1
|
Liu Y, Huang S, Dong G, Hou C, Zhao Y, Zhang D. Computational identification of DNA damage-relevant lncRNAs for predicting therapeutic efficacy and clinical outcomes in cancer. Comput Biol Med 2024; 171:108107. [PMID: 38412692 DOI: 10.1016/j.compbiomed.2024.108107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/12/2024] [Accepted: 02/04/2024] [Indexed: 02/29/2024]
Abstract
OBJECTIVES The role of long non-coding RNAs (lncRNAs) in cancer treatment, particularly in modulating DNA repair programs, is an emerging field that warrants systematic exploration. This study aimed to systematically identify the lncRNA regulators that potentially regulate DNA damage response (DDR). METHODS Using genome-wide mRNA and lncRNA expression profiles of the same tumor patients, we proposed a novel computational framework. This framework performed Gene Set Variation Analysis to calculate DDR pathway enrichment score, which relies on weighting by tumor purity to obtain DDR activity score for each patient. Then, an in-depth differential expression profiling was conducted to identify pathway activity lncRNAs between high- and low-activity groups, utilizing a bootstrap-based randomization method. RESULTS We comprehensively charted the landscape of DDR-relevant lncRNAs across 23 epithelial-based cancer types. Its effectiveness was validated by assessing the consistency of these lncRNAs within various datasets of the same cancer type (hypergeometric test P < 0.001), examining the expression perturbation of these lncRNAs in response to treatment and demonstrating its application in prioritizing clinically-related lncRNAs. Furthermore, leveraging 820 epithelial ovarian cancer patients from four public datasets, we applied these lncRNAs identified by DDRLnc to establish and validate a risk stratification model to evaluate the benefits of platinum-based adjuvant chemotherapy for the improvement of clinical treatment outcomes. CONCLUSIONS Comprehensive pan-cancer analysis illustrates the utility of computational framework in identifying potentially lncRNAs involved in DDR, thereby offering novel insights into the complex realm of cancer research, and it will become a valuable tool for identifying potential therapeutic targets for cancer.
Collapse
Affiliation(s)
- Yixin Liu
- Modern Education Technology Center, Harbin Medical University, Harbin, 150080, China
| | - Shan Huang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Guanghui Dong
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Chang Hou
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Yuming Zhao
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, 150040, China.
| | - Dandan Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150007, China.
| |
Collapse
|
2
|
Lu S, Zhang X, Cai Z, Xi Z, Wang F, Wang X, Li W, Dai P. Identification of novel lncRNA prognostic biomarkers and their associated ceRNAs in bladder urothelial carcinoma. J Biochem Mol Toxicol 2023; 37:e23441. [PMID: 37393523 DOI: 10.1002/jbt.23441] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 04/19/2023] [Accepted: 06/14/2023] [Indexed: 07/03/2023]
Abstract
Bladder urothelial carcinoma (BUCA) is a common malignant tumor with a high rate of metastasis and recurrence. The lack of specific and sensitive biomarkers for the prognostic assessment makes it important to seek alternatives. Recent studies have demonstrated that long noncoding RNAs (lncRNAs) function as competitive endogenous RNAs (ceRNAs) and play an important role in BUCA prognosis. Therefore, this study aimed to establish a prognosis-related lncRNAs-microRNAs (miRNAs)-messenger RNA (mRNA) (pceRNA) network and identify novel prognostic biomarkers. Integrated weighted coexpression analysis, functional clustering, and ceRNA network were used for the prognostic assessment of BUCA. The transcriptome sequencing datasets of lncRNA, miRNA, and mRNA from The Cancer Genome Atlas database were used for the identification of key lncRNAs and construction of the lncRNAs expression signature for prognostic prediction of BUCA patients. Then, 14 differentially expressed lncRNAs (DE-lncRNAs) were identified as candidate prognostic RNAs based on the ceRNAs network and functional clustering. In the Cox regression analysis, two (AC008676.1 and ADAMTS9-AS1) of all DE-lncRNAs were significantly associated with overall survival (OS) of BUCA patients. This two DE-lncRNA signature was significantly correlated with OS and was an independent prognostic factor, which was confirmed in an independent dataset of GSE216037. Moreover, we constructed the pceRNA network that includes 2 DE-lncRNAs, 9 DE-miRNAs, and 10 DE-mRNAs. Pathway enrichment analysis showed that AC008676.1 and ADAMTS9-AS1 are involved in several cancer-related pathways such as proteoglycans in cancer and TGF-beta signaling pathway. The novel-identified DE-lncRNA prognostic signature and the pceRNA network in this study will be valuable risk predictors and diagnostic markers for BUCA.
Collapse
Affiliation(s)
- Sihai Lu
- School of Life Sciences, Northwest University, Xi'an, China
- Shaanxi Lifegen Co. Ltd., Xi'an, China
- National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, China
| | | | - Zhiye Cai
- School of Life Sciences, Northwest University, Xi'an, China
| | - Ziyi Xi
- School of Life Sciences, Northwest University, Xi'an, China
| | - Fei Wang
- School of Life Sciences, Northwest University, Xi'an, China
| | - Xuan Wang
- School of Life Sciences, Northwest University, Xi'an, China
| | - Wenqi Li
- School of Life Sciences, Northwest University, Xi'an, China
| | - Penggao Dai
- School of Life Sciences, Northwest University, Xi'an, China
- Shaanxi Lifegen Co. Ltd., Xi'an, China
| |
Collapse
|
3
|
Wei L, Zhang X, Yao Y, Zheng W, Tian J. LncRNA HOTTIP impacts the proliferation and differentiation of fibroblast-like synoviocytes in ankylosing spondylitis through the microRNA-30b-3p/PGK1 axis. J Orthop Surg Res 2023; 18:237. [PMID: 36964567 PMCID: PMC10039568 DOI: 10.1186/s13018-023-03653-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/26/2023] [Indexed: 03/26/2023] Open
Abstract
OBJECTIVE Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been reported to exert regulatory effects on biological processes. This study intended to assess the role of the lncRNA HOXA transcript at the distal tip (HOTTIP)/miR-30b-3p/phosphoglycerate kinase 1 (PGK1) axis in ankylosing spondylitis (AS). METHODS Levels of HOTTIP, miR-30b-3p and PGK1 in AS synovial tissues and cultured AS fibroblast-like synoviocytes (ASFLSs) were assessed. The ASFLSs were identified and, respectively, treated with altered expression of HOTTIP and miR-30b-3p, and then, the proliferation and differentiation of the ASFLSs were assessed. The AS mouse models were established by injection of proteoglycan and Freund's complete adjuvant and then were treated with altered expression of HOTTIP and miR-30b-3p, and the pathological changes and apoptosis of synoviocytes in mice' synovial tissues were measured. The relationship of HOTTIP, miR-30b-3p and PGK1 was verified. RESULTS HOTTIP and PGK1 were elevated, while miR-30b-3p was reduced in AS synovial tissues and ASFLSs. Elevated miR-30b-3p or inhibited HOTTIP restrained proliferation and differentiation of ASFLSs and also improved the pathological changes and promoted apoptosis of synoviocytes in mice's synovial tissues. PGK1 was a target of miR-30b-3p, and miR-30b-3p could directly bind to HOTTIP. Silencing miR-30b-3p or overexpressing PGK1 reversed the improvement of AS by knocking down HOTTIP or up-regulating miR-30b-3p. CONCLUSION Our study suggests that reduced HOTTIP ameliorates AS progression by suppressing the proliferation and differentiation of ASFLSs through the interaction of miR-30b-3p and PGK1.
Collapse
Affiliation(s)
- Li Wei
- Department of Orthopaedic Ward 1, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Harbin, 150000, Heilongjiang, China
| | - Xin Zhang
- Department of Orthopaedic Ward 1, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Harbin, 150000, Heilongjiang, China
| | - Yu Yao
- Department of Orthopaedic Ward 1, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Harbin, 150000, Heilongjiang, China
| | - Weizhuo Zheng
- Department of Orthopaedic Ward 1, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Harbin, 150000, Heilongjiang, China
| | - Jun Tian
- Department of Orthopaedic Ward 1, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Harbin, 150000, Heilongjiang, China.
| |
Collapse
|
4
|
Wang J, Zhu Y, Ai X, Wan H, Jia W, Chu J, Xu B, Kong X, Kong L. Long noncoding RNA 02027 inhibits proliferation, migration and invasion of hepatocellular carcinoma via miR-625-3p/PDLIM5 pathway. J Gene Med 2023:e3485. [PMID: 36811210 DOI: 10.1002/jgm.3485] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 01/02/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Long non-coding RNAs have been established to promote or inhibit the oncogenic and tumorigenic potential of various cancers, acting as competing endogenous RNAs (ceRNAs) for specific microRNAs. The primary objective of the study was to investigate the underlying mechanism by which the LINC02027/miR-625-3p/PDLIM5 axis affects proliferation, migration and invasion in hepatocellular carcinoma (HCC). METHODS The differentially expressed gene was selected based on gene sequencing and bioinformation database analysis of HCC and adjacent non-tumor tissues. The expression of LINC02027 in HCC tissues and cells and its regulatory effect on the development of HCC were detected by colony formation, cell counting kit-8 assays, wound healing assays, Transwell assays and subcutaneous tumorigenesis assays in nude mice. According to the results of database prediction, quantitative real-time polymerase chain reaction and dual-luciferase reporter assay, the downstream microRNA and target gene were searched. Finally, HCC cells were transfected with lentivirus and used for cell function assays in vitro and in vivo. RESULTS Downregulation of LINC02027 was detected in HCC tissues and cell lines and was associated with poor prognosis. The overexpression of LINC02027 suppressed the proliferation, migration and invasion of HCC cells. Mechanistically, LINC02027 inhibited epithelial-to-mesenchymal transition. As a ceRNA, LINC02027 inhibited the malignant ability of HCC by competitively binding to miR-625-3p to regulate the expression of PDLIM5. CONCLUSIONS The LINC02027/miR-625-3p/PDLIM5 axis inhibits the development of HCC.
Collapse
Affiliation(s)
- Jinyi Wang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, China
| | - Yong Zhu
- Department of General Surgery, Anhui Public Clinical Center, The First Affiliated Hospital of Anhui Medical University North District, Hefei, China
| | - Xiaoming Ai
- Department of General Surgery, BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hong Wan
- Department of General Surgery, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Wenbo Jia
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, China
| | - Jian Chu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, China
| | - Bin Xu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, China
| | - Xiangxu Kong
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, China
| | - Lianbao Kong
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, China
| |
Collapse
|
5
|
Silencing of Long Noncoding RNA TUG1 Ameliorates Atherosclerosis-Induced Myocardial Injury by Upregulating microRNA-30b-3p and Downregulating Brd4. J Cardiovasc Pharmacol 2023; 81:45-54. [PMID: 36166514 DOI: 10.1097/fjc.0000000000001367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/27/2022] [Indexed: 01/27/2023]
Abstract
ABSTRACT Long noncoding RNAs and microRNAs (miRNAs) are emerging biomarkers involved in human diseases, and we focused on the roles of long noncoding RNA taurine upregulated gene 1 (TUG1) and miR-30b-3p in the related mechanisms of atherosclerosis-induced myocardial injury. ApoE-deficient mice were fed with high-fat diet to establish atherosclerotic models and then were subjected to either TUG1 downregulation or miR-30b-3p upregulation treatment. The serum myocardial enzymes, inflammatory biomarkers, pathological changes, intramyocardial macrophage infiltration, and apoptosis of cardiomyocytes in atherosclerotic mice were determined. The expression of TUG1, miR-30b-3p, and bromodomain protein 4 (Brd4) in atherosclerotic models was evaluated. Moreover, the correlations of TUG1, miR-30b-3p, and Brd4 were verified. TUG1 and Brd4 were increased while miR-30b-3p was decreased in atherosclerotic mice. The silenced TUG1 or elevated miR-30b-3p attenuated atherosclerosis-induced myocardial injury mainly by reducing serum myocardial enzyme content and inflammatory response, improving pathological changes, and preventing macrophage infiltration and cardiomyocyte apoptosis in atherosclerotic mice. Mechanistically, TUG1 could competitively bind with miR-30b-3p to prevent the degradation of its target gene Brd4. This study reveals that the silencing of TUG1 ameliorates atherosclerosis-induced myocardial injury by upregulating miR-30b-3p and downregulating Brd4, which may provide novel targets for atherosclerosis treatment.
Collapse
|
6
|
Zhu Y, Chen J, Zhou L, Zhang L, Liu Y, Zhuang Y, Peng L, Huang YT. A Platinum Resistance-Related lncRNA Signature for Risk Classification and Prognosis Prediction in Patients with Serous Ovarian Cancer. JOURNAL OF ONCOLOGY 2022; 2022:7625138. [PMID: 37223641 PMCID: PMC10202609 DOI: 10.1155/2022/7625138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/13/2022] [Accepted: 09/16/2022] [Indexed: 11/11/2022]
Abstract
Accurate risk stratification for patients with serous ovarian cancer (SOC) is pivotal for treatment decisions. In this study, we identified a lncRNA-based signature for predicting platinum resistance and prognosis stratification for SOC patients. We analyzed the RNA-sequencing data and the relevant clinical information of 295 SOC samples obtained from The Cancer Genome Atlas (TCGA) database and 180 normal ovarian tissues from the Genotype-Tissue Expression (GTEx) database. A total of 284 differentially expressed lncRNAs were screened out between platinum-sensitive and platinum-resistant groups by univariate Cox regression analysis. Then, a signature consisting of eight prognostic lncRNAs was used to construct a lncRNA score model by least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox regression analysis. The ROC analysis showed that this signature had a good predictive performance for chemotherapy response in the training set (AUC = 0.8524) and the testing and whole sets with 0.8142 and 0.8393 of AUC, respectively. Dichotomized by the risk score of lncRNAs (lncScore), the high-risk patients showed significantly shorter progression-free survival (PFS) and overall survival (OS). Based on the final Cox model, a nomogram comprising the 8-lncRNA signature and 3 clinicopathological risk factors was then established for clinical application to predict the 1, 2, and 3-year PFS of SOC patients. The gene set enrichment analysis (GSEA) revealed that genes in the high-risk group were active in ATP synthesis, coupled electron transport, and mitochondrial respiratory chain complex assembly. Overall, our findings demonstrated the potential clinical significance of the 8-lncRNA-based classifier as a novel biomarker for outcome prediction and therapy decisions in SOC patients with platinum treatment.
Collapse
Affiliation(s)
- Yan Zhu
- Health Care Center, The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong, China
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen 518001, Guangdong, China
| | - Jiongyu Chen
- Central Laboratory, Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Li Zhou
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Lina Zhang
- Health Care Center, The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Yuxin Liu
- Health Care Center, The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Yixuan Zhuang
- Department of Pathology, Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Lin Peng
- Central Laboratory, Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Yi-Teng Huang
- Health Care Center, The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong, China
| |
Collapse
|
7
|
Wang T, Wu Z, Li S, Chen Z, Chen Y, Yang Z. Identification of Gefitinib Resistance-Related lncRNA-miRNA-mRNA Regulatory Networks and Corresponding Prognostic Signature in Patients with Lung Adenocarcinoma. Int J Gen Med 2022; 15:7155-7168. [PMID: 36118184 PMCID: PMC9477152 DOI: 10.2147/ijgm.s369718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 09/01/2022] [Indexed: 12/24/2022] Open
Abstract
Purpose To identify and characterize gefitinib resistance-related (GefR-related) lncRNAs and construct a prediction model for lung adenocarcinoma (LUAD). Methods Differential expression analysis between PC9 and gefitinib-resistant PC9 (PC9GR) cell samples was performed to screen GefR-related lncRNAs and mRNAs based on the GSE34228 dataset. These lncRNAs, mRNAs, and their corresponding microRNAs (miRNAs) were used to construct the GefR-related network and PPI networks. Functional enrichment analyses were conducted using the STRING database. A prognostic signature was developed using the TCGA dataset. The reliability of the signature was tested using the Kaplan–Meier method and ROC curve. Lastly, the FZD4-associated ceRNA subnetwork was selected to confirm the in vitro expressions of the GefR-related lncRNAs using RT-qPCR assay. Results A GefR-related ceRNA network that consists of 35 miRNAs, 26 lncRNAs, and 179 mRNAs was constructed. Then, 20 hub genes were screened from the targeted mRNAs of the constructed PPI network, and enrichment analysis identified relevant enriched pathways. We also constructed a prognostic signature for LUAD based on nine mRNAs in the GefR-related ceRNA network. The 9-mRNA signature was an independent predictor of LUAD, the AUC produced by ROC analysis showed a good predictive power of the model, and Kaplan–Meier analysis showed poorer outcomes in the high-risk group, relative to the low-risk group. Lastly, MIR137HG and ZNF295-AS1 levels were found to be associated with gefitinib resistance and exerted their functions through the ceRNA mechanism. Conclusion We established a prognostic signature and identified two lncRNAs (MIR137HG and ZNF295-AS1) with potential significant roles in gefitinib resistance.
Collapse
Affiliation(s)
- Taoli Wang
- Department of Oncology, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, People’s Republic of China
| | - Zhulin Wu
- Department of Oncology, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, People’s Republic of China
| | - Shiguang Li
- Department of Oncology, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, People’s Republic of China
| | - Zhong Chen
- Department of Oncology, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, People’s Republic of China
| | - Yiqi Chen
- Department of Oncology, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, People’s Republic of China
| | - Zhenjiang Yang
- Department of Oncology, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, People’s Republic of China
- Correspondence: Zhenjiang Yang; Taoli Wang, Department of Oncology, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, People’s Republic of China, Tel +86-755-23612697, Email ;
| |
Collapse
|
8
|
Du Y, Chen Y, Wu T, Fan X, Lin W, Jiang Z. miR-2682-3p antagonizes its host lncRNA-MIR137HG by interacting with the same target FUS to regulate the progression of gastric cancer. BMC Cancer 2022; 22:689. [PMID: 35733138 PMCID: PMC9219209 DOI: 10.1186/s12885-022-09740-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/02/2022] [Indexed: 12/24/2022] Open
Abstract
Background The mechanism of long non-coding RNA MIR137HG in human gastric cancer (GC) is currently unknown. In the present study, we aimed to explore the function and mechanism of MIR137HG in gastric cancer. Methods The expression of lncRNA-MIR137HG in 69 gastric cancer samples and their paired surgical margin (SM) tissue samples were tested by QRT-PCR. UCSC was used to find the gene location relationship among MIR137HG and its embedded miRNAs. TargetScan was used to predict the targets of miR-2682-3p. Starbase was used to predict the candidate proteins that interacted with MIR137HG. Western blot, co-focus, and RIP assay were used to verify the direct interaction between MIR137HG and FUS (fused in sarcoma/translocated in liposarcoma, FUS/TLS), while dual-luciferase reporter assay was used to confirm the interaction between miR-2682-3p and FUS. Cell migration assays, colony formation, and xenografts assay were used to investigate the function of MIR137HG and miR-2682-3p to tumor growth and metastasis. Western blot assay was used to explore the downstream candidate protein of FUS. Results Data showed that MIR137HG expressed significantly higher in GC than in SM. MIR137HG promoted colony formation and migration in vitro and promoted tumor formation and metastasis in vivo. MIR137HG is distributed in both the nucleus and cytoplasm. It was co-located with FUS and could directly interact with FUS, which might interact with other proteins, such as MET(MET-proto-oncogene, receptor tyrosine kinase), RHOC(ras homolog family member), and CTNNB1(catenin beta1). These proteins may involve different signaling pathways to regulate gastric cancer progression. By contrast, the embedded miR-2682-3p could antagonize the series functions of its host lncRNA-MIR137HG by targeting FUS. Conclusions lncRNA-MIR137HG promoted growth and metastasis in gastric cancer by interacting with FUS, while miR-2682-3p could inhibit the function of MIR137HG via the same target FUS. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09740-9.
Collapse
Affiliation(s)
- Yantao Du
- The Affiliated Hospital of Medical School of Ningbo University, Renmin Road No.247, Ningbo, 315020, Zhejiang, China. .,Ningbo Institute of Medical Science, Yangshan Road No.42-46, Ningbo, 315020, Zhejiang, China.
| | - Yichen Chen
- The Affiliated Hospital of Medical School of Ningbo University, Renmin Road No.247, Ningbo, 315020, Zhejiang, China.,Ningbo Institute of Medical Science, Yangshan Road No.42-46, Ningbo, 315020, Zhejiang, China
| | - Tao Wu
- The Affiliated Hospital of Medical School of Ningbo University, Renmin Road No.247, Ningbo, 315020, Zhejiang, China
| | - Xiaodan Fan
- Medical School of Ningbo University, Fenghua Road No.818, Ningbo, 315211, Zhejiang, China
| | - Wei Lin
- The Affiliated Hospital of Medical School of Ningbo University, Renmin Road No.247, Ningbo, 315020, Zhejiang, China.,Zhejiang Pharmaceutical College, Ningbo, 315100, ZhejiangZhejiang, China
| | - Zhouhua Jiang
- Ningbo Medical Centre Lihui Li Eastern Hospital, Ningbo University, Jiangnan Road No.1111, Ningbo, 330212, Zhejiang, China. .,Ningbo Women and Children Hospital, Ningbo Liuting Road No.339, Ningbo, 315012, Zhejiang, China.
| |
Collapse
|
9
|
Identification of Novel Prognostic Signatures for Clear Cell Renal Cell Carcinoma Based on ceRNA Network Construction and Immune Infiltration Analysis. DISEASE MARKERS 2022; 2022:4033583. [PMID: 35320950 PMCID: PMC8938059 DOI: 10.1155/2022/4033583] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/20/2022] [Accepted: 03/02/2022] [Indexed: 12/11/2022]
Abstract
Objective. Clear cell renal cell carcinoma (ccRCC) carries significant morbidity and mortality globally and is often resistant to conventional radiotherapy and chemotherapy. Immune checkpoint blockade (ICB) has received attention in ccRCC patients as a promising anticancer treatment. Furthermore, competitive endogenous RNA (ceRNA) networks are crucial for the occurrence and progression of various tumors. This study was aimed at identifying reliable prognostic signatures and exploring potential mechanisms between ceRNA regulation and immune cell infiltration in ccRCC patients. Methods and Results. Gene expression profiling and clinical information of ccRCC samples were obtained from The Cancer Genome Atlas (TCGA) database. Through comprehensive bioinformatic analyses, differentially expressed mRNAs (DEmRNAs;
), lncRNAs (DElncRNAs;
), and miRNAs (DEmiRNAs;
) were identified to establish ceRNA networks. The CIBERSORT algorithm was applied to calculate the proportion of 22 types of tumor-infiltrating immune cells (TIICs) in ccRCC tissues. Subsequently, univariate Cox, Lasso, and multivariate Cox regression analyses were employed to construct ceRNA-related and TIIC-related prognostic signatures. In addition, we explored the relationship between the crucial genes and TIICs via coexpression analysis, which revealed that the interactions between MALAT1, miR-1271-5p, KIAA1324, and follicular helper T cells might be closely correlated with the progression of ccRCC. Ultimately, we preliminarily validated that the potential MALAT1/miR-1271-5p/KIAA1324 axis was consistent with the ceRNA theory by qRT-PCR in the ccRCC cell lines. Conclusion. On the basis of the ceRNA networks and TIICs, we constructed two prognostic signatures with excellent predictive value and explored possible molecular regulatory mechanisms, which might contribute to the improvement of prognosis and individualized treatment for ccRCC patients.
Collapse
|
10
|
He Y, Wu Y, Liu Z, Li B, Jiang N, Xu P, Xu A. Identification of Signature Genes Associated With Invasiveness and the Construction of a Prognostic Model That Predicts the Overall Survival of Bladder Cancer. Front Genet 2021; 12:694777. [PMID: 34589112 PMCID: PMC8473900 DOI: 10.3389/fgene.2021.694777] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/25/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Bladder cancer has become the tenth most diagnosed cancer worldwide. The prognosis has been shown to differ between non-muscle invasive bladder cancer (NMIBC) and muscle invasive bladder cancer (MIBC). We aimed to identify signature genes that are associated with the invasiveness and survival of bladder cancer and to identify potential treatments. Methods: We downloaded gene expression profiles of bladder cancer from the Gene Expression Omnibus database to identify differentially expressed genes and perform weighted gene co-expression network analysis. Functional enrichment was analyzed by GO and KEGG analyses. Hub genes were identified from the significant module. Another dataset was also acquired to verify the expression of hub genes. Univariate and multivariate Cox regression analyses were applied to the dataset downloaded from The Cancer Genome Atlas database. Risk scores were calculated and the effect was evaluated by Kaplan-Meier survival analysis. A nomogram was constructed and validated using training and testing samples, respectively. Analysis of the tumor immune microenvironment was conducted with the CIBERSORT algorithm. Results: In total, 1,245 differentially expressed genes (DEGs) were identified. A distinct module was identified that was significantly correlated to invasiveness. The genes within this module were found to be significantly associated with extracellular exosomes, GTPase activity, metabolic pathways, etc. Three hub genes (VSIG2, PPFIBP2, and DENND2D) were identified as biomarkers of invasiveness; two of these (PPFIBP2 and DENND2D) were closely associated with prognosis. The risk score was regarded as an independent prognostic factor. The nomogram was associated with acceptable accuracy for predicting 1- and 5-year overall survival. The infiltrating levels of resting NK cells, activated natural killer (NK) cells, CD8+ T cells, activated memory CD4+ T cells, and T follicular helper cells, were significantly higher in the group with lower risk scores. The group with higher risk scores showed predominant infiltration by regulatory T cells (Tregs). Conclusion: We successfully identified three signature genes related to invasiveness and constructed a nomogram of bladder cancer with acceptable performance. Differences suggested by risk scores between groups of patients showing diverse patterns of immune cell infiltration may be beneficial for selecting therapeutic approaches and predicting prognosis.
Collapse
Affiliation(s)
- Yang He
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yongxin Wu
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zhe Liu
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Boping Li
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Ning Jiang
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Peng Xu
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Abai Xu
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Department of Urology, The First People's Hospital of Kashgar Prefecture, Kashgar, China
| |
Collapse
|
11
|
He X, Xiao H, Yang R, Chen H, Wang B. lncRNA LOC339524 inhibits the proliferation of bladder cancer cells by targeting the miR-875-5p/COPS7A signaling axis. Exp Ther Med 2021; 22:1202. [PMID: 34584547 PMCID: PMC8422399 DOI: 10.3892/etm.2021.10636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/21/2021] [Indexed: 12/28/2022] Open
Abstract
It has been reported that long non-coding RNAs (lncRNAs) play a crucial role in the progression of various types of cancer. The role of numerous lncRNAs in a variety of cancer types has been investigated. However, the underlying mechanisms of the majority of lncRNAs in bladder cancer (BCa) remain to be elucidated. In the present study, abnormally expressed lncRNAs in BCa and para-carcinoma tissues were identified through screening the Cancer RNA-Seq Nexus database and were validated using reverse transcription-quantitative PCR. It was found that LOC339524 expression levels were markedly downregulated in BCa tissues and cells (J82, T24, UM-UC-3 and 5637). LOC339524 overexpression was revealed to suppress the proliferation of BCa cells. LOC339524 was also discovered to act as a sponge for microRNA (miR)-875-5p, as identified using dual luciferase reporter assays and biotin pull-down analysis. LOC339524 downregulated the expression of miR-875-5p and knockdown of miR-875-5p expression inhibited the proliferation of bladder cancer cells. In addition, COP9 signalosome subunit 7A (COPS7A) was identified to be the target gene of miR-875-5p and COPS7A expression level was upregulated following LOC339524 overexpression. lncRNA LOC339524 was proposed to function as a competitive endogenous RNA to facilitate the expression of COPS7A by binding to miR-875-5p. In conclusion, the findings of the present study suggested that LOC339524 may inhibit cell proliferation in BCa by targeting the miR-875-5p/COPS7A signaling axis.
Collapse
Affiliation(s)
- Xuan He
- Department of Oncology, Daping Hospital, Army Medical University, Chongqing 400042, P.R. China
| | - He Xiao
- Department of Oncology, Daping Hospital, Army Medical University, Chongqing 400042, P.R. China
| | - Rui Yang
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Hang Chen
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Bin Wang
- Department of Oncology, Daping Hospital, Army Medical University, Chongqing 400042, P.R. China
| |
Collapse
|
12
|
Wei J, Fang DL, Huang CK, Hua SL, Lu XS. Screening a novel signature and predicting the immune landscape of metastatic osteosarcoma in children via immune-related lncRNAs. Transl Pediatr 2021; 10:1851-1866. [PMID: 34430433 PMCID: PMC8349967 DOI: 10.21037/tp-21-226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 06/15/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The immune microenvironment plays an essential role in osteosarcoma (OSs); however, differences in immune-related long non-coding ribonucleic acids (irlncRNAs) in children with localized OSs and metastatic OSs have not yet been investigated. METHODS The clinical data and the transcriptome of OSs were obtained from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database, and the immune-related genes were derived from the imported dataset. The correlations between immune-related genes and lncRNAs were examined. Next, the differential expressions of the irlncRNA pairs (IRLPs) in localized OSs and distant metastatic OSs were analyzed, and a prognostic model was constructed based on the significant differentially expressed IRLPs. We also analyzed the association between the IRLPs' signature risk score and the infiltration of the immune cells. Finally, we investigated the correlation between risk score and drug resistance. RESULTS Thirty upregulated and 22 downregulated lncRNAs were identified in the localized and metastatic OSs samples. Univariate and multivariate cox regression analyses were undertaken to select 6 lncRNA pairs to establish the prognostic signature, the model was valuable in predicting OSs prognosis. Further, the expression of the finally selected irlncRNAs indicated that VPS9D1-AS1 (P=0.031), AP003086.2 (P=0.041), AL031847.1 (P=0.008), AL020997.3 (P=0.020), AC011444.1 (P=0.025), and AC006449.2 (P=0.003) were significantly upregulated in metastasis patients, but USP27X-AS1 (P=0.046), AL008721.2 (P=0.005), AC002091.1 (P=0.033), and AL118558.4 (P=0.049) were significantly overexpressed in localized patients. The overexpression of AC002091.1 (P=0.038) and AL118558.4 (P=0.004) resulted in better overall survival, but the upregulation of AC011444.1 (P=0.045), AL031847.1 (P=0.020), VPS9D1-AS1 (P=0.039), and AC006449.2 (0.006) led to a poor outcome. Differences in immune cell infiltration indicated that metastatic patients and localized have significant difference of 4 (CD4) T cells (P=0.006), monocytes (P=0.029), activated mast cells (P=0.018), and neutrophils (P=0.026), and a high abundance of activated dendritic cells (P=0.010) and activated mast cells (P=0.049) resulted in poor prognosis. Patients in the high-risk-score group were resistant to axitinib, but sensitive to dasatinib, bortezomib, and cisplatin. CONCLUSIONS In the present study, IRLPs were used to construct a novel and practical model for predicting the prognosis of localized and metastatic OSs in children.
Collapse
Affiliation(s)
- Jie Wei
- Department of Hematology, Baise People's Hospital, Baise, China
| | - Da-Lang Fang
- Department of Breast and Thyroid Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Cheng Kua Huang
- Department of Traumatology, Baise People's Hospital, Baise, China
| | - Shu-Liang Hua
- Department of Traumatology, Baise People's Hospital, Baise, China
| | - Xiao-Sheng Lu
- Department of Traumatology, Baise People's Hospital, Baise, China
| |
Collapse
|
13
|
Wu Y, Wang T, Xia L, Zhang M. LncRNA WDFY3-AS2 promotes cisplatin resistance and the cancer stem cell in ovarian cancer by regulating hsa-miR-139-5p/SDC4 axis. Cancer Cell Int 2021; 21:284. [PMID: 34051810 PMCID: PMC8164817 DOI: 10.1186/s12935-021-01993-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Ovarian cancer (OC) is a high-mortality gynecological cancer that is typically treated with cisplatin, although such treatment often results in chemoresistance. Ovarian cancer resistance is usually related to cell stemness. Herein, we explored the function of lncRNA WDFY3-AS2 in OC cell resistance to cisplatin (DDP). METHODS Cisplatin resistant OC A2780 cell lines (A2780-DDP) were established by long-term exposure to cisplatin. CCK-8 assay were performed to evaluate the viability of A2780, and A2780-DDP cells. Quantitative RT-PCR was used to examine the expression of lncRNA WDFY3-AS2, miR-139-5p, and SDC4 in A2780-DDP cell lines. After treatment with cisplatin, cell apoptosis and CD44+CD166+-positive cells were measured by flow cytometry. The transwell assays were employed to measure the effect of WDFY3-AS2 on cell migration, and invasion. In addition, tumorsphere formation assay was used to enrich OC cancer stem cells (CSCs) from A2780-DDP cells. The expression of CSC markers (SOX2, OCT4, and Nanog) was detected by western blotting. The regulatory mechanism was confirmed by RNA pull down, and luciferase reporter assays. Furthermore, xenograft tumor in nude mice was used to assess the impact of WDFY3-AS2 on cisplatin resistance in OC in vivo. RESULTS WDFY3-AS2 was highly expressed in OC A2780-DDP cells, and silencing WDFY3-AS2 significantly inhibited proliferation, migration and invasion but increased apoptosis in OC A2780-DDP cells. Additionally, WDFY3-AS2 significantly promoted the A2780-DDP cells tumorspheres. WDFY3-AS2 was predicted to impact OC by sponging miR-139-5p and regulating SDC4. The xenografts inoculated with A2780-DDP cells additionally confirmed that tumor growth in vivo was reduced by si-WDFY3-AS2 transfection. MiR-139-5p inhibitor or SDC4 overexpression could restore the suppressive influence of silenced WDFY3-AS2 on tumor growth. CONCLUSIONS Together, WDFY3-AS2 may lead to change of cisplatin resistance by the expression of miR-139-5p/SDC4 in the OC A2870-DDP cells both in vitro and in vivo. Our finding may provide a drug target for the drug resistance of OC.
Collapse
Affiliation(s)
- Yue Wu
- Department of Integrated Chinese and Western Medicine Oncology, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, Anhui, China
- The Traditional and Western Medicine (TCM)-Integrated Cancer Center of Anhui Medical University, 81 Meishan Road, Hefei, 230032, China
| | - Ting Wang
- Department of Integrated Chinese and Western Medicine Oncology, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, Anhui, China
- The Traditional and Western Medicine (TCM)-Integrated Cancer Center of Anhui Medical University, 81 Meishan Road, Hefei, 230032, China
| | - Lin Xia
- Graduate School of Anhui, University of Traditional Chinese Medicine, Hefei, 230012, Anhui, China
| | - Mei Zhang
- Department of Integrated Chinese and Western Medicine Oncology, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, Anhui, China.
- The Traditional and Western Medicine (TCM)-Integrated Cancer Center of Anhui Medical University, 81 Meishan Road, Hefei, 230032, China.
| |
Collapse
|
14
|
Zhang R, Yang F, Fan H, Wang H, Wang Q, Yang J, Song T. Long non-coding RNA TUG1/microRNA-187-3p/TESC axis modulates progression of pituitary adenoma via regulating the NF-κB signaling pathway. Cell Death Dis 2021; 12:524. [PMID: 34021124 PMCID: PMC8140116 DOI: 10.1038/s41419-021-03812-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 01/27/2023]
Abstract
The molecule mechanisms of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in human diseases have been broadly studied recently, therefore, our research aimed to assess the effect of lncRNA taurine upregulated gene 1 (TUG1)/miR-187-3p/tescalcin (TESC) axis in pituitary adenoma (PA) by regulating the nuclear factor-kappa B (NF-κB) signaling pathway. We observed that TUG1 was upregulated in PA tissues and was associated with invasion, knosp grade and tumor size. TUG1 particularly bound to miR-187-3p. TUG1 knockdown inhibited cell proliferation, invasion, migration, and epithelial–mesenchymal transition, promoted apoptosis, and regulated the expression of NF-κB p65 and inhibitor of κB (IκB)-α in PA cells lines in vitro, and also inhibited tumor growth in vivo, and these effects were reversed by miR-187-3p reduction. Similarly, miR-187-3p elevation inhibited PA cell malignant behaviors and modulated the expression of NF-κB p65 and IκB-α in PA cells, and reduced in vivo tumor growth as well. TUG1 inhibition downregulated TESC, which was targeted by miR-187-3p. In conclusion, this study suggests that TUG1 sponges miR-187-3p to affect PA development by elevating TESC and regulating the NF-κB signaling pathway.
Collapse
Affiliation(s)
- Rui Zhang
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021, Jinan, Shandong, China
| | - Fan Yang
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021, Jinan, Shandong, China
| | - Haitao Fan
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021, Jinan, Shandong, China
| | - Haocong Wang
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021, Jinan, Shandong, China
| | - Qinghao Wang
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021, Jinan, Shandong, China
| | - Jianxin Yang
- Department of Neurosurgery, The People's Hospital of Qingzhou, 262500, Qingzhou, Shandong, China
| | - Tao Song
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021, Jinan, Shandong, China.
| |
Collapse
|
15
|
Comprehensive analysis of long non-coding RNA and mRNA expression profile in rectal cancer. Chin Med J (Engl) 2021; 133:1312-1321. [PMID: 32224706 PMCID: PMC7289300 DOI: 10.1097/cm9.0000000000000753] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Rectal cancer (RC) is a malignant tumor that seriously threatens human health. Long non-coding RNAs (lncRNAs) play a vital role in tumor regulation. Nevertheless, their exact expression features and functions remain obscure, and therefore was the aim of the current study. METHODS We utilized the Affymetrix human GeneChip to screen differentially expressed profiles of lncRNAs and mRNAs from the cancer tissues and matched paracancer tissues of 6 RC patients. Gene Ontology (GO) and pathway enrichment analyses identified crucial functions and pathways of the aberrantly expressed mRNAs. We used quantitative real-time polymerase chain reaction to verify the significant expression differences of 11 candidate lncRNAs between the cancer and paracancer tissues. LncRNA-mRNA coexpression networks were built by calculating the Pearson correlation value to identify significant correlation pairs. Online bioinformatics tools GEPIA2, ONCOMINE, and PROGgeneV2 were used to mine the expression and prognosis of three crucial mRNAs and six verified lncRNAs. Competing endogenous RNA networks were constructed by predicting microRNA response elements and calculating free energy. RESULTS We found 1658 differentially expressed lncRNAs (778 up-regulated and 880 down-regulated) and 1783 aberrantly expressed mRNAs (909 up-regulated and 874 down-regulated). GO and pathway enrichment analyses revealed the vital functions of the differentially expressed mRNAs, including cell proliferation, cell migration, angiogenesis, and cellular response to zinc ion. The canonical signaling pathways mainly included the interleukin-17, cell cycle, Wnt, and mineral absorption signaling pathways. Six lncRNAs including AC017002.2 (P = 0.039), cancer susceptibility 19 (CASC19) (P = 0.021), LINC00152 (P = 0.013), NONHSAT058834 (P = 0.007), NONHSAT007692 (P = 0.045), and ENST00000415991.1 (P = 0.045) showed significant differences in expression levels between the cancer tissue and paracancer tissue groups. AC017002.2, NONHSAT058834, NONHSAT007692, and ENST00000415991.1 have not yet been reported in RC. The crucial mRNAs myelocytomatosis viral oncogene (MYC), transforming growth factor beta induced (TGFBI), and solute carrier family 7 member 5 (SLC7A5) were selected. AC017002.2 and LINC00152 were positively correlated with MYC, TGFBI, and cytochrome P450 family 2 sub-family B member 6 (All r > 0.900, P < 0.050). NONHSAT058834 was positively associated with MYC (r = 0.930, P < 0.001), and CASC19 was positively correlated with SLC7A5 (r = 0.922, P < 0.001). CONCLUSION This study offers convincing evidence of differentially expressed lncRNAs and mRNAs as potential biomarkers in RC.
Collapse
|
16
|
Huang M, Long Y, Jin Y, Ya W, Meng D, Qin T, Su L, Zhou W, Wu J, Huang C, Huang Q. Comprehensive analysis of the lncRNA-miRNA-mRNA regulatory network for bladder cancer. Transl Androl Urol 2021; 10:1286-1301. [PMID: 33850763 PMCID: PMC8039630 DOI: 10.21037/tau-21-81] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are essential regulators for various human cancers. However, these lncRNAs need to be further classified for cancer. In the present study, we identified novel competing endogenous RNA (ceRNA) network for bladder cancer (BC) and explored the gene functions of the ceRNA regulatory network. Methods Differential gene expression analysis were performed on The Cancer Genome Atlas Urothelial Bladder Carcinoma (TCGA-BLCA) datasets to identify differentially expressed messenger RNAs (mRNAs), lncRNAs, and microRNAs (miRNAs). Based on the competing endogenous RNA (ceRNA) hypothesis, a lncRNA-miRNA-mRNA network was constructed using the StarBase database and visualization by Cytoscape software. Functional enrichment analyses of Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were performed via R package ClusterProfiler. The protein-protein interaction network was constructed by STRING database and visualization by Cytoscape. Finally, we used CIBERSORT and the TIMER database to analyze the immune infiltrations for BC. Results The regulatory network was constructed via TCGA BLCA cohort. The differential expressions of lncRNA, miRNA, and mRNA were 186, 200, and 2,661, respectively. There were 106 lncRNA, miRNA, and mRNA included in the ceRNA network. In this network, Calcium Voltage-gated Channel Auxiliary Subunit Alpha2delta1 (CACNA2D1, P<0.001), domain containing engulfment adaptor1 (GULP1, P=0.001), latent transforming growth factor beta binding protein 1 (LTBP1, P=0.006), myosin light chain kinase (MYLK, P=0.001), serpin family E member 2 (SERPINE2, P=0.002), spectrin beta non-erythrocytic 2 (SPTBN2, P=0.047), and hsa-miR-590-3p (P<0.001) significantly affected the prognosis of BC patients. Functional enrichment analyses showed that the biological functions included negative regulation of protein phosphorylation, cell morphogenesis, and sensory organ morphogenesis. Important cancer pathways of KEGG included parathyroid hormone synthesis secretion action, the notch signaling pathway, MAPK signaling pathway, the Rap1 signaling pathway, signaling pathways regulating the pluripotency of stem cells, and the transforming growth factor-β signaling pathway. Our findings demonstrated that the ceRNA network has important biological functions and a significant influence on the prognosis of BC. Conclusions The lncRNA-miRNA-mRNA network constructed in the present study could provide useful insight into the underlying tumorigenesis of BC, and can determine new molecular biomarkers for the diagnosis and therapeutical treatment of BC.
Collapse
Affiliation(s)
- Minyu Huang
- Department of Urology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yi Long
- Department of Urology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yuzhu Jin
- Department of Urology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Wentong Ya
- Department of Urology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Dongdong Meng
- Department of Urology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Tianzi Qin
- Department of Urology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Lize Su
- Department of Urology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Wei Zhou
- Department of Urology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Jichao Wu
- Department of Urology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Chunhe Huang
- Department of Infectious Disease, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Qun Huang
- Department of Urology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| |
Collapse
|
17
|
Fu Y, Liu Q, Bao Q, Wen J, Liu Z, Hu Y, He G, Peng C, Xu Y, Zhang W. Development and analysis of long non-coding RNA-associated competing endogenous RNA network for osteosarcoma metastasis. Hereditas 2021; 158:9. [PMID: 33593435 PMCID: PMC7887822 DOI: 10.1186/s41065-021-00174-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 02/08/2021] [Indexed: 11/25/2022] Open
Abstract
Background Osteosarcoma is the primary bone malignant neoplasm that often develops metastasis. Increasing evidences have shown that non-coding RNAs (ncRNAs) relate to the progression of osteosarcoma. However, the ncRNAs’ roles in osteosarcoma metastasis are still unknown. Methods Differentially expressed (DE) RNAs were identified from Gene Expression Omnibus (GEO) database. Protein-protein interaction (PPI) of DE messenger RNAs (DEmRNAs) was built through STRING database. The target mRNAs and long ncRNAs (lncRNAs) of microRNAs (miRNA) were predicted through miRDB, Targetscan and Genecode databases, which then cross-checked with previously obtained DERNAs to construct competing endogenous RNA (ceRNA) network. All networks were visualized via Cytoscape and the hub RNAs were screened out through Cytoscape plug-in Cytohubba. The gene functional and pathway analyses were performed through DAVID and MirPath databases. The survival analyses of hub RNAs were obtained through Kaplan-Meier (KM) survival curves. Results Five hundred sixty-four DEmRNAs, 16 DElncRNAs and 22 DEmiRNAs were screened out. GO functional and KEGG pathway analyses showed that DERNAs were significantly associated with tumor metastasis. The ceRNA network including 6 lncRNAs, 55 mRNAs and 20 miRNAs were constructed and the top 10 hub RNAs were obtained. Above all, PI3K/AKT signaling pathway was identified as the most important osteosarcoma metastasis-associated pathway and its hub ceRNA module was constructed. The survival analyses showed that the RNAs in hub ceRNA module closely related to osteosarcoma patients’ prognosis. Conclusions The current study provided a new perspective on osteosarcoma metastasis. More importantly, the RNAs in hub ceRNA module might act as the novel therapeutic targets and prognostic factors for osteosarcoma patients. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-021-00174-0.
Collapse
Affiliation(s)
- Yucheng Fu
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, PR China
| | - Qi Liu
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, PR China
| | - Qiyuan Bao
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, PR China
| | - Junxiang Wen
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, PR China
| | - Zhuochao Liu
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, PR China
| | - Yuehao Hu
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, PR China
| | - Guoyu He
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, PR China
| | - Cheng Peng
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, PR China
| | - Yiqi Xu
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, PR China
| | - Weibin Zhang
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, PR China.
| |
Collapse
|
18
|
Liu T, Zhang Y, Liu W, Zhao J. LncRNA NEAT1 Regulates the Development of Parkinson's Disease by Targeting AXIN1 Via Sponging miR-212-3p. Neurochem Res 2021; 46:230-240. [PMID: 33241432 DOI: 10.1007/s11064-020-03157-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 10/10/2020] [Accepted: 10/21/2020] [Indexed: 12/21/2022]
Abstract
Long non-coding RNA (lncRNA) nuclear-enriched assembly transcript 1 (NEAT1) has been reported to be highly expressed in Parkinson's disease (PD). However, the mechanism of NEAT1 in PD progression has not been fully elucidated. 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine injection (MPTP) was used to construct PD mouse models in vivo, and 1-methyl-4-phenyl pyridine (MPP+) was used to build PD cell models in vitro. Quantitative real-time polymerase chain reaction (qRT-PCR) was employed to test the expression of NEAT1, microRNA (miR)-212-3p and axis inhibition protein 1 (AXIN1). The viability, apoptosis and inflammation of cells were determined using cell counting kit 8 (CCK8) assay, flow cytometry and enzyme-linked immunosorbent assay (ELISA), respectively. Then, the protein levels of apoptosis-related markers and AXIN1 were measured by western blot (WB) analysis. Furthermore, dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay were performed to verify the interaction between miR-212-3p and NEAT1 or AXIN1. NEAT1 was upregulated in PD mouse models and cell models. Function experiments confirmed that NEAT1 knockdown could promote the viability, suppress the apoptosis and inflammation of MPP+-stimulated SK-N-SH cells to restrain PD progression. MiR-212-3p was downregulated in PD, and its inhibitor could reverse the suppression effect of NEAT1 knockdown on PD progression. Additionally, AXIN1 was a target of miR-212-3p, and its overexpression could invert the inhibition effect of miR-212-3p mimic on PD progression. Furthermore, AXIN1 expression was inhibited by NEAT1 silencing and promoted by NEAT1 overexpression, while these effect could be recovered by miR-212-3p inhibitor and mimic, respectively. Our results demonstrated that NEAT1 knockdown suppressed PD progression through regulating the miR-212-3p/AXIN1 pathway, indicating that NEAT1 might be a therapeutic target for neuroprotection in PD.
Collapse
Affiliation(s)
- Tao Liu
- Department of Neurology, Tianjin Hospital of ITCWM Nankai Hospital, No. 6 Changjiang Road, Nankai District, Tianjin, 300100, China.
| | - Yang Zhang
- Department of Acupuncture & Physiotherapy, Tianjin Hospital of ITCWM Nankai Hospital, Tianjin, 300100, China
| | - Weihong Liu
- Department of Traditional Chinese Medicine, Tianjin Fourth Central Hospital, Tianjin, 300140, China
| | - Jinsheng Zhao
- Department of Acupuncture & Physiotherapy, Tianjin Hospital of ITCWM Nankai Hospital, Tianjin, 300100, China
| |
Collapse
|
19
|
Jiang A, Liu N, Bai S, Wang J, Gao H, Zheng X, Fu X, Ren M, Zhang X, Tian T, Ruan Z, Yao Y, Liang X. The Construction and Analysis of Tumor-Infiltrating Immune Cells and ceRNA Networks in Bladder Cancer. Front Genet 2021; 11:605767. [PMID: 33391354 PMCID: PMC7775311 DOI: 10.3389/fgene.2020.605767] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
Background Bladder cancer (BLCA) is the 11th most common malignancy worldwide. Although significant improvements have been made in screening, diagnosis, and precise management in recent years, the prognosis of BLCA remains bleak. Objectives This study aimed to investigate the prognostic significance of tumor-infiltrating immune cells and construct ceRNA networks in BLCA patients. Methods The expression data of BLCA patients were obtained from The Cancer Genome Atlas (TCGA) database. A competing endogenous RNA (ceRNA) network was constructed to identify the hub genes involved in the prognosis of BLCA. The CIBERSORT algorithm was utilized to investigate the infiltration levels of 22 subsets of immune cells. Ultimately, the nomogram was generated to visualize the survival probability of each patient, with the calibration curve being performed to assess its performance. Furthermore, the Pearson correlation test was used to explore the correlation between the identified hub genes in the ceRNA network and the prognostic-related immune cells. Results A total of eight elements in the ceRNA network were considered as key members and correlated with the prognosis of BLCA, including ELN, SREBF1, DSC2, TTLL7, DIP2C, SATB1, hsa-miR-20a-5p, and hsa-miR-29c-3p. T cells CD8, T cells follicular helper (Tfh), and neutrophils were identified as independent prognostic factors in BLCA. The co-expression analysis showed that there was a significant correlation between the identified hub genes and immune cells. Conclusion Our results suggest that the mechanism of hsa-miR-29c-3p regulates the expression of ELN and DSC2, and the infiltration of Tfh and neutrophils might play pivotal roles in the progression of BLCA.
Collapse
Affiliation(s)
- Aimin Jiang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Na Liu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Shuheng Bai
- Department of Radiotherapy Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jingjing Wang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Huan Gao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaoqiang Zheng
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiao Fu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Mengdi Ren
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaoni Zhang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Tao Tian
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhiping Ruan
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yu Yao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xuan Liang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| |
Collapse
|
20
|
Cheng C, Li H, Zheng J, Xu J, Gao P, Wang J. FENDRR Sponges miR-424-5p to Inhibit Cell Proliferation, Migration and Invasion in Colorectal Cancer. Technol Cancer Res Treat 2020; 19:1533033820980102. [PMID: 33356998 PMCID: PMC7768317 DOI: 10.1177/1533033820980102] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Objective: LncRNAs are non-coding RNAs exerting vital roles in the occurrence and
development of various cancer types. This study tended to describe the
expression pattern of FENDRR in colorectal cancer (CRC), and further
investigate the role of FENDRR in CRC cell biological behaviors. Methods: Gene expression profile of colon cancer was accessed from the TCGA database,
and then processed for differential analysis for identification of
differentially expressed lncRNAs and miRNAs. Some in vitro
experiments like qRT-PCR, MTT, colony formation assay, wound healing assay
and Transwell assay were performed to assess the effect of FENDRR on cell
biological behaviors. Dual-luciferase reporter assay was conducted to
further validate the targeting relationship between FENDRR and miR-424-5p,
and rescue experiments were carried out for determining the mechanism of
FENDRR/miR-424-5p underlying the proliferation, migration and invasion of
CRC cells. Results: Bioinformatics analysis suggested that FENDRR was significantly
down-regulated in CRC tissue, and low FENDRR was intimately correlated to
poor prognosis. FENDRR overexpression could greatly inhibit cell
proliferation, migration and invasion. Besides, there was a negative
correlation between FENDRR and miR-424-5p. Dual-luciferase reporter assay
indicated that miR-424-5p was a direct target of FENDRR. Rescue experiments
discovered that FENDRR exerted its role in cell proliferation, migration and
invasion in CRC via targeting miR-424-5p. Conclusion: FENDRR is poorly expressed in CRC tissue and cells, and low FENDRR is
responsible for the inhibition of cell proliferation, migration and invasion
of CRC by means of targeting miR-424-5p.
Collapse
Affiliation(s)
- Chuan Cheng
- Department of Colorectal and Anal Surgery, Lishui Municipal Central Hospital, Zhejiang Province, China
| | - Huixia Li
- Department of Colorectal and Anal Surgery, Lishui Municipal Central Hospital, Zhejiang Province, China
| | - Jiujian Zheng
- Department of Colorectal and Anal Surgery, Lishui Municipal Central Hospital, Zhejiang Province, China
| | - Jie Xu
- Department of Colorectal and Anal Surgery, Lishui Municipal Central Hospital, Zhejiang Province, China
| | - Peng Gao
- Department of Colorectal and Anal Surgery, Lishui Municipal Central Hospital, Zhejiang Province, China
| | - Jianping Wang
- Department of Colorectal and Anal Surgery, Lishui Municipal Central Hospital, Zhejiang Province, China
| |
Collapse
|
21
|
Han L, Jia L, Zan Y. Long intergenic noncoding RNA smad7 (Linc-smad7) promotes the epithelial-mesenchymal transition of HCC by targeting the miR-125b/SIRT6 axis. Cancer Med 2020; 9:9123-9137. [PMID: 33037850 PMCID: PMC7724296 DOI: 10.1002/cam4.3515] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 09/06/2020] [Accepted: 09/15/2020] [Indexed: 12/16/2022] Open
Abstract
Long intergenic noncoding RNA smad7 (Linc-smad7) has been recently identified as a new long non-coding RNA (lncRNA). However, the role of Linc-smad7 in the tumourigenesis of human cancers remains unknown. This study uncovered that Linc-smad7 was increased in HCC samples and HCC cell lines using RT-qPCR assays. Furthermore, the overexpression of Linc-smad7 indicated poor clinicopathological features and outcomes for HCC patients. In addition, Linc-smad7 promoted HCC cells proliferation, migration, invasion and EMT, as determined by MTT, colony formation, Transwell assays and western blot analysis. Functionally, it was demonstrated that Linc-smad7 could bind with microRNA-125b (miR-125b), and the restoration of miR-125b rescued the promoting effects of Linc-smad7 on HCC cells. Finally, it was observed that sirtuin 6 (SIRT6) was positively regulated by Linc-smad7 in HCC as the direct target of miR-125b, and decreased SIRT6 reversed the effects of Linc-smad7 on promoting HCC. In conclusion, the current study first identified Linc-smad7 is increased in HCC, facilitating HCC cells proliferation, migration, invasion and EMT via regulating the miR-125b/SIRT6 axis.
Collapse
Affiliation(s)
- Lili Han
- Department of OncologyThe Second Affiliated HospitalCollege of MedicineXi'an Jiaotong UniversityXi'anShaanxiChina
| | - Lijun Jia
- Department of OncologyThe Second Affiliated HospitalCollege of MedicineXi'an Jiaotong UniversityXi'anShaanxiChina
| | - Ying Zan
- Department of OncologyThe Second Affiliated HospitalCollege of MedicineXi'an Jiaotong UniversityXi'anShaanxiChina
| |
Collapse
|
22
|
Yu H, Cheng Y, Li W, Li Z, Wu P, Qiu S, Zeng B, Huang B. A novel lncRNA-miRNA-mRNA competitive endogenous RNA network for uveal melanoma prognosis constructed by weighted gene co-expression network analysis. Life Sci 2020; 260:118409. [PMID: 32926921 DOI: 10.1016/j.lfs.2020.118409] [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: 06/07/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 02/07/2023]
Abstract
AIMS Uveal melanoma (UM) is the most common and aggressive intraocular tumor in adults, and long-term survival of UM patients remains poor. Abnormal competitive endogenous RNA (ceRNA) networks promote the initiation and progression of many tumors and may thus serve as useful prognostic indicators. Here, we do a comprehensive analysis of long non-coding RNA (lncRNA)-microRNA (miRNA)-mRNA ceRNA networks as prognostic markers for UM. MATERIALS AND METHODS The Cancer Genome Atlas UM dataset was used to identify survival-related mRNA and lncRNA modules through weighted gene co-expression network analysis (WGCNA). Prognostic miRNAs were identified using univariate Cox proportional hazard regression. We then used Cox and least absolute shrinkage and selection operator regression to screen for prognostic hub mRNAs and establish a hub ceRNA network. A nomogram of five hub mRNAs was constructed and Kaplan-Meier survival analysis performed. KEY FINDINGS Six mRNA modules were constructed, two of which involved 1490 mRNAs that significantly correlated with survival. Among the three lncRNA modules constructed, one involved 199 survival-related lncRNAs. Five hub prognostic mRNAs were identified and a hub ceRNA network constructed, consisting of six lncRNAs, four miRNAs, and five mRNAs, with high prognostic value. SIGNIFICANCE We describe a hub ceRNA network of survival-associated lncRNAs, miRNAs, and mRNA that may underlie a critical post-translational regulatory mechanism determining UM aggression. These hub RNAs may be valuable prognostic markers and therapeutic targets in UM.
Collapse
Affiliation(s)
- Huan Yu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Yaqi Cheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Weihua Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Zhiquan Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Peixin Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Sujuan Qiu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Baozhu Zeng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Bing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China.
| |
Collapse
|
23
|
Zhu X, Jiang L, Yang H, Chen T, Wu X, Lv K. Analyzing the lncRNA, miRNA, and mRNA-associated ceRNA networks to reveal potential prognostic biomarkers for glioblastoma multiforme. Cancer Cell Int 2020; 20:393. [PMID: 32821246 PMCID: PMC7429694 DOI: 10.1186/s12935-020-01488-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/07/2020] [Indexed: 02/08/2023] Open
Abstract
Background Glioblastoma multiforme (GBM) is the most seriously brain tumor with extremely poor prognosis. Recent research has demonstrated that competitive endogenous RNA (ceRNA) network which long noncoding RNAs (lncRNAs) act as microRNA (miRNA) sponges to regulate mRNA expression were closely related to tumor development. However, the regulatory mechanisms and functional roles of ceRNA network in the pathogenesis of GBM are remaining poorly understood. Methods In this study, we systematically analyzed the expression profiles of lncRNA and mRNA (GSE51146 dataset) and miRNA (GSE65626 dataset) from GEO database. Then, we constructed a ceRNA network with the dysregulated genes by bioinformatics methods. The TCGA and GSE4290 dataset were used to confirm the expression and prognostic value of candidate mRNAs. Results In total, 3413 differentially expressed lncRNAs and mRNAs, 305 differentially expressed miRNAs were indentified in GBM samples. Then a ceRNA network containing 3 lncRNAs, 5 miRNAs, and 60 mRNAs was constructed. The overall survival analysis of TCGA databases indicated that two mRNAs (C1s and HSD3B7) were remarkly related with the prognosis of GBM. Conclusion The ceRNA network may increase our understanding to the pathogenesis of GBM. In general, the candidate mRNAs from the ceRNA network can be predicted as new therapeutic targets and prognostic biomarkers for GBM.
Collapse
Affiliation(s)
- Xiaolong Zhu
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001 People's Republic of China.,Non-coding RNA Research Center of Wannan Medical College, Wuhu, 241001 China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, 241001 People's Republic of China
| | - Lan Jiang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001 People's Republic of China.,Non-coding RNA Research Center of Wannan Medical College, Wuhu, 241001 China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, 241001 People's Republic of China
| | - Hui Yang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001 People's Republic of China.,Non-coding RNA Research Center of Wannan Medical College, Wuhu, 241001 China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, 241001 People's Republic of China
| | - Tianbing Chen
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001 People's Republic of China.,Non-coding RNA Research Center of Wannan Medical College, Wuhu, 241001 China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, 241001 People's Republic of China
| | - Xingwei Wu
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001 People's Republic of China.,Non-coding RNA Research Center of Wannan Medical College, Wuhu, 241001 China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, 241001 People's Republic of China
| | - Kun Lv
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001 People's Republic of China.,Non-coding RNA Research Center of Wannan Medical College, Wuhu, 241001 China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, 241001 People's Republic of China
| |
Collapse
|
24
|
Cheng S, Xia B, Li H, Li Y, Lv X, Zhang Y, Huang Y. Long non-coding RNA SATB2-AS1 inhibits microRNA-155-3p to suppress breast cancer cell growth by promoting breast cancer metastasis suppressor 1-like. Cancer Cell Int 2020; 20:321. [PMID: 32694943 PMCID: PMC7367385 DOI: 10.1186/s12935-020-01411-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/08/2020] [Indexed: 12/23/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) play vital roles in human cancers. Nevertheless, the effects of lncRNAs and miRNAs on breast cancer (BC) remain to be further investigated. This study was designed to testify the roles of lncRNA antisense transcript of SATB2 protein (SATB2-AS1) and microRNA-155-3p (miR-155-3p) in BC progression. Methods Levels of SATB2-AS1, miR-155-3p and breast cancer metastasis suppressor 1-like (BRMS1L) in BC were determined. The prognostic role of SATB2-AS1 in BC patients was assessed. The screened cells were respectively introduced with altered SATB2-AS1 or miR-155-3p to figure out their roles in malignant phenotypes of BC cells. The effect of varied SATB2-AS1 and miR-155-3p on BC cells in vivo was observed. Dual luciferase reporter gene assay and RNA-pull down assay were implemented to detect the targeting relationship of SATB2-AS1, miR-155-3p, and BRMS1L. Results SATB2-AS1 and BRMS1L were decreased while miR-155-3p was increased in BC cells and tissues. Patients with lower SATB2-AS1 expression had poor prognosis. Elevated SATB2-AS1 and inhibited miR-155-3p were able to restrain malignant behaviors of BC cells in vitro, as well as decelerate tumor growth in vivo. Oppositely, inhibited SATB2-AS1 and amplified miR-155-3p had converse effects on BC cell growth. MiR-155-3p mimic abrogated the impact of overexpressed SATB2-AS1. SATB2-AS1 could sponge miR-155-3p, and BRMS1L was the target gene of miR-155-3p. Conclusion Elevated SATB2-AS1 and inhibited miR-155-3p could suppress the malignant phenotypes of BC cells, thereby restricting the development of BC.
Collapse
Affiliation(s)
- Shaoqiang Cheng
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, China
| | - Bingshu Xia
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, China
| | - Hongbin Li
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, China
| | - Yuying Li
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, China
| | - Xinxin Lv
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, China
| | - Yue Zhang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, China
| | - Yuanxi Huang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, China
| |
Collapse
|
25
|
Zhang Q, Guan F, Fan T, Li S, Ma S, Zhang Y, Guo W, Liu H. LncRNA WDFY3-AS2 suppresses proliferation and invasion in oesophageal squamous cell carcinoma by regulating miR-2355-5p/SOCS2 axis. J Cell Mol Med 2020; 24:8206-8220. [PMID: 32536038 PMCID: PMC7348145 DOI: 10.1111/jcmm.15488] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/09/2020] [Accepted: 05/24/2020] [Indexed: 12/19/2022] Open
Abstract
Long non‐coding RNAs (lncRNAs) widely participate in ESCC development and progression; however, the prognostic factors and therapeutic strategies implicated in ESCC development and progression remain to be under investigation. The purpose of the current study was to explore whether WDFY3‐AS2 may be a potential prognostic factor and investigate its biological functions in ESCC. Here, WDFY3‐AS2 was frequently down‐regulated in ESCC tissues and cells, and its expression was correlated with TNM stage, lymph node metastasis and poor prognosis of ESCC patients. Moreover, WDFY3‐AS2 down‐regulation significantly promoted cell proliferation and invasion, whereas WDFY3‐AS2 up‐regulation markedly suppressed cell proliferation and invasion in ESCC EC9706 and TE1 cells, coupled with EMT phenotype alterations. WDFY3‐AS2 functioned as a competing endogenous RNA (ceRNA) for sponging miR‐2355‐5p, further resulted in the up‐regulation of its target gene SOCS2, followed by suppression of JAK2/Stat5 signalling pathway, to suppress ESCC cell proliferation and invasion in EC9706 and TE1 cells. These findings suggest that WDFY3‐AS2 may participate in ESCC development and progression, and may be a novel prognostic factor for ESCC patients, and thus targeting WDFY3‐AS2/miR‐2355‐5p/SOCS2 signalling axis may be a novel therapeutic strategy for ESCC patients.
Collapse
Affiliation(s)
- Qing Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Fangxia Guan
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Tianli Fan
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Shenglei Li
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shanshan Ma
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yanting Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Wenna Guo
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Hongtao Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| |
Collapse
|