Italy.
- Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131, Naples, Italy.
| | - Alessandro Fiorenzano
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131, Naples, Italy
- Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131, Naples, Italy
- Developmental and Regenerative Neurobiology, Wallenberg Neuroscience Center, and Lund Stem Cell Centre, Department of Experimental Medical Science, Lund University, 22184, Lund, Sweden
| | - Emilia Pascale
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131, Naples, Italy
- Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131, Naples, Italy
| | - Eduardo Jorge Patriarca
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131, Naples, Italy
- Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131, Naples, Italy
| | - Gabriella Minchiotti
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131, Naples, Italy
- Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131, Naples, Italy
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178
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Li Y, Zhang D, Zhang Y, Xu X, Bi L, Zhang M, Yu B, Zhang Y. Association of lncRNA polymorphisms with triglyceride and total cholesterol levels among myocardial infarction patients in Chinese population. Gene 2019; 724:143684. [PMID: 30898706 DOI: 10.1016/j.gene.2019.02.085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 01/21/2019] [Accepted: 02/22/2019] [Indexed: 01/02/2023]
Abstract
AIM The long noncoding RNAs (lncRNAs) have gradually been reported to be an important class of RNAs with pivotal roles in the development and progression of myocardial infarction (MI). In this study, we hypothesized that genetic variant of cyclin-dependent kinase inhibitor 2B antisense RNA (ANRIL) and metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) may affect the prognosis of MI patients. METHODS The study included 401 Han Chinese MI patients and 409 controls. Four lncRNA tag single nucleotide polymorphisms (SNPs)-ANRIL rs9632884 and rs1537373, MALAT1 rs619586 and rs3200401-were selected. SNP genotyping was performed by an improved multiplex ligation detection reaction assay. RESULTS rs9632884 and rs3200401 SNPs were significantly associated with lipid levels in both controls and MI patients (P < 0.003-0.046). Several SNPs interacted with sex and age to modify total cholesterol, low-density lipoprotein cholesterol, and creatinine levels to modify the risk of MI. No association between the lncRNAs SNPs and susceptibility to MI was found (P > 0.05 for all). CONCLUSIONS Taken together, this study provides additional evidence that genetic variation of the ANRIL rs9632884 and MALAT1 rs3200401 can mediate lipid levels in MI patients.
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Affiliation(s)
- Yilan Li
- Department of Cardiology, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin 150001, China
| | - Dandan Zhang
- Department of Cardiology, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin 150001, China
| | - Yanxiu Zhang
- Department of Cardiology, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Xueming Xu
- Department of Cardiology, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Lei Bi
- Department of Cardiology, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Meiling Zhang
- Department of Cardiology, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin 150001, China
| | - Bo Yu
- Department of Cardiology, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin 150001, China
| | - Yao Zhang
- Department of Cardiology, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin 150001, China.
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179
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Hao L, Wang J, Liu N. Long noncoding RNA TALNEC2 regulates myocardial ischemic injury in H9c2 cells by regulating miR-21/PDCD4-medited activation of Wnt/β-catenin pathway. J Cell Biochem 2019; 120:12912-12923. [PMID: 30861181 DOI: 10.1002/jcb.28562] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/27/2018] [Accepted: 01/09/2019] [Indexed: 12/22/2022]
Abstract
The goal of this study was to explore the role of tumor associated long noncoding RNA expressed on chromosome 2 (TALNEC2) in protecting against myocardial ischemic injury, as well as its underlying molecular mechanism. We established a cell model of myocardial injury through treating H9c2 cells with hypoxia, and the expression level of TALNEC2 was analyzed. Further, in vitro studies investigated the functional role of TALNEC2 dysregulation in hypoxia injury by assessing cell proliferation, migration, invasion, and apoptosis. Moreover, the expression of miR-21 was determined after dysregulation of TALNEC2, and whether TALNEC2-regulated hypoxia injury in H9c2 cells via regulating miR-21 expression were explored. Furthermore, the regulatory relationship between TALNEC2 and Wnt/β-catenin pathway was also investigated. TALNEC2 was highly expressed in the serum from patients with myocardial ischemic compared with that in healthy persons. Hypoxia-induced injury in H9c2 cells. Overexpression of TALNEC2 aggravated hypoxia injury in H9c2 cells. TALNEC2 could negative regulate the miR-21 expression, and overexpression of TALNEC2 aggravated hypoxia injury by downregulation of miR-21. Moreover, miR-21 negatively regulated the PDCD4 expression, and PDCD4 was a target of miR-21. Further studies disclosed that the overexpression of TALNEC2 further activated the Wnt/β-catenin pathway in hypoxia-treated H9c2 cells, implying that the Wnt/β-catenin pathway was a downstream mechanism mediating the role of TALNEC2 in regulating hypoxia injury in H9c2 cells. These findings confirmed the key functions of TALNEC2 in regulating myocardial ischemic injury. Upregulation of TALNEC2 may aggravate hypoxia injury in H9c2 cells via regulating miR-21/PDCD4-medited activation of the Wnt/β-catenin pathway. TALNEC2 may serve as a promising therapeutic target in myocardial ischemia.
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Affiliation(s)
- Lin Hao
- Department of Cardiology, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Juan Wang
- Department of Cardiology, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Na Liu
- Department of Cardiology, The Second Hospital of Shandong University, Jinan, Shandong, China
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180
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Zhang H, Liu Y, Yan L, Wang S, Zhang M, Ma C, Zheng X, Chen H, Zhu D. Long noncoding RNA Hoxaas3 contributes to hypoxia-induced pulmonary artery smooth muscle cell proliferation. Cardiovasc Res 2019; 115:647-657. [DOI: 10.1093/cvr/cvy250] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
Abstract
Abstract
Aims
Long noncoding RNAs (lncRNAs) are involved in the regulation of vascular smooth muscle cells and cardiovascular pathology. However, the contribution of lncRNAs to pulmonary hypertension (PH) remains largely unknown. The over-proliferation of pulmonary artery smooth muscle cells (PASMCs) causes pulmonary arterial smooth muscle hypertrophy and stenosis of the pulmonary vascular lumen, resulting in PH. Here, we investigated the biological role of a novel lncRNA, Hoxa cluster antisense RNA 3 (Hoxaas3), in the regulation of cell proliferation in PH.
Methods and results
Hoxaas3 was up-regulated in the lung vasculature of hypoxic mice and in PASMCs under hypoxic conditions. Histone H3 Lysine 9 acetylation of Hoxaas3 promoted gene expression. Moreover, high expression of Hoxaas3 was associated with cell proliferation and modulated cell cycle distribution by up-regulating Homeobox a3 at the mRNA and protein levels.
Conclusion
This study defined the role and mechanism of action of Hoxaas3 in the regulation of cell proliferation in PH, which should facilitate the development of new therapeutic strategies for the treatment of this disease.
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Affiliation(s)
- Hongyue Zhang
- College of Pharmacy, Harbin Medical University, No.157, Baojian Road, Harbin, Heilongjiang, China
- Central Laboratory of Harbin Medical University-Daqing, No.38, Xinyang Road, Daqing, Heilongjiang, China
| | - Ying Liu
- College of Pharmacy, Harbin Medical University, No.157, Baojian Road, Harbin, Heilongjiang, China
- Central Laboratory of Harbin Medical University-Daqing, No.38, Xinyang Road, Daqing, Heilongjiang, China
| | - Lixin Yan
- College of Pharmacy, Harbin Medical University, No.157, Baojian Road, Harbin, Heilongjiang, China
- Central Laboratory of Harbin Medical University-Daqing, No.38, Xinyang Road, Daqing, Heilongjiang, China
| | - Siqi Wang
- College of Pharmacy, Harbin University of Commerce, No.138, Tongda Road, Harbin, Heilongjiang, China
| | - Min Zhang
- College of Pharmacy, Harbin Medical University, No.157, Baojian Road, Harbin, Heilongjiang, China
- Central Laboratory of Harbin Medical University-Daqing, No.38, Xinyang Road, Daqing, Heilongjiang, China
| | - Cui Ma
- College of Medical Laboratory Science and Technology, Harbin Medical University-Daqing, No.38, Xinyang Road, Daqing, Heilongjiang, China
| | - Xiaodong Zheng
- Department of Pathophysiology, Harbin Medical University-Daqing, Daqing, No.38, Xinyang Road, Daqing, Heilongjiang, China
| | - He Chen
- Department of Obstetrics and gynecology, The Second affiliated Hospital of Harbin Medical University, No.246, Xuefu Road, Harbin, Heilongjiang, China
| | - Daling Zhu
- College of Pharmacy, Harbin Medical University, No.157, Baojian Road, Harbin, Heilongjiang, China
- Central Laboratory of Harbin Medical University-Daqing, No.38, Xinyang Road, Daqing, Heilongjiang, China
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181
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Shihabudeen Haider Ali MS, Cheng X, Moran M, Haemmig S, Naldrett MJ, Alvarez S, Feinberg MW, Sun X. LncRNA Meg3 protects endothelial function by regulating the DNA damage response. Nucleic Acids Res 2019; 47:1505-1522. [PMID: 30476192 PMCID: PMC6379667 DOI: 10.1093/nar/gky1190] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 11/05/2018] [Accepted: 11/09/2018] [Indexed: 01/10/2023] Open
Abstract
The role of long non-coding RNAs (lncRNAs) in regulating endothelial function through the DNA damage response (DDR) remains poorly understood. In this study, we demonstrate that lncRNA maternally expressed gene 3 (Meg3) interacts with the RNA binding protein polypyrimidine tract binding protein 3 (PTBP3) to regulate gene expression and endothelial function through p53 signaling ─ a major coordinator of apoptosis and cell proliferation triggered by the DDR. Meg3 expression is induced in endothelial cells (ECs) upon p53 activation. Meg3 silencing induces DNA damage, activates p53 signaling, increases the expression of p53 target genes, promotes EC apoptosis, and inhibits EC proliferation. Mechanistically, Meg3 silencing reduces the interaction of p53 with Mdm2, induces p53 expression, and promotes the association of p53 with the promoters of a subset of p53 target genes. PTBP3 silencing recapitulates the effects of Meg3 deficiency on the expression of p53 target genes, EC apoptosis and proliferation. The Meg3-dependent association of PTBP3 with the promoters of p53 target genes suggests that Meg3 and PTBP3 restrain p53 activation. Our studies reveal a novel role of Meg3 and PTBP3 in regulating p53 signaling and endothelial function, which may serve as novel targets for therapies to restore endothelial homeostasis.
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Affiliation(s)
| | - Xiao Cheng
- Department of Biochemistry, University of Nebraska-Lincoln, Beadle Center, 1901 Vine St, Lincoln, NE 68588, USA
| | - Matthew Moran
- Department of Biochemistry, University of Nebraska-Lincoln, Beadle Center, 1901 Vine St, Lincoln, NE 68588, USA
| | - Stefan Haemmig
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael J Naldrett
- Proteomics and Metabolomics Facility, Center for Biotechnology, University of Nebraska-Lincoln, Beadle Center, 1901 Vine St, Lincoln, NE 68588, USA
| | - Sophie Alvarez
- Proteomics and Metabolomics Facility, Center for Biotechnology, University of Nebraska-Lincoln, Beadle Center, 1901 Vine St, Lincoln, NE 68588, USA
| | - Mark W Feinberg
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xinghui Sun
- Department of Biochemistry, University of Nebraska-Lincoln, Beadle Center, 1901 Vine St, Lincoln, NE 68588, USA
- Nebraska Center for the Prevention of Obesity Diseases through Dietary Molecules, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
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182
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Barangi S, Hayes AW, Reiter R, Karimi G. The therapeutic role of long non-coding RNAs in human diseases: A focus on the recent insights into autophagy. Pharmacol Res 2019; 142:22-29. [PMID: 30742900 DOI: 10.1016/j.phrs.2019.02.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/06/2019] [Accepted: 02/07/2019] [Indexed: 12/15/2022]
Abstract
Long non-coding RNA (lncRNA) is a class of non-coding RNA with ≥200 nucleotides in length which are involved as critical regulators in various cellular processes. LncRNAs contribute to the development and progression of many human diseases. Autophagy is a key catabolic process which helps to maintain the cellular homeostasis through the decay of damaged or unwanted proteins and dysfunctional cytoplasmic organelles. The impairment of the autophagy process has been described in numerous diseases. The autophagy possess can have either a protective or a detrimental role in cells depending on its activation status and other cellular conditions. LncRNAs have been shown to have an important function in the regulation of important biological processes such as autophagy. The relationship between lncRNAs and autophagy has been shown to be involved in the progression and possibly in the prevention of many diseases. In this review, recent findings on the regulatory roles of lncRNAs in the cell autophagy pathway, as well as their relevance to different diseases such as cardiovascular disease, cerebral ischemic stroke and cancer are highlighted.
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Affiliation(s)
- Samira Barangi
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - A Wallace Hayes
- University of South Florida College of Public Health, USA; Michigan State University, East Lansing, MI, USA
| | - Russel Reiter
- University of Texas, Health Science Center at San Antonio, Department of Cellular and Structural Biology, USA
| | - Gholamreza Karimi
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Pharmaceutical Research Centre, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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183
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Wu L, Li Y, Zhang D, Huang Z, Du B, Wang Z, Yang L, Zhang Y. LncRNA NEXN-AS1 attenuates proliferation and migration of vascular smooth muscle cells through sponging miR-33a/b. RSC Adv 2019; 9:27856-27864. [PMID: 35530470 PMCID: PMC9070771 DOI: 10.1039/c9ra06282c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 08/27/2019] [Indexed: 12/27/2022] Open
Abstract
Non-protein-coding RNAs (lncRNAs) are emerging as important regulators in disease pathogenesis, including atherosclerosis (AS). Here, we investigated the role and underlying mechanisms of nexilin F-actin binding protein antisense RNA 1 (NEXN-AS1) on the proliferation and migration of vascular smooth muscle cells (VSMCs). Our data revealed that ox-LDL treatment resulted in decreased NEXN-AS1 expression and increased miR-33a/b levels in human aorta VSMCs (HA-VSMCs) in dose- and time-dependent manners. Overexpression of NEXN-AS1 mitigated the proliferation and migration of HA-VSMCs under ox-LDL stimulation using CCK-8 and wound-healing assays. Moreover, dual-luciferase reporter and RNA immunoprecipitation assays verified that NEXN-AS1 acted as molecular sponges of miR-33a and miR-33b in HA-VSMCs. MiR-33a or miR-33b silencing attenuated the proliferation and migration of ox-LDL-treated HA-VSMCs. Furthermore, miR-33a or miR-33b mediated the inhibitory effects of NEXN-AS1 overexpression on the proliferation and migration of ox-LDL-treated HA-VSMCs. Our study suggested that high level of NEXN-AS1 mitigated VSMC proliferation and migration under ox-LDL stimulation at least partly through sponging miR-33a and miR-33b, illuminating NEXN-AS1 as a novel therapeutic approach for AS treatment. Non-protein-coding RNAs (lncRNAs) are emerging as important regulators in disease pathogenesis, including atherosclerosis (AS).![]()
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Affiliation(s)
- Leiming Wu
- Department of Cardiology
- The First Affiliated Hospital of Zhengzhou University
- Zhengzhou 450052
- China
| | - Yapeng Li
- Department of Cardiology
- The First Affiliated Hospital of Zhengzhou University
- Zhengzhou 450052
- China
| | - Dianhong Zhang
- Department of Cardiology
- The First Affiliated Hospital of Zhengzhou University
- Zhengzhou 450052
- China
| | - Zhen Huang
- Department of Cardiology
- The First Affiliated Hospital of Zhengzhou University
- Zhengzhou 450052
- China
| | - Binbin Du
- Department of Cardiology
- The First Affiliated Hospital of Zhengzhou University
- Zhengzhou 450052
- China
| | - Zheng Wang
- Department of Cardiology
- The First Affiliated Hospital of Zhengzhou University
- Zhengzhou 450052
- China
| | - Lulu Yang
- Department of Cardiology
- The First Affiliated Hospital of Zhengzhou University
- Zhengzhou 450052
- China
| | - Yanzhou Zhang
- Department of Cardiology
- The First Affiliated Hospital of Zhengzhou University
- Zhengzhou 450052
- China
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184
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Hurtado Del Pozo C, Garreta E, Izpisúa Belmonte JC, Montserrat N. Modeling epigenetic modifications in renal development and disease with organoids and genome editing. Dis Model Mech 2018; 11:dmm035048. [PMID: 30459215 PMCID: PMC6262817 DOI: 10.1242/dmm.035048] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Understanding epigenetic mechanisms is crucial to our comprehension of gene regulation in development and disease. In the past decades, different studies have shown the role of epigenetic modifications and modifiers in renal disease, especially during its progression towards chronic and end-stage renal disease. Thus, the identification of genetic variation associated with chronic kidney disease has resulted in better clinical management of patients. Despite the importance of these findings, the translation of genotype-phenotype data into gene-based medicine in chronic kidney disease populations still lacks faithful cellular or animal models that recapitulate the key aspects of the human kidney. The latest advances in the field of stem cells have shown that it is possible to emulate kidney development and function with organoids derived from human pluripotent stem cells. These have successfully recapitulated not only kidney differentiation, but also the specific phenotypical traits related to kidney function. The combination of this methodology with CRISPR/Cas9 genome editing has already helped researchers to model different genetic kidney disorders. Nowadays, CRISPR/Cas9-based approaches also allow epigenetic modifications, and thus represent an unprecedented tool for the screening of genetic variants, epigenetic modifications or even changes in chromatin structure that are altered in renal disease. In this Review, we discuss these technical advances in kidney modeling, and offer an overview of the role of epigenetic regulation in kidney development and disease.
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Affiliation(s)
- Carmen Hurtado Del Pozo
- Pluripotency for organ regeneration. Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Technology (BIST), 08028 Barcelona, Spain
| | - Elena Garreta
- Pluripotency for organ regeneration. Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Technology (BIST), 08028 Barcelona, Spain
| | | | - Nuria Montserrat
- Pluripotency for organ regeneration. Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Technology (BIST), 08028 Barcelona, Spain
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185
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Long noncoding RNA RMRP upregulation aggravates myocardial ischemia-reperfusion injury by sponging miR-206 to target ATG3 expression. Biomed Pharmacother 2018; 109:716-725. [PMID: 30551524 DOI: 10.1016/j.biopha.2018.10.079] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 07/30/2018] [Accepted: 10/14/2018] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVE Coronary heart disease is a common cause of death and disability worldwide and mainly results from myocardial ischemia-reperfusion (I/R) injury. This study aimed to elucidate the roles and possible mechanism of long noncoding RNA Component Of Mitochondrial RNA Processing Endoribonuclease (RMRP) in protecting against ischemic myocardial injury. MATERIAL AND METHODS The H9c2 cardiomyocytes were cultured under hypoxia condition to induce myocardial injury. The RMRP expression under hypoxia condition was determined, followed by investigation of the effects of RMRP dysregulation on hypoxia-induced injury in H9c2 cells. In addition, the regulatory relationship between RMRP and miR-206 was detected, and the potential target of miR-206 was identified. Besides, the association of RMRP and activation of PI3K/AKT/mTOR signaling pathway was explored. Furthermore, an in vivo rat model of myocardial I/R injury was established by subjection to 60 min ischemia and subsequently 24 h reperfusion for validation of the role of RMRP in regulating myocardial I/R injury in vivo. RESULTS The results showed that overexpression of RMRP aggravated hypoxia-induced injury in H9c2 cells. Moreover, miR-206 was negatively regulated by RMRP and overexpression of RMRP aggravated hypoxia injury by downregulation of miR-206. Furthermore, ATG3 was a target of miR-206, and he effects of miR-206 on hypoxia injury were through targeting ATG3. Besides, overexpression of RMRP activated PI3K/AKT/mTOR pathway in hypoxia-treated H9c2 cells, which were reversed by miR-206 overexpression at the same time. Furthermore, in an in vivo rat model of myocardial I/R injury, suppression of RMPR improved cardiac function and inhibited apoptosis after myocardial I/R injury. CONCLUSIONS Our findings reveal that upregulation of RMRP may aggravate myocardial I/R injury possible by downregulation of miR-206 and subsequently upregulation of ATG3. Activation of PI3K/Akt/mTOR pathway may be a key downstream mechanism mediating the cardioprotection of RMPR/miR-206/ATG3 axis against myocardial I/R injury.
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Dai L, Zhang G, Cheng Z, Wang X, Jia L, Jing X, Wang H, Zhang R, Liu M, Jiang T, Yang Y, Yang M. Knockdown of LncRNA MALAT1 contributes to the suppression of inflammatory responses by up-regulating miR-146a in LPS-induced acute lung injury. Connect Tissue Res 2018; 59:581-592. [PMID: 29649906 DOI: 10.1080/03008207.2018.1439480] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND Acute lung injury (ALI) is a type of severe pulmonary inflammatory disease with high rates of morbidity and mortality. Now, an increasing number of studies suggest that lncRNAs may act as key regulators of the inflammatory response and play a crucial role in the pathogenesis of many inflammatory diseases. Our study firstly explored the function and underlying mechanism of lncRNA metastasis-associated lung adenocarcinoma transcription 1 (MALAT1) in regulating the inflammatory response of lipopolysaccharide (LPS)-induced ALI in rats. METHODS The ALI rats were constructed by intratracheal instillation with LPS. Hematoxylin and eosin (HE) for histological examination were performed to detect histopathological changes in the lung tissues. Enzyme-linked immunosorbent assay (ELISA) was used to determine the concentrations of cytokines TNF-α, IL-6, and IL-1β in the supernatants of the bronchoalveolar lavage fluid (BALF). Quantitative real-time PCR (qRT-PCR) analysis was employed to assess the expression of MALAT1, miR-146a, TNF-α, IL-6, and IL-1β in lung tissues. Luciferase reporter assay and RNA immunoprecipitation (RIP) assay were used to detect the relationship between MALAT1 and miR-146a. RESULTS The results revealed that MALAT1 knockdown played a protective role in the LPS-induced ALI rat model. In addition, knockdown of MALAT1 in vitro inhibited LPS-induced inflammatory response in murine alveolar macrophages cell line MH-S and murine alveolar epithelial cell line MLE-12. This study found that MALAT1 acts as a molecular sponge for miR-146a and MALAT1 negatively regulated miR-146a expression. Mechanistically, MALAT1 overexpression alleviated the inhibitory effect of miR-146a on LPS-induced inflammatory response in MH-S. CONCLUSIONS Together, our study provided the first evidence that MALAT1 knockdown could suppress inflammatory response by up-regulating miR-146a in LPS-induced ALI, which provided a potential therapeutic target for the treatment of ALI.
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Affiliation(s)
- Lingling Dai
- a Department of respiration , Hospital of Zhengzhou University , Zhengzhou , China
| | - Guojun Zhang
- a Department of respiration , Hospital of Zhengzhou University , Zhengzhou , China
| | - Zhe Cheng
- a Department of respiration , Hospital of Zhengzhou University , Zhengzhou , China
| | - Xi Wang
- a Department of respiration , Hospital of Zhengzhou University , Zhengzhou , China
| | - Liuqun Jia
- a Department of respiration , Hospital of Zhengzhou University , Zhengzhou , China
| | - Xiaogang Jing
- a Department of respiration , Hospital of Zhengzhou University , Zhengzhou , China
| | - Huan Wang
- a Department of respiration , Hospital of Zhengzhou University , Zhengzhou , China
| | - Rui Zhang
- a Department of respiration , Hospital of Zhengzhou University , Zhengzhou , China
| | - Meng Liu
- a Department of respiration , Hospital of Zhengzhou University , Zhengzhou , China
| | - Tianci Jiang
- a Department of respiration , Hospital of Zhengzhou University , Zhengzhou , China
| | - Yuanjian Yang
- a Department of respiration , Hospital of Zhengzhou University , Zhengzhou , China
| | - Meng Yang
- a Department of respiration , Hospital of Zhengzhou University , Zhengzhou , China
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Abstract
Only a small fraction of the human genome corresponds to protein-coding genes. Historically, the vast majority of genomic sequence was dismissed as transcriptionally silent, but recent large-scale investigations have instead revealed a rich array of functionally significant elements, including non-protein-coding transcripts, within the noncoding regions of the human genome. Long noncoding RNAs (lncRNAs), a class of noncoding transcripts with lengths >200 nucleotides, are pervasively transcribed in the genome, and have been shown to bind DNA, RNA, and protein. LncRNAs exert effects through a variety of mechanisms that include guiding chromatin-modifying complexes to specific genomic loci, providing molecular scaffolds, modulating transcriptional programs, and regulating miRNA expression. An increasing number of experimental studies are providing evidence that lncRNAs mediate disease pathogenesis, thereby challenging the concept that protein-coding genes are the sole contributors to the development of human disease. This chapter highlights recent findings linking lncRNAs with human diseases of complex etiology, including hepatocellular carcinoma, Alzheimer's disease, and diabetes.
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Pant T, Dhanasekaran A, Fang J, Bai X, Bosnjak ZJ, Liang M, Ge ZD. Current status and strategies of long noncoding RNA research for diabetic cardiomyopathy. BMC Cardiovasc Disord 2018; 18:197. [PMID: 30342478 PMCID: PMC6196023 DOI: 10.1186/s12872-018-0939-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/12/2018] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are endogenous RNA transcripts longer than 200 nucleotides which regulate epigenetically the expression of genes but do not have protein-coding potential. They are emerging as potential key regulators of diabetes mellitus and a variety of cardiovascular diseases. Diabetic cardiomyopathy (DCM) refers to diabetes mellitus-elicited structural and functional abnormalities of the myocardium, beyond that caused by ischemia or hypertension. The purpose of this review was to summarize current status of lncRNA research for DCM and discuss the challenges and possible strategies of lncRNA research for DCM. A systemic search was performed using PubMed and Google Scholar databases. Major conference proceedings of diabetes mellitus and cardiovascular disease occurring between January, 2014 to August, 2018 were also searched to identify unpublished studies that may be potentially eligible. The pathogenesis of DCM involves elevated oxidative stress, myocardial inflammation, apoptosis, and autophagy due to metabolic disturbances. Thousands of lncRNAs are aberrantly regulated in DCM. Manipulating the expression of specific lncRNAs, such as H19, metastasis-associated lung adenocarcinoma transcript 1, and myocardial infarction-associated transcript, with genetic approaches regulates potently oxidative stress, myocardial inflammation, apoptosis, and autophagy and ameliorates DCM in experimental animals. The detail data regarding the regulation and function of individual lncRNAs in DCM are limited. However, lncRNAs have been considered as potential diagnostic and therapeutic targets for DCM. Overexpression of protective lncRNAs and knockdown of detrimental lncRNAs in the heart are crucial for defining the role and function of lncRNAs of interest in DCM, however, they are technically challenging due to the length, short life, and location of lncRNAs. Gene delivery vectors can provide exogenous sources of cardioprotective lncRNAs to ameliorate DCM, and CRISPR–Cas9 genome editing technology may be used to knockdown specific lncRNAs in DCM. In summary, current data indicate that LncRNAs are a vital regulator of DCM and act as the promising diagnostic and therapeutic targets for DCM.
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Affiliation(s)
- Tarun Pant
- Department of Medicine, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.,Centre for Biotechnology, Anna University, Chennai, Tamil Nadu, India
| | | | - Juan Fang
- Department of Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Xiaowen Bai
- Department of Cell Biology, Neurology & Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.,Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Zeljko J Bosnjak
- Department of Medicine, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.,Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Mingyu Liang
- Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Zhi-Dong Ge
- Department of Ophthalmology, Stanford School of Medicine, 1651 Page Mill Road, Stanford, CA, 94304, USA.
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van der Heijden CDCC, Noz MP, Joosten LAB, Netea MG, Riksen NP, Keating ST. Epigenetics and Trained Immunity. Antioxid Redox Signal 2018; 29:1023-1040. [PMID: 28978221 PMCID: PMC6121175 DOI: 10.1089/ars.2017.7310] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
SIGNIFICANCE A growing body of clinical and experimental evidence has challenged the traditional understanding that only the adaptive immune system can mount immunological memory. Recent findings describe the adaptive characteristics of the innate immune system, underscored by its ability to remember antecedent foreign encounters and respond in a nonspecific sensitized manner to reinfection. This has been termed trained innate immunity. Although beneficial in the context of recurrent infections, this might actually contribute to chronic immune-mediated diseases, such as atherosclerosis. Recent Advances: In line with its proposed role in sustaining cellular memories, epigenetic reprogramming has emerged as a critical determinant of trained immunity. Recent technological and computational advances that improve unbiased acquisition of epigenomic profiles have significantly enhanced our appreciation for the complexities of chromatin architecture in the contexts of diverse immunological challenges. CRITICAL ISSUES Key to resolving the distinct chromatin signatures of innate immune memory is a comprehensive understanding of the precise physiological targets of regulatory proteins that recognize, deposit, and remove chemical modifications from chromatin as well as other gene-regulating factors. Drawing from a rapidly expanding compendium of experimental and clinical studies, this review details a current perspective of the epigenetic pathways that support the adapted phenotypes of monocytes and macrophages. FUTURE DIRECTIONS We explore future strategies that are aimed at exploiting the mechanism of trained immunity to improve the prevention and treatment of infections and immune-mediated chronic disorders.
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Affiliation(s)
| | - Marlies P Noz
- 1 Department of Internal Medicine, Radboud University Medical Center , Nijmegen, The Netherlands
| | - Leo A B Joosten
- 1 Department of Internal Medicine, Radboud University Medical Center , Nijmegen, The Netherlands
| | - Mihai G Netea
- 1 Department of Internal Medicine, Radboud University Medical Center , Nijmegen, The Netherlands .,2 Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn , Bonn, Germany
| | - Niels P Riksen
- 1 Department of Internal Medicine, Radboud University Medical Center , Nijmegen, The Netherlands
| | - Samuel T Keating
- 1 Department of Internal Medicine, Radboud University Medical Center , Nijmegen, The Netherlands
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190
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Long B, Li N, Xu XX, Li XX, Xu XJ, Liu JY, Wu ZH. Long noncoding RNA LOXL1-AS1 regulates prostate cancer cell proliferation and cell cycle progression through miR-541-3p and CCND1. Biochem Biophys Res Commun 2018; 505:561-568. [DOI: 10.1016/j.bbrc.2018.09.160] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 09/25/2018] [Indexed: 12/19/2022]
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191
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Kato M. Noncoding RNAs as therapeutic targets in early stage diabetic kidney disease. Kidney Res Clin Pract 2018; 37:197-209. [PMID: 30254844 PMCID: PMC6147183 DOI: 10.23876/j.krcp.2018.37.3.197] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 07/18/2018] [Accepted: 07/18/2018] [Indexed: 02/01/2023] Open
Abstract
Diabetic kidney disease (DKD) is a major renal complication of diabetes that leads to renal dysfunction and end-stage renal disease (ESRD). Major features of DKD include accumulation of extracellular matrix proteins and glomerular hypertrophy, especially in early stage. Transforming growth factor-β plays key roles in regulation of profibrotic genes and signal transducers such as Akt kinase and MAPK as well as endoplasmic reticulum stress, oxidant stress, and autophagy related to hypertrophy in diabetes. Many drugs targeting the pathogenic signaling in DKD (mostly through protein-coding genes) are under development. However, because of the limited number of protein-coding genes, noncoding RNAs (ncRNAs) including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) are attracting more attention as potential new drug targets for human diseases. Some miRNAs and lncRNAs regulate each other (by hosting, enhancing transcription from the neighbor, hybridizing each other, and changing chromatin modifications) and create circuits and cascades enhancing the pathogenic signaling in DKD. In this short and focused review, the functional significance of ncRNAs (miRNAs and lncRNAs) in the early stages of DKD and their therapeutic potential are discussed.
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Affiliation(s)
- Mitsuo Kato
- Beckman Research Institute of City of Hope, Duarte, CA, USA
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192
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Zhang X, Li DY, Reilly MP. Long intergenic noncoding RNAs in cardiovascular diseases: Challenges and strategies for physiological studies and translation. Atherosclerosis 2018; 281:180-188. [PMID: 30316538 DOI: 10.1016/j.atherosclerosis.2018.09.040] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/05/2018] [Accepted: 09/27/2018] [Indexed: 12/25/2022]
Abstract
Long intergenic noncoding RNAs (lincRNAs) are increasingly recognized as important mediators of many biological processes relevant to human pathophysiologies, including cardiovascular diseases. In vitro studies have provided important knowledge of cellular functions and mechanisms for an increasing number of lincRNAs. Dysregulated lncRNAs have been associated with cell fate programming and development, vascular diseases, atherosclerosis, dyslipidemia and metabolic syndrome, and cardiac pathological hypertrophy. However, functional interrogation of individual lincRNAs in physiological and disease states is largely limited. The complex nature of lincRNA actions and poor species conservation of human lincRNAs pose substantial challenges to physiological studies in animal model systems and in clinical translation. This review summarizes recent findings of specific lincRNA physiological studies, including MALAT1, MeXis, Lnc-DC and others, in the context of cardiovascular diseases, examines complex mechanisms of lincRNA actions, reviews in vivo research strategies to delineate lincRNA functions and highlights challenges and approaches for physiological studies of primate-specific lincRNAs.
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Affiliation(s)
- Xuan Zhang
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Daniel Y Li
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Muredach P Reilly
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA; Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, 10032, USA.
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193
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Jin B, Jin H, Wu H, Xu J, Li B. Long non-coding RNA SNHG15 promotes CDK14 expression via miR-486 to accelerate non-small cell lung cancer cells progression and metastasis. J Cell Physiol 2018; 233:7164-7172. [PMID: 29630731 PMCID: PMC6001572 DOI: 10.1002/jcp.26543] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 02/16/2018] [Indexed: 01/01/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been validated to play important role in multiple cancers, including non-small cell lung cancer (NSCLC). In present study, our team investigate the biologic role of SNHG15 in the NSCLC tumorigenesis. LncRNA SNHG15 was significantly upregulated in NSCLC tissue samples and cells, and its overexpression was associated with poor prognosis of NSCLC patients. In vitro, loss-of-functional cellular experiments showed that SNHG15 silencing significantly inhibited the proliferation, promoted the apoptosis, and induced the cycle arrest at G0//G1 phase. In vivo, xenograft assay showed that SNHG15 silencing suppressed tumor growth of NSCLC cells. Besides, SNHG15 silencing decreased CDK14 protein expression both in vivo and vitro. Bioinformatics tools and luciferase reporter assay confirmed that miR-486 both targeted the 3'-UTR of SNHG15 and CDK14 and was negatively correlated with their expression levels. In summary, our study conclude that the ectopic overexpression of SNHG15 contribute to the NSCLC tumorigenesis by regulating CDK14 protein via sponging miR-486, providing a novel insight for NSCLC pathogenesis and potential therapeutic strategy for NSCLC patients.
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Affiliation(s)
- Bing Jin
- Department of Chest SurgeryNanyang City Center HospitalNanyangChina
| | - Hua Jin
- Department of RespirationJinshan Hospital Affiliated to Fudan UniversityShanghaiChina
| | - Hai‐Bo Wu
- Fudan UniversityYangpu District, ShanghaiChina
| | - Jian‐Jun Xu
- Fudan UniversityYangpu District, ShanghaiChina
| | - Bing Li
- Central LaboratoryJinshan Hospital Affiliated to Fudan UniversityJinshan District, ShanghaiChina
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195
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Guan H, Mei Y, Mi Y, Li C, Sun X, Zhao X, Liu J, Cao W, Li Y, Wang Y. Downregulation of lncRNA ANRIL suppresses growth and metastasis in human osteosarcoma cells. Onco Targets Ther 2018; 11:4893-4899. [PMID: 30147340 PMCID: PMC6098425 DOI: 10.2147/ott.s170293] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND This study was designed to research the potential function of lncRNA ANRIL in osteosarcoma (OS). MATERIALS AND METHODS Quantitative real-time PCR, cell counting kit-8, wound healing assay, Transwell assay, flow cytometric analysis, caspase activity analysis, and Western blot were carried out. RESULTS ANRIL was remarkably upregulated in human OS tissues and cells, and knockdown of ANRIL significantly suppressed MG63 cell proliferation, migration, and invasion and promoted apoptosis. Moreover, our mechanistic research findings verified that ANRIL-influenced growth and apoptosis may be partly through regulation of caspase-3 and Bcl-2. Migration and invasion were influenced via ANRIL-mediated regulation of MTA1, TIMP-2, and E-cadherin. CONCLUSION Our finding demonstrates that ANRIL plays vital roles in OS growth and metastasis.
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Affiliation(s)
- Hongya Guan
- Translational Medical Center, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450007, People's Republic of China
| | - Yingwu Mei
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, People's Republic of China,
| | - Yang Mi
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, People's Republic of China,
| | - Cheng Li
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, People's Republic of China
| | - Xiaoya Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, People's Republic of China,
| | - Xuefeng Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, People's Republic of China,
| | - Jia Liu
- Translational Medical Center, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450007, People's Republic of China
| | - Wei Cao
- Translational Medical Center, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450007, People's Republic of China
| | - Yuebai Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, People's Republic of China,
| | - Yisheng Wang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, People's Republic of China
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Poller W, Dimmeler S, Heymans S, Zeller T, Haas J, Karakas M, Leistner DM, Jakob P, Nakagawa S, Blankenberg S, Engelhardt S, Thum T, Weber C, Meder B, Hajjar R, Landmesser U. Non-coding RNAs in cardiovascular diseases: diagnostic and therapeutic perspectives. Eur Heart J 2018; 39:2704-2716. [PMID: 28430919 PMCID: PMC6454570 DOI: 10.1093/eurheartj/ehx165] [Citation(s) in RCA: 273] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/14/2017] [Accepted: 03/15/2017] [Indexed: 02/06/2023] Open
Abstract
Recent research has demonstrated that the non-coding genome plays a key role in genetic programming and gene regulation during development as well as in health and cardiovascular disease. About 99% of the human genome do not encode proteins, but are transcriptionally active representing a broad spectrum of non-coding RNAs (ncRNAs) with important regulatory and structural functions. Non-coding RNAs have been identified as critical novel regulators of cardiovascular risk factors and cell functions and are thus important candidates to improve diagnostics and prognosis assessment. Beyond this, ncRNAs are rapidly emgerging as fundamentally novel therapeutics. On a first level, ncRNAs provide novel therapeutic targets some of which are entering assessment in clinical trials. On a second level, new therapeutic tools were developed from endogenous ncRNAs serving as blueprints. Particularly advanced is the development of RNA interference (RNAi) drugs which use recently discovered pathways of endogenous short interfering RNAs and are becoming versatile tools for efficient silencing of protein expression. Pioneering clinical studies include RNAi drugs targeting liver synthesis of PCSK9 resulting in highly significant lowering of LDL cholesterol or targeting liver transthyretin (TTR) synthesis for treatment of cardiac TTR amyloidosis. Further novel drugs mimicking actions of endogenous ncRNAs may arise from exploitation of molecular interactions not accessible to conventional pharmacology. We provide an update on recent developments and perspectives for diagnostic and therapeutic use of ncRNAs in cardiovascular diseases, including atherosclerosis/coronary disease, post-myocardial infarction remodelling, and heart failure.
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Affiliation(s)
- Wolfgang Poller
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Center of Molecular Medicine, Johann Wolfgang Goethe Universität, Theodor-Stern-Kai 7, Frankfurt am Main, Germany
- DZHK, Site Rhein-Main, Frankfurt, Germany
| | - Stephane Heymans
- Center for Heart Failure Research, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, Netherlands
| | - Tanja Zeller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Jan Haas
- Institute for Cardiomyopathies Heidelberg (ICH), Universitätsklinikum Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany
- DZHK, Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Mahir Karakas
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - David-Manuel Leistner
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Philipp Jakob
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama, Japan
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo, Japan
| | - Stefan Blankenberg
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Stefan Engelhardt
- Institute for Pharmacology and Toxikology, Technische Universität München, Biedersteiner Strasse 29, München, Germany
- DZHK, Site Munich, Munich, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
| | - Christian Weber
- DZHK, Site Munich, Munich, Germany
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität, Pettenkoferstrasse 8a/9, Munich, Germany
| | - Benjamin Meder
- Institute for Cardiomyopathies Heidelberg (ICH), Universitätsklinikum Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany
- DZHK, Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Roger Hajjar
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ulf Landmesser
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
- Berlin Institute of Health, Kapelle-Ufer 2, Berlin, Germany
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Xing Q, Huang Y, Wu Y, Ma L, Cai B. Integrated analysis of differentially expressed profiles and construction of a competing endogenous long non-coding RNA network in renal cell carcinoma. PeerJ 2018; 6:e5124. [PMID: 30038853 PMCID: PMC6054097 DOI: 10.7717/peerj.5124] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/01/2018] [Indexed: 12/28/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) play crucial roles in the initiation and progression of renal cell carcinoma (RCC) by competing in binding to miRNAs, and related competitive endogenous RNA (ceRNA) networks have been constructed in several cancers. However, the coexpression network has been poorly explored in RCC. Methods We collected RCC RNA expression profile data and relevant clinical features from The Cancer Genome Atlas (TCGA). A cluster analysis was explored to show different lncRNA expression patterns. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses and gene set enrichment analysis (GSEA) were performed to analyze the functions of the intersecting mRNAs. Targetscan and miRanda bioinformatics algorithms were used to predict potential relationships among RNAs. Univariate Cox proportional hazards regression was conducted to determine the RNA expression levels and survival times. Results Bioinformatics analysis revealed that the expression profiles of hundreds of aberrantly expressed lncRNAs, miRNAs, and mRNAs were significantly changed between different stages of tumors and non-tumor groups. By combining the data predicted by databases with intersection RNAs, a ceRNA network consisting of 106 lncRNAs, 26 miRNAs and 69 mRNAs was established. Additionally, a protein interaction network revealed the main hub nodes (VEGFA, NTRK2, DLG2, E2F2, MYB and RUNX1). Furthermore, 63 lncRNAs, four miRNAs and 31 mRNAs were significantly associated with overall survival. Conclusion Our results identified cancer-specific lncRNAs and constructed a ceRNA network for RCC. A survival analysis related to the RNAs revealed candidate biomarkers for further study in RCC.
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Affiliation(s)
- Qianwei Xing
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Yeqing Huang
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - You Wu
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Limin Ma
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Bo Cai
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
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198
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Yang R, Liu S, Wen J, Xue L, Zhang Y, Yan D, Wang G, Liu Z. Inhibition of maternally expressed gene 3 attenuated lipopolysaccharide-induced apoptosis through sponging miR-21 in renal tubular epithelial cells. J Cell Biochem 2018; 119:7800-7806. [PMID: 29923218 DOI: 10.1002/jcb.27163] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/18/2018] [Indexed: 12/20/2022]
Abstract
Acute kidney injury (AKI) results in retention of waste products and dysregulation of extracellular volume and electrolytes, thus leading to a variety of complications. Recent advances in long noncoding RNAs suggested their close relationship with disease progression. In the current study, we investigated the role and mechanism of maternally expressed gene 3 (MEG3) on AKI pathogenesis. Real-time polymerase chain reaction found that the expression of MEG3 was significantly increased in both kidney tissues and TKPTS cells induced by lipopolysaccharide (LPS). Western blot assay showed that the expression of apoptosis regulator Bcl-2 was increased in MEG3-inhibited TKPTS cells. Flow cytometry assay confirmed that LPS-induced apoptosis was significantly attenuated after transfection of si-MEG3. The RNAhybrid informatics algorithm predicted that there was a strong binding capacity between miR-21 and MEG3. Luciferase reporter assay confirmed that MEG3 could function as a competing endogenous RNA of miR-21. The antiapoptotic effect of si-MEG3 could be neutralized by a miR-21 inhibitor, demonstrated by the decreased expression of Bcl-2 and flow cytometry results. Further investigation showed that programmed cell death protein 4 (PDCD4), a validated target of miR-21, was highly expressed in both injured kidney tissues and LPS-stimulated TKPTS cells. Meanwhile, the protein expression of PDCD4 was significantly reduced by inhibition of MEG3, but retrieved by coinhibition of MEG3 and miR-21. In conclusion, our results demonstrated that inhibition of MEG3 could attenuate LPS-induced apoptosis in TKPTS cells by regulating the miR-21/PDCD4 pathway, suggesting that the MEG3/miR-21/PDCD4 axis could be developed as a potential therapeutic target of AKI.
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Affiliation(s)
- Ru Yang
- Department of Rheumatology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Suxuan Liu
- Department of Cardiovascular Surgery, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Jian Wen
- Department of Rheumatology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Leixi Xue
- Department of Rheumatology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yi Zhang
- Department of Rheumatology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Dong Yan
- Department of Rheumatology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Guokun Wang
- Department of Cardiovascular Surgery, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Zhichun Liu
- Department of Rheumatology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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199
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Song L, Qiao G, Xu Y, Ma L, Jiang W. Role of non-coding RNAs in cardiotoxicity of chemotherapy. Surg Oncol 2018; 27:526-538. [PMID: 30217315 DOI: 10.1016/j.suronc.2018.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 05/30/2018] [Accepted: 06/07/2018] [Indexed: 01/06/2023]
Abstract
The long-time paradoxical situation of non-coding RNAs (ncRNAs) has been terminated for they emerge as executive at full spectrum of gene expression and translation. More recently, it has been demonstrated that some ncRNAs apparently are associated with chemotherapy, causing cardiotoxicity, which taint long-term recovery of patients in growing body of evidence. The current review focused on up-to-date knowledge on regulation change and molecular signaling of ncRNAs, at mean time evaluate their potentials as diagnostic biomarkers or therapeutic targets to monitor and protect cardio function.
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Affiliation(s)
- Lina Song
- Department of Oncology, Shanghai Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Guanglei Qiao
- Department of Oncology, Shanghai Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yingjie Xu
- Department of Cardiology, Shanghai Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Lijun Ma
- Department of Oncology, Shanghai Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
| | - Weihua Jiang
- Department of Oncology, Shanghai Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
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200
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Abstract
Long non-coding RNAs (lncRNAs) refer to functional cellular RNAs molecules longer than 200 nucleotides in length. Unlike microRNAs, which have been widely studied, little is known about the enigmatic role of lncRNAs. However, lncRNAs have motivated extensively attention in the past few years and are emerging as potentially important regulators in pathological processes, including in cancer. We now understand that lncRNAs play role in cancer through their interactions with DNA, protein, and RNA in many instances. Moreover, accumulating evidence has recognized that large classes of lncRNAs are functional for ovarian cancer. Nevertheless, the biological phenomena and molecular mechanisms of lncRNAs in ovarian cancer remain to be better identified. In this review, we outline the dysregulated expression of lncRNAs and their potential clinical implications in ovarian cancer, with a particular emphasis on discussing the well characterized mechanisms underlying lncRNAs in ovarian cancer.
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Affiliation(s)
- Lei Zhan
- Department of gynecology and obstetrics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601 China
| | - Jun Li
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032 China
| | - Bing Wei
- Department of gynecology and obstetrics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601 China
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