51
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Liu B, Cui X, Zheng S, Dong K, Dong R. Aberrant KLK4 gene promoter hypomethylation in pediatric hepatoblastomas. Oncol Lett 2017; 13:1360-1364. [PMID: 28454262 DOI: 10.3892/ol.2017.5558] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/24/2016] [Indexed: 12/20/2022] Open
Abstract
DNA methylation has a crucial role in cancer biology and has been recognized as an activator of oncogenes and inactivator of tumor suppressor genes, both of which are mechanisms for tumorigenesis. Kallikrein-related peptidase 4 (KLK4), has been suggested to be an oncogene in various types of cancer. The aim of the present study was to assess the DNA methylation patterns of the KLK4 gene in cancerous samples harvested from patients with hepatoblastoma (HB). KLK4 mRNA expression levels were detected using reverse transcription-quantitative polymerase chain reaction and assessed its DNA methylation patterns using high-throughput mass spectrometry on a matrix-assisted laser desorption/ionization time-of-flight mass array. A total of 10 HB and 10 normal liver tissue samples were obtained from patients with HB. The results of the present study showed that a significantly higher level of KLK4 mRNA expression levels were detected in HB tissues, as compared with the matched controls. Furthermore, the KLK4 gene promoter region was distinctively less methylated in the HB samples compared with the controls and negatively correlated with KLK4 mRNA expression levels. These findings indicate that aberrant methylation of KLK4 may contribute to its upregulated mRNA expression in HB.
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Affiliation(s)
- Baihui Liu
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defects and Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai 201102, P.R. China
| | - Ximao Cui
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defects and Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai 201102, P.R. China
| | - Shan Zheng
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defects and Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai 201102, P.R. China
| | - Kuiran Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defects and Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai 201102, P.R. China
| | - Rui Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defects and Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai 201102, P.R. China
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Dong R, Liu GB, Liu BH, Chen G, Li K, Zheng S, Dong KR. Targeting long non-coding RNA-TUG1 inhibits tumor growth and angiogenesis in hepatoblastoma. Cell Death Dis 2016; 7:e2278. [PMID: 27362796 PMCID: PMC5108331 DOI: 10.1038/cddis.2016.143] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/11/2016] [Accepted: 04/11/2016] [Indexed: 02/07/2023]
Abstract
Hepatoblastoma is the most common liver tumor of early childhood, which is usually characterized by unusual hypervascularity. Recently, long non-coding RNAs (lncRNA) have emerged as gene regulators and prognostic markers in several cancers, including hepatoblastoma. We previously reveal that lnRNA-TUG1 is upregulated in hepatoblastoma specimens by microarray analysis. In this study, we aim to elucidate the biological and clinical significance of TUG1 upregulation in hepatoblastoma. We show that TUG1 is significantly upregulated in human hepatoblastoma specimens and metastatic hepatoblastoma cell lines. TUG1 knockdown inhibits tumor growth and angiogenesis in vivo, and decreases hepatoblastoma cell viability, proliferation, migration, and invasion in vitro. TUG1, miR-34a-5p, and VEGFA constitutes to a regulatory network, and participates in regulating hepatoblastoma cell function, tumor progression, and tumor angiogenesis. Overall, our findings indicate that TUG1 upregulation contributes to unusual hypervascularity of hepatoblastoma. TUG1 is a promising therapeutic target for aggressive, recurrent, or metastatic hepatoblastoma.
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Affiliation(s)
- R Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defect, Shanghai, China.,Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai, China
| | - G-B Liu
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China
| | - B-H Liu
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China
| | - G Chen
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China
| | - K Li
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defect, Shanghai, China.,Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai, China
| | - S Zheng
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defect, Shanghai, China.,Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai, China
| | - K-R Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defect, Shanghai, China.,Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai, China
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53
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Cui X, Liu B, Zheng S, Dong K, Dong R. Genome-wide analysis of DNA methylation in hepatoblastoma tissues. Oncol Lett 2016; 12:1529-1534. [PMID: 27446465 DOI: 10.3892/ol.2016.4789] [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] [Received: 04/03/2015] [Accepted: 06/02/2016] [Indexed: 12/17/2022] Open
Abstract
DNA methylation has a crucial role in cancer biology. In the present study, a genome-wide analysis of DNA methylation in hepatoblastoma (HB) tissues was performed to verify differential methylation levels between HB and normal tissues. As alpha-fetoprotein (AFP) has a critical role in HB, AFP methylation levels were also detected using pyrosequencing. Normal and HB liver tissue samples (frozen tissue) were obtained from patients with HB. Genome-wide analysis of DNA methylation in these tissues was performed using an Infinium HumanMethylation450 BeadChip, and the results were confirmed with reverse transcription-quantitative polymerase chain reaction. The Infinium HumanMethylation450 BeadChip demonstrated distinctively less methylation in HB tissues than in non-tumor tissues. In addition, methylation enrichment was observed in positions near the transcription start site of AFP, which exhibited lower methylation levels in HB tissues than in non-tumor liver tissues. Lastly, a significant negative correlation was observed between AFP messenger RNA expression and DNA methylation percentage, using linear Pearson's R correlation coefficients. The present results demonstrate differential methylation levels between HB and normal tissues, and imply that aberrant methylation of AFP in HB could reflect HB development. Expansion of these findings could provide useful insight into HB biology.
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Affiliation(s)
- Ximao Cui
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defects and Key Laboratory of Neonatal Diseases, Ministry of Health, Shanghai 201102, P.R. China
| | - Baihui Liu
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defects and Key Laboratory of Neonatal Diseases, Ministry of Health, Shanghai 201102, P.R. China
| | - Shan Zheng
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defects and Key Laboratory of Neonatal Diseases, Ministry of Health, Shanghai 201102, P.R. China
| | - Kuiran Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defects and Key Laboratory of Neonatal Diseases, Ministry of Health, Shanghai 201102, P.R. China
| | - Rui Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defects and Key Laboratory of Neonatal Diseases, Ministry of Health, Shanghai 201102, P.R. China
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Chen D, Sun Q, Cheng X, Zhang L, Song W, Zhou D, Lin J, Wang W. Genome-wide analysis of long noncoding RNA (lncRNA) expression in colorectal cancer tissues from patients with liver metastasis. Cancer Med 2016; 5:1629-39. [PMID: 27165481 PMCID: PMC4867661 DOI: 10.1002/cam4.738] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/03/2016] [Accepted: 03/25/2016] [Indexed: 12/15/2022] Open
Abstract
The liver is the most frequent site of metastasis in colorectal cancer (CRC), in which long noncoding RNAs (lncRNAs) may play a crucial role. In this study, we performed a genome‐wide analysis of lncRNA expression to identify novel targets for the further study of liver metastasis in CRC. Samples obtained from CRC patients were analyzed using Arraystar human 8 × 60K lncRNA/mRNA v3.0 microarrays chips to find differentially expressed lncRNAs and mRNAs. The results were confirmed by quantitative reverse transcription‐polymerase chain reaction (qRT‐PCR). The differentially expressed lncRNAs and mRNAs were identified through fold change filtering. Gene ontology (GO) and pathway analyses were performed using standard enrichment computational methods. In the CRC tissues from patients with liver metastasis, 2636 lncRNAs were differentially expressed, including 1600 up‐regulated and 1036 down‐regulated over two‐fold compared with the CRC tissues without metastasis. Among the 1584 differentially expressed mRNAs, 548 were up‐regulated and 1036 down‐regulated. GO and pathway analysis of the up‐regulated and down‐regulated mRNAs yielded different results. The up‐regulated mRNAs were associated with single‐organism process (biological process), membrane part (cellular component), and transporter activity (molecular function), whereas the down‐regulated mRNAs were associated with cellular process, membrane, and binding, respectively. In the pathway analysis, 27 gene pathways associated with the up‐regulated mRNAs and 51 gene pathways associated with the down‐regulated mRNAs were targeted. The significant changes in NQO2 (NM_000904) mRNA and six associated lncRNAs were selected for validation by qRT‐PCR. Aberrantly expressed lncRNAs may play an important role in the liver metastasis of CRC. The further study can provide useful insights into the biology and, ultimately, the prevention of liver metastasis.
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Affiliation(s)
- Dong Chen
- Department of Colorectal Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qiang Sun
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, Zhejiang, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang, China
| | - Xiaofei Cheng
- Department of Colorectal Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lufei Zhang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, Zhejiang, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang, China
| | - Wei Song
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, Zhejiang, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang, China
| | - Dongkai Zhou
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, Zhejiang, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang, China
| | - Jianjiang Lin
- Department of Colorectal Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Weilin Wang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, Zhejiang, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang, China
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55
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Zhou M, Wang X, Shi H, Cheng L, Wang Z, Zhao H, Yang L, Sun J. Characterization of long non-coding RNA-associated ceRNA network to reveal potential prognostic lncRNA biomarkers in human ovarian cancer. Oncotarget 2016; 7:12598-611. [PMID: 26863568 PMCID: PMC4914307 DOI: 10.18632/oncotarget.7181] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/24/2016] [Indexed: 12/14/2022] Open
Abstract
Accumulating evidence has underscored the important roles of long non-coding RNAs (lncRNAs) acting as competing endogenous RNAs (ceRNAs) in cancer initiation and progression. In this study, we used an integrative computational method to identify miRNA-mediated ceRNA crosstalk between lncRNAs and mRNAs, and constructed global and progression-related lncRNA-associated ceRNA networks (LCeNETs) in ovarian cancer (OvCa) based on "ceRNA hypothesis". The constructed LCeNETs exhibited small world, modular architecture and high functional specificity for OvCa. Known OvCa-related genes tended to be hubs and occurred preferentially in the functional modules. Ten lncRNA ceRNAs were identified as potential candidates associated with stage progression in OvCa using ceRNA-network driven method. Finally, we developed a ten-lncRNA signature which classified patients into high- and low-risk subgroups with significantly different survival outcomes. Our study will provide novel insight for better understanding of ceRNA-mediated gene regulation in progression of OvCa and facilitate the identification of novel diagnostic and therapeutic lncRNA ceRNAs for OvCa.
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Affiliation(s)
- Meng Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, PR China
| | - Xiaojun Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, PR China
| | - Hongbo Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, PR China
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, PR China
| | - Zhenzhen Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, PR China
| | - Hengqiang Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, PR China
| | - Lei Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, PR China
| | - Jie Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, PR China
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56
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Abstract
In mammals and other eukaryotes, most of the genome is transcribed in a developmentally regulated manner to produce large numbers of long noncoding RNAs (lncRNAs). Genome-wide studies have identified thousands of lncRNAs lacking protein-coding capacity. RNA in situ hybridization technique is especially beneficial for the visualization of RNA (mRNA and lncRNA) expression in a heterogeneous population of cells/tissues; however its utility has been hampered by complicated procedures typically developed and optimized for the detection of a specific gene and therefore not amenable to a wide variety of genes and tissues.Recently, bDNA has revolutionized RNA in situ detection with fully optimized, robust assays for the detection of any mRNA and lncRNA targets in formalin-fixed paraffin-embedded (FFPE) and fresh frozen tissue sections using manual processing.
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Affiliation(s)
- Botoul Maqsodi
- Affymetrix, 3420 Central Expressway, Santa Clara, CA, 95051, USA
| | - Corina Nikoloff
- Affymetrix, 3420 Central Expressway, Santa Clara, CA, 95051, USA.
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57
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Audas TE, Lee S. Stressing out over long noncoding RNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:184-91. [PMID: 26142536 DOI: 10.1016/j.bbagrm.2015.06.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 06/17/2015] [Accepted: 06/19/2015] [Indexed: 12/26/2022]
Abstract
Genomic studies have revealed that humans possess far fewer protein-encoding genes than originally predicted. These over-estimates were drawn from the inherent developmental and stimuli-responsive complexity found in humans and other mammals, when compared to lower eukaryotic organisms. This left a conceptual void in many cellular networks, as a new class of functional molecules was necessary for "fine-tuning" the basic proteomic machinery. Transcriptomics analyses have determined that the vast majority of the genetic material is transcribed as noncoding RNA, suggesting that these molecules could provide the functional diversity initially sought from proteins. Indeed, as discussed in this review, long noncoding RNAs (lncRNAs), the largest family of noncoding transcripts, have emerged as common regulators of many cellular stressors; including heat shock, metabolic deprivation and DNA damage. These stimuli, while divergent in nature, share some common stress-responsive pathways, notably inhibition of cell proliferation. This role intrinsically makes stress-responsive lncRNA regulators potential tumor suppressor or proto-oncogenic genes. As the list of functional RNA molecules continues to rapidly expand it is becoming increasingly clear that the significance and functionality of this family may someday rival that of proteins. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Timothy E Audas
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Stephen Lee
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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58
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Guo X, Gao L, Wang Y, Chiu DKY, Wang T, Deng Y. Advances in long noncoding RNAs: identification, structure prediction and function annotation. Brief Funct Genomics 2015; 15:38-46. [PMID: 26072035 PMCID: PMC5863772 DOI: 10.1093/bfgp/elv022] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Long noncoding RNAs (lncRNAs), generally longer than 200 nucleotides and with poor protein coding potential, are usually considered collectively as a heterogeneous class of RNAs. Recently, an increasing number of studies have shown that lncRNAs can involve in various critical biological processes and a number of complex human diseases. Not only the primary sequences of many lncRNAs are directly interrelated to a specific functional role, strong evidence suggests that their secondary structures are even more interrelated to their known functions. As functional molecules, lncRNAs have become more and more relevant to many researchers. Here, we review recent, state-of-the-art advances in the three levels (the primary sequence, the secondary structure and the function annotation) of the lncRNA research, as well as computational methods for lncRNA data analysis.
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59
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Li J, Li P, Zhao W, Yang R, Chen S, Bai Y, Dun S, Chen X, Du Y, Wang Y, Zang W, Zhao G, Zhang G. Expression of long non-coding RNA DLX6-AS1 in lung adenocarcinoma. Cancer Cell Int 2015; 15:48. [PMID: 26052251 PMCID: PMC4458341 DOI: 10.1186/s12935-015-0201-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/22/2015] [Indexed: 12/17/2022] Open
Abstract
Background Lung adenocarcinoma (LAC), the primary histological type of non-small cell lung cancer (NSCLC), has displayed an increasing incidence and mortality worldwide. However, therapeutic approaches were limited. Dysregulation of some lncRNAs has been shown in various types of cancers including LAC. The aim of the present study was to vertify lncRNA DLX6-AS1 expression in LAC. Methods Microarray assay revealed expression profile of lncRNAs in LAC. qRT-PCR ( quantitative reverse transcription PCR) was performed to identify lncRNA DLX6-AS1 expression level in 72 paired LAC and adjacent normal lung tissues. qRT-PCR and Western blotting were used to verify that down-regulation lncRNA DLX6-AS1 decreased DLX6 (distal-less homeobox 6) mRNA and protein expression. Results Microarray analysis identified up-regulation of 272 lncRNAs and down-regulation of 635 lncRNAs in LAC tissues. The expression level of lncRNA DLX6-AS1 in LAC tissues was significantly higher compared to paired adjacent normal lung tissues (P< 0.05). In addition, its expression level was closed correlated with both histological differentiation (P = 0.004) and TNM stage (P = 0.033). qRT-PCR and Western blotting analysis showed that DLX6 mRNA and protein levels were lower in si-LncRNA group than in the NC (negative control) and Blank groups. Conclusions Microarray analysis identified that lncRNA DLX6-AS1 was up-regulated in LAC tissues. High DLX6-AS1 expression levels were significantly associated with both histological differentiation and TNM stage. Down-regulation of lncRNA DLX6-AS1 expression decreased the DLX6 mRNA and protein levels.
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Affiliation(s)
- Juan Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan China
| | - Ping Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan China
| | - Wei Zhao
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan China
| | - Rui Yang
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan China
| | - Shanshan Chen
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan China
| | - Yong Bai
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan China
| | - Shaozhi Dun
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan China
| | - Xiaonan Chen
- College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan China
| | - Yuwen Du
- College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan China
| | - Yuanyuan Wang
- College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan China
| | - Wenqiao Zang
- College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan China
| | - Guoqiang Zhao
- College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan China
| | - Guojun Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan China
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Wang P, Lu S, Mao H, Bai Y, Ma T, Cheng Z, Zhang H, Jin Q, Zhao J, Mao H. Identification of biomarkers for the detection of early stage lung adenocarcinoma by microarray profiling of long noncoding RNAs. Lung Cancer 2015; 88:147-53. [DOI: 10.1016/j.lungcan.2015.02.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/09/2015] [Accepted: 02/13/2015] [Indexed: 11/24/2022]
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61
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Systems biology of myasthenia gravis, integration of aberrant lncRNA and mRNA expression changes. BMC Med Genomics 2015; 8:13. [PMID: 25889429 PMCID: PMC4380247 DOI: 10.1186/s12920-015-0087-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 02/26/2015] [Indexed: 12/20/2022] Open
Abstract
Background A novel class of transcripts, long non-coding RNAs (lncRNAs), has recently emerged as a key player in several biological processes, and important roles for these molecules have been reported in a number of complex human diseases, such as autoimmune diseases, neurological disorders, and various cancers. However, the aberrant lncRNAs implicated in myasthenia gravis (MG) remain unknown. The aim of the present study was to explore the abnormal expression of lncRNAs in peripheral blood mononuclear cells (PBMCs) and examine mRNA regulatory relationship networks among MG patients with or without thymoma. Methods Microarray assays were performed, and the outstanding differences between lncRNAs or mRNA expression were verified through RT-PCR. The lncRNAs functions were annotated for the target genes using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway. The potential regulatory relationships between the lncRNAs and target genes were analyzed using the ‘cis’ and ‘trans’ model. Outstanding lncRNAs were organized to generate a TF-lncRNA-gene network using Cytoscape software. Results The lncRNA and mRNA expression profile analysis revealed subsets of differentially expressed genes in MG patients with or without thymoma. A total of 12 outstanding dysregulated expression lncRNAs, such as lncRNA oebiotech_11933, were verified through real-time PCR. Several GO terms including the cellular response to interferon-γ, platelet degranulation, chemokine receptor binding and cytokine interactions were very important in MG pathogenesis. The chromosome locations of some lncRNAs and associated co-expression genes were demonstrated using ‘cis’ analysis. The results of the ‘trans’ analysis revealed that some TFs (i.e., CTCF, TAF1and MYC) regulate lncRNA and gene expression. The outstanding lncRNAs in each group were implicated in the regulation of the TF-lncRNA-target gene network. Conclusion The results of the present study provide a perspective on lncRNA expression in MG. We identify a subset of aberrant lncRNAs and mRNAs as potential biomarkers for the diagnosis of MG. The GO and KEGG pathway analysis provides an annotation to determine the functions of these lncRNAs. The results of the ‘cis’ and ‘trans’ analyses provide information concerning the modular regulation of lncRNAs. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0087-z) contains supplementary material, which is available to authorized users.
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62
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Wu AM, Ni WF, Huang ZY, Li QL, Wu JB, Xu HZ, Yin LH. Analysis of differentially expressed lncRNAs in differentiation of bone marrow stem cells into neural cells. J Neurol Sci 2015; 351:160-167. [PMID: 25820029 DOI: 10.1016/j.jns.2015.03.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 02/11/2015] [Accepted: 03/05/2015] [Indexed: 12/24/2022]
Abstract
Many studies have reported micro RNAs involved in the differentiation of bone marrow mesenchymal stem cells (BMSCs) into neural cells; however, the roles of long non-coding RNAs (lncRNAs) in the differentiation of BMSCs into neural cells remain poorly understood. We used microarray assays to compare the lncRNA and messenger RNA (mRNA) expression profiles in BMSCs and neural-induced BMSCs. We found a total of 24 lncRNAs and 738 mRNAs that were upregulated and 32 lncRNAs and 682 mRNAs that were downregulated in samples induced for 3h; 27 lncRNAs and 864 mRNAs that were upregulated and 37 lncRNAs and 968 mRNAs that were downregulated in 6h samples; and 23 lncRNAs and 1159 mRNAs that were upregulated or downregulated in both the 3h and 6h samples. For 23 differentially lncRNAs and 83 differentially mRNAs, 256 matched lncRNA-mRNA pairs were found. GO (Gene ontology) analysis showed that these lncRNAs were associated with biological processes, cellular components, and molecular functions. Twenty-five pathways were identified by pathway analysis. Then, RT-qPCR validation of the differentially expressed H19, Esco2, Pcdhb18, and RGD1560277 genes confirmed the microarray data. Our study revealed the expression patterns of lncRNAs in the differentiation of BMSCs into neural cells, and many lncRNAs were differentially expressed in induced BMSCs, suggesting that they may play key roles in processes of differentiation. Our findings may promote the use of BMSCs to treat neurodegenerative diseases and trauma.
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Affiliation(s)
- Ai-Min Wu
- Laboratory of Internal Medicine, The First Affiliated Hospital of Wenzhou Medical University, 2# Fuxue Road, Wenzhou 325027, People's Republic of China; The Department of Spinal Surgery, Second Affiliated Hospital of Wenzhou Medical University, Zhejiang Spinal Research Center, 109# XueYuan Western Road, Wenzhou, Zhejiang 325027, People's Republic of China
| | - Wen-Fei Ni
- The Department of Spinal Surgery, Second Affiliated Hospital of Wenzhou Medical University, Zhejiang Spinal Research Center, 109# XueYuan Western Road, Wenzhou, Zhejiang 325027, People's Republic of China
| | - Zhe-Yu Huang
- The Department of Spinal Surgery, Second Affiliated Hospital of Wenzhou Medical University, Zhejiang Spinal Research Center, 109# XueYuan Western Road, Wenzhou, Zhejiang 325027, People's Republic of China
| | - Qing-Long Li
- The Department of Spinal Surgery, Second Affiliated Hospital of Wenzhou Medical University, Zhejiang Spinal Research Center, 109# XueYuan Western Road, Wenzhou, Zhejiang 325027, People's Republic of China
| | - Jian-Bo Wu
- Laboratory of Internal Medicine, The First Affiliated Hospital of Wenzhou Medical University, 2# Fuxue Road, Wenzhou 325027, People's Republic of China
| | - Hua-Zi Xu
- The Department of Spinal Surgery, Second Affiliated Hospital of Wenzhou Medical University, Zhejiang Spinal Research Center, 109# XueYuan Western Road, Wenzhou, Zhejiang 325027, People's Republic of China
| | - Li-Hui Yin
- Laboratory of Internal Medicine, The First Affiliated Hospital of Wenzhou Medical University, 2# Fuxue Road, Wenzhou 325027, People's Republic of China.
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63
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Yang QQ, Deng YF. Genome-wide analysis of long non-coding RNA in primary nasopharyngeal carcinoma by microarray. Histopathology 2015; 66:1022-30. [PMID: 25406670 DOI: 10.1111/his.12616] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/14/2014] [Indexed: 12/22/2022]
Abstract
AIMS Alterations in the expression of several long non-coding RNAs (lncRNAs) have been found in primary nasopharyngeal carcinoma (NPC). However, the effect of lncRNA expression on primary NPC as well as the molecular mechanism of lncRNA remains vague. This study was to identify differentially expressed lncRNAs involved in NPC on a genome-wide scale and predict their potential functions. METHODS AND RESULTS Using high-throughput microarray with 30,586 lncRNA and 26,109 mRNA probes, 856 lncRNAs and 767 mRNAs were expressed differentially between NPC and chronic nasopharyngitis tissues. Bioinformatic analysis (clustering analysis, gene ontology analysis and pathway analysis) was used for further research. Differentially expressed lncRNAs were subgrouped into three types and differentially expressed mRNAs were clustered into 28 pathways. The first coexpression network analysis revealed that 46 lncRNAs interacting with three mRNAs involved the Janus kinase-signal transducer and activator of transcription (JAK-STAT) signalling pathway. Quantitative real-time polymerase chain reaction (PCR) verified 11 up- and down-regulated lncRNAs and eight mRNAs in NPC. The second coexpression network analysis showed that 23 significantly aberrantly expressed mRNAs interacted with three validated lncRNAs. CONCLUSIONS This study could provide new insight into the molecular mechanisms of lncRNAs and their potential role in NPC for further study. These differentially expressed lncRNAs may act as novel biomarkers and therapeutic targets for NPC.
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Affiliation(s)
- Qing-Qing Yang
- Union School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian, China
| | - Yan-Fei Deng
- Union School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian, China.,Department of Otolaryngology, Zhongshan Hospital, Xiamen University, Xiamen, Fujian, China
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Cogill SB, Wang L. Co-expression Network Analysis of Human lncRNAs and Cancer Genes. Cancer Inform 2014; 13:49-59. [PMID: 25392693 PMCID: PMC4218681 DOI: 10.4137/cin.s14070] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Revised: 06/27/2014] [Accepted: 07/01/2014] [Indexed: 12/30/2022] Open
Abstract
We used gene co-expression network analysis to functionally annotate long noncoding RNAs (lncRNAs) and identify their potential cancer associations. The integrated microarray data set from our previous study was used to extract the expression profiles of 1,865 lncRNAs. Known cancer genes were compiled from the Catalogue of Somatic Mutations in Cancer and UniProt databases. Co-expression analysis identified a list of previously uncharacterized lncRNAs that showed significant correlation in expression with core cancer genes. To further annotate the lncRNAs, we performed a weighted gene co-expression network analysis, which resulted in 37 co-expression modules. Three biologically interesting modules were analyzed in depth. Two of the modules showed relatively high expression in blood and brain tissues, whereas the third module was found to be downregulated in blood cells. Hub lncRNA genes and enriched functional annotation terms were identified within the modules. The results suggest the utility of this approach as well as potential roles of uncharacterized lncRNAs in leukemia and neuroblastoma.
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Affiliation(s)
- Steven B Cogill
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Liangjiang Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
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Affiliation(s)
- Chen Gao
- Departments of Anesthesiology, Physiology and Medicine, Molecular Biology Institute, David Geffen School of Medicine at University of California at Los Angeles
| | - Yibin Wang
- Departments of Anesthesiology, Physiology and Medicine, Molecular Biology Institute, David Geffen School of Medicine at University of California at Los Angeles
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