101
|
Zhou Y, Sun W, Qin Z, Guo S, Kang Y, Zeng S, Yu L. LncRNA regulation: New frontiers in epigenetic solutions to drug chemoresistance. Biochem Pharmacol 2020; 189:114228. [PMID: 32976832 DOI: 10.1016/j.bcp.2020.114228] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 02/09/2023]
Abstract
Long-noncoding RNAs (lncRNAs) have been shown to participate in sensitizing or de-sensitizing cancer cells to chemical drugs during cancer therapeutics. Notably, a plethora of lncRNAs have been confirmed to be associated with epigenetic controllers and regulate histone protein modification or DNA methylation states in the process of gene transcription. This correlation between lncRNAs and epigenetic regulators can induce the expression of core genes to trigger drug resistance. In addition, epigenetic signatures are considered to be effective and attractive biomarkers for monitoring drug therapeutic effects because they are inheritable, dynamic, and reversible. Therefore, the regulatory mechanism between lncRNAs and epigenetic machinery can serve as a novel indicator and target to overcome or reverse drug resistance in cancer therapy. In this review, we also presented a curated selection of computational tools (including online databases and network analysis) in the area of epigenetics. A classic workflow for lncRNA expression network analysis is presented, providing guidance for non-bioinformaticians to identify significant correlation between lncRNAs and other biomolecules.
Collapse
Affiliation(s)
- Ying Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Wen Sun
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Zhiyuan Qin
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Suhang Guo
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yu Kang
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.
| |
Collapse
|
102
|
Zhao B, Qu X, Lv X, Wang Q, Bian D, Yang F, Zhao X, Ji Z, Ni J, Fu Y, Xin G, Yu H. Construction and Characterization of a Synergistic lncRNA-miRNA Network Reveals a Crucial and Prognostic Role of lncRNAs in Colon Cancer. Front Genet 2020; 11:572983. [PMID: 33101392 PMCID: PMC7522580 DOI: 10.3389/fgene.2020.572983] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/24/2020] [Indexed: 12/18/2022] Open
Abstract
Non-coding RNAs such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been found to be indispensable factors in carcinogenesis and cancer development. Numerous studies have explored the regulatory functions of these molecules and identified the synergistic interactions among lncRNAs or miRNAs, while those between lncRNAs and miRNAs remain to be investigated. In this study, we constructed and characterized an lncRNA–miRNA synergistic network following a four-step approach by integrating the regulatory pairs and expression profiles. The synergistic interactions with more shared regulatory mRNAs were found to have higher interactional intensity. Through the analysis of nodes in the network, we found that lncRNAs played roles that are more central and had similar synergistic interactions with their neighbors when compared with miRNAs. In addition, known colon adenocarcinoma (COAD)-related RNAs were found to be enriched in this synergistic network, with higher degrees, betweenness, and closeness. Finally, we proposed a risk score model to predict the clinical outcome for COAD patients based on two prognostic hub lncRNAs, MEG3 and ZEB1-AS1. Moreover, the hierarchical networks of these two lncRNAs could contribute to the understanding of the biological mechanism of tumorigenesis. For each lncRNA–miRNA interaction in the hub-related subnetwork and two hierarchical networks, we performed RNAup method to evaluate their binding energy. Our results identified two important lncRNAs with prognostic roles in colon cancer and dissected their regulatory mechanism involving synergistic interaction with miRNAs.
Collapse
Affiliation(s)
- Bin Zhao
- Department of Proctology, First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Xiusheng Qu
- Department of Chemoradiotherapy, First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Xin Lv
- Department of General Surgery, Samii Medical Center, Shenzhen, China
| | - Qingdong Wang
- Department of Anesthesiology, First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Deqiang Bian
- Scientific Research Departments, First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Fan Yang
- Department of Proctology, First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Xingwang Zhao
- Department of Proctology, First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Zhiwu Ji
- Department of Proctology, First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Jian Ni
- Department of Proctology, First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Yan Fu
- Department of Proctology, First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Guorong Xin
- Department of Proctology, First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Haitao Yu
- Department of Proctology, First Affiliated Hospital of Jiamusi University, Jiamusi, China
| |
Collapse
|
103
|
Zhang H, Zhu C, He Z, Chen S, Li L, Sun C. LncRNA PSMB8-AS1 contributes to pancreatic cancer progression via modulating miR-382-3p/STAT1/PD-L1 axis. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:179. [PMID: 32891166 PMCID: PMC7487636 DOI: 10.1186/s13046-020-01687-8] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/23/2020] [Indexed: 12/19/2022]
Abstract
Background Accumulating evidence demonstrates the essential role of long non-coding RNA (lncRNA) in various types of cancers, including pancreatic cancer. However, the functions and regulation mechanism of lncRNA PMSB8-AS1 in pancreatic cancer are largely unclear. Methods Quantitative reverse transcription PCR (qRT-PCR) is used to examine the expression of PMSB8-AS1 in PC tissues and PC cell lines. The effect of PMSB8-AS1 on the proliferation of PC cells was detected using CCK8 assay, colony assay, and flow cytometry. The effect of PMSB8-AS1 on the migration and invasion of pancreatic cancer cells was detected using a wound-healing assay and transwell migration assay. Bioinformatic analysis, double luciferase reporting assay, western blot, and rescue experiments were used to detect the regulatory relationship between PMSB8-AS1, miR-382–3p, STAT1, and PD-L1. Results PMSB8-AS1 expression was upregulated in PC tissues and cell lines and positively associated with the worst survival in patients with PC. The in vitro and in vivo assays demonstrated that overexpression of PMSB8-AS1 significantly promoted pancreatic cancer cell proliferation, migration, and invasion, whereas knockdown of PMSB8-AS1 suppressed cell proliferation, migration, invasion, and EMT, and decreased apoptosis of PC cells. Besides, PMSB8-AS1 directly bound to miR-382–3p downregulated its expression. Besides, PMSB8-AS1 reversed the effect of miR-382–3p on the growth and metastasis of PC cells, which might be targeted on STAT1. Furthermore, STAT1 is the transcriptional factor that activates the expression of PD-L1. Conclusion lncRNA PMSB8-AS1 promotes pancreatic cancer progression via STAT1 by sponging miR-382–3p involving regulation PD-L1.
Collapse
Affiliation(s)
- Hao Zhang
- College of Basic Medicine, Guizhou Medical University, Guiyang, China.,College of Clinical Medicine, Guizhou Medical University, Guiyang, China.,Department of Hepatic-Biliary-Pancreatic Surgery, the Affiliated Hospital of Guizhou Medical University, No.9, Beijing Road, Guiyang, 550000, Guizhou Province, China
| | - Changhao Zhu
- College of Basic Medicine, Guizhou Medical University, Guiyang, China.,College of Clinical Medicine, Guizhou Medical University, Guiyang, China.,Department of Hepatic-Biliary-Pancreatic Surgery, the Affiliated Hospital of Guizhou Medical University, No.9, Beijing Road, Guiyang, 550000, Guizhou Province, China
| | - Zhiwei He
- College of Basic Medicine, Guizhou Medical University, Guiyang, China.,College of Clinical Medicine, Guizhou Medical University, Guiyang, China.,Department of Hepatic-Biliary-Pancreatic Surgery, the Affiliated Hospital of Guizhou Medical University, No.9, Beijing Road, Guiyang, 550000, Guizhou Province, China
| | - Shiyu Chen
- College of Basic Medicine, Guizhou Medical University, Guiyang, China.,College of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Lin Li
- College of Basic Medicine, Guizhou Medical University, Guiyang, China.,College of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Chengyi Sun
- College of Basic Medicine, Guizhou Medical University, Guiyang, China. .,College of Clinical Medicine, Guizhou Medical University, Guiyang, China. .,Department of Hepatic-Biliary-Pancreatic Surgery, the Affiliated Hospital of Guizhou Medical University, No.9, Beijing Road, Guiyang, 550000, Guizhou Province, China.
| |
Collapse
|
104
|
Xu C, Zhai J, Fu Y. Overexpression of Nuclear Enriched Autosomal Transcript 1 Facilitates Cell Proliferation, Migration Invasion, and Suppresses Apoptosis in Endometrial Cancer by Targeting MicroRNA-202-3p/T Cell Immunoglobulin and Mucin Domain 4 Axis. Cancer Biother Radiopharm 2020; 37:815-823. [PMID: 32882142 DOI: 10.1089/cbr.2020.3902] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background: Endometrial cancer (EC) is an intractable gynecological cancer with increasing incidence and mortality worldwide. Accumulating studies indicated that long noncoding RNA nuclear enriched autosomal transcript 1 (NEAT1) was a novel oncogene implicated in a variety of cancers. However, whether NEAT1 could accelerate cell growth in EC is unclear. Methods: NEAT1, microRNA (miR)-202-3p, and T cell immunoglobulin and mucin domain 4 (TIMD4) levels were detected by quantitative real-time polymerase chain reaction. Cell proliferation and apoptosis were examined by cell counting kit-8 and flow cytometry. Transwell assay was employed for the evaluation of cell migration and invasion. The relationship between miR-202-3p and NEAT1 or TIMD4 was determined by luciferase reporter system. TIMD4 protein expression was assessed by Western blot assay. Results: NEAT1 was upregulated, whereas miR-202-3p was downregulated in EC tumors and cells. Depletion of NEAT1 restrained EC cell proliferation, migration, invasion, and improved apoptosis. MiR-202-3p was targeted by NEAT1 and could bind to TIMD4. Subsequently, it is observed that miR-202-3p inhibitor neutralized NEAT1 silencing mediated suppression on EC cell progression. Meanwhile, TIMD4 rescued miR-202-3p induced inhibition on cell progression in EC. Furthermore, it was obvious that NEAT1 facilitated TIMD4 expression by absorbing miR-202-3p in EC. Conclusions: Upregulation of NEAT1 accelerated EC cell progression through sponging miR-202-3p to facilitate TIMD4 expression, providing potential novel treatment method for EC.
Collapse
Affiliation(s)
- Caiyan Xu
- Department of Gynecologic and Obstetric, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Jianjun Zhai
- Department of Gynecologic and Obstetric, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yujing Fu
- Department of Gynecologic and Obstetric, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
105
|
Comprehensive Analysis of Long Non-coding RNA-Associated Competing Endogenous RNA Network in Duchenne Muscular Dystrophy. Interdiscip Sci 2020; 12:447-460. [PMID: 32876881 DOI: 10.1007/s12539-020-00388-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/18/2020] [Accepted: 08/24/2020] [Indexed: 12/20/2022]
Abstract
Duchenne muscular dystrophy (DMD) is one of the most severe neuromuscular disorders. Long non-coding RNAs (lncRNAs) are a group of non-coding transcripts, which could regulate messenger RNA (mRNA) by binding the mutual miRNAs, thus acting as competing endogenous RNAs (ceRNAs). So far, the role of lncRNA in DMD pathogenesis remains unclear. In the current study, expression profile from a total of 33 DMD patients and 12 healthy people were downloaded from Gene Expression Omnibus (GEO) database (GSE38417 and GSE109178). Differentially expressed (DE) lncRNAs were discovered and targeted mRNAs were predicted. The ceRNA network of lncRNAs-miRNAs-mRNAs was then constructed. Genome Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of the putative mRNAs in the ceRNA network were performed through Database for Annotation, Visualization and Integration Discovery (DAVID) website. Topological property of the network was analyzed using Cytoscape to disclose the hub lncRNAs. According to our assessments, 19 common DElncRNAs and 846 common DEmRNAs were identified in DMD compared to controls. The created ceRNA network contained 6 lncRNA nodes, 69 mRNA nodes, 27 miRNA nodes and 102 edges, while four hub lncRNAs (XIST, AL132709, LINC00310, ALDH1L1-AS2) were uncovered. In conclusion, our latest bioinformatic analysis demonstrated that lncRNA is likely involved in DMD. This work highlights the importance of lncRNA and provides new insights for exploring the molecular mechanism of DMD. The created ceRNA network contained 6 lncRNA nodes, 69 mRNA nodes, 27 miRNA nodes and 102 edges, while four hub lncRNAs (XIST, AL132709, LINC00310, ALDH1L1-AS2) were uncovered. Remarkably, KEGG analysis indicated that targeted mRNAs in the network were mainly enriched in "microRNAs in cancer" and "proteoglycans in cancer". Our study may offer novel perspectives on the pathogenesis of DMD from the point of lncRNAs. This work might be also conducive for exploring the molecular mechanism of increased incidence of tumorigenesis reported in DMD patients and experimental models.
Collapse
|
106
|
Guo Z, Han L, Fu Y, Wu Z, Ma Y, Li Y, Wang H, Jiang L, Liang S, Wang Z, Li F, Xiao W, Wang J, Wang Y. Systematic Evaluation of the Diagnostic and Prognostic Significance of Competitive Endogenous RNA Networks in Prostate Cancer. Front Genet 2020; 11:785. [PMID: 32849794 PMCID: PMC7406720 DOI: 10.3389/fgene.2020.00785] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 07/01/2020] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNA (lncRNA)-mediated competitive endogenous RNA (ceRNA) networks act as essential mechanisms in tumor initiation and progression, but their diagnostic and prognostic significance in prostate cancer (PCa) remains poorly understood. Presently, using the RNA expression data derived from multiple independent PCa-related studies, we constructed a high confidence and PCa-specific core ceRNA network by employing three lncRNA-gene inference approaches and key node filter strategies and then established a logistic model and risk score formula to evaluate its diagnostic and prognostic values, respectively. The core ceRNA network consists of 10 nodes, all of which are significantly associated with clinical outcomes. Combination of expression of the 10 ceRNAs with a logistic model achieved AUC of ROC and PR curve up to ∼96 and 99% in excluding normal prostate samples, respectively. Additionally, a risk score formula constructed with the ceRNAs exhibited significant association with disease-free survival. More importantly, utilizing the expression of RNAs in the core ceRNA network as a molecular signature, the TCGA-PRAD cohort was divided into four novel clinically relevant subgroups with distinct expression patterns, highlighting a feasible way for improving patient stratification in the future. Overall, we constructed a PCa-specific core ceRNA network, which provides diagnostic and prognostic value.
Collapse
Affiliation(s)
- Zihu Guo
- College of Life Science, Northwest A&F University, Yangling, China.,College of Life Science, Northwest University, Xi'an, China
| | - Liang Han
- Department of Andrology, Fangshan Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yingxue Fu
- College of Life Science, Northwest A&F University, Yangling, China
| | - Ziyin Wu
- State Key Laboratory of New-Tech for Chinese Medicine Pharmaceutical Process, Lianyungang, China
| | - Yaohua Ma
- College of Life Science, Northwest University, Xi'an, China
| | - Yueping Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Shihezi University, Shihezi, China
| | - Haiqing Wang
- College of Life Science, Northwest University, Xi'an, China
| | - Li Jiang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Shihezi University, Shihezi, China
| | - Shengnan Liang
- School of Chemistry and Pharmacy, Northwest A&F University, Yangling, China
| | - Zhenzhong Wang
- State Key Laboratory of New-Tech for Chinese Medicine Pharmaceutical Process, Lianyungang, China
| | - Furong Li
- Translational Medicine Collaborative Innovation Center, The Second Clinical Medical College (Shenzhen People's Hospital), Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Shenzhen, China
| | - Wei Xiao
- State Key Laboratory of New-Tech for Chinese Medicine Pharmaceutical Process, Lianyungang, China
| | - Jingbo Wang
- Translational Medicine Collaborative Innovation Center, The Second Clinical Medical College (Shenzhen People's Hospital), Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Shenzhen, China
| | - Yonghua Wang
- College of Life Science, Northwest A&F University, Yangling, China.,College of Life Science, Northwest University, Xi'an, China
| |
Collapse
|
107
|
Li J, Jiang X, Li Z, Huang L, Ji D, Yu L, Zhou Y, Cui Y. SP1-induced HOXD-AS1 promotes malignant progression of cholangiocarcinoma by regulating miR-520c-3p/MYCN. Aging (Albany NY) 2020; 12:16304-16325. [PMID: 32857725 PMCID: PMC7485728 DOI: 10.18632/aging.103660] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022]
Abstract
The purpose of this article is to explore the function and mechanism of HOXD-AS1 in cholangiocarcinoma. TCGA, StarBase and JASPAR were applied to predict the differential expression and molecular mechanism. The qRT-PCR was conducted to detect molecular expression. The effect of HOXD-AS1 on tumor proliferation, metastasis and stemness was measured through corresponding experiments. ChIP, luciferase reporter and RIP assays were implemented to explore the regulatory mechanism of HOXD-AS1 in CCA. In this study, HOXD-AS1 expression was significantly upregulated in CCA tissues and cells compared with control groups, respectively. Increased HOXD-AS1 was markedly correlated with lymph node invasion, advanced TNM stage and poor survival of CCA patients. Moreover, HOXD-AS1 was confirmed to be an unfavorable independent prognostic factor for CCA patients. Functionally, gain- and loss-of-function experiments demonstrated that HOXD-AS1 facilitated tumor proliferation, migration, invasion, EMT, stemness and drug resistance in vitro and in vivo. For the mechanism, transcription factor SP1-induced HOXD-AS1 upregulated oncogene MYCN through competitively binding to miR-520c-3p. Furthermore, HOXD-AS1-induced malignant phenotypes were rescued by interfering miR-520c-3p and MYCN, respectively. SP1/HOXD-AS1/miR-520c-3p/MYCN plays a vital role in initiation and progression of CCA, and HOXD-AS1 is expected to be an efficient biomarker and therapeutic target.
Collapse
Affiliation(s)
- Jinglin Li
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, China
| | - Xingming Jiang
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, China
| | - Zhenglong Li
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, China
| | - Lining Huang
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, China
| | - Daolin Ji
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, China
| | - Liang Yu
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, China
| | - Yongxu Zhou
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, China
| | - Yunfu Cui
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, China
| |
Collapse
|
108
|
Zhang Y, Lan X, Wang Y, Liu C, Cui T. CRNDE mediates the viability and epithelial-mesenchymal transition of renal cell carcinoma via miR-136-5p. J Recept Signal Transduct Res 2020; 41:234-244. [PMID: 32808846 DOI: 10.1080/10799893.2020.1805629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Long non-coding RNAs (lncRNAs) regulate epithelial-mesenchymal transition (EMT) and the mutual adhesion and development of renal cell carcinoma (RCC). The underlying molecular mechanism of EMT and RCC cells in the treatment of RCC was less reported. In this study, the related functional lncRNA and miRNA in RCC tissues were predicted by bioinformatics analysis and verified by quantitative real-time PCR (qRT-PCR). The RNA interference technology was applied to measure the effects of the predicted lncRNAs and miRNAs on RCC cells. The expressions of EMT-related mRNAs and proteins were determined using qRT-PCR and Western-blot experiments. CRNDE was overexpressed and miR-136-5p was low-expressed in RCC. Upregulation of CRNDE could promote the viability, migration, invasion of RCC, while downregulation of CRNDE produced the opposite effects. Both the upregulation and downregulation of CRNDE alternated the protein expressions related to EMT, while miR-136-5p resulted in the opposite effects on CRNDE. Moreover, the promotive effect of overexpressed CRNDE on RCC cells could be blocked by miR-136-5p mimic. CRNDE can mediate miR-136-5p, promote the development of EMT and RCC cells, showing the potential to serve as a novel biomarker and therapeutic target in RCC treatment.
Collapse
Affiliation(s)
- Yanhui Zhang
- Department of Urology, Qingdao Central Hospital, Qingdao, China
| | - Xiaopeng Lan
- Department of Urology, Qingdao Central Hospital, Qingdao, China
| | - Yizhen Wang
- Department of Urology, Qingdao Central Hospital, Qingdao, China
| | - Chunlei Liu
- Department of Urology, Qingdao Central Hospital, Qingdao, China
| | - Tao Cui
- Department of Urology, Qingdao Central Hospital, Qingdao, China
| |
Collapse
|
109
|
Li Y, Wang JS, Zhang T, Wang HC, Li LP. Identification of New Therapeutic Targets for Gastric Cancer With Bioinformatics. Front Genet 2020; 11:865. [PMID: 33014013 PMCID: PMC7461879 DOI: 10.3389/fgene.2020.00865] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/16/2020] [Indexed: 01/06/2023] Open
Abstract
We aimed to identify new targets affecting gastric cancer (GC) prognosis. Six target genes were identified from hub genes based on their relationship with important factors affecting tumor progression, like immune infiltration, purity, tumor mutation burden (TMB), and tumor microenvironment (TME) score. The effect of target genes' somatic mutations and copy number alteration (CNA) was examined to determine their effect on GC prognosis. Six target genes (FBN1, FN1, HGF, MMP9, THBS1, and VCAN) were identified. Reduced expression of each target gene, except MMP9, indicated better prognosis and lower grade in GC. FBN1, THBS1, and VCAN showed lower expression in stage I GC. Non-silencing mutations of the six genes played a role in significantly higher TMB and TME scores. THBS1 mutation was associated with earlier stage GC, and VCAN mutation was associated with lower grade GC. However, patients with target gene CNA displayed higher tumor purity. MMP9, THBS1, and VCAN CNA was associated with lower grade GC, while FBN1 CNA reflected earlier T stage. Additionally, the target genes may affect GC prognosis by influencing multiple oncogenic signaling pathways. FBN1, FN1, HGF, MMP9, THBS1, and VCAN may be new GC prognostic targets by affecting tumor purity, TMB, TME score, and multiple oncogenic signaling pathways.
Collapse
Affiliation(s)
- Yang Li
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jin-Shen Wang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tao Zhang
- Department of Biostatistics, School of Public Health, Shandong University, Jinan, China
| | - Hong-Chang Wang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Le-Ping Li
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| |
Collapse
|
110
|
Integrative Analysis of Three Novel Competing Endogenous RNA Biomarkers with a Prognostic Value in Lung Adenocarcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2837906. [PMID: 32802839 PMCID: PMC7424383 DOI: 10.1155/2020/2837906] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/23/2020] [Indexed: 12/20/2022]
Abstract
Increasing evidence has shown competitive endogenous RNAs (ceRNAs) play key roles in numerous cancers. Nevertheless, the ceRNA network that can predict the prognosis of lung adenocarcinoma (LUAD) is still lacking. The aim of the present study was to identify the prognostic value of key ceRNAs in lung tumorigenesis. Differentially expressed (DE) RNAs were identified between LUAD and adjacent normal samples by limma package in R using The Cancer Genome Atlas database (TCGA). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway function enrichment analysis was performed using the clusterProfiler package in R. Subsequently, the LUAD ceRNA network was established in three steps based on ceRNA hypothesis. Hub RNAs were identified using degree analysis methods based on Cytoscape plugin cytoHubba. Multivariate Cox regression analysis was implemented to calculate the risk score using the candidate ceRNAs and overall survival information. The survival differences between the high-risk and low-risk ceRNA groups were determined by the Kaplan-Meier and log-rank test using survival and survminer package in R. A total of 2,989 mRNAs, 185 lncRNAs, and 153 miRNAs were identified. GO and KEGG pathway function enrichment analysis showed that DE mRNAs were mainly associated with “sister chromatid segregation,” “regulation of angiogenesis,” “cell adhesion molecules (CAMs),” “cell cycle,” and “ECM-receptor interaction.” LUAD-related ceRNA network was constructed, which comprised of 54 nodes and 78 edges. Top ten hub RNAs (hsa-miR-374a-5p, hsa-miR-374b-5p, hsa-miR-340-5p, hsa-miR-377-3p, hsa-miR-21-5p, hsa-miR-326, SNHG1, RALGPS2, and PITX2) were identified according to their degree. Kaplan-Meier survival analyses demonstrated that hsa-miR-21-5p and RALGPS2 had a significant prognostic value. Finally, we found that a high risk of three novel ceRNA interactions (SNHG1-hsa-miR-21-5p-RALGPS2, SNHG1-hsa-miR-326-RALGPS2, and SNHG1-hsa-miR-377-3p-RALGPS2) was positively associated with worse prognosis. Three novel ceRNAs (SNHG1-hsa-miR-21-5p-RALGPS2, SNHG1-hsa-miR-326-RALGPS2, and SNHG1-hsa-miR-377-3p-RALGPS2) might be potential biomarkers for the prognosis and treatment of LUAD.
Collapse
|
111
|
Teng H, Li M, Qian L, Yang H, Pang M. Long non‑coding RNA SNHG16 inhibits the oxygen‑glucose deprivation and reoxygenation‑induced apoptosis in human brain microvascular endothelial cells by regulating miR‑15a‑5p/bcl‑2. Mol Med Rep 2020; 22:2685-2694. [PMID: 32945414 PMCID: PMC7453539 DOI: 10.3892/mmr.2020.11385] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 06/03/2020] [Indexed: 12/20/2022] Open
Abstract
MicroRNA (miR) 15a-5p can promote ischemia/reperfusion (I/R)-induced apoptosis of cerebral vascular endothelial cells, which is inhibited by long non-coding RNAs (lncRNAs). The present study investigated the potential of lncRNAs targeting miR-15a-5p to regulate oxygen-glucose deprivation and reoxygenation (OGD-R)-induced apoptosis of human brain microvascular endothelial cells (hBMECs). hBMECs were transfected with or without miR-15a-5p or its mutant, together with p-small nucleolar RNA host gene 16 (SNHG16) or its mutant. Following OGD-R, proliferation, apoptosis and miR-15a-5p, SNHG16 and Bcl-2 expression levels were determined using MTT, flow cytometry, reverse transcription-quantitative PCR or western blotting. The potential interaction of SNHG16 with miR-15a-5p was analyzed by pull-down, luciferase and immunoprecipitation assays. OGD-R induced apoptosis of hBMECs and increased miR-15a-5p expression levels in a time-dependent manner. miR-15a-5p overexpression decreased the proliferation of hBMECs and promoted apoptosis by decreasing Bcl-2 expression levels. SNHG16 was pulled-down by miR-15a-5p and anti-Ago2. miR-15a-5p overexpression significantly decreased SNHG16-regulated luciferase activity and hBMEC survival by increasing apoptosis. SNHG16 overexpression decreased miR-15a-5p expression levels in hBMECs. SNHG16 gradually decreased following OGD-R and its overexpression decreased miR-15a-5p expression levels and promoted the proliferation of hBMECs by decreasing apoptosis. SNHG16 enhanced Bcl-2 expression levels in hBMECs, which was abrogated by miR-15a-5p. Bioinformatics suggest that SNHG16 may antagonize the binding of miR-15a-5p to the 3′UTR of Bcl-2 mRNA. These findings suggest that SNHG16 may protect hBMECs from OGD-R-induced apoptosis by antagonizing the miR-15a-5p/bcl-2 axis. Thus, targeting SNHG16-based mechanisms may provide novel therapeutic strategies for treatment of ischemic stroke.
Collapse
Affiliation(s)
- Hongwei Teng
- Department of Neurosurgery, Binhai County People's Hospital, Yancheng, Jiangsu 224500, P.R. China
| | - Ming Li
- Department of Laboratory Medicine, Binhai County People's Hospital, Yancheng, Jiangsu 224500, P.R. China
| | - Lei Qian
- Department of Laboratory Medicine, Binhai County People's Hospital, Yancheng, Jiangsu 224500, P.R. China
| | - Hua Yang
- Department of Neurosurgery, Binhai County People's Hospital, Yancheng, Jiangsu 224500, P.R. China
| | - Mingzhi Pang
- Department of Neurosurgery, Wuxi No. 2 Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214002, P.R. China
| |
Collapse
|
112
|
Glaß M, Dorn A, Hüttelmaier S, Haemmerle M, Gutschner T. Comprehensive Analysis of LincRNAs in Classical and Basal-Like Subtypes of Pancreatic Cancer. Cancers (Basel) 2020; 12:cancers12082077. [PMID: 32727085 PMCID: PMC7464731 DOI: 10.3390/cancers12082077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/09/2020] [Accepted: 07/23/2020] [Indexed: 02/07/2023] Open
Abstract
Pancreatic ductal adenocarcinomas (PDAC) belong to the deadliest malignancies in the western world. Mutations in TP53 and KRAS genes along with some other frequent polymorphisms occur almost universally and are major drivers of tumour initiation. However, these mutations cannot explain the heterogeneity in therapeutic responses and differences in overall survival observed in PDAC patients. Thus, recent classifications of PDAC tumour samples have leveraged transcriptome-wide gene expression data to account for epigenetic, transcriptional and post-transcriptional mechanisms that may contribute to this deadly disease. Intriguingly, long intervening RNAs (lincRNAs) are a special class of long non-coding RNAs (lncRNAs) that can control gene expression programs on multiple levels thereby contributing to cancer progression. However, their subtype-specific expression and function as well as molecular interactions in PDAC are not fully understood yet. In this study, we systematically investigated the expression of lincRNAs in pancreatic cancer and its molecular subtypes using publicly available data from large-scale studies. We identified 27 deregulated lincRNAs that showed a significant different expression pattern in PDAC subtypes suggesting context-dependent roles. We further analyzed these lincRNAs regarding their common expression patterns. Moreover, we inferred clues on their functions based on correlation analyses and predicted interactions with RNA-binding proteins, microRNAs, and mRNAs. In summary, we identified several PDAC-associated lincRNAs of prognostic relevance and potential context-dependent functions and molecular interactions. Hence, our study provides a valuable resource for future investigations to decipher the role of lincRNAs in pancreatic cancer.
Collapse
Affiliation(s)
- Markus Glaß
- Institute of Molecular Medicine, Section for Cell Biology, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany; (M.G.); (S.H.)
| | - Agnes Dorn
- Institute of Pathology, Section for Experimental Pathology, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany;
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Section for Cell Biology, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany; (M.G.); (S.H.)
| | - Monika Haemmerle
- Institute of Pathology, Section for Experimental Pathology, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany;
- Correspondence: (M.H.); (T.G.)
| | - Tony Gutschner
- Junior Research Group ‘RNA Biology and Pathogenesis’, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany
- Correspondence: (M.H.); (T.G.)
| |
Collapse
|
113
|
Wang X, Zhang X, Dang Y, Li D, Lu G, Chan WY, Leung PCK, Zhao S, Qin Y, Chen ZJ. Long noncoding RNA HCP5 participates in premature ovarian insufficiency by transcriptionally regulating MSH5 and DNA damage repair via YB1. Nucleic Acids Res 2020; 48:4480-4491. [PMID: 32112110 PMCID: PMC7192606 DOI: 10.1093/nar/gkaa127] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 02/18/2020] [Indexed: 12/14/2022] Open
Abstract
The genetic etiology of premature ovarian insufficiency (POI) has been well established to date, however, the role of long noncoding RNAs (lncRNAs) in POI is largely unknown. In this study, we identified a down-expressed lncRNA HCP5 in granulosa cells (GCs) from biochemical POI (bPOI) patients, which impaired DNA damage repair and promoted apoptosis of GCs. Mechanistically, we discovered that HCP5 stabilized the interaction between YB1 and its partner ILF2, which could mediate YB1 transferring into the nucleus of GCs. HCP5 silencing affected the localization of YB1 into nucleus and reduced the binding of YB1 to the promoter of MSH5 gene, thereby diminishing MSH5 expression. Taken together, we identified that the decreased expression of HCP5 in bPOI contributed to dysfunctional GCs by regulating MSH5 transcription and DNA damage repair via the interaction with YB1, providing a novel epigenetic mechanism for POI pathogenesis.
Collapse
Affiliation(s)
- Xiaoyan Wang
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China.,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong 250012, China
| | - Xinyue Zhang
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China.,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong 250012, China
| | - Yujie Dang
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China.,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong 250012, China
| | - Duan Li
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China.,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong 250012, China
| | - Gang Lu
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China
| | - Wai-Yee Chan
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China
| | - Peter C K Leung
- Department of Obstetrics and Gynaecology, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Shidou Zhao
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China.,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong 250012, China.,CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China
| | - Yingying Qin
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China.,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong 250012, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China.,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong 250012, China.,Shanghai Key Laboratory of Assisted Reproduction and Reproductive Genetics, Shanghai 200127, China.,Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| |
Collapse
|
114
|
Lou W, Ding B, Zhong G, Yao J, Fan W, Fu P. RP11-480I12.5-004 Promotes Growth and Tumorigenesis of Breast Cancer by Relieving miR-29c-3p-Mediated AKT3 and CDK6 Degradation. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:916-931. [PMID: 32810693 PMCID: PMC7452110 DOI: 10.1016/j.omtn.2020.07.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/11/2022]
Abstract
Pseudogenes have been reported to exert oncogenic or tumor-suppressive functions in cancer. However, the expression, role, and mechanism of pseudogene-derived RNAs in breast cancer remain unclear. The RNA levels and prognostic values of pseudogenes in breast cancer were determined. The levels of RP11-480I12.5 in cell lines and clinical samples were validated by quantitative real-time PCR. In vitro effects of RP11-480I12.5 on cell growth were measured by cell counting kit-8 (CCK-8) assay, colony formation assay, cell counting assay, and flow cytometry analysis. Xenograft model was established to detect its in vivo effect. The potential mechanism of RP11-480I12.5 was also studied by a combination of bioinformatic analysis and experimental confirmation. Finally, the possible functional parental genes of RP11-480I12.5 in breast cancer were explored. After a series of bioinformatic analyses, RP11-480I12.5 was selected as the most potential pseudogene in breast cancer. RP11-480I12.5 expression was significantly upregulated in breast cancer cell lines and clinical breast cancer tissues. Knockdown of RP11-480I12.5 markedly suppressed cell proliferation and colony formation, induced cell apoptosis of breast cancer in vitro, and inhibited tumor growth in vivo. Four transcripts of RP11-480I12.5 (001/002/003/004) were identified. Only overexpression of RP11-480I12.5-004 significantly enhanced cell growth of breast cancer both in vitro and in vivo. RP11-480I12.5-004 mainly located in cytoplasm and increased AKT3 and CDK6 mRNA expression, at least in part, by competitively binding to miR-29c-3p. Six parental genes of RP11-480I12.5 were found, among which TUBA1B and TUBA1C were statistically linked to RP11-480I12.5 expression, possessed prognostic values, and were upregulated in breast cancer. Our findings suggested that pseudogene-derived long non-coding RNA (lncRNA) RP11-480I12.5-004 promoted growth and tumorigenesis of breast cancer via increasing AKT3 and CDK6 expression by competitively binding to miR-29c-3p.
Collapse
Affiliation(s)
- Weiyang Lou
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, Zhejiang 310003, China; Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation, Zhejiang University, Hangzhou 310003, Zhejiang, Province, China.
| | - Bisha Ding
- Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation, Zhejiang University, Hangzhou 310003, Zhejiang, Province, China
| | - Guansheng Zhong
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, Zhejiang 310003, China
| | - Jia Yao
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, Zhejiang 310003, China
| | - Weimin Fan
- Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation, Zhejiang University, Hangzhou 310003, Zhejiang, Province, China
| | - Peifen Fu
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, Zhejiang 310003, China.
| |
Collapse
|
115
|
Agbana YL, Abi ME, Ni Y, Xiong G, Chen J, Yun F, Yi Z, Zhang Q, Yang Z, Kuang Y, Zhu Y. LINC00511 as a prognostic biomarker for human cancers: a systematic review and meta-analysis. BMC Cancer 2020; 20:682. [PMID: 32698787 PMCID: PMC7376647 DOI: 10.1186/s12885-020-07188-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/16/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Long intergenic non-coding RNA 00511 (LINC00511) is highly expressed in diverse cancers and has a correlation with poor clinical outcomes for cancer patients. In view of contradictory data among published data, we aim to evaluate the prognostic role of LINC00511 for cancer patients. METHODS In the present study, a meta-analysis of related studies has been performed to investigate the prognostic significance of LINC00511 in cancer patients. Relevant studies published before December 22, 2019 were systematically searched online in PubMed, EMBASE, Web of Science, and the Cochrane Library databases. The relationship between LINC00511 expression and cancer patients' survival, including overall survival (OS), disease-free survival (DFS)/relapse-free survival (RFS) and progression-free survival (PFS), was evaluated using pooled hazard ratios (HRs) with their corresponding 95% confidence intervals (CIs). The association between LINC00511 expression and clinicopathological features was assessed using odd ratios (ORs) and their corresponding 95% CIs. RESULTS A total of 14 eligible studies with 1883 patients were enrolled in the present meta-analysis. The results demonstrated that elevated expression of LINC00511 was significantly associated with poor OS (HR = 2.62; 95% CI: 2.00-3.45; p < 0.001), PFS (HR = 1.80; 95% CI: 1.29-2.51; p = 0.001) and DFS/RFS (HR = 2.90; 95% CI: 1.04-8.12; p = 0.04). Additionally, High LINC00511 expression was associated with large tumor size (OR = 3.10; 95% CI: 1.97-4.86; p < 0.00001), lymph node metastasis (OR = 3.11; 95% CI: 2.30-4.21; p < 0.00001), advanced clinical stage (OR = 3.95; 95% CI: 2.68-5.81; p < 0.00001), distant metastasis (OR = 2.39; 95% CI: 1.16-4.93; p = 0.02), and disease recurrence (OR = 4.62; 95% CI: 2.47-8.65; p < 0.00001). Meanwhile, no correlation was found between LINC00511 expression and age, gender, and histological grade. These findings were consolidated by the results of bioinformatics analysis. CONCLUSIONS Based on our findings, LINC00511 may serve as a novel prognostic biomarker for cancer patients.
Collapse
Grants
- 31660246, 31960200,81960462,31960145,81460421,81760455, 81560037,91660135 National Natural Science Foundation of China
- 2017FE468(-003), 2018FE468(-001), 2017FE468(-132) Yunnan Province, Kunming Medical University joint Foundation for Applied Basic Research
- National Natural Science Foundation of China
- Yunnan Province, Kunming Medical University joint Foundation for Applied Basic Research
Collapse
Affiliation(s)
- Yannick Luther Agbana
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650500 Yunnan Province China
| | - Manzama-Esso Abi
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan Province China
| | - Yueli Ni
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650500 Yunnan Province China
| | - Guohang Xiong
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650500 Yunnan Province China
| | - Jing Chen
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650500 Yunnan Province China
| | - Fang Yun
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650500 Yunnan Province China
| | - Zihan Yi
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650500 Yunnan Province China
| | - Qiao Zhang
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650500 Yunnan Province China
| | - Zhe Yang
- Department of Pathology, The First Affiliated Hospital of Kunming Medical University, Wuhua District, Kunming, 650032 Yunnan Province China
| | - Yingmin Kuang
- Department of Organ Transplantation, The First Affiliated Hospital of Kunming Medical University, Wuhua District, Kunming, 650032 Yunnan Province China
| | - Yuechun Zhu
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650500 Yunnan Province China
| |
Collapse
|
116
|
Wang XF, Liang B, Chen C, Zeng DX, Zhao YX, Su N, Ning WW, Yang W, Huang JA, Gu N, Zhu YH. Long Intergenic Non-protein Coding RNA 511 in Cancers. Front Genet 2020; 11:667. [PMID: 32733536 PMCID: PMC7358593 DOI: 10.3389/fgene.2020.00667] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/01/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Long intergenic non-protein coding RNA 511 (LINC00511) is upregulated in diverse cancers and involved in prognosis. This study aimed to evaluate the prognostic profile of LINC00511 in cancer patients. Methods: Published studies evaluating the prognosis of LINC00511 in patients with different cancers were identified from Medline, Embase, and Web of Science. Analysis of the association between LINC00511 and clinicopathological characteristics was conducted. GEPIA was used to validation and functional analysis and LnCeVar was used to get genomic variations. Results: We eventually included 9 studies, and the combined results showed LINC00511 was significantly associated with decreased OS (HR = 3.18, 95% CI = 2.29 ~ 4.42, P < 0.001) albeit with mild heterogeneity (I2 = 58.1%, Ph = 0.014), similarly in cancer type subgroups: breast cancer, digestive system cancer, and cervical cancer (all P < 0.001). There is no publication bias and meta-regression indicated follow-up time maybe heterogeneity of the results (P = 0.008). Additionally, LINC00511 appeared to be correlated with age, clinical stage, tumor size, and lymph node metastasis. Those findings were confirmed in GEPIA. Through LnCeVars, gene ontology and functional pathways were enriched, and dysregulated hallmarks and related ceRNA network of LINC00511 were disturbed. Conclusions: LINC00511 could be predictive of poor OS and lymph node metastasis in multiple cancers, in another word, LINC00511 serves as an unfavorable prognostic factor, and its mechanism is related to ceRNA.
Collapse
Affiliation(s)
- Xiao-Fei Wang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Bo Liang
- Nanjing University of Chinese Medicine, Nanjing, China
| | - Cheng Chen
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Da-Xiong Zeng
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yu-Xiu Zhao
- Hospital of Traditional Chinese Medicine (T.C.M) Affiliated to Southwest Medical University, Luzhou, China
| | - Nan Su
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Wei-Wei Ning
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Wen Yang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jian-An Huang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Ning Gu
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Ye-Han Zhu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| |
Collapse
|
117
|
Ma ZJ, Wang Y, Li HF, Liu MH, Bi FR, Ma L, Ma H, Yan HL. LncZEB1-AS1 regulates hepatocellular carcinoma bone metastasis via regulation of the miR-302b-EGFR-PI3K-AKT axis. J Cancer 2020; 11:5118-5128. [PMID: 32742459 PMCID: PMC7378930 DOI: 10.7150/jca.45995] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/09/2020] [Indexed: 12/15/2022] Open
Abstract
In patients with hepatocellular carcinoma (HCC), disease progression and associated bone metastasis (BM) can markedly reduce quality of life. While the long non-coding RNA (lncRNA) zinc finger E-box binding homeobox 1 antisense 1 (ZEB1-AS1) has been shown to function as a key regulator of oncogenic processes in HCC and other tumor types, whether it plays a role in controlling HCC BM remains to be established. In the current study, we detected the significant upregulation of lncZEB1-AS1 in HCC tissues, and we found this expression to be associated with BM progression. When we knocked down this lncRNA in HCC cells, we found that this significantly reduced their migratory, invasive, and metastatic activity both in vitro and in vivo. At a mechanistic level, we found that lncZEB1-AS1 was able to target miR-302b and to thereby increase PI3K-AKT pathway activation and EGFR expression, resulting in the enhanced expression of downstream matrix metalloproteinase genes in HCC cells. In summary, our results provide novel evidence that lncZEB1-AS1 can promote HCC BM through a mechanism dependent upon the activation of PI3K-AKT signaling, thus highlighting a potentially novel therapeutic avenue for the treatment of such metastatic progression in HCC patients.
Collapse
Affiliation(s)
- Zhen-Jiang Ma
- Department of Orthopedics, the Third Affiliated Hospital of Second Military Medical University, Shanghai 201805, P.R. China.,Department of Orthopedics, Shanghai Ninth People's Hospital, Shanghai 200011, P.R. China
| | - Yao Wang
- Department of Laboratory Medicine, Changhai Hospital, Second Military Medical University, Shanghai, P.R. China.,Department of Laboratory Medicine, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu 214000, China
| | - Hui-Fen Li
- Department of Interventional, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, P.R. China
| | - Ming-Hua Liu
- Department of Laboratory Medicine, Changhai Hospital, Second Military Medical University, Shanghai, P.R. China
| | - Feng-Rui Bi
- Department of Laboratory Medicine, Changhai Hospital, Second Military Medical University, Shanghai, P.R. China
| | - Long Ma
- Department of Laboratory Medicine, Changhai Hospital, Second Military Medical University, Shanghai, P.R. China
| | - Hui Ma
- Department of Orthopedics, the Third Affiliated Hospital of Second Military Medical University, Shanghai 201805, P.R. China
| | - Hong-Li Yan
- Department of Laboratory Medicine, Changhai Hospital, Second Military Medical University, Shanghai, P.R. China
| |
Collapse
|
118
|
Identification and Verification of Biomarker in Clear Cell Renal Cell Carcinoma via Bioinformatics and Neural Network Model. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6954793. [PMID: 32626756 PMCID: PMC7317307 DOI: 10.1155/2020/6954793] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/10/2020] [Accepted: 05/22/2020] [Indexed: 12/20/2022]
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is the most common subtype of kidney cancer, which represents the 9th most frequently diagnosed cancer. However, the molecular mechanism of occurrence and development of ccRCC is indistinct. Therefore, the research aims to identify the hub biomarkers of ccRCC using numerous bioinformatics tools and functional experiments. Methods The public data was downloaded from the Gene Expression Omnibus (GEO) database, and the differently expressed genes (DEGs) between ccRCC and normal renal tissues were identified with GEO2R. Protein-protein interaction (PPI) network of the DEGs was constructed, and hub genes were screened with cytoHubba. Then, ten ccRCC tumor samples and ten normal kidney tissues were obtained to verify the expression of hub genes with the RT-qPCR. Finally, the neural network model was constructed to verify the relationship among the genes. Results A total of 251 DEGs and ten hub genes were identified. AURKB, CCNA2, TPX2, and NCAPG were highly expressed in ccRCC compared with renal tissue. With the increasing expression of AURKB, CCNA2, TPX2, and NCAPG, the pathological stage of ccRCC increased gradually (P < 0.05). Patients with high expression of AURKB, CCNA2, TPX2, and NCAPG have a poor overall survival. After the verification of RT-qPCR, the expression of hub genes was same as the public data. And there were strong correlations between the AURKB, CCNA2, TPX2, and NCAPG with the verification of the neural network model. Conclusion After the identification and verification, AURKB, CCNA2, TPX2, and NCAPG might be related to the occurrence and malignant progression of ccRCC.
Collapse
|
119
|
Weng W, Zhang Z, Huang W, Xu X, Wu B, Ye T, Shan Y, Shi K, Lin Z. Identification of a competing endogenous RNA network associated with prognosis of pancreatic adenocarcinoma. Cancer Cell Int 2020; 20:231. [PMID: 32536819 PMCID: PMC7288603 DOI: 10.1186/s12935-020-01243-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 05/04/2020] [Indexed: 12/11/2022] Open
Abstract
Background Emerging evidence suggests that competing endogenous RNAs plays a crucial role in the development and progress of pancreatic adenocarcinoma (PAAD). The objective was to identify a new lncRNA-miRNA-mRNA network as prognostic markers, and develop and validate a multi-mRNAs-based classifier for predicting overall survival (OS) in PAAD. Methods Data on pancreatic RNA expression and clinical information of 445 PAAD patients and 328 normal subjects were downloaded from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC) and Genotype-Tissue Expression (GTEx). The weighted correlation network analysis (WGCNA) was used to analyze long non-coding RNA (lncRNA) and mRNA, clustering genes with similar expression patterns. MiRcode was used to predict the sponge microRNAs (miRNAs) corresponding to lncRNAs. The downstream targeted mRNAs of miRNAs were identified by starBase, miRDB, miRTarBase and Targetscan. A multi-mRNAs-based classifier was develop using least absolute shrinkage and selection operator method (LASSO) COX regression model, which was tested in an independent validation cohort. Results A lncRNA-miRNA-mRNA co-expression network which consisted of 60 lncRNAs, 3 miRNAs and 3 mRNAs associated with the prognosis of patients with PAAD was established. In addition, we constructed a 14-mRNAs-based classifier based on a training cohort composed of 178 PAAD patients, of which the area under receiver operating characteristic (AUC) in predicting 1-year, 3-year, and 5-year OS was 0.719, 0.806 and 0.794, respectively. The classifier also shown good prediction function in independent verification cohorts, with the AUC of 0.604, 0.639 and 0.607, respectively. Conclusions A novel competitive endogenous RNA (ceRNA) network associated with progression of PAAD could be used as a reference for future molecular biology research.
Collapse
Affiliation(s)
- Wanqing Weng
- Zhejiang Provincial Key Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000 Zhejiang People's Republic of China.,Precision Medicine Center Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000 Zhejiang People's Republic of China
| | - Zhongjing Zhang
- Zhejiang Provincial Key Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000 Zhejiang People's Republic of China
| | - Weiguo Huang
- Zhejiang Provincial Key Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000 Zhejiang People's Republic of China
| | - Xiangxiang Xu
- Zhejiang Provincial Key Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000 Zhejiang People's Republic of China
| | - Boda Wu
- Zhejiang Provincial Key Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000 Zhejiang People's Republic of China.,Precision Medicine Center Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000 Zhejiang People's Republic of China
| | - Tingbo Ye
- Zhejiang Provincial Key Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000 Zhejiang People's Republic of China
| | - Yunfeng Shan
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000 Zhejiang People's Republic of China
| | - Keqing Shi
- Zhejiang Provincial Key Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000 Zhejiang People's Republic of China.,Precision Medicine Center Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000 Zhejiang People's Republic of China
| | - Zhuo Lin
- Department of Liver Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000 Zhejiang People's Republic of China
| |
Collapse
|
120
|
Shi J, Huang Y, Wen C, He S, Wu L, Zhou H. Genome-wide identification and characterization of long non-coding RNAs involved in acquired resistance to gefitinib in non-small-cell lung cancer. Comput Biol Chem 2020; 87:107288. [PMID: 32521497 DOI: 10.1016/j.compbiolchem.2020.107288] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 12/28/2022]
Abstract
Acquired resistance is a major obstacle to the therapeutic efficacy of gefitinib in non-small-cell lung cancer (NSCLC). Current knowledge about the role of long non-coding RNAs (lncRNAs) in this phenomenon is insufficient. In this study, we searched RNA sequencing data for lncRNAs associated with acquired resistance to gefitinib in NSCLC, and constructed a functional lncRNA-mRNA co-expression network and protein-protein interaction (PPI) network to analyze their putative target genes and biological functions. The expression levels of 14 outstanding dysregulated lncRNAs and mRNA were verified using real-time PCR. Changes in the expression levels of 39 lncRNAs and 121 mRNAs showed common patterns in our two pairs of gefitinib-sensitive and gefitinib-resistant NSCLC cell lines. The co-expression network included 1235 connections among these common differentially expressed lncRNAs and mRNAs. The significantly enriched signaling pathways based on dysregulated mRNAs were mainly involved in the Hippo signaling pathway; proteoglycans in cancer; and valine, leucine, and isoleucine biosynthesis. The results show that LncRNAs play an important part in acquired gefitinib resistance in NSCLC by regulating mRNA expression and function, and may represent potential new molecular biomarkers and therapeutic targets for gefitinib-resistant NSCLC.
Collapse
Affiliation(s)
- Jingjing Shi
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Yutang Huang
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Chunjie Wen
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Shuai He
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Lanxiang Wu
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China.
| | - Honghao Zhou
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China; Pharmacogenetics Research Institute, Institute of Clinical Pharmacology, Central South University, Changsha 410078, China
| |
Collapse
|
121
|
Zhao F, Wei C, Cui MY, Xia QQ, Wang SB, Zhang Y. Prognostic value of microRNAs in pancreatic cancer: a meta-analysis. Aging (Albany NY) 2020; 12:9380-9404. [PMID: 32420903 PMCID: PMC7288910 DOI: 10.18632/aging.103214] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/17/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND The prognostic impact of microRNA (miRNA) expression levels in pancreatic cancer (PC) has been estimated for years, but the outcomes are controversial and heterogeneous. Therefore, we comprehensively reviewed the evidence collected on miRNA expression in PC to determine this effect. RESULTS PC patients with high miR-21 (HR=2.61, 95%CI=1.68-4.04), miR-451a (HR=2.23, 95%CI=1.23-4.04) or miR-1290 (HR=1.43, 95%CI=1.04-1.95) levels in blood had significantly poorer OS (P<0.05). Furthermore, PC patients with high miR-10b (HR=1.73, 95%CI=1.09-2.76), miR-17-5p (HR=1.91, 95%CI=1.30-2.80), miR-21 (HR=1.90, 95%CI=1.61-2.25), miR-23a (HR=2.18, 95%CI=1.52-3.13), miR-155 (HR=2.22, 95%CI=1.27-3.88), miR-203 (HR=1.65, 95%CI=1.14-2.40), miR-221 (HR=1.72, 95%CI=1.08-2.74), miR-222 levels (HR=1.72, 95%CI=1.02-2.91) or low miR-29c (HR=1.39, 95%CI=1.08-1.79), miR-126 (HR=1.55, 95%CI=1.23-1.95), miR-218 (HR=2.62, 95%CI=1.41-4.88) levels in tissues had significantly shorter OS (P<0.05). CONCLUSIONS In summary, blood miR-21, miR-451a, miR-1290 and tissue miR-10b, miR-17-5p, miR-21, miR-23a, miR-29c, miR-126, miR-155, miR-203, miR-218, miR-221, miR-222 had significant prognostic value. METHODS We searched PubMed, EMBASE, Web of Science and Cochrane Database of Systematic Reviews to recognize eligible studies, and 57 studies comprising 5445 PC patients and 15 miRNAs were included to evaluate the associations between miRNA expression levels and overall survival (OS) up to June 1, 2019. Summary hazard ratios (HR) with 95% confidence intervals (CI) were calculated to assess the effect.
Collapse
Affiliation(s)
- Fei Zhao
- , Department of Traditional Chinese Medicine, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Chao Wei
- College of Integrated Traditional Chinese and Western Medicine, Jining Medical University, Jining, Shandong, China
| | - Meng-Ying Cui
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Qiang-Qiang Xia
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Shuai-Bin Wang
- Department of Urology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yue Zhang
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| |
Collapse
|
122
|
Chen H, Chen L. An integrated analysis of the competing endogenous RNA network and co-expression network revealed seven hub long non-coding RNAs in osteoarthritis. Bone Joint Res 2020; 9:90-98. [PMID: 32435461 PMCID: PMC7229307 DOI: 10.1302/2046-3758.93.bjr-2019-0140.r2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aims This study aimed to uncover the hub long non-coding RNAs (lncRNAs) differentially expressed in osteoarthritis (OA) cartilage using an integrated analysis of the competing endogenous RNA (ceRNA) network and co-expression network. Methods Expression profiles data of ten OA and ten normal tissues of human knee cartilage were obtained from the Gene Expression Omnibus (GEO) database (GSE114007). The differentially expressed messenger RNAs (DEmRNAs) and lncRNAs (DElncRNAs) were identified using the edgeR package. We integrated human microRNA (miRNA)-lncRNA/mRNA interactions with DElncRNA/DEmRNA expression profiles to construct a ceRNA network. Likewise, lncRNA and mRNA expression profiles were used to build a co-expression network with the WGCNA package. Potential hub lncRNAs were identified based on an integrated analysis of the ceRNA network and co-expression network. StarBase and Multi Experiment Matrix databases were used to verify the lncRNAs. Results We detected 1,212 DEmRNAs and 49 DElncRNAs in OA and normal knee cartilage. A total of 75 dysregulated lncRNA-miRNA interactions and 711 dysregulated miRNA-mRNA interactions were obtained in the ceRNA network, including ten DElncRNAs, 69 miRNAs, and 72 DEmRNAs. Similarly, 1,330 dysregulated lncRNA-mRNA interactions were used to construct the co-expression network, which included ten lncRNAs and 407 mRNAs. We finally identified seven hub lncRNAs, named MIR210HG, HCP5, LINC00313, LINC00654, LINC00839, TBC1D3P1-DHX40P1, and ISM1-AS1. Subsequent enrichment analysis elucidated that these lncRNAs regulated extracellular matrix organization and enriched in osteoclast differentiation, the FoxO signalling pathway, and the tumour necrosis factor (TNF) signalling pathway in the development of OA. Conclusion The integrated analysis of the ceRNA network and co-expression network identified seven hub lncRNAs associated with OA. These lncRNAs may regulate extracellular matrix changes and chondrocyte homeostasis in OA progress. Cite this article:Bone Joint Res. 2020;9(3):90–98.
Collapse
Affiliation(s)
- Haitao Chen
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Liaobin Chen
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| |
Collapse
|
123
|
Gao S, Ding B, Lou W. microRNA-Dependent Modulation of Genes Contributes to ESR1's Effect on ERα Positive Breast Cancer. Front Oncol 2020; 10:753. [PMID: 32500028 PMCID: PMC7243797 DOI: 10.3389/fonc.2020.00753] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/20/2020] [Indexed: 12/16/2022] Open
Abstract
Background: Dysregulation of ESR1 accounts for endocrine therapy resistance and metastasis of ERα positive breast cancer. However, the underlying molecular mechanism of ESR1 in ERα positive breast cancer remains insufficiency. Notably, to date, a comprehensive miRNA-mRNA regulatory network involved in modulation of ESR1 in development and progression of ERα positive breast cancer is still not established. Methods: Microarray miRNA and mRNA expression profiling from GEO database were used to obtained significant DE-miRNAs and DE-mRNAs in ERα positive breast cancer. Functional enrichment analysis was conducted by Enrichr database. STRING database was utilized to construct protein-protein interaction network, after which hub genes were identified through Cytoscape. Kaplan-Meier plotter was introduced to perform survival analysis. The relationship between ESR1-miRNA or miRNA-target gene pairs were experimentally validated. Results: 74 DE-miRNAs, including 19 upregulated and 55 downregulated miRNAs, and 830 DE-mRNAs, including 359 upregulated and 471 downregulated mRNAs, in ERα positive breast cancer were identified. Potential DE-mRNAs were statistically enriched in several cancer-associated pathways, such as cell cycle and pathway in cancer. Fifty-one hub genes with node degree more than 10 were screened. Twenty-seven of 51 hub genes had significant prognostic values in ERα positive breast cancer. Based on the 27 hub genes, a miRNA-hub gene network, containing 26 miRNAs, was established. Seven of 26 miRNAs were found to possess prognostic predictive roles for patients with ERα positive breast cancer by combination of TCGA and METABRIC data. Intriguingly, ESR1 positively correlated and regulated the 7 miRNAs and the 7 miRNAs inversely correlated and modulated their corresponding downstream targets in MCF-7 and T47D cells, supporting the accuracy of in silico analysis. The relationship between ESR1-miRNA, miRNA-mRNA, or ESR1-mRNA pairs was validated in clinical ERα positive breast cancer. Conclusions: In total, the current findings from this work add substantially to the understanding of ESR1's molecular regulatory mechanism in ERα positive breast cancer.
Collapse
Affiliation(s)
- Shan Gao
- Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China.,Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Bisha Ding
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Weiyang Lou
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| |
Collapse
|
124
|
Yuan B, Guan Q, Yan T, Zhang X, Xu W, Li J. LncRNA HCP5 Regulates Pancreatic Cancer Progression by miR-140-5p/CDK8 Axis. Cancer Biother Radiopharm 2020; 35:711-719. [PMID: 32407143 DOI: 10.1089/cbr.2019.3294] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background: Pancreatic cancer (PC) is a leading cause of cancer-related deaths worldwide. Human leukocyte antigen complex P5 (HCP5), a member of long noncoding RNAs (lncRNAs), was reported to be associated with the poor prognosis of PC. However, the mechanism of HCP5 in regulating the progression of PC remains poorly defined. Materials and Methods: Quantitative real-time polymerase chain reaction was performed to detect the expression levels of HCP5, microRNA (miR)-140-5p, and cyclin-dependent kinase 8 (CDK8) in PC tissues and cells. Cell counting kit-8 (CCK-8) assay was utilized to check cell proliferation. Transwell assay was employed to evaluate the abilities of cell migration and invasion. Xenograft tumor model was established to investigate the biological role of HCP5 in PC in vivo. The interaction between miR-140-5p and HCP5 or CDK8 was predicted by starBase or TargetScan, respectively. The dual-luciferase reporter assay was conducted to corroborate the interaction. The protein level of CDK8 was measured by Western blot. Results: HCP5 and CDK8 were significantly upregulated in PC tissues and cells, opposite to the expression of miR-140-5p. High expression of HCP5 contributed to the low survival rate and HCP5 silencing inhibited proliferation, migration, and invasion of PC cells in vitro. Simultaneously, in vivo experiments indicated that downregulation of HCP5 suppressed tumor growth. In addition, miR-140-5p was a target of HCP5 and bound to the 3'-untranslated region (3'UTR) of CDK8. Further studies revealed that overexpression of CDK8 reversed the miR-140-5p-mediated inhibitory effect on PC progression. Moreover, downregulation of miR-140-5p or upregulation of CDK8 inverted the silencing-mediated repressive impact of HCP5 on PC progression. Conclusion: Downregulation of HCP5 impeded PC progression by downregulating CDK8 via sponging miR-140-5p.
Collapse
Affiliation(s)
- Bo Yuan
- Department of Hepatobiliary Surgery, Dongying City People's Hospital, Dongying, China
| | - Qiang Guan
- Department of Hepatobiliary Surgery, Dongying City People's Hospital, Dongying, China
| | - Tinghai Yan
- Department of Oncology, Wudi County People's Hospital, Binzhou, China
| | - Xiaobin Zhang
- Department of Hepatobiliary Surgery, Dongying City People's Hospital, Dongying, China
| | - Wuzhong Xu
- Department of Hepatobiliary Surgery, Dongying City People's Hospital, Dongying, China
| | - Jiangong Li
- Department of Hepatobiliary Surgery, Dongying City People's Hospital, Dongying, China
| |
Collapse
|
125
|
Ding F, Jiang K, Sheng Y, Li C, Zhu H. RETRACTED: LncRNA MIR7-3HG executes a positive role in retinoblastoma progression via modulating miR-27a-3p/PEG10 axis. Exp Eye Res 2020; 193:107960. [PMID: 32035086 DOI: 10.1016/j.exer.2020.107960] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/13/2020] [Accepted: 02/04/2020] [Indexed: 12/18/2022]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the authors since upon institutional inspection, the reproducibility of the CCK-8 assay was not sufficient and considered not to be valid and therefore could not support the conclusions of the article.
Collapse
Affiliation(s)
- Fengkui Ding
- Department of Ophthalmology, Jining No.1 People's Hospital, No.6 Jiankang Road, Jining, Shandong Province, 272011, PR China
| | - Kai Jiang
- Department of Ophthalmology, Yuhuangding Hospital, Yantai, Shandong Province, 264000, PR China
| | - Yanjuan Sheng
- Department of Ophthalmology, The Second People's Hospital of Jinan, Jinan, Shandong Province, 250001, PR China
| | - Chuanbao Li
- Department of Ophthalmology, Affiliated Hospital of Jining Medical University, Jining, Shandong Province, 272067, PR China
| | - Huaicheng Zhu
- Department of Ophthalmology, Jining No. 1 People's Hospital, Affiliated Jining No. 1 People's Hospital of Jining Medical University, Jining Medical University, Jining, Shandong Province, 272000, PR China.
| |
Collapse
|
126
|
Zhang J, Lou W. A Key mRNA-miRNA-lncRNA Competing Endogenous RNA Triple Sub-network Linked to Diagnosis and Prognosis of Hepatocellular Carcinoma. Front Oncol 2020; 10:340. [PMID: 32257949 PMCID: PMC7092636 DOI: 10.3389/fonc.2020.00340] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 02/26/2020] [Indexed: 01/27/2023] Open
Abstract
Growing evidence has illustrated critical roles of competing endogenous RNA (ceRNA) regulatory network in human cancers including hepatocellular carcinoma. In this study, we aimed to find promising diagnostic and prognostic biomarkers for patients with hepatocellular carcinoma. Three novel unfavorable prognosis-associated genes (CELSR3, GPSM2, and CHEK1) was first identified. We also demonstrated that these genes were significantly upregulated in hepatocellular carcinoma cell lines and tissues. Next, 154 potential miRNAs of CELSR3, GPSM2, and CHEK1 were predicted. CHEK1-hsa-mir-195-5p/hsa-mir-497-5p and GPSM2-hsa-mir-122-5p axes were defined as two key pathways in carcinogenesis of hepatocellular carcinoma by combination of in silico analysis and experimental validation. Subsequently, lncRNAs binding to hsa-mir-195-5p, hsa-mir-497-5p, and hsa-mir-122-5p were predicted via starBase and miRNet databases. After performing expression analysis and survival analysis for these predicted lncRNAs, we showed that nine lncRNAs (SNHG1, SNHG12, LINC00511, HCG18, FGD5-AS1, CERS6-AS1, NUTM2A-AS1, SNHG16, and ASB16-AS1) were markedly increased in hepatocellular carcinoma and their upregulation indicated poor prognosis. Moreover, a similar mRNA-miRNA-lncRNA analysis for six “known” genes (CLEC3B, DNASE1L3, PTTG1, KIF2C, XPO5, and UBE2S) was performed. Subsequently, a comprehensive mRNA-miRNA-lncRNA triple ceRNA network linked to prognosis of patients with hepatocellular carcinoma was established. Moreover, all RNAs in this network exhibited significantly diagnostic values for patients with hepatocellular carcinoma. In summary, the current study constructed a mRNA-miRNA-lncRNA ceRNA network associated with diagnosis and prognosis of hepatocellular carcinoma.
Collapse
Affiliation(s)
- Junjie Zhang
- Department of Hepatobiliary Surgery, The First People's Hospital of Fuyang Hangzhou, Hangzhou, China
| | - Weiyang Lou
- Department of Breast Surgery, The First Affiliated Hospital of Zhejiang University, College of Medicine, Zhejiang University, Hangzhou, China
| |
Collapse
|
127
|
Zhang HP, Liu XL, Chen JJ, Cheng K, Bai SJ, Zheng P, Zhou CJ, Wang W, Wang HY, Zhong LM, Xie P. Circulating microRNA 134 sheds light on the diagnosis of major depressive disorder. Transl Psychiatry 2020; 10:95. [PMID: 32179735 PMCID: PMC7075934 DOI: 10.1038/s41398-020-0773-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/15/2020] [Accepted: 02/25/2020] [Indexed: 12/11/2022] Open
Abstract
Major depressive disorder (MDD) is a prevalent and debilitating psychiatric mood disorder that lacks objective laboratory-based tests to support its diagnosis. A class of microRNAs (miRNAs) has been found to be centrally involved in regulating many molecular processes fundamental to central nervous system function. Among these miRNAs, miRNA-134 (miR-134) has been reported to be related to neurogenesis and synaptic plasticity. In this study, the hypothesis that plasma miR-134 can be used to diagnose MDD was tested. Perturbation of peripheral and central miR-134 in a depressive-like rat model was also examined. By reverse-transcription quantitative PCR, miR-134 was comparatively measured in a small set of plasma samples from MDD and healthy control (HC) subjects. To determine its diagnostic efficacy, plasma miR-134 levels were assessed in 100 MDD, 50 bipolar disorder (BD), 50 schizophrenic (SCZ), and 100 HC subjects. A chronic unpredictable mild stress (CUMS) rat model was also developed to evaluate miR-134 expression in plasma, hippocampus (HIP), prefrontal cortex (PFC), and olfactory bulb. We found that plasma miR-134 was significantly downregulated in MDD subjects. Diagnostically, plasma miR-134 levels could effectively distinguish MDD from HC with 79% sensitivity and 84% specificity, while distinguishing MDD from HC, BD, and SCZ subjects with 79% sensitivity and 76.5% specificity. Congruent with these clinical findings, CUMS significantly reduced miR-134 levels in the rat plasma, HIP, and PFC. Although limited by the relatively small sample size, these results demonstrated that plasma miR-134 displays potential ability as a biomarker for MDD.
Collapse
Affiliation(s)
- Han-ping Zhang
- grid.452206.7Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016 China ,grid.203458.80000 0000 8653 0555NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, Chongqing Medical University, Chongqing, 400016 China
| | - Xiao-lei Liu
- grid.414902.aDepartment of Neurology, The First Affiliated Hospital of Kunming Medical University, Yunan, China
| | - Jian-jun Chen
- grid.203458.80000 0000 8653 0555Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016 China
| | - Ke Cheng
- grid.452206.7Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016 China ,grid.203458.80000 0000 8653 0555NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, Chongqing Medical University, Chongqing, 400016 China
| | - Shun-Jie Bai
- grid.452206.7Department of Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016 China
| | - Peng Zheng
- grid.452206.7Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016 China ,grid.203458.80000 0000 8653 0555NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, Chongqing Medical University, Chongqing, 400016 China
| | - Chan-juan Zhou
- grid.203458.80000 0000 8653 0555NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, Chongqing Medical University, Chongqing, 400016 China
| | - Wei Wang
- grid.452206.7Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016 China ,grid.203458.80000 0000 8653 0555NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, Chongqing Medical University, Chongqing, 400016 China
| | - Hai-yang Wang
- grid.452206.7Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016 China ,grid.203458.80000 0000 8653 0555NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, Chongqing Medical University, Chongqing, 400016 China
| | - Lian-mei Zhong
- grid.414902.aDepartment of Neurology, The First Affiliated Hospital of Kunming Medical University, Yunan, China
| | - Peng Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China. .,NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, Chongqing Medical University, Chongqing, 400016, China. .,Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing, 400016, China.
| |
Collapse
|
128
|
Dell'Aquila E, Fulgenzi CAM, Minelli A, Citarella F, Stellato M, Pantano F, Russano M, Cursano MC, Napolitano A, Zeppola T, Vincenzi B, Tonini G, Santini D. Prognostic and predictive factors in pancreatic cancer. Oncotarget 2020; 11:924-941. [PMID: 32206189 PMCID: PMC7075465 DOI: 10.18632/oncotarget.27518] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 02/17/2020] [Indexed: 12/13/2022] Open
Abstract
Pancreatic cancer is one of the leading causes of cancer death worldwide. Its high mortality rate has remained unchanged for years. Radiotherapy and surgery are considered standard treatments in early and locally advanced stages. Chemotherapy is the only option for metastatic patients. Two treatment regimens, i. e. the association of 5-fluorouracil- irinotecan-oxaliplatin (FOLFIRINOX) and the association of nab-paclitaxel with gemcitabine, have been shown to improve outcomes for metastatic pancreatic adenocarcinoma patients. However, there are not standardized predictive biomarkers able to identify patients who benefit most from treatments. CA19-9 is the most studied prognostic biomarker, its predictive role remains unclear. Other clinical, histological and molecular biomarkers are emerging in prognostic and predictive settings. The aim of this review is to provide an overview of prognostic and predictive markers used in clinical practice and to explore the most promising fields of research in terms of treatment selection and tailored therapy in pancreatic cancer.
Collapse
Affiliation(s)
| | | | - Alessandro Minelli
- Department of Medical Oncology, University Campus Bio-Medico, Rome 00128, Italy
| | - Fabrizio Citarella
- Department of Medical Oncology, University Campus Bio-Medico, Rome 00128, Italy
| | - Marco Stellato
- Department of Medical Oncology, University Campus Bio-Medico, Rome 00128, Italy
| | - Francesco Pantano
- Department of Medical Oncology, University Campus Bio-Medico, Rome 00128, Italy
| | - Marco Russano
- Department of Medical Oncology, University Campus Bio-Medico, Rome 00128, Italy
| | | | - Andrea Napolitano
- Department of Medical Oncology, University Campus Bio-Medico, Rome 00128, Italy
| | - Tea Zeppola
- Department of Medical Oncology, University Campus Bio-Medico, Rome 00128, Italy
| | - Bruno Vincenzi
- Department of Medical Oncology, University Campus Bio-Medico, Rome 00128, Italy
| | - Giuseppe Tonini
- Department of Medical Oncology, University Campus Bio-Medico, Rome 00128, Italy
| | - Daniele Santini
- Department of Medical Oncology, University Campus Bio-Medico, Rome 00128, Italy
| |
Collapse
|
129
|
Lou W, Ding B, Fu P. Pseudogene-Derived lncRNAs and Their miRNA Sponging Mechanism in Human Cancer. Front Cell Dev Biol 2020; 8:85. [PMID: 32185172 PMCID: PMC7058547 DOI: 10.3389/fcell.2020.00085] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/30/2020] [Indexed: 12/28/2022] Open
Abstract
Pseudogenes, abundant in the human genome, are traditionally considered as non-functional “junk genes.” However, recent studies have revealed that pseudogenes act as key regulators at DNA, RNA or protein level in diverse human disorders (including cancer), among which pseudogene-derived long non-coding RNA (lncRNA) transcripts are extensively investigated and has been reported to be frequently dysregulated in various types of human cancer. Growing evidence demonstrates that pseudogene-derived lncRNAs play important roles in cancer initiation and progression by serving as competing endogenous RNAs (ceRNAs) through competitively binding to shared microRNAs (miRNAs), thus affecting both their cognate genes and unrelated genes. Herein, we retrospect those current findings about expression, functions and potential ceRNA mechanisms of pseudogene-derived lncRNAs in human cancer, which may provide us with some crucial clues in developing potential targets for cancer therapy in the future.
Collapse
Affiliation(s)
- Weiyang Lou
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation, Zhejiang University, Hangzhou, China
| | - Bisha Ding
- Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation, Zhejiang University, Hangzhou, China
| | - Peifen Fu
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| |
Collapse
|
130
|
Yang X, Xin N, Qu HJ, Wei L, Han Z. Long noncoding RNA TUG1 facilitates cell ovarian cancer progression through targeting MiR-29b-3p/MDM2 axis. Anat Rec (Hoboken) 2020; 303:3024-3034. [PMID: 31930662 DOI: 10.1002/ar.24367] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/05/2019] [Accepted: 11/24/2019] [Indexed: 12/21/2022]
Abstract
Ovarian cancer (OC) is one of the most aggressive female cancers in the world. OC trends to be diagnosed at an advanced stage with abdominal metastasis. Our study explored the biological function and underlying mechanism of lncRNA on OC cell proliferation and migration. The expression of turine up-regulated gene 1 (TUG1) in human OC tissues and cell lines was measured by qRT-PCR. OC cell proliferation, viability, migration, and invasion were measured by MTT assays, colony formation assays, and transwell assays in vitro. Furthermore, the nude mice xenograft model was established to determine the effects of TUG1 in vivo. The relationship between TUG1 and miR-29b-3p, as well as miR-29b-3p and MDM2 were identified using the luciferase reporter assays. We showed that the expression of TUG1 and MDM2 were significantly increased, but the expression of miR-29b-3p was remarkably decreased in OC tissues and cell lines. Knockdown of TUG1 strongly inhibited the ability of cell proliferation, colony formation, migration, and invasion in vitro. The relationship between TUG1 and miR-29b-3p, or miR-29b-3p and MDM2 were predicted by StarBase and miRanda online software. Besides, miR-29b-3p reversed the positive effect of TUG1 on the OC cell proliferation, migration, and invasion through inhibiting MDM2 expression and increasing p53 phosphorylation level. Moreover, knockdown of TUG1 suppressed tumor growth in vivo. Taken all together, this study shows that TUG1 plays a crucial oncogenic role and facilitates cell proliferation, migration, and invasion in OC through regulating miR-29b-3p/MDM2 axis.
Collapse
Affiliation(s)
- Xiaoqiu Yang
- Department of Pharmacy, Huangdao District Central Hospital, Qingdao, China
| | - Nana Xin
- Department of Pharmacy, Songshan Hospital, Medical College of Qingdao University, Qingdao, China
| | - Hai-Jun Qu
- Department of Pharmacy, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lina Wei
- Department of Pharmacy, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhiwu Han
- Department of Pharmacy, Affiliated Hospital of Qingdao University, Qingdao, China
| |
Collapse
|
131
|
Jiang X, Li J, Wang W, Hu Z, Guan C, Zhao Y, Li W, Cui Y. AR-induced ZEB1-AS1 represents poor prognosis in cholangiocarcinoma and facilitates tumor stemness, proliferation and invasion through mediating miR-133b/HOXB8. Aging (Albany NY) 2020; 12:1237-1255. [PMID: 31978895 PMCID: PMC7053610 DOI: 10.18632/aging.102680] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/25/2019] [Indexed: 02/07/2023]
Abstract
Zinc finger E-box binding homeobox 1 antisense 1 (ZEB1-AS1) has displayed vital regulatory function in various tumors. However, the biological function of ZEB1-AS1 in cholangiocarcinoma (CCA) remains unclear. In this study, we confirmed that ZEB1-AS1 expression was increased in CCA tissues and cells, respectively. Upregulated ZEB1-AS1 was related to lymph node invasion, advanced TNM stage and poor survival of CCA patients. ZEB1-AS1 exhibited high sensitivity and specificity to be an independent poor prognostic factor of patients with CCA. Functionally, knocking down ZEB1-AS1 attenuated tumor cell stemness, restrained cellular viability in vitro and in vivo, and inhibited CCA cell migration and invasion by reversing epithelial-mesenchymal transition. For the mechanism, androgen receptor (AR) directly promoted ZEB1-AS1 expression, and further ZEB1-AS1 increased oncogene homeobox B8 (HOXB8) by sponging miR-133b. In addition, malignant phenotypes of CCA promoted by ZEB1-AS1 dysregulation were rescued separately through interfering miR-133b and HOXB8, suggesting AR/ZEB1-AS1/miR-133b/HOXB8 exerted crucial functions in tumorigenesis and progression of CCA.
Collapse
Affiliation(s)
- Xingming Jiang
- Department of General Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Jinglin Li
- Department of General Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Weina Wang
- Department of Anesthesiology, Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Zengtao Hu
- Department of General Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Canghai Guan
- Department of General Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Yuqiao Zhao
- Department of General Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Wenzhi Li
- Department of Anesthesiology, Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Yunfu Cui
- Department of General Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| |
Collapse
|
132
|
Wang Z, Wang W, Zhao W, Wang Z, Yang J, Wang W, Teng P, Su X, Li D, Zhang X, Wang H, Hao M. Folate inhibits miR-27a-3p expression during cervical carcinoma progression and oncogenic activity in human cervical cancer cells. Biomed Pharmacother 2020; 122:109654. [PMID: 31918266 DOI: 10.1016/j.biopha.2019.109654] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/30/2019] [Accepted: 11/06/2019] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Folate deficiency has been long implicated in cancer development. Although the role of folate in preventing cervical cancer is still unclear, emerging evidence shows that microRNAs (miRs) have great influence on tumor cell migration and invasion. OBJECTIVES The purpose of this study was to conduct an integrated analysis of miR expression in squamous cell carcinoma tissues with adequate or deficient serum folate. Further, study conducted tissue validation and functional analysis of miRs to uncover novel pathogenic mechanisms on the role of folate in squamous cell carcinoma (SCC). MATERIALS AND METHODS miR expression profiles were obtained from five paired primary SCC tumors with sufficient or deficient serum folate levels through Affymetrix GeneChip microRNA 4.0. This was followed by an integrated bioinformatics analysis and expanded sample size to verify core miRs by molecular biological validation. HeLa and SiHa cells with different concentrations of folate were used to clarify the roles of miR-27a on cell proliferation, migration, and invasion. MiR-27a expression was measured by the quantitative real-time polymerase chain reaction. Cell counting proliferation, wound healing, and transwell invasion assays were used to determine cell survival, proliferation, migration, and invasion abilities, respectively. RESULTS Our study found increasing miR-27a expression in serum of normal, high-grade squamous intraepithelial lesion (HSIL), and SCC tissues (in order of magnitude), which trend was negatively correlated with serum folate content. Further, there were significant differences in cellular miR-27a expression between 200 nM and 500 nM folate concentrations, with higher folate concentrations showing lower proliferation, migration, and invasion in SCC. Finally, miR-27a promoted proliferation and invasion in HeLa cells, whereas a miR-27a inhibitor blocked cell proliferation and invasion. CONCLUSION There is a significant association between miR-27a expression and folate during cervical carcinoma progression. Therefore, miR-27a could be used as a new biomarker for SCC diagnosis and prediction, suggesting a new therapeutic strategy for SCC treatment.
Collapse
Affiliation(s)
- Zhe Wang
- Department of Obstetrics and Gynecology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Wenhao Wang
- Department of Obstetrics and Gynecology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Weihong Zhao
- Department of Obstetrics and Gynecology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Zhilian Wang
- Department of Obstetrics and Gynecology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jing Yang
- Department of Obstetrics and Gynecology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Wei Wang
- Department of Obstetrics and Gynecology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Peng Teng
- Department of Obstetrics and Gynecology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiaoqiang Su
- Department of Obstetrics and Gynecology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Dongyan Li
- Department of Obstetrics and Gynecology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xi Zhang
- Department of Obstetrics and Gynecology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Hui Wang
- Department of Obstetrics and Gynecology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Min Hao
- Department of Obstetrics and Gynecology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China.
| |
Collapse
|
133
|
Qiao S, Qi K, Liu C, Xu C, Ma J, Xu X, Li C, Wang Z. Long intergenic non-coding RNA 511 correlates with improved prognosis, and hinders osteosarcoma progression both in vitro and in vivo. J Clin Lab Anal 2020; 34:e23164. [PMID: 31893577 PMCID: PMC7246352 DOI: 10.1002/jcla.23164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/24/2019] [Accepted: 10/29/2019] [Indexed: 12/15/2022] Open
Abstract
Background This study aimed to investigate the correlation of long intergenic non‐coding RNA 511 (LINC00511) with clinicopathological characteristics and overall survival (OS) in osteosarcoma patients and to explore its function in osteosarcoma in vitro and in vivo. Methods Tumor tissues and adjacent tissues from 45 osteosarcoma patients were acquired, and LINC00511 expression was detected. In vitro, LINC00511 expression was detected in osteosarcoma cell lines and osteoblast cell line. LINC00511 overexpression‐treated (OE‐LINC00511) and nonsense overexpression‐treated (OE‐control) MG‐63 and Saos‐2 cells were cultured, followed by the assessment of cell proliferation, apoptosis, migration, and invasion. In vivo, tumor weight and volume were measured in OE‐LINC00511 and OE‐control xenografted mice. Results LINC00511 expression was decreased in tumor tissues compared with adjacent tissues (P < .001), and its high expression correlated with increased tumor cell necrosis rate to neoadjuvant chemotherapy (P = .025) and prolonged OS (P = .010). In vitro, LINC00511 expression was decreased in osteosarcoma cell lines (including MG‐63, U‐2OS, Saos‐2, and HOS) compared with osteoblast cell line (All P < .001). Cell proliferation was decreased at 48 hours (Both P < .01) and 72 hours (Both P < .001) (in MG‐63 and Saos‐2 cells); cell apoptosis was increased (P < .05) (in Saos‐2 cells); cell migration and invasion were decreased (All P < .01) (in MG‐63 cells and Saos‐2 cells) in OE‐LINC00511 compared with OE‐control. In vivo, tumor volume was reduced at week 4 (P < .001), week 5 (P < .001), week 6 (P < .001) in OE‐LINC00511 compared with OE‐control. Tumor weight was declined in OE‐LINC00511 than OE‐control (P < .001). Conclusions LINC00511 acts as a potential biomarker and therapeutic option for osteosarcoma.
Collapse
Affiliation(s)
- Suchi Qiao
- The Outpatient Department, 905 Hospital of Navy, Second Military Medical University, Shanghai, China.,Department of Orthopedics, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Ke Qi
- Department of Orthopedics, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Chang Liu
- Department of Orthopedics, 900 Hospital of the Joint Logistics Team, Fuzhou, China
| | - Changli Xu
- Department of Orthopedics, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Jun Ma
- Department of Orthopedics, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Xinmin Xu
- The Outpatient Department, 905 Hospital of Navy, Second Military Medical University, Shanghai, China.,Department of Orthopedics, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Cheng Li
- Department of Orthopedics, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Zhiwei Wang
- Department of Orthopedics, Changhai Hospital, Second Military Medical University, Shanghai, China
| |
Collapse
|
134
|
Dysregulation of pseudogene/lncRNA-hsa-miR-363-3p-SPOCK2 pathway fuels stage progression of ovarian cancer. Aging (Albany NY) 2019; 11:11416-11439. [PMID: 31794425 PMCID: PMC6932902 DOI: 10.18632/aging.102538] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/19/2019] [Indexed: 02/07/2023]
Abstract
Objective: Ovarian cancer is one of the most common and lethal cancer types in women. The molecular mechanism of ovarian cancer progression is still unclear. Results: Here, we first reported that expression levels of three genes, GJB2, S100A2 and SPOCK2, were significantly higher in advanced stage than that in early stage of ovarian cancer, and upregulation of them indicated poor prognosis of patients with ovarian cancer. Subsequently, 8, 6 and 20 miRNAs were predicted to target GJB2, S100A2 and SPOCK2, respectively. Among these miRNA-mRNA pairs, hsa-miR-363-3p-SPOCK2 axis was the most potential in suppressing progression of ovarian cancer. Mechanistically, we found that hsa-miR-363-3p-SPOCK2 axis was involved in regulation of actin cytoskeleton. Moreover, 6 pseudogenes and 8 lncRNAs were identified to potentially inhibit hsa-miR-363-3p-SPOCK2 axis in ovarian cancer. Conclusions: Collectively, we elucidate a regulatory role of pseudogene/lncRNA-hsa-miR-363-3p-SPOCK2 pathway in progression of ovarian cancer, which may provide effective therapeutic approaches and promising prognostic biomarkers for ovarian cancer. Materials and methods: Differentially expressed genes (DEGs) in ovarian cancer were first screened using GSE12470, after which DEGs expression were validated using GEPIA. Kaplan-Meier analysis was employed to assess the prognostic values. Potential miRNAs were predicted by seven target prediction databases, and upstream lncRNAs and pseudogenes of hsa-miR-363-3p were forecasted through miRNet or starBase. UALCAN and starBase were used to obtain the co-expressed genes of SPOCK. Enrichment analysis for these co-expressed genes was performed by Enrichr.
Collapse
|
135
|
Competing endogenous network analysis identifies lncRNA Meg3 activates inflammatory damage in UVB induced murine skin lesion by sponging miR-93-5p/epiregulin axis. Aging (Albany NY) 2019; 11:10664-10683. [PMID: 31761787 PMCID: PMC6914409 DOI: 10.18632/aging.102483] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/08/2019] [Indexed: 02/05/2023]
Abstract
In this study, we obtained the RNA expression data of murine skin tissues of control, and UVB irradiated groups. After the re-annotation of lncRNAs, a gene expression similarity analysis was done by WGCNA. The target mRNA prediction of lncRNAs, miRNAs, and ceRNA regulatory networks were constructed by five lncRNAs, 14 miRNAs and 54 mRNAs, respectively. Based on the ceRNA network of UVB-induced skin lesions, it was evident that the dysregulation of Meg3 has critical effects on the UVB-induced inflammatory lesion of murine skin tissues. The overexpression of Meg3 after UVB irradiation was observed in primary murine skin fibroblasts, and the up-regulated Meg3 expression was related to the activation of the inflammatory cytokines. These functional experiments demonstrated that the RNA silencing of Meg3 in murine skin fibroblasts could suppress the expression of the cytokines (in vitro) and UVB-induced skin lesions (in vivo). Moreover, the Meg3 functioned as a competing endogenous RNA (ceRNA) that acted as a sponge for miR-93-5p and thereby modulated the expression of Epiregulin (Ereg). Our results proved that Meg3 was involved in UVB-induced skin inflammation and that the ceRNA networks, which includes miR-93-5p and Ereg, could prove to be a potential therapeutic target for UVB-induced skin damage.
Collapse
|
136
|
Hu P, Cui H, Lei T, Li S, Mai E, Jia F. Linc00511 Indicates A Poor Prognosis Of Liver Hepatocellular Carcinoma. Onco Targets Ther 2019; 12:9367-9376. [PMID: 31807017 PMCID: PMC6850899 DOI: 10.2147/ott.s228231] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/18/2019] [Indexed: 12/24/2022] Open
Abstract
Objective To uncover the specific function of linc00511 in the progression of liver hepatocellular carcinoma (LIHC) and the underlying mechanism. Patients and methods GEPIA dataset containing 9736 LIHC samples and 857 normal samples were downloaded from TCGA. Expression pattern and prognostic potential of linc00511 in LIHC were analyzed. Subsequently, expression level of linc00511 in LIHC tissues collected in our hospital and cell lines were determined by quantitative real-time polymerase chain reaction (qRT-PCR). Differential expressions of linc00511 in LIHC with different tumor grades and metastatic status were compared. After transfection of si-linc00511, proliferative and migratory changes in Huh7 and Hep3B cells were assessed by cell counting kit-8 (CCK-8), 5-ethynyl-2ʹ-deoxyuridine (EdU) and Transwell assay. Lastly, Pearson correlation analysis and qRT-PCR were conducted to investigate the interaction between linc00511 and miR-29c. Results Linc00511 was upregulated in LIHC tissues and cell lines. Its level was positively correlated to TNM staging, lymphatic metastasis and poor prognosis in LIHC patients. Knockdown of linc00511 attenuated proliferative and migratory abilities in Huh7 and Hep3B cells. In addition, miR-29c was downregulated in LIHC and negatively linked to linc00511 level. A negative interaction between linc00511 and miR-29c could be a regulatory feedback influencing the progression of LIHC. Conclusion Linc00511 accelerates the proliferation and migration in LIHC, thus aggravating tumor progression. Meanwhile, linc00511 could be utilized as a hallmark predicting poor prognosis in LIHC patients.
Collapse
Affiliation(s)
- Pingan Hu
- Department of Hepatobiliary Surgery, Luoyang Center Hospital, Luoyang, People's Republic of China
| | - Huxiao Cui
- Department of Hepatobiliary Surgery, Xuchang Central Hospital, Xuchang, People's Republic of China
| | - Ting Lei
- Department of Hepatobiliary Surgery, Luoyang Center Hospital, Luoyang, People's Republic of China
| | - Siqiao Li
- Department of Hepatobiliary Surgery, Luoyang Center Hospital, Luoyang, People's Republic of China
| | - Erhui Mai
- Department of Hepatobiliary Surgery, Luoyang Center Hospital, Luoyang, People's Republic of China
| | - Fuxin Jia
- Department of Hepatobiliary Surgery, Luoyang Center Hospital, Luoyang, People's Republic of China
| |
Collapse
|
137
|
Liu Y, Wang J, Dong L, Xia L, Zhu H, Li Z, Yu X. Long Noncoding RNA HCP5 Regulates Pancreatic Cancer Gemcitabine (GEM) Resistance By Sponging Hsa-miR-214-3p To Target HDGF. Onco Targets Ther 2019; 12:8207-8216. [PMID: 31632071 PMCID: PMC6781945 DOI: 10.2147/ott.s222703] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 08/27/2019] [Indexed: 01/22/2023] Open
Abstract
Background Gemcitabine (GEM) is one of the most widely chemotherapy drugs in PC. However, the chemotherapy resistance always occurs after a period of treatment indicating poor prognosis. lncRNA may play an essential role in PC and serve as a prognosis biomarkers in PC with GEM-resistance. In our study, we aim to investigate the role of lncRNA HCP5 in PC. Materials and methods QRT-PCR detected the expression of lncRNA HCP5. The effects of knockdown lncRNA HCP5 on the proliferation, migration, invasion, cell apoptosis and autophagy were investigated in GEM-resistance PC cells. Bioinformatic analysis, luciferase reporter assay and RNA immunoprecipitation assay were performed to predict for potential miRNAs that can interact with lncRNA HCP5 and mRNAs that can interact with miR-214-3p. Results Our study revealed that lncRNA HCP5 expression was upregulated in PC tissues, especially increased expression in GEM-resistant PC tissues and GEM-resistant PC cells. Wound healing, Transwell assays, flow cytometry, Western blot, luciferase reporter assay and RNA immunoprecipitation (RIP) results demonstrated lncRNA HCP5 acted as a ceRNA to regulate GEM-resistance PC cells' proliferation, invasion, migration, cell apoptosis and autophagy by targeting HDGF via miR-214-3p. Conclusion Our results revealed that lncRNA HCP5 is highly expressed in HCC, and development of GEM-resistance PC cells involving the processes of proliferation, invasive, migration, cell apoptosis and autophagy through the miR-214-3p/HDGF axis. Targeting lncRNA HCP5 may improve gemcitabine-based therapeutic efficacy.
Collapse
Affiliation(s)
- Yunfei Liu
- Department of Hepatobiliary and Pancreatic Surgery II, Third Xiangya Hospital, Central South University, Changsha 410006, China
| | - Jiale Wang
- Department of Hepatobiliary and Pancreatic Surgery II, Third Xiangya Hospital, Central South University, Changsha 410006, China
| | - Luo Dong
- Department of Hepatobiliary and Pancreatic Surgery II, Third Xiangya Hospital, Central South University, Changsha 410006, China
| | - Li Xia
- Department of Hepatobiliary and Pancreatic Surgery II, Third Xiangya Hospital, Central South University, Changsha 410006, China
| | - Hongwei Zhu
- Department of Hepatobiliary and Pancreatic Surgery II, Third Xiangya Hospital, Central South University, Changsha 410006, China
| | - Zhiqiang Li
- Department of Hepatobiliary and Pancreatic Surgery II, Third Xiangya Hospital, Central South University, Changsha 410006, China
| | - Xiao Yu
- Department of Hepatobiliary and Pancreatic Surgery II, Third Xiangya Hospital, Central South University, Changsha 410006, China
| |
Collapse
|
138
|
Chen J, Lou W, Ding B, Wang X. Overexpressed pseudogenes, DUXAP8 and DUXAP9, promote growth of renal cell carcinoma and serve as unfavorable prognostic biomarkers. Aging (Albany NY) 2019; 11:5666-5688. [PMID: 31409759 PMCID: PMC6710046 DOI: 10.18632/aging.102152] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 07/31/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND Growing studies have reported that pseudogenes play key roles in multiple human cancers. However, expression and roles of pseudogenes in renal cell carcinoma remains absent. RESULTS 31 upregulated and 16 downregulated pseudogenes were screened. Higher expression of DUXAP8 and DUXAP9 indicated poorer prognosis of kidney cancer. 33 and 5 miRNAs were predicted to potentially binding to DUXAP8 and DUXAP9, respectively. miR-29c-3p was identified as the most potential binding miRNAs of DUXAP8 and DUXAP9 based on expression, survival and correlation analyses. 254 target genes of miR-29c-3p were forecast. 47 hub genes with node degree >= 10 were identified. Subsequent analysis for the top 10 hub genes demonstrated that COL1A1 and COL1A2 may be two functional targets of DUXAP8 and DUXAP9. Expression of DUXAP8, DUXAP9, COL1A1 and COL1A2 were significantly increased in cancer samples compared to normal controls while miR-29c-3p expression was decreased. Luciferase reporter assay revealed that miR-29c-3p could directly bind to DUXAP8, DUXAP9, COL1A1 and COL1A2. Functional experiments showed that DUXAP8 and DUXAP9 enhanced but miR-29c-3p weakened growth of renal cell carcinoma. CONCLUSIONS In conclusion, upregulated DUXAP8 and DUXAP9 promote growth of renal cell carcinoma and serve as two promising prognostic biomarkers. METHODS Dysregulated pseudogenes were obtained by dreamBase and GEPIA. The binding miRNAs of pseudogene and targets of miRNA were predicted using starBase and miRNet. Kaplan-Meier plotter was utilized to perform survival analysis, and Enrichr database was introduced to conduct functional enrichment analysis. Hub genes were identified through STRING and Cytoscape. qRT-PCR, luciferase reporter assay, cell counting assay and colony formation assay were performed to validate in silico analytic results.
Collapse
Affiliation(s)
- Jing Chen
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Zhejiang Province, Hangzhou 313100, China.,First Affiliated Hospital of Jiaxing University, Zhejiang Province, Jiaxing 314000, China
| | - Weiyang Lou
- Department of Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 313100, China
| | - Bisha Ding
- Department of Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 313100, China
| | - Xian Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Zhejiang Province, Hangzhou 313100, China
| |
Collapse
|
139
|
Zhang H, Wang Y, Lu J. Identification of lung-adenocarcinoma-related long non-coding RNAs by random walking on a competing endogenous RNA network. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:339. [PMID: 31475209 DOI: 10.21037/atm.2019.06.69] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Background Identification of novel risk long non-coding RNAs (lncRNAs) in lung adenocarcinoma (LUAD) is still a significant challenge in cancer research. Methods In this study, we first constructed a LUAD-specific competing endogenous RNA (ceRNA) network using both experimental- and computational-supported datasets. Then, a random walking with restart method was performed to predict LUAD-associated risk lncRNAs based on the ceRNA network. The role of lncRNA MAPKAPK5-AS1 was assessed by siRNA transfection, followed by a colony formation assay, the CCK-8 assay, and immunofluorescence on A549 cells. Results Our method achieved an area under the curve (AUC) value of over 0.83. Of the several potential novel LUAD-related lncRNAs identified, the highest ranked lncRNA was SNHG12, which, interestingly, was also shown to promote tumorigenesis and metastasis in LUAD in a recent study. Furthermore, we found that the expression of MAPKAPK5-AS1, which was ranked second, was higher in both LUAD tissues and three LUAD cell lines. After the silencing of MAPKAPK5-AS1 by siRNA transfection, a colony formation assay revealed fewer colonies, and a CCK-8 assay revealed significantly suppressed growth of A549 cells. Moreover, immunofluorescence staining of Ki-67, a proliferation marker, revealed that the proliferation capability of A549 was dramatically reduced following MAPKAPK5-AS1 downregulation. AO/EB staining showed an increased proportion of apoptotic cells among A549 cells depleted of MAPKAPK5-AS1. Conclusions In brief, the lncRNAs were predicted to serve as potential biomarkers for the diagnosis, treatment, and prognosis of LUAD.
Collapse
Affiliation(s)
- Hongyan Zhang
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Yuan Wang
- Department of Rehabilitation, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Jibin Lu
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| |
Collapse
|