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A Computationally Constructed lncRNA-Associated Competing Triplet Network in Clear Cell Renal Cell Carcinoma. DISEASE MARKERS 2022; 2022:8928282. [DOI: 10.1155/2022/8928282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 10/04/2022] [Accepted: 10/11/2022] [Indexed: 11/19/2022]
Abstract
Long noncoding RNAs (lncRNAs) are revealed to be involved in the tumorigenesis and progression of human malignancies mediated by microRNA (miRNA) via the competing endogenous RNA (ceRNA) mechanism, a newly proposed “RNA language.” However, the lncRNA-associated competing triplet (lncACT) network among ceRNA transcripts in clear cell renal cell carcinoma (ccRCC) is currently lacking. We carried out differential expression analysis to identify aberrantly expressed lncRNAs, miRNAs, and mRNAs by analyzing the RNA-seq data of 420 ccRCC tissues and 71 noncancerous kidney tissues obtained from The Cancer Genome Atlas (TCGA). Then, a ccRCC-specific ceRNA network was built using computational algorithms, including miRcode, TargetScan, miRanda, and miRTarBase. In total, 1491 dysregulated lncRNAs were found between normal renal tissues and ccRCC (fold
and false discovery
). A ceRNA network that comprised of 46 DElncRNAs, 11 DEmiRNAs, and 55 DEmRNAs was established by integrating the lncRNA/miRNA and miRNA/mRNA interactions into lncACTs. Several lncRNAs were identified to be significantly associated with clinical features of ccRCC patients. Notably, four key lncRNAs (TCL6, HOTTIP, HULC, and PCGEM1) were tightly correlated with both patients’ clinical characteristics and overall survival (log-rank
), indicating their potential important roles in ccRCC. HOTTIP may be a potential prognostic and therapeutic molecular marker for ccRCC patients. Collectively, our results provide a comprehensive view of the lncRNA-associated ceRNA regulatory network for a better understanding of the mechanisms and prognosis biomarkers for ccRCC.
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Miao C, Liang C, Li P, Liu B, Qin C, Yuan H, Liu Y, Zhu J, Cui Y, Xu A, Wang S, Su S, Li J, Shao P, Wang Z. TRIM37 orchestrates renal cell carcinoma progression via histone H2A ubiquitination-dependent manner. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:195. [PMID: 34130705 PMCID: PMC8204444 DOI: 10.1186/s13046-021-01980-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 05/12/2021] [Indexed: 01/02/2023]
Abstract
Background Ubiquitylation modification is one of the multiple post-transcriptional process to regulate cellular physiology, including cell signaling, cycle regulation, DNA repair and transcriptional regulation. Members of TRIM family proteins could be defined as E3 ubiquitin ligases as they contain a RING-finger domain, and alterations of TRIM proteins are involved into a broad range of diverse disorders including cancer. TRIM37 is a novel discovered E3 ubiquitin ligase and acts as a oncoprotein in multiple human neoplasms, however its biological role in RCC still remains elusive. Methods RCC microarray chips and public datasets were screened to identify novel TRIMs member as TRIM37, which was dysregulated in RCC. Gain or loss of functional cancer cell models were constructed, and in vitro and in vivo assays were performed to elucidate its tumorigenic phenotypes. Interactive network analyses were utilized to define intrinsic mechanism. Results We identified TRIM37 was upregulated in RCC tumors, and its aberrant function predicted aggressive neoplastic phenotypes, poorer survival endings. TRIM37 promoted RCC cells EMT and malignant progression via TGF-β1 signaling activation, as a consequence of directly mediated by ubiquitinating-H2A modifications. Conclusions Our findings identified a previously unappreciated role of TRIM37 in RCC progression and prognostic prediction. Importantly, we declared a novel ubiquitination-dependent link between TRIM ubiquitin ligases and TGF-β1 signaling in regulating cancerous malignancies. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01980-0.
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Affiliation(s)
- Chenkui Miao
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Chao Liang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Pu Li
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Bianjiang Liu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Chao Qin
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Han Yuan
- Center for Quantitative Medicine, Duke-NUS Medical School, National University of Singapore, Singapore, SG, 169857, Singapore
| | - Yiyang Liu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Jundong Zhu
- Department of Urology, The First People's Hospital of Changzhou, Changzhou, 213003, China
| | - Yankang Cui
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Aiming Xu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Shangqian Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Shifeng Su
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Jie Li
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Pengfei Shao
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
| | - Zengjun Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
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The Role of Epigenetics in the Progression of Clear Cell Renal Cell Carcinoma and the Basis for Future Epigenetic Treatments. Cancers (Basel) 2021; 13:cancers13092071. [PMID: 33922974 PMCID: PMC8123355 DOI: 10.3390/cancers13092071] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The accumulated evidence on the role of epigenetic markers of prognosis in clear cell renal cell carcinoma (ccRCC) is reviewed, as well as state of the art on epigenetic treatments for this malignancy. Several epigenetic markers are likely candidates for clinical use, but still have not passed the test of prospective validation. Development of epigenetic therapies, either alone or in combination with tyrosine-kinase inhibitors of immune-checkpoint inhibitors, are still in their infancy. Abstract Clear cell renal cell carcinoma (ccRCC) is curable when diagnosed at an early stage, but when disease is non-confined it is the urologic cancer with worst prognosis. Antiangiogenic treatment and immune checkpoint inhibition therapy constitute a very promising combined therapy for advanced and metastatic disease. Many exploratory studies have identified epigenetic markers based on DNA methylation, histone modification, and ncRNA expression that epigenetically regulate gene expression in ccRCC. Additionally, epigenetic modifiers genes have been proposed as promising biomarkers for ccRCC. We review and discuss the current understanding of how epigenetic changes determine the main molecular pathways of ccRCC initiation and progression, and also its clinical implications. Despite the extensive research performed, candidate epigenetic biomarkers are not used in clinical practice for several reasons. However, the accumulated body of evidence of developing epigenetically-based biomarkers will likely allow the identification of ccRCC at a higher risk of progression. That will facilitate the establishment of firmer therapeutic decisions in a changing landscape and also monitor active surveillance in the aging population. What is more, a better knowledge of the activities of chromatin modifiers may serve to develop new therapeutic opportunities. Interesting clinical trials on epigenetic treatments for ccRCC associated with well established antiangiogenic treatments and immune checkpoint inhibitors are revisited.
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Zhang B, Chu W, Wen F, Zhang L, Sun L, Hu B, Wang J, Su Q, Mei Y, Cao J, Zheng J, Mou X, Dong H, Lin X, Wang N, Ji H. Dysregulation of Long Non-coding RNAs and mRNAs in Plasma of Clear Cell Renal Cell Carcinoma Patients Using Microarray and Bioinformatic Analysis. Front Oncol 2020; 10:559730. [PMID: 33330027 PMCID: PMC7729199 DOI: 10.3389/fonc.2020.559730] [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: 05/07/2020] [Accepted: 08/17/2020] [Indexed: 11/13/2022] Open
Abstract
Objective: The roles of long non-coding RNAs (lncRNAs) in the diagnosis of clear cell renal cell carcinoma (ccRCC) are still not well-defined. We aimed to identify differentially expressed lncRNAs and mRNAs in plasma of ccRCC patients and health controls systematically. Methods: Expression profile of plasma lncRNAs and mRNAs in ccRCC patients and healthy controls was analyzed based on microarray assay. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway-based approaches were used to investigate biological function and signaling pathways mediated by the differentially expressed mRNAs. SOCS2-AS1 was selected for validation using Real-Time PCR. The differentially expressed lncRNAs and mRNAs were further compared with E-MTAB-1830 datasets using Venn and the NetworkAnalyst website. The GEPIA and ULCAN websites were utilized for the evaluation of the expression level of differentially expressed mRNA and their association with overall survival (OS). Results: A total of 3,664 differentially expressed lncRNAs were identified in the plasma of ccRCC patients, including 1,511 up-regulated and 2,153 down-regulated lncRNAs (fold change ≥2 and P < 0.05), respectively. There were 2,268 differentially expressed mRNAs, including 932 up-regulated mRNAs and 1,336 down-regulated mRNAs, respectively (fold change ≥2 and P < 0.05). Pathway analysis based on deregulated mRNAs was mainly involved in melanogenesis and Hippo signaling pathway (P < 0.05). In line with the lncRNA microarray findings, the SOCS2-AS1 was down-regulated in ccRCC plasma and tissues, as well as in cell lines. Compared with the E-MTAB-1830 gene expression profiles, we identified 18 lncRNAs and 87 mRNAs differently expressed in both plasma and neoplastic tissues of ccRCC. The expression of 10 mRNAs (EPB41L4B, CCND1, GGT1, CGNL1, CYSLTR1, PLAUR, UGT3A1, PROM2, MUC12, and PCK1) was correlated with the overall survival (OS) rate in ccRCC patients based on the GEPIA and ULCAN websites. Conclusions: We firstly reported differentially expressed lncRNAs in ccRCC patients and healthy controls systemically. Several differentially expressed lncRNAs and mRNAs were identified, which might serve as diagnostic or prognostic markers. The biological function of these lncRNAs and mRNAs should be further validated. Our study may contribute to the future treatment of ccRCC and provide novel insights into cancer biology.
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Affiliation(s)
- Bing Zhang
- Department of Urology, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, China
| | - Wei Chu
- Department of Pathology, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, China
| | - Feifei Wen
- Department of Pathology, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, China
| | - Li Zhang
- Department of Anesthesiology, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, China
| | - Lixia Sun
- Department of Pathology, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, China
| | - Baoguang Hu
- Department of Gastrointestinal Surgery, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, China
| | - Jingjing Wang
- Department of Pathology, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, China
| | - Qingguo Su
- Department of Urology, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, China
| | - Yanhui Mei
- Department of Urology, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, China
| | - Jingyuan Cao
- Department of Urology, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, China
| | - Jing Zheng
- Clinical Medicine Laboratory, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, China
| | - Xiaodong Mou
- Department of Pathology, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, China
| | - Hongliang Dong
- Clinical Medicine Laboratory, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, China
| | - Xiaoyan Lin
- Department of Pathology, Shandong Province Hospital, Jinan, China
| | - Nan Wang
- Clinical Medicine Laboratory, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, China
| | - Hong Ji
- Department of Pathology, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, China
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Outeiro-Pinho G, Barros-Silva D, Correia MP, Henrique R, Jerónimo C. Renal Cell Tumors: Uncovering the Biomarker Potential of ncRNAs. Cancers (Basel) 2020; 12:cancers12082214. [PMID: 32784737 PMCID: PMC7465320 DOI: 10.3390/cancers12082214] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 12/24/2022] Open
Abstract
Renal cell tumors (RCT) remain as one of the most common and lethal urological tumors worldwide. Discrimination between (1) benign and malignant disease, (2) indolent and aggressive tumors, and (3) patient responsiveness to a specific therapy is of major clinical importance, allowing for a more efficient patient management. Nonetheless, currently available tools provide limited information and novel strategies are needed. Over the years, a putative role of non-coding RNAs (ncRNAs) as disease biomarkers has gained relevance and is now one of the most prolific fields in biological sciences. Herein, we extensively sought the most significant reports on ncRNAs as potential RCTs' diagnostic, prognostic, predictive, and monitoring biomarkers. We could conclude that ncRNAs, either alone or in combination with currently used clinical and pathological parameters, might represent key elements to improve patient management, potentiating the implementation of precision medicine. Nevertheless, most ncRNA biomarkers require large-scale validation studies, prior to clinical implementation.
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Affiliation(s)
- Gonçalo Outeiro-Pinho
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (G.O.-P.); (D.B.-S.); (M.P.C.); (R.H.)
| | - Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (G.O.-P.); (D.B.-S.); (M.P.C.); (R.H.)
| | - Margareta P. Correia
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (G.O.-P.); (D.B.-S.); (M.P.C.); (R.H.)
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (G.O.-P.); (D.B.-S.); (M.P.C.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira n. 228, 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (G.O.-P.); (D.B.-S.); (M.P.C.); (R.H.)
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira n. 228, 4050-313 Porto, Portugal
- Correspondence: ; Tel.: +351-225084000; Fax: +351-225084199
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Che J, Yao X, Wang C, Zheng J, Guo C. Hypoxia promoted renal cell carcinoma cell migration through regulating lncRNA-ENST00000574654.1. Am J Transl Res 2020; 12:3884-3894. [PMID: 32774742 PMCID: PMC7407743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/28/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Hypoxia is common in solid tumor masses that has functional consequences for tumor progression. Previous studies demonstrated that nearly 80% renal cell carcinoma (RCC) are under hypoxia. However, effect and its mechanism of hypoxia on RCC cell invasion remains to be defined. METHODS The shRNA expression vectors, which were constructed to express a short hairpin RNA against lncRNA and overexpression of lncRNA, were transfected into the RCC cell lines (SW839 and OSRC-2). Levels of lncRNA-ENST00000574654.1, VEGF-A and VEGF-C mRNA and protein were examined by real-time quantitative-fluorescent PCR and Western blot analysis, respectively. The effects of lncRNA silencing and overexpression on cell invasion of SW839 and OSRC-2 cells were evaluated with cell migration assay. RESULTS Hypoxia significantly stimulated cell invasion in both RCC cell lines (SW839: 2.38 ± 0.19 of normoxia vs 7.83 ± 0.38 of hypoxia, P < 0.05; and OSRC-2: 1.00 ± 0.08 of normoxia vs 5.88 ± 0.32 of hypoxia, P < 0.05). LncRNA microarray analysis found that lncRNA-ENST00000574654.1 was down-regulated under hypoxia. Consistently, over-expression of lncRNA-ENST00000574654.1 resulted in significant blockade of hypoxia-induced RCC migration. Furthermore, expression of lncRNA-ENST00000574654.1 was regulated by HIF-1α and VEGA-A through interacting with hnRNP, which in turn regulated the RCC cell invasion. CONCLUSIONS These findings suggested that hypoxia promoted RCC cell invasion through HIF-1α/lncRNA (ENST00000574654.1)/hnRNP/VEGF-A pathway. Targeting this pathway could potentially improve therapeutic outcomes of renal cell carcinoma.
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Affiliation(s)
- Jianping Che
- Department of Urology, The Affiliated Shanghai Tenth People’s Hospital, Nanjing Medical UniversityShanghai 200072, China
| | - Xudong Yao
- Department of Urology, Shanghai Tenth People’s Hospital, Tongji UniversityShanghai 200072, China
| | - Chunguang Wang
- Department of Urology, Shanghai Tenth People’s Hospital, Tongji UniversityShanghai 200072, China
| | - Junhua Zheng
- Department of Urology, Shanghai General Hospital, Shanghai Jiaotong UniversityShanghai 200080, China
| | - Changcheng Guo
- Department of Urology, Shanghai Tenth People’s Hospital, Tongji UniversityShanghai 200072, China
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Xiao SH, Li GX, Quan L. Long non-coding RNA BX357664 inhibits cell proliferation and metastasis in human lung cancer. Oncol Lett 2019; 17:2607-2614. [PMID: 30854036 PMCID: PMC6365958 DOI: 10.3892/ol.2019.9886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 06/18/2018] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been investigated in human carcinogenesis. The lncRNA BX357664 has emerged as a novel lncRNA that was initially recognized by a microarray analysis. The present study aimed to identify the expression and functional roles of lncRNA BX357664 in lung cancer. The transcription level of BX357664 was initially revealed to be downregulated in clinical lung cancer tissues and in a series of lung cancer cell lines. Clinical data demonstrated that the high expression of BX357664 was associated with tumor size, distant metastasis and Tumor-Node-Metastasis stage. Following the overexpression of BX357664 in A549 and 95D cells, the potential of cells to form colonies, as well as the proliferation and motility abilities, were revealed to be decreased. Furthermore, the cell cycle was arrested in the G0/G1 phase by BX357664 modulation. Transwell analysis and a wound-healing assay also demonstrated that overexpression of BX357664 in A549 and 95D cells significantly inhibited cell migration and invasion. These data suggested that BX357664 inhibits cell proliferation and metastasis in lung cancer. The results of the present study provided evidence that BX357664 is a novel lncRNA that may aid in the diagnosis and treatment of lung cancer.
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Affiliation(s)
- Shu-Hui Xiao
- Department of Clinical Laboratory Medicine, The People's Hospital of Linyi, Linyi, Shandong 276003, P.R. China
| | - Gong-Xiang Li
- Department of Clinical Laboratory Medicine, The People's Hospital of Linyi, Linyi, Shandong 276003, P.R. China
| | - Lingli Quan
- The First Department of Respiratory of Central Hospital of Zhuzhou, Zhuzhou, Hunan 412000, P.R. China
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8
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Long non-coding RNA HOTTIP affects renal cell carcinoma progression by regulating autophagy via the PI3K/Akt/Atg13 signaling pathway. J Cancer Res Clin Oncol 2018; 145:573-588. [DOI: 10.1007/s00432-018-2808-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 11/30/2018] [Indexed: 12/12/2022]
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9
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Xing Q, Huang Y, Wu Y, Ma L, Cai B. Integrated analysis of differentially expressed profiles and construction of a competing endogenous long non-coding RNA network in renal cell carcinoma. PeerJ 2018; 6:e5124. [PMID: 30038853 PMCID: PMC6054097 DOI: 10.7717/peerj.5124] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/01/2018] [Indexed: 12/28/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) play crucial roles in the initiation and progression of renal cell carcinoma (RCC) by competing in binding to miRNAs, and related competitive endogenous RNA (ceRNA) networks have been constructed in several cancers. However, the coexpression network has been poorly explored in RCC. Methods We collected RCC RNA expression profile data and relevant clinical features from The Cancer Genome Atlas (TCGA). A cluster analysis was explored to show different lncRNA expression patterns. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses and gene set enrichment analysis (GSEA) were performed to analyze the functions of the intersecting mRNAs. Targetscan and miRanda bioinformatics algorithms were used to predict potential relationships among RNAs. Univariate Cox proportional hazards regression was conducted to determine the RNA expression levels and survival times. Results Bioinformatics analysis revealed that the expression profiles of hundreds of aberrantly expressed lncRNAs, miRNAs, and mRNAs were significantly changed between different stages of tumors and non-tumor groups. By combining the data predicted by databases with intersection RNAs, a ceRNA network consisting of 106 lncRNAs, 26 miRNAs and 69 mRNAs was established. Additionally, a protein interaction network revealed the main hub nodes (VEGFA, NTRK2, DLG2, E2F2, MYB and RUNX1). Furthermore, 63 lncRNAs, four miRNAs and 31 mRNAs were significantly associated with overall survival. Conclusion Our results identified cancer-specific lncRNAs and constructed a ceRNA network for RCC. A survival analysis related to the RNAs revealed candidate biomarkers for further study in RCC.
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Affiliation(s)
- Qianwei Xing
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Yeqing Huang
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - You Wu
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Limin Ma
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Bo Cai
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
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10
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11
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Li M, Wang Y, Cheng L, Niu W, Zhao G, Raju JK, Huo J, Wu B, Yin B, Song Y, Bu R. Long non-coding RNAs in renal cell carcinoma: A systematic review and clinical implications. Oncotarget 2018; 8:48424-48435. [PMID: 28467794 PMCID: PMC5564659 DOI: 10.18632/oncotarget.17053] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/20/2017] [Indexed: 12/27/2022] Open
Abstract
Renal cell carcinoma is one of the most common malignancy in adults, its prognosis is poor in an advanced stage and early detection is difficult due to the lack of molecular biomarkers. The identification of novel biomarkers for RCC is an urgent and meaningful project. Long non-coding RNA (lncRNA) is transcribed from genomic regions with a minimum length of 200 bases and limited protein-coding potential. Recently, lncRNAs have been greatly studied in a variety of cancer types. They participate in a wide variety of biological processes including cancer biology. In this review, we provide a new insight of the profiling of lncRNAs in RCC and their roles in renal carcinogenesis, with an emphasize on their potential in diagnosis, prognosis and potential roles in RCC therapy.
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Affiliation(s)
- Ming Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Ying Wang
- Department of Nuclear Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China.,Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Wanting Niu
- Department of Orthopedics, Brigham and Women's Hospital, VA Boston Healthcare System, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Guoan Zhao
- School of Network Education, Beijing University of Posts and Telecommunications, Hebei, Beijing 100088, P.R. China
| | - Jithin K Raju
- Department of Clinical Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Jun Huo
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Bin Wu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Bo Yin
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Yongsheng Song
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Renge Bu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
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12
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Liu F, Wang X, Liu H, Wang Y, Liu X, Hao X, Li H. LncRNA BX357664 inhibits cell proliferation and invasion and promotes cell apoptosis in human colorectal cancer cells. Oncol Lett 2018; 15:8237-8244. [PMID: 29844809 PMCID: PMC5958819 DOI: 10.3892/ol.2018.8435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 11/21/2017] [Indexed: 12/13/2022] Open
Abstract
Colorectal cancer represents a great burden for patients worldwide. Long noncoding RNA BX357664 is an RNA that was identified by microarray technique in renal cell carcinoma. The function of BX357664 in solid tumors remains largely unknown. The present study aimed to investigate the expression profile and functional role of BX357664 in human colorectal cancer progression. The transcription levels of BX357664 were initially examined in vivo and in vitro. An overexpression plasmid was constructed in order to examine the effects of BX357664 overexpression on cell proliferation, apoptosis, migration and invasion. The results demonstrated that BX357664 was significantly downregulated in clinical colorectal cancer tissues and cell lines. Overexpression of BX357664 decreased cell proliferation rates and cell colony formation capacities in HCT116 and HT-29 cells. Following BX357664 overexpression, HCT116 and HT-29 cells exhibited reduced migration and invasion capacities. Would closure was also blunted by >50% following overexpression of BX357664 in HCT-116 and HT-29 cells. In addition, the cell cycle regulators Cyclin B1, CDC25C and Cyclin D1 as well as the mesenchymal marker N-cadherin were downregulated, whereas the epithelial marker E-cadherin was upregulated by BX357664 overexpression. Finally, HCT116 and HT-29 cell apoptosis was induced and activities of caspase-3 and caspase-9 increased significantly following BX357664 overexpression. The present data suggested that BX257664 negatively regulated cell proliferation and metastasis and promoted cell apoptosis in colorectal cancer. These observations provided novel evidence that BX357664 might serve as a tumor suppressor and a potential therapeutic target in the treatment of colorectal cancer in the clinic.
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Affiliation(s)
- Fengjun Liu
- Department of General Surgery, Shandong University Qilu Hospital, Jinan, Shandong 250012, P.R. China
| | - Xinsheng Wang
- Department of General Surgery, Shandong University Qilu Hospital, Jinan, Shandong 250012, P.R. China.,Department of General Surgery, Anqiu People's Hospital, Anqiu, Shandong 262100, P.R. China
| | - Haiyan Liu
- Department of Rehabilitation, Anqiu Maternal and Child Health Care Hospital, Anqiu, Shandong 262100, P.R. China
| | - Yang Wang
- Department of General Surgery, Weifang People's Hospital, Weifang, Shandong 261000, P.R. China
| | - Xiaoqian Liu
- Department of Obstetrics, Anqiu Maternal and Child Health Care Hospital, Anqiu, Shandong 262100, P.R. China
| | - Xiaochen Hao
- Department of Internal Medicine Cardiovascular, Anqiu People's Hospital, Anqiu, Shandong 262100, P.R. China
| | - Hongguang Li
- Department of Urology Surgery, Anqiu People's Hospital, Anqiu, Shandong 262100, P.R. China
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13
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Long noncoding RNA BX357664 regulates cell proliferation and epithelial-to-mesenchymal transition via inhibition of TGF-β1/p38/HSP27 signaling in renal cell carcinoma. Oncotarget 2018; 7:81410-81422. [PMID: 27806310 PMCID: PMC5348402 DOI: 10.18632/oncotarget.12937] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 09/12/2016] [Indexed: 02/06/2023] Open
Abstract
Antisense long noncoding RNAs (lncRNAs) are reported to play a regulating role in carcinogenesis of various human malignancies. However, the function of lncRNAs and their underlying mechanism in renal cell carcinoma (RCC) is still unknown. The aims of this study are to investigate the expression of lncRNA BX357664 in RCC and to explore its function in RCC cell lines. As a result, BX357664 was downregulated in RCC according to previous microarray analysis and qualitative real-time polymerase chain reaction. After the upregulation of BX357664, reduced migration, invasion, and proliferation capabilities in RCC cells were detected. Furthermore, Western blot analysis was conducted to identify the influence of BX357664 on epithelial-to-mesenchymal transition, matrix metalloproteinase 2, matrix metalloproteinase 9, and transforming growth factor-beta 1 (TGF-β1)/p38/HSP27 signaling pathway in RCC. Subsequently, upregulating the protein level of TGF-β1 in the presence of BX357664 could rescue the suppression of the malignant behavior mediated by BX357664, indicating that BX357664 attributed its inhibitory role to the suppression of TGF-β1. Therefore, we investigated a novel lncRNA BX357664, which might exhibit its inhibitory role in RCC metastasis and progression by blocking the TGF-β1/p38/HSP27 pathway.
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14
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Jin L, Quan J, Pan X, He T, Hu J, Li Y, Gui Y, Yang S, Mao X, Chen Y, Lai Y. Identification of lncRNA EGOT as a tumor suppressor in renal cell carcinoma. Mol Med Rep 2017; 16:7072-7079. [PMID: 28901455 DOI: 10.3892/mmr.2017.7470] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 07/13/2017] [Indexed: 11/06/2022] Open
Abstract
Renal cell carcinoma (RCC) is the most common type of kidney cancer and the prognosis of metastatic RCC remains poor, with a high rate of recurrence and mortality. Long non‑coding RNA (lncRNA) is a class of RNA which serves important roles in multiple cellular processes and tumorigenesis. In the present study, the expression and function of lncRNA eosinophil granule ontogeny transcript (EGOT) were examined in RCC. In 24 paired tissues (RCC tissues and adjacent normal tissues) the results of reverse transcription‑quantitative polymerase chain reaction analysis revealed that EGOT was downregulated in 22 RCC tissues compared with paired tissues. Upregulation of lncRNA EGOT by transfection of 786‑O and ACHN RCC cells with pcDNA3.1‑EGOT suppressed cell proliferation, migration and invasion, and induced RCC cell apoptosis. The results demonstrated that EGOT may serve as a tumor suppressor in RCC and may be a potential prognostic biomarker of RCC.
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Affiliation(s)
- Lu Jin
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Jing Quan
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Xiang Pan
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Tao He
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Jia Hu
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Yifan Li
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Yaoting Gui
- Department of Urology, Anhui Medical University, Hefei, Anhui 230032, P.R. China
| | - Shangqi Yang
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Xiangming Mao
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Yun Chen
- Department of Ultrasound, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Yongqing Lai
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
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15
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Jin L, Fu H, Quan J, Pan X, He T, Hu J, Li Y, Li H, Yang Y, Ye J, Zhang F, Ni L, Yang S, Lai Y. Overexpression of long non-coding RNA differentiation antagonizing non-protein coding RNA inhibits the proliferation, migration and invasion and promotes apoptosis of renal cell carcinoma. Mol Med Rep 2017; 16:4463-4468. [PMID: 28765964 DOI: 10.3892/mmr.2017.7135] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 05/15/2017] [Indexed: 11/06/2022] Open
Abstract
Renal cell carcinoma (RCC) is the third most common cancer in the urological system; however, the pathogenesis remains unknown. Accumulating evidence has demonstrated that long non‑coding RNAs are dysregulated in various tumors and serves an important role in tumorigenesis and development. In the present study, expression of lncRNA differentiation antagonizing non‑protein coding RNA (DANCR) in 24 paired RCC and adjacent normal tissues was detected by reverse transcription‑quantitative polymerase chain reaction. The results revealed that DANCR is downregulated in RCC tissues compared with adjacent normal tissues. Subsequent study revealed that overexpression of lncRNA DANCR by transfection of pcDNA3.1‑DANCR could suppress 786‑O and ACHN (RCC cell) proliferation, migration and invasion, and induce apoptosis compared with cells transfected with the pcDNA3.1 vector. The results revealed that DANCR functions as a tumor suppressor in RCC. In conclusion, the present study, to the best of our knowledge, was the first to reveal DANCR as a tumor suppressor. The results implicate DANCR as a potential biomarker of RCC, and further study will be focused on the clinical significance and signaling pathways of DANCR.
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Affiliation(s)
- Lu Jin
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Huifang Fu
- The Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Shenzhen, Guangdong 518036, P.R. China
| | - Jing Quan
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Xiang Pan
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Tao He
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Jia Hu
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Yifan Li
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Hang Li
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Yu Yang
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Jing Ye
- The Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Shenzhen, Guangdong 518036, P.R. China
| | - Fangting Zhang
- The Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Shenzhen, Guangdong 518036, P.R. China
| | - Liangchao Ni
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Shangqi Yang
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
| | - Yongqing Lai
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, P.R. China
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16
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Downregulation of a novel long non-coding RNA, LOC389332, is associated with poor prognosis and tumor progression in clear cell renal cell carcinoma. Exp Ther Med 2017; 13:1137-1142. [PMID: 28450954 DOI: 10.3892/etm.2017.4080] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 10/28/2016] [Indexed: 01/17/2023] Open
Abstract
It has been demonstrated that various long non-coding RNAs (lncRNAs) may have key roles in various types of cancer. Clear cell renal cell carcinoma (ccRCC) is the most common subtype of all RCCs, accounting for 70-80% of all cases. The present study identified a novel lncRNA and investigated its clinical significance and physiological function in ccRCC. The expression pattern of the novel lncRNA LOC389332 in 30 ccRCC tissue samples was examined using reverse-transcription quantitative polymerase chain reaction. The results demonstrated that LOC389332 expression was markedly lower in ccRCC tissues compared with that in matched adjacent non-tumor tissues. Of note, downregulation of LOC389332 expression was significantly associated with the tumor American Joint Commission on Cancer stage (P=0.001), Fuhrman grade (P=0.001) and lymph node metastasis (P<0.001). Furthermore, patients with ccRCC with lower levels of LOC389332 expression had a shorter overall survival time than those with higher LOC389332 expression. A gain-of-function study was used to evaluate the biological function of LOC389332 in ccRCC and the results suggested that restoration of LOC389332 expression inhibited the growth and migration of the 786-O and 769-P cell lines. Therefore, the results of the present study demonstrated that LOC389332 is a novel lncRNA involved in ccRCC progression and may be a potential diagnostic and prognostic biomarker. Ectopic overexpression of LOC389332 may represent a therapeutic strategy for ccRCC.
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17
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Ellinger J, Gevensleben H, Müller SC, Dietrich D. The emerging role of non-coding circulating RNA as a biomarker in renal cell carcinoma. Expert Rev Mol Diagn 2016; 16:1059-1065. [PMID: 27649770 DOI: 10.1080/14737159.2016.1239531] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Bodily fluids like serum and plasma contain significant amounts of tumor-derived circulating cell-free RNA, which holds the potential to serve as diagnostic biomarker. Consequently, liquid biopsies comprising circulating cell-free RNA might help to facilitate personalized treatment strategies for patients with renal cell carcinoma (RCC). Areas covered: The present review provides a summary of the literature obtained by a PubMed search and covers the current knowledge on circulating non-coding cell-free RNA in patients with RCC. Expert commentary: Altered circulating microRNA and long non-coding RNAs signatures allow for the discrimination of patients with RCC and healthy individuals. On the other hand, little is known about non-coding RNA expression in benign tumors. Cell-free microRNA expression levels may help to identify patients at risk for disease recurrence. However, accurate determination of cell-free RNAs is methodologically challenging and currently no biomarker candidate has reached a sufficient level of clinical validation. Thus, short-term implementation of cell-free circulating microRNA into clinical routine seems unlikely.
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Affiliation(s)
- Jörg Ellinger
- a Department of Urology , University Hospital Bonn , Bonn , Germany
| | | | - Stefan C Müller
- a Department of Urology , University Hospital Bonn , Bonn , Germany
| | - Dimo Dietrich
- b Institute of Pathology , University Hospital Bonn , Bonn , Germany.,c Department of Otolaryngology, Head and Neck Surgery , University Hospital Bonn , Bonn , Germany
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18
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Chen J, Miao Z, Xue B, Shan Y, Weng G, Shen B. Long Non-coding RNAs in Urologic Malignancies: Functional Roles and Clinical Translation. J Cancer 2016; 7:1842-1855. [PMID: 27698924 PMCID: PMC5039368 DOI: 10.7150/jca.15876] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/29/2016] [Indexed: 12/31/2022] Open
Abstract
Early diagnosis and surveillance for metastasis and recurrences are critical issues of urologic cancer. Deregulation of long non-coding RNAs (lncRNAs) has been implicated in urologic malignancies and represents potential markers or therapeutic targets. However, the utility of lncRNA as biomarkers appears to be overstated due to heterogeneous or irreproducible results from different studies. Thus, a critical and cautious review on the biomarker potential of lncRNAs is needed. This review provides an update on new findings of lncRNA-based markers for urologic cancer. The diverse mechanisms and associated examples of lncRNAs involved during the carcinogenesis of prostate cancer, bladder cancer and renal cancer were discussed in a more balanced and critical manner, as were the suitability of lncRNAs as diagnostic or prognostics markers.
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Affiliation(s)
- Jiajia Chen
- Center for Systems Biology, Soochow University, Suzhou 215006, China; School of Chemistry, Biological Engineering, Suzhou University of Science and Technology, Suzhou 215011, China
| | - Zhijun Miao
- Center for Systems Biology, Soochow University, Suzhou 215006, China; Suzhou Dushuhu Hospital, Clinic Center, Soochow University, Suzhou 215123, China
| | - Boxin Xue
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Yuxi Shan
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Guobin Weng
- Ningbo Urologic and Nephrotic Hospital, Ningbo 315000, China
| | - Bairong Shen
- Center for Systems Biology, Soochow University, Suzhou 215006, China
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19
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Ren X, Lan T, Chen Y, Shao Z, Yang C, Peng J. lncRNA uc009yby.1 promotes renal cell proliferation and is associated with poor survival in patients with clear cell renal cell carcinomas. Oncol Lett 2016; 12:1929-1934. [PMID: 27602119 DOI: 10.3892/ol.2016.4856] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 04/15/2016] [Indexed: 01/20/2023] Open
Abstract
The expression and function of long non-coding RNAs (lncRNAs) in clear cell renal cell carcinoma (ccRCC) remains unclear. The present study measured the expression profiles of three lncRNAs (uc009yby.1, ENST00000514034, and ENST00000450687) using reverse transcription-quantitative polymerase chain reaction, and assessed their signatures in distinguishing ccRCC from matched normal tissues via analysis of receiver operating characteristic (ROC) curves. The expression of uc009yby.1 was inhibited by transfection of renal cells with small interfering RNA, and then the cell proliferation was evaluated by using a Cell Counting Kit-8. The results showed that the expressions of uc009yby.1 and ENST00000514034 were markedly increased in ccRCC compared with the matched normal tissues (P<0.0001 and P=0.0008, respectively), whereas the ENST00000450687 expression was not significantly altered. ROC curves yielded an area under the curve (AUC) value of 0.7000 for uc009yby.1, with sensitivity of 54.29% and specificity of 82.86%; and an AUC value of 0.6627 for ENST00000514034, with sensitivity of 60.00% and specificity of 67.14%. Furthermore, knockdown of uc009yby.1 suppressed renal cell proliferation (Day 0, P=0.7844; Day 1, P=0.0018; Day 2, P=0.0001; Day 3, P<0.000; Day 4, P<0.0001). Taken together, these findings suggest that the expression profiles of uc009yby.1 and ENST00000514034 may serve as novel biomarkers for ccRCC detection, and that uc009yby.1 is strongly associated with renal cell proliferation.
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Affiliation(s)
- Xingfeng Ren
- Nephrology Department, Wuhan General Hospital of Guangzhou Military Region, Wuhan, Hubei 430030, P.R. China
| | - Tianbiao Lan
- Nephrology Department, Wuhan General Hospital of Guangzhou Military Region, Wuhan, Hubei 430030, P.R. China
| | - Yan Chen
- Nephrology Department, Wuhan General Hospital of Guangzhou Military Region, Wuhan, Hubei 430030, P.R. China
| | - Ziyun Shao
- Nephrology Department, Wuhan General Hospital of Guangzhou Military Region, Wuhan, Hubei 430030, P.R. China
| | - Cheng Yang
- Nephrology Department, Wuhan General Hospital of Guangzhou Military Region, Wuhan, Hubei 430030, P.R. China
| | - Jun Peng
- Nephrology Department, Wuhan General Hospital of Guangzhou Military Region, Wuhan, Hubei 430030, P.R. China
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20
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GFOD1 and peejar are promising markers for clear-cell renal cell carcinoma disease progression. Oncotarget 2016; 7:38004-38009. [PMID: 27191742 PMCID: PMC5122367 DOI: 10.18632/oncotarget.9379] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/26/2016] [Indexed: 11/29/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is a common genitourinary malignancy. The molecular pathogenesis of ccRCC remains unclear and biomarkers for daily practice were still limited. We performed an integrative analysis of two public ccRCC microarray datasets, E-GEOD-22541 and E-MTAB-1050, The candidate differential expression genes (DEG) were then confirmed in the E-GEOD-53757 dataset. In addition, an independent cohort of 50 ccRCC and 36 non-tumor kidney tissues were analyzed to examine the selected DGEs by qRT-PCR. We identified and validated two DEGs, namely GFOD1 and peejar, which were significantly up-regulated in ccRCC compared with normal renal tissues (p < 0.001). Moreover, the expression of these two genes are related to histological grade and stage and decrease of their expression correlated with disease progression (p < 0.05). Furthermore, we found the expression of peejar was positively correlated with the expression of GFOD1 in ccRCC tissue, with Pearson correlation coefficiency reaching 0.939 (p < 0.001). GFOD1 and peejar were novel genes correlated with ccRCC disease progression and patients' poor prognosis.
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21
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Seles M, Hutterer GC, Kiesslich T, Pummer K, Berindan-Neagoe I, Perakis S, Schwarzenbacher D, Stotz M, Gerger A, Pichler M. Current Insights into Long Non-Coding RNAs in Renal Cell Carcinoma. Int J Mol Sci 2016; 17:573. [PMID: 27092491 PMCID: PMC4849029 DOI: 10.3390/ijms17040573] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/08/2016] [Accepted: 04/12/2016] [Indexed: 02/07/2023] Open
Abstract
Renal cell carcinoma (RCC) represents a deadly disease with rising mortality despite intensive therapeutic efforts. It comprises several subtypes in terms of distinct histopathological features and different clinical presentations. Long non-coding RNAs (lncRNAs) are non-protein-coding transcripts in the genome which vary in expression levels and length and perform diverse functions. They are involved in the inititation, evolution and progression of primary cancer, as well as in the development and spread of metastases. Recently, several lncRNAs were described in RCC. This review emphasises the rising importance of lncRNAs in RCC. Moreover, it provides an outlook on their therapeutic potential in the future.
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Affiliation(s)
- Maximilian Seles
- Department of Urology, Medical University of Graz, A-8036 Graz, Austria.
| | - Georg C Hutterer
- Department of Urology, Medical University of Graz, A-8036 Graz, Austria.
| | - Tobias Kiesslich
- Department of Internal Medicine I, Salzburger Landeskliniken (SALK), Paracelsus Medical University, A-5020 Salzburg, Austria.
- Laboratory for Tumour Biology and Experimental Therapies, Institute of Physiology and Pathophysiology, Paracelsus Medical University, A-5020 Salzburg, Austria.
| | - Karl Pummer
- Department of Urology, Medical University of Graz, A-8036 Graz, Austria.
| | - Ioana Berindan-Neagoe
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
- Research Center of Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania.
- Department of Experimental Pathology, The Oncology Institute Ion Chiricuta, 400015 Cluj-Napoca, Romania.
| | - Samantha Perakis
- Institute of Human Genetics, Medical University of Graz, A-8036 Graz, Austria.
| | - Daniela Schwarzenbacher
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, A-8036 Graz, Austria.
| | - Michael Stotz
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, A-8036 Graz, Austria.
| | - Armin Gerger
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, A-8036 Graz, Austria.
- Center for Biomarker Research in Medicine, Medical University of Graz, A-8036 Graz, Austria.
| | - Martin Pichler
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, A-8036 Graz, Austria.
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22
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Ellinger J, Alam J, Rothenburg J, Deng M, Schmidt D, Syring I, Miersch H, Perner S, Müller SC. The long non-coding RNA lnc-ZNF180-2 is a prognostic biomarker in patients with clear cell renal cell carcinoma. Am J Cancer Res 2015; 5:2799-2807. [PMID: 26609485 PMCID: PMC4633906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 08/05/2015] [Indexed: 06/05/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is among the most common human malignancies. Long non-coding RNAs (lncRNA) regulate various cellular functions and have been implicated in ccRCC pathogenesis. In order to decipher the molecular biology of this tumor and to identify potential prognostic biomarkers and therapeutic targets, we re-evaluated published lncRNA expression profiling data. An expression profile of 49 lncRNAs allowed discrimination of localized and advanced ccRCC. The expression profile of six lncRNAs transcripts (lnc-ACO1625, lnc-CYP4A22-2/3, lnc-PEAK1.1-1, lnc-PCYOX1L, lnc-VCAN-1, lnc-ZNF180-2) with potential prognostic interest were validated in a cohort of 50 normal renal, 57 localized ccRCC and 45 advanced ccRCC tissues. lnc-ZNF180-2 levels were similar in localized ccRCC and normal renal tissue, but we observed a significant increase of lnc-ZNF180-2 expression in advanced ccRCC tissue. Furthermore, lnc-ZNF180-2 expression levels were an independent predictor of progression-free survival, cancer-specific survival and overall survival in ccRCC patients. We also observed that lnc-CYP4A22-2/3 expression levels allowed discrimination of ccRCC and normal renal tissue. In conclusion, lncRNAs are involved in renal carcinogenesis, and quantification of lnc-ZNF180-2 may be useful for the prediction of ccRCC patients outcome following nephrectomy.
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Affiliation(s)
- Jörg Ellinger
- Department of Urology, University Hospital BonnBonn, Germany
| | - Jahedul Alam
- Department of Urology, University Hospital BonnBonn, Germany
| | | | - Mario Deng
- Section for Prostate Cancer Research, Institute of Pathology, University Hospital BonnBonn, Germany
| | - Doris Schmidt
- Department of Urology, University Hospital BonnBonn, Germany
| | - Isabella Syring
- Department of Urology, University Hospital BonnBonn, Germany
| | - Herdis Miersch
- Department of Urology, University Hospital BonnBonn, Germany
| | - Sven Perner
- Section for Prostate Cancer Research, Institute of Pathology, University Hospital BonnBonn, Germany
| | - Stefan C Müller
- Department of Urology, University Hospital BonnBonn, Germany
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23
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Zhao J, Liu Y, Zhang W, Zhou Z, Wu J, Cui P, Zhang Y, Huang G. Long non-coding RNA Linc00152 is involved in cell cycle arrest, apoptosis, epithelial to mesenchymal transition, cell migration and invasion in gastric cancer. Cell Cycle 2015; 14:3112-23. [PMID: 26237576 DOI: 10.1080/15384101.2015.1078034] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer remains a serious threat to public health with high incidence and mortality worldwide. Accumulating evidence demonstrates that long non-coding RNAs (lncRNAs) play important roles in regulating gene expression and are involved in various pathological processes, including gastric cancer. To investigate the possible role of dysregulated lncRNAs in gastric cancer development, we performed lncRNA microarray and identified 3141 significantly differentially expressed lncRNAs in gastric cancer tissues. Next, some of deregulated lncRNAs were validated among about 60 paired gastric cancer specimens such as Linc00261, DKFZP434K028, RPL34-AS1, H19, HOTAIR and Linc00152. Our results found that the decline of DKFZP434K028 and RPL34-AS1, and the increased expression of Linc00152 positively correlated with larger tumor size. The high expression levels of HOTAIR were associated with lymphatic metastasis and poor differentiation. Since the biological roles of Linc00152 are largely unknown in gastric cancer pathogenesis, we assessed its functions by silencing its up-regulation in gastric cancer cells. We found that Linc00152 knockdown could inhibit cell proliferation and colony formation, promote cell cycle arrest at G1 phase, trigger late apoptosis, reduce the epithelial to mesenchymal transition (EMT) program, and suppress cell migration and invasion. Taken together, we delineate the gastric cancer lncRNA signature and demonstrate the oncogenic functions of Linc00152. These findings may have implications for developing lncRNA-based biomarkers for diagnosis and therapeutics for gastric cancer.
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Affiliation(s)
- Jing Zhao
- a Department of Infectious Diseases ; Huashan Hospital; Shanghai Medical College; Fudan University ; Shanghai , China.,b Department of General Surgery ; Huashan Hospital; Shanghai Medical College; Fudan University ; Shanghai , China
| | - Yongchao Liu
- b Department of General Surgery ; Huashan Hospital; Shanghai Medical College; Fudan University ; Shanghai , China
| | - Wenhong Zhang
- a Department of Infectious Diseases ; Huashan Hospital; Shanghai Medical College; Fudan University ; Shanghai , China
| | - Zhongwen Zhou
- c Department of pathology ; Huashan Hospital; Shanghai Medical College; Fudan University ; Shanghai , China
| | - Jing Wu
- a Department of Infectious Diseases ; Huashan Hospital; Shanghai Medical College; Fudan University ; Shanghai , China
| | - Peng Cui
- a Department of Infectious Diseases ; Huashan Hospital; Shanghai Medical College; Fudan University ; Shanghai , China
| | - Ying Zhang
- a Department of Infectious Diseases ; Huashan Hospital; Shanghai Medical College; Fudan University ; Shanghai , China.,d Department of Molecular Microbiology and Immunology ; Bloomberg School of Public Health; Johns Hopkins University ; Baltimore , MD USA
| | - Guangjian Huang
- b Department of General Surgery ; Huashan Hospital; Shanghai Medical College; Fudan University ; Shanghai , China
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24
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Identification of novel differentially expressed lncRNA and mRNA transcripts in clear cell renal cell carcinoma by expression profiling. GENOMICS DATA 2015; 5:173-5. [PMID: 26484251 PMCID: PMC4584005 DOI: 10.1016/j.gdata.2015.06.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 06/08/2015] [Accepted: 06/11/2015] [Indexed: 01/09/2023]
Abstract
Clear cell renal cell carcinoma (ccRCC) is a common human malignancy. Despite numerous efforts, there is still no reliable biomarker or combination of biomarkers available for daily practice. Our study was designed to explore the expression profile of messenger RNA (mRNA) and long non-coding RNA (lncRNA) transcripts in ccRCC in order to identify potential diagnostic biomarkers for patients with ccRCC. Total RNA from corresponding normal and malignant tissue of 15 patients with ccRCC was isolated. Expression profiling was performed using a custom Agilent gene expression microarray which allowed the analysis of 34,144 mRNA and 32,183 lncRNA transcripts. We observed that a subset of mRNA (n = 1064; 3.1%) and lncRNA (n = 1308; 4.1%) transcripts are dysregulated (fold change > 2) in ccRCC tissue. The relative higher number of differentially expressed lncRNAs indicates that lncRNA profiling may be better suited for diagnostic purposes; a number of so far unknown RNAs with potential diagnostic interest in ccRCC are identified by our gene expression profiling study. The data are deposited in the Gene Expression Omnibus (GSE61763).
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Blondeau JJ, Deng M, Syring I, Schrödter S, Schmidt D, Perner S, Müller SC, Ellinger J. Identification of novel long non-coding RNAs in clear cell renal cell carcinoma. Clin Epigenetics 2015; 7:10. [PMID: 25685243 PMCID: PMC4326488 DOI: 10.1186/s13148-015-0047-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/15/2015] [Indexed: 12/18/2022] Open
Abstract
Background Long non-coding RNAs (lncRNA) play an important role in carcinogenesis; knowledge on lncRNA expression in renal cell carcinoma is rudimental. As a basis for biomarker development, we aimed to explore the lncRNA expression profile in clear cell renal cell carcinoma (ccRCC) tissue. Results Microarray experiments were performed to determine the expression of 32,183 lncRNA transcripts belonging to 17,512 lncRNAs in 15 corresponding normal and malignant renal tissues. Validation was performed using quantitative real-time PCR in 55 ccRCC and 52 normal renal specimens. Computational analysis was performed to determine lncRNA-microRNA (MiRTarget2) and lncRNA-protein (catRAPID omics) interactions. We identified 1,308 dysregulated transcripts (expression change >2-fold; upregulated: 568, downregulated: 740) in ccRCC tissue. Among these, aberrant expression was validated using PCR: lnc-BMP2-2 (mean expression change: 37-fold), lnc-CPN2-1 (13-fold), lnc-FZD1-2 (9-fold), lnc-ITPR2-3 (15-fold), lnc-SLC30A4-1 (15-fold), and lnc-SPAM1-6 (10-fold) were highly overexpressed in ccRCC, whereas lnc-ACACA-1 (135-fold), lnc-FOXG1-2 (19-fold), lnc-LCP2-2 (2-fold), lnc-RP3-368B9 (19-fold), and lnc-TTC34-3 (314-fold) were downregulated. There was no correlation between lncRNA expression with clinical-pathological parameters. Computational analyses revealed that these lncRNAs are involved in RNA-protein networks related to splicing, binding, transport, localization, and processing of RNA. Small interfering RNA (siRNA)-mediated knockdown of lnc-BMP2-2 and lnc-CPN2-1 did not influence cell proliferation. Conclusions We identified many novel lncRNA transcripts dysregulated in ccRCC which may be useful for novel diagnostic biomarkers. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0047-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Mario Deng
- Institute of Pathology, University Hospital Bonn, Bonn, Germany ; Department of Prostate Cancer Research, University Hospital Bonn, Bonn, Germany ; Center of Integrated Oncology, University Hospital Bonn, Bonn, Germany
| | - Isabella Syring
- Department of Urology, University Hospital Bonn, Bonn, Germany ; Department of Prostate Cancer Research, University Hospital Bonn, Bonn, Germany
| | - Sarah Schrödter
- Department of Urology, University Hospital Bonn, Bonn, Germany
| | - Doris Schmidt
- Department of Urology, University Hospital Bonn, Bonn, Germany
| | - Sven Perner
- Institute of Pathology, University Hospital Bonn, Bonn, Germany ; Department of Prostate Cancer Research, University Hospital Bonn, Bonn, Germany ; Center of Integrated Oncology, University Hospital Bonn, Bonn, Germany
| | - Stefan C Müller
- Department of Urology, University Hospital Bonn, Bonn, Germany
| | - Jörg Ellinger
- Department of Urology, University Hospital Bonn, Bonn, Germany
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