201
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Sahu M, Mallick B. Modulation of specific cell cycle phases in human embryonic stem cells by lncRNA RNA decoys. J Mol Recognit 2018; 32:e2763. [DOI: 10.1002/jmr.2763] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/19/2018] [Accepted: 08/13/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Mousumi Sahu
- RNAi and Functional Genomics Laboratory, Department of Life Science; National Institute of Technology; Rourkela Odisha India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Laboratory, Department of Life Science; National Institute of Technology; Rourkela Odisha India
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202
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Zhao B, Xu H, Ai X, Adalat Y, Tong Y, Zhang J, Yang S. Expression profiles of long noncoding RNAs in lung adenocarcinoma. Onco Targets Ther 2018; 11:5383-5390. [PMID: 30233202 PMCID: PMC6134945 DOI: 10.2147/ott.s167633] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Purpose This study aimed to analyze expression profiles of long noncoding RNAs (lncRNAs) in lung adenocarcinoma. Methods lncRNA microarray technology was employed to detect lncRNA profiles of 3 pairs of lung adenocarcinoma tissues and adjacent tissues. Results We found 134 upregulated lncRNAs and 460 downregulated lncRNAs in lung adenocarcinoma tissues compared to adjacent tissues. Among them, LINC00152, LINC00691, and LINC00578 showed the most significant changes of upregulation, while LINC00668, LINC00710, and LINC00607 showed the most significant changes of downregulation. Fluorescent quantitative polymerase chain reaction (PCR) analysis of tissue samples from an additional 90 patients with lung adenocarcinoma showed significantly increased levels of LINC00152, LINC00691, and LINC00578 and decreased levels of LINC00668, LINC00710, and LINC00607 in lung adenocarcinoma tissues. In addition, LINC00578 was closely associated with the existence of metastasis of lung adenocarcinoma, but the other 5 lncRNAs showed no significant correlation with clinicopathologic characteristics such as age, gender, tumor stage, and the existence of metastasis. Further follow-up study showed that LINC00578 expression was closely associated with the survival of patients with lung adenocarcinoma. Conclusion We revealed the expression profiles of lncRNAs in lung adenocarcinoma and identified LINC00578 as a promising biomarker and therapeutic target for lung adenocarcinoma.
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Affiliation(s)
- Bing Zhao
- Department of Day Oncology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, People's Republic of China
| | - Hang Xu
- Intensive Care Unit, The Sixth Affiliated Hospital, Xinjiang Medical University, Urumqi, Xinjiang, People's Republic of China
| | - Xiaoye Ai
- Department of Day Oncology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, People's Republic of China
| | - Yasheng Adalat
- Department of Day Oncology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, People's Republic of China
| | - Ying Tong
- Department of Day Oncology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, People's Republic of China
| | - Jiazhennan Zhang
- Department of Day Oncology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, People's Republic of China
| | - Shune Yang
- Department of Breast Cancer and Lymphoma, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, People's Republic of China,
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203
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Liu JX, Li W, Li JT, Liu F, Zhou L. Screening key long non-coding RNAs in early-stage colon adenocarcinoma by RNA-sequencing. Epigenomics 2018; 10:1215-1228. [PMID: 30182733 DOI: 10.2217/epi-2017-0155] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AIM We aim to identify the key long noncoding RNAs (lncRNAs) in early-stage colon adenocarcinoma (COAD). PATIENTS & METHODS Compared with colonic intraepithelial neoplasia, differentially expressed lncRNAs (DElncRNAs) in early-stage COAD were obtained by RNA-sequencing. Our previous work has obtained the differentially expressed mRNAs and miRNAs (DEmRNAs and DEmiRNAs) in early-stage COAD. DEmiRNA-DElncRNA-DEmRNA interaction analysis and functional annotation were performed. Validation of expression and receiver-operating characteristic analyses were performed based on The Cancer Genome Atlas. RESULTS Seventy-nine significantly DElncRNAs in early-stage COAD were obtained. MiR-153-3p-TUG1-DAPK1/ARNT2/KLK3/PLD1/SMAD2 and miR-153-3p-SNHG17-COL11A1/IGFBP3/KLF6 interactions were associated with early-stage COAD. Five DElncRNAs (ELFN1-AS1, LINC01234, SNHG17, UCA1 and LOC101929549) involved in early-stage COAD with potential diagnostic value. CONCLUSION LncRNAs involve in early-stage COAD by interaction with COAD-regulated genes and miRNAs.
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Affiliation(s)
- Ji-Xi Liu
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing 100029, PR China
| | - Wen Li
- Department of Surgical ICU, China-Japan Friendship Hospital, Beijing 100029, PR China
| | - Jing-Tao Li
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing 100029, PR China
| | - Fang Liu
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing 100029, PR China
| | - Lei Zhou
- Department of General Surgery, China-Japan Friendship Hospital, Beijing 100029, PR China
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204
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Ren G, Zhu J, Li J, Meng X. Noncoding RNAs in acute kidney injury. J Cell Physiol 2018; 234:2266-2276. [PMID: 30146769 DOI: 10.1002/jcp.27203] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 07/16/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Gui‐Ling Ren
- Department of PharmacyThe 105 Hospital of Chinese People’s Liberation ArmyHefei China
| | - Jie Zhu
- Department of PharmacyThe 105 Hospital of Chinese People’s Liberation ArmyHefei China
| | - Jun Li
- Department of PharmacologySchool of Pharmacy, Anhui Medical UniversityHefei China
- Anhui Institute of Innovative Drugs, Anhui Medical UniversityHefei China
| | - Xiao‐Ming Meng
- Department of PharmacologySchool of Pharmacy, Anhui Medical UniversityHefei China
- Anhui Institute of Innovative Drugs, Anhui Medical UniversityHefei China
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205
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Aberrantly expressed messenger RNAs and long noncoding RNAs in degenerative nucleus pulposus cells co-cultured with adipose-derived mesenchymal stem cells. Arthritis Res Ther 2018; 20:182. [PMID: 30115120 PMCID: PMC6097446 DOI: 10.1186/s13075-018-1677-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/17/2018] [Indexed: 02/07/2023] Open
Abstract
Background Stem cell therapy is considered as a promising alternative to treat intervertebral disc degeneration (IDD). Extensive work had been done on identifying and comparing different types of candidate stem cells, both in vivo and in vitro. However, few studies have shed light on degenerative nucleus pulposus cells (NPCs), especially their biological behavior under the influence of exogenous stem cells, specifically the gene expression and regulation pattern. In the present study, we aimed to determine messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs), which are differentially expressed during the co-culturing process with adipose-derived mesenchymal stem cells (ASCs) and to explore the involved signaling pathways and the regulatory networks. Methods We compared degenerative NPCs co-cultured with ASCs with those cultured solely using lncRNA-mRNA microarray analysis. Based on these data, we investigated the significantly regulated signaling pathways based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Moreover, 23 micro RNAs (miRNAs), which were demonstrated to be involved in IDD were chosen; we investigated their theoretic regulatory importance associated with our microarray data. Results We found 632 lncRNAs and 1682 mRNAs were differentially expressed out of a total of 40,716 probes. We then confirmed the microarray data by real-time PCR. Furthermore, we demonstrated 197 upregulated, and 373 downregulated Gene Ontology terms and 176 significantly enriched pathways, such as the mitogen-activated protein kinase (MAPK) pathway. Also, a signal-net was constructed to reveal the interplay among differentially expressed genes. Meanwhile, a mRNA-lncRNA co-expression network was constructed for the significantly changed mRNAs and lncRNAs. Also, the competing endogenous RNA (ceRNA) network was built. Conclusion Our results present the first comprehensive identification of differentially expressed lncRNAs and mRNAs of degenerative NPCs, altered by co-culturing with ASCs, and outline the gene expression regulation pattern. These may provide valuable information for better understanding of stem cell therapy and potential candidate biomarkers for IDD treatment. Electronic supplementary material The online version of this article (10.1186/s13075-018-1677-x) contains supplementary material, which is available to authorized users.
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206
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Liu P, Zhang M, Niu Q, Zhang F, Yang Y, Jiang X. Knockdown of long non-coding RNA ANRIL inhibits tumorigenesis in human gastric cancer cells via microRNA-99a-mediated down-regulation of BMI1. ACTA ACUST UNITED AC 2018; 51:e6839. [PMID: 30156609 PMCID: PMC6110352 DOI: 10.1590/1414-431x20186839] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 06/25/2018] [Indexed: 12/19/2022]
Abstract
Long non-coding RNA antisense non-coding RNA in the INK4 locus (ANRIL) has been reported to promote tumorigenesis via regulating microRNA (miR)-99a in gastric cancer cells. However, the role of each component involved in it is still not well understood. This study aimed to verify the role of ANRIL in gastric cancer as well as the underlying mechanisms. ANRIL levels in clinical gastric cancer tissues and cell lines were tested by qPCR. Effects of ANRIL silence on cell viability, migration and invasion, apoptosis, and miR-99a expression in MKN-45 and SGC-7901 cells were measured using CCK-8, Transwell assay, flow cytometry, and qPCR assays, respectively. Then, effects of miR-99a inhibition on ANRIL-silenced cells were evaluated. B-lymphoma Mo-MLV insertion region 1 (BMI1) expression, after abnormal expression of ANRIL and miR-99a, was determined. Finally, expression of key proteins in the apoptotic, Notch, and mTOR pathways was assessed. ANRIL level was elevated in gastric cancer tissues and cell lines. Knockdown of ANRIL suppressed cell viability, migration, and invasion, and increased apoptosis through up-regulating miR-99a. Furthermore, ANRIL silence down-regulated BMI1 via up-regulating miR-99a. BMI1 silence down-regulated Bcl-2 and key kinases in the Notch and mTOR pathways and up-regulated p16 and cleaved caspases. We verified the tumor suppressive effects of ANRIL knockdown in gastric cancer cells via crosstalk with miR-99a. Together, we provided a novel regulatory mechanism for ANRIL in gastric cancer, in which ANRIL silence down-regulated BMI1 via miR-99a, along with activation of the apoptotic pathway and inhibition of the Notch and mTOR pathways.
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Affiliation(s)
- Pei Liu
- Department of Infectious Diseases, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Mingming Zhang
- Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao, Shandong, China
| | - Qinghui Niu
- Department of Infectious Diseases, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Fengjuan Zhang
- Department of Infectious Diseases, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Yuling Yang
- Department of Infectious Diseases, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Xiangjun Jiang
- Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao, Shandong, China
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207
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Mousavi MJ, Jamshidi A, Chopra A, Aslani S, Akhlaghi M, Mahmoudi M. Implications of the noncoding RNAs in rheumatoid arthritis pathogenesis. J Cell Physiol 2018; 234:335-347. [DOI: 10.1002/jcp.26911] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/13/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Mohammad Javad Mousavi
- Rheumatology Research Center, Tehran University of Medical Sciences Tehran Iran
- Department of Hematology Faculty of Allied Medicine, Bushehr University of Medical Sciences Bushehr Iran
- Department of Immunology School of Medicine, Tehran University of Medical Sciences Tehran Iran
| | - Ahmadreza Jamshidi
- Rheumatology Research Center, Tehran University of Medical Sciences Tehran Iran
| | - Arvind Chopra
- Centre for Rheumatic Diseases Pune Maharashtra India
| | - Saeed Aslani
- Rheumatology Research Center, Tehran University of Medical Sciences Tehran Iran
| | - Massoomeh Akhlaghi
- Rheumatology Research Center, Tehran University of Medical Sciences Tehran Iran
| | - Mahdi Mahmoudi
- Rheumatology Research Center, Tehran University of Medical Sciences Tehran Iran
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208
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Spiniello M, Knoener RA, Steinbrink MI, Yang B, Cesnik AJ, Buxton KE, Scalf M, Jarrard DF, Smith LM. HyPR-MS for Multiplexed Discovery of MALAT1, NEAT1, and NORAD lncRNA Protein Interactomes. J Proteome Res 2018; 17:3022-3038. [PMID: 29972301 DOI: 10.1021/acs.jproteome.8b00189] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
RNA-protein interactions are integral to the regulation of gene expression. RNAs have diverse functions and the protein interactomes of individual RNAs vary temporally, spatially, and with physiological context. These factors make the global acquisition of individual RNA-protein interactomes an essential endeavor. Although techniques have been reported for discovery of the protein interactomes of specific RNAs they are largely laborious, costly, and accomplished singly in individual experiments. We developed HyPR-MS for the discovery and analysis of the protein interactomes of multiple RNAs in a single experiment while also reducing design time and improving efficiencies. Presented here is the application of HyPR-MS to simultaneously and selectively isolate the interactomes of lncRNAs MALAT1, NEAT1, and NORAD. Our analysis features the proteins that potentially contribute to both known and previously undiscovered roles of each lncRNA. This platform provides a powerful new multiplexing tool for the efficient and cost-effective elucidation of specific RNA-protein interactomes.
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Affiliation(s)
- Michele Spiniello
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Rachel A Knoener
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Maisie I Steinbrink
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Molecular and Environmental Toxicology , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Bing Yang
- Department of Urology , University of Wisconsin School of Medicine and Public Health , Madison , Wisconsin 53705 , United States
| | - Anthony J Cesnik
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Katherine E Buxton
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Mark Scalf
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - David F Jarrard
- Molecular and Environmental Toxicology , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Department of Urology , University of Wisconsin School of Medicine and Public Health , Madison , Wisconsin 53705 , United States.,Carbone Comprehensive Cancer Center , University of Wisconsin-Madison , Madison , Wisconsin 53792 , United States
| | - Lloyd M Smith
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Genome Center of Wisconsin , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
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209
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Liu H, Li H, Jin L, Li G, Hu S, Ning C, Guo J, Shuai S, Li X, Li M. Long Noncoding RNA GAS5 Suppresses 3T3-L1 Cells Adipogenesis Through miR-21a-5p/PTEN Signal Pathway. DNA Cell Biol 2018; 37:767-777. [PMID: 30020817 DOI: 10.1089/dna.2018.4264] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Emerging studies indicated that both long noncoding RNAs and micro-RNAs play crucial roles in the mediation of adipogenesis, which is closely linked to obesity-related diseases. However, the mechanisms of lncRNA-miRNAs coregulating in adipogenesis are still largely unknown. In this study, we determined that lncRNA growth arrest-specific 5 (GAS5) presented an opposite expression pattern with miR-21a-5p in 3T3-L1 adipocytes development. To explore the role of GAS5 in adipogenesis, pcDNA3.1-GAS5 expression vectors and GAS5-siRNAs were used to perform GAS5 overexpression and knockdown, respectively. Ectopic expression of GAS5 dramatically reduced miR-21a-5p level and suppressed the proliferation of 3T3-L1 preadipocytes, while silencing GAS5 slightly increased miR-21a-5p expression but had no significant influence on the cell viability. In addition, overexpression of GAS5 remarkably decreased the mRNA and protein levels of adipogenic marker genes, and resulted in a notable reduction of lipid accumulation. In contrast, overexpressing miR-21a-5p significantly facilitated differentiation of 3T3-L1 cells. By target gene prediction and luciferase reporter assay, we suggested that GAS5 might indirectly improve the expression of phosphatase and tensin homolog (PTEN) by repressing miR-21a-5p in a miRNA-based regulatory mechanism. Together, GAS5 plays a suppressive role in 3T3-L1 cells adipogenesis, which further highlights the importance of lncRNAs in adipogenesis.
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Affiliation(s)
- Haifeng Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu, Sichuan, People's Republic of China
| | - Huan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu, Sichuan, People's Republic of China
| | - Long Jin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu, Sichuan, People's Republic of China
| | - Guilin Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu, Sichuan, People's Republic of China
| | - Silu Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu, Sichuan, People's Republic of China
| | - Chunyou Ning
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu, Sichuan, People's Republic of China
| | - Jiazhong Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu, Sichuan, People's Republic of China
| | - Surong Shuai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu, Sichuan, People's Republic of China
| | - Xuewei Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu, Sichuan, People's Republic of China
| | - Mingzhou Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu, Sichuan, People's Republic of China
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210
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Zhang D, Qin H, Leng Y, Li X, Zhang L, Bai D, Meng Y, Wang J. LncRNA MEG3 overexpression inhibits the development of diabetic retinopathy by regulating TGF-β1 and VEGF. Exp Ther Med 2018; 16:2337-2342. [PMID: 30186476 DOI: 10.3892/etm.2018.6451] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/27/2018] [Indexed: 01/12/2023] Open
Abstract
In view of the high incidence of diabetic retinopathy and the functionality of long non-coding RNA (lncRNA) maternally expressed gene 3 (MEG3) in different disease models, the present study aimed to investigate the role of MEG3 in diabetic retinopathy. In the study, patients with diabetic retinopathy, diabetic patients without retinopathy as well as healthy people were included. Fasting blood was extracted from each participant. Serum MEG3 levels were detected by everse transcription-quantitative polymerase chain reaction (RT-qPCR) and serum vascular endothelial growth factor (VEGF) and transforming growth factor-β1 (TGF-β1) levels were detected by ELISA. Also, the effects of high glucose treatment on the expression of MEG3 and VEGF and the effects of MEG3 overexpression on expression of VEGF and TGF-β1 in high glucose-treated ARPE-19 cells were detected by RT-qPCR and western blot analysis to determine the mRNA and protein levels, respectively. It was indicated that serum levels of MEG3 were significantly lower, while the serum levels of VEGF and TGF-β1 were significantly higher in patients with diabetic retinopathy and diabetic patients without retinopathy compared with the healthy controls. Furthermore, slight differences were found between patients with diabetic retinopathy and diabetic patients without retinopathy; however, these differences were not significant. The findings indicated that high glucose upregulated the expression of VEGF mRNA and downregulated the expression of MEG3, MEG3 overexpression reduced the increased expression levels of VEGF and TGF-β1 induced by high glucose treatment. Therefore, it was concluded that lncRNA MEG3 overexpression may inhibit the development of diabetic retinopathy by inhibiting TGF-β1 and VEGF expression.
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Affiliation(s)
- Daning Zhang
- Department of Ophthalmology, Affiliated Hospital of Beihua University, Jilin 132011, P.R. China
| | - Haixiang Qin
- Department of Legal Medical Experts, Public Security Bureau of Jilin City, Jilin 132011, P.R. China
| | - Ying Leng
- Department of Ophthalmology, Affiliated Hospital of Beihua University, Jilin 132011, P.R. China
| | - Xiangjun Li
- Department of Ophthalmology, Affiliated Hospital of Beihua University, Jilin 132011, P.R. China
| | - Lei Zhang
- Department of Ophthalmology, Affiliated Hospital of Beihua University, Jilin 132011, P.R. China
| | - Dan Bai
- Department of Ophthalmology, Affiliated Hospital of Beihua University, Jilin 132011, P.R. China
| | - Yujun Meng
- Department of Ophthalmology, Affiliated Hospital of Beihua University, Jilin 132011, P.R. China
| | - Jingyi Wang
- Department of Ophthalmology, Affiliated Hospital of Beihua University, Jilin 132011, P.R. China
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211
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Li BL, Wan XP. The role of lncRNAs in the development of endometrial carcinoma. Oncol Lett 2018; 16:3424-3429. [PMID: 30127944 DOI: 10.3892/ol.2018.9065] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 07/03/2017] [Indexed: 01/23/2023] Open
Abstract
Endometrial carcinoma (EC) is one of the most common types of gynecological cancer. Long noncoding RNAs (lncRNAs) are associated with the carcinogenesis and progression of EC. In the following review, the emerging role of lncRNAs in EC initiation and progression is considered. The profile of lncRNAs is becoming higher as the contribution of lncRNAs to carcinogenesis through diverse mechanisms is being increasingly recognized, including in EC. A number of lncRNA-profiling studies have identified aberrantly expressed lncRNAs in EC tissue, and the regulatory network associated with these lncRNAs may be critical in EC progression. Additionally, certain lncRNAs may have diagnostic and/or prognostic significance. The potential function of lncRNAs as prospective therapeutic and prognostic targets in EC will be evaluated.
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Affiliation(s)
- Bi-Lan Li
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, P.R. China
| | - Xiao-Ping Wan
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, P.R. China
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212
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Imsnc761 and DDX6 synergistically suppress cell proliferation and promote apoptosis via p53 in testicular embryonal carcinoma cells. Biosci Rep 2018; 38:BSR20180271. [PMID: 29769412 PMCID: PMC6028756 DOI: 10.1042/bsr20180271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/02/2018] [Accepted: 05/10/2018] [Indexed: 12/25/2022] Open
Abstract
Intermediate-sized non-coding RNAs (imsncRNAs) have been shown to play important regulatory roles in the development of several eukaryotic organisms. In the present research, we selected imsncRNA 761 (imsnc761) as a research target. Expression analyses in a previous study showed that imsnc761 was down-regulated in maturation-arrested testis tissues as compared with the level in normal controls. In the present study, we found that imsnc761 could interact with DEAD-box helicase 6 (DDX6) to induce NTERA-2 (NT2 (testicular embryonal carcinoma cell)) cell apoptosis and proliferation inhibition via the p53 pathway. This interaction between imsnc761 and DDX6 also inhibited mitochondrial function and specific gene transcription and translation. To facilitate further research, we used label-free quantitation method to analyze the associated differences in Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways and biological processes. This confirmed the changes in several specific pathways, which matched our molecular experimental results.
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213
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Zhou M, Hu L, Zhang Z, Wu N, Sun J, Su J. Recurrence-Associated Long Non-coding RNA Signature for Determining the Risk of Recurrence in Patients with Colon Cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 12:518-529. [PMID: 30195788 PMCID: PMC6076224 DOI: 10.1016/j.omtn.2018.06.007] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 06/21/2018] [Accepted: 06/21/2018] [Indexed: 01/18/2023]
Abstract
Patients with colon cancer are often faced a high risk of disease recurrence within 5 years of treatment that is the major cause of cancer mortality. Reliable molecular markers were required to improve the most effective personalized therapy. Here, we identified a recurrence-associated six-lncRNA (long non-coding RNA) signature (LINC0184, AC105243.1, LOC101928168, ILF3-AS1, MIR31HG, and AC006329.1) that can effectively distinguish between high and low risk of cancer recurrence from 389 patients of a discovery dataset, and validated its robust performance in four independent datasets comprising a total of 906 colon cancer patients. We found that the six-lncRNA signature was an independent predictive factor of disease recurrence in multivariate analysis and was superior to the performance of clinical factors and known gene signature. Furthermore, in silico functional analysis showed that the six-lncRNA-signature-associated coding genes are significantly enriched in proliferation and angiogenesis, cell death, as well as critical cancer pathways that could play important roles in colon cancer recurrence. Together, the six-lncRNA signature holds great potential for recurrence risk assessment and personalized management of colon cancer patients.
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Affiliation(s)
- Meng Zhou
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, China
| | - Long Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Zicheng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jie Sun
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, China.
| | - Jianzhong Su
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, China.
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214
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Song S, Yang M, Li Y, Rouzi M, Zhao Q, Pu Y, He X, Mwacharo JM, Yang N, Ma Y, Jiang L. Genome-wide discovery of lincRNAs with spatiotemporal expression patterns in the skin of goat during the cashmere growth cycle. BMC Genomics 2018; 19:495. [PMID: 29940837 PMCID: PMC6019838 DOI: 10.1186/s12864-018-4864-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 06/12/2018] [Indexed: 01/03/2023] Open
Abstract
Background Long intergenic noncoding RNAs (lincRNAs) have been recognized in recent years as key regulators of biological processes. However, lincRNAs in goat remain poorly characterized both across various tissues and during different developmental stages in goat (Capra hircus). Results We performed the genome-wide discovery of the lincRNAs in goat by combining the RNA-seq dataset that were generated from 28 cashmere goat skin samples and the 12 datasets of goat tissues downloaded from the NCBI database. We identified a total of 5546 potential lincRNA transcripts that overlapped 3641 lincRNA genes. These lincRNAs exhibited a tissue-specific pattern. Specifically, there are 584 lincRNAs expressed exclusively in only one tissue, and 91 were highly expressed in hair follicle (HF). In addition, 2350 protein-coding genes and 492 lincRNAs were differentially expressed in the skin of goat. The majority exhibited the remarkable differential expression during the transition of the goat skin from the May–June to August–October time point, which covered the different seasons. Fundamental biological processes, such as skin development, were significantly enriched in these genes. Furthermore, we identified several lincRNAs highly expressed in the HF, which exhibited not only the co-expression pattern with the key factors to the HF development but also the activated expression in the August to October time point. Intriguingly, one of spatiotemporal lincRNAs, linc-chig1598 could be a potential regulator of distal-less homeobox 3 expression during the secondary hair follicle growth. Conclusions This study will facilitate future studies aimed at unravelling the function of lincRNAs in hair follicle development. Electronic supplementary material The online version of this article (10.1186/s12864-018-4864-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shen Song
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100094, China
| | - Min Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Yefang Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Marhaba Rouzi
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Qianjun Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,Small Ruminant Genomics Group, International Center for Agricultural Research in the Dry Areas (ICARDA), P. O. Box 5689, Addis Ababa, Ethiopia
| | - Yabin Pu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,Small Ruminant Genomics Group, International Center for Agricultural Research in the Dry Areas (ICARDA), P. O. Box 5689, Addis Ababa, Ethiopia
| | - Xiaohong He
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,Small Ruminant Genomics Group, International Center for Agricultural Research in the Dry Areas (ICARDA), P. O. Box 5689, Addis Ababa, Ethiopia
| | - Joram M Mwacharo
- Small Ruminant Genomics Group, International Center for Agricultural Research in the Dry Areas (ICARDA), P. O. Box 5689, Addis Ababa, Ethiopia
| | - Ning Yang
- Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100094, China
| | - Yuehui Ma
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China. .,Small Ruminant Genomics Group, International Center for Agricultural Research in the Dry Areas (ICARDA), P. O. Box 5689, Addis Ababa, Ethiopia.
| | - Lin Jiang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China. .,Small Ruminant Genomics Group, International Center for Agricultural Research in the Dry Areas (ICARDA), P. O. Box 5689, Addis Ababa, Ethiopia.
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215
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Liu AN, Qu HJ, Yu CY, Sun P. Knockdown of LINC01614 inhibits lung adenocarcinoma cell progression by up-regulating miR-217 and down-regulating FOXP1. J Cell Mol Med 2018; 22:4034-4044. [PMID: 29934982 PMCID: PMC6111824 DOI: 10.1111/jcmm.13483] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 10/31/2017] [Indexed: 02/06/2023] Open
Abstract
We tried to identify the function of LINC01614 in lung adenocarcinoma (LUAD) and reveal its underlying mechanisms. qRT‐PCR was applied to assess the expression of LINC016014 in LUAD tissues, noncancerous tissues and cells. Through colony formation assay, MTT assay and apoptosis analysis, we examined the variation of cell proliferation and apoptosis ability after silencing LINC01614. Moreover, the targeting interactions among LINC01614, miR‐217 and FOXP1 were validated via luciferase reporter assay, and then, we regulated the expression of miR‐217 and FOXP1 to ascertain their importance in cell proliferation and apoptosis. LINC01614 and FOXP1 were found to be up‐regulated in LUAD tumours and cells, whereas miR‐217 was down‐regulated. The experiment showed that target‐specific selectivity exists between LINC01614‐miR‐217 and miR‐217‐FOXP1 3′UTR. Furthermore, we disclosed that inhibition of LINC01614 could activate miR‐217, which subsequently restrained FOXP1. It was proved that LINC01614 promoted FOXP1 by inhibiting miR‐217, which ultimately stimulated the development of LUAD.
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Affiliation(s)
- Ai-Na Liu
- Department of Medical Oncology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University Medical College, Yantai, Shandong, China
| | - Hua-Jun Qu
- Department of Medical Oncology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University Medical College, Yantai, Shandong, China
| | - Cai-Yan Yu
- Department of Medical Oncology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University Medical College, Yantai, Shandong, China
| | - Ping Sun
- Department of Medical Oncology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University Medical College, Yantai, Shandong, China
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216
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Abstract
Long non-coding RNAs (lncRNAs) refer to functional cellular RNAs molecules longer than 200 nucleotides in length. Unlike microRNAs, which have been widely studied, little is known about the enigmatic role of lncRNAs. However, lncRNAs have motivated extensively attention in the past few years and are emerging as potentially important regulators in pathological processes, including in cancer. We now understand that lncRNAs play role in cancer through their interactions with DNA, protein, and RNA in many instances. Moreover, accumulating evidence has recognized that large classes of lncRNAs are functional for ovarian cancer. Nevertheless, the biological phenomena and molecular mechanisms of lncRNAs in ovarian cancer remain to be better identified. In this review, we outline the dysregulated expression of lncRNAs and their potential clinical implications in ovarian cancer, with a particular emphasis on discussing the well characterized mechanisms underlying lncRNAs in ovarian cancer.
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Affiliation(s)
- Lei Zhan
- Department of gynecology and obstetrics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601 China
| | - Jun Li
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032 China
| | - Bing Wei
- Department of gynecology and obstetrics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601 China
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217
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Liu Y, Li M, Bo X, Li T, Ma L, Zhai T, Huang T. Systematic Analysis of Long Non-Coding RNAs and mRNAs in the Ovaries of Duroc Pigs During Different Follicular Stages Using RNA Sequencing. Int J Mol Sci 2018; 19:ijms19061722. [PMID: 29891752 PMCID: PMC6032137 DOI: 10.3390/ijms19061722] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/05/2018] [Accepted: 06/06/2018] [Indexed: 01/22/2023] Open
Abstract
The dynamic process involving the selection and maturation of follicles is regulated and controlled by a highly synchronized and exquisitely timed cascade of gene expression. Studies have shown that long non-coding RNA (lncRNA) is essential for the normal maintenance of animal reproductive function and has an important regulatory function in ovarian development and hormone secretion. In this study, a total of 2076 lncRNAs (1362 known lncRNAs and 714 new lncRNAs) and 25,491 mRNAs were identified in libraries constructed from Duroc ovaries on days 0, 2 and 4 of follicle development. lncRNAs were shorter, had fewer exons, exhibited a shorter ORF (Open Reading Frame) length and lower expression levels, and were less conserved than mRNAs. Furthermore, 1694 transcripts (140 lncRNAs and 1554 mRNAs) were found to be differentially expressed in pairwise comparisons. A total of 6945 co-localized mRNAs were detected in cis in 2076 lncRNAs. The most enriched GO (Gene Ontology) terms were related to developmental processes. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis revealed that the differentially expressed lncRNAs targeted mRNAs, and the differentially expressed mRNAs were related to the TGF-β signaling pathway, the PI3K-Akt signaling pathway, the Retinol metabolic pathway and the Wnt signaling pathway. This study deepened our understanding of the genetic basis and molecular mechanisms of follicular development in pigs.
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Affiliation(s)
- Yi Liu
- College of Animal Science and Technology, Shihezi University, 221 North Fourth Road, Shihezi 832000, China.
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Sciences, 221 Wu Yi Road, Shihezi 832000, China.
| | - Mengxun Li
- College of Animal Science and Technology, Shihezi University, 221 North Fourth Road, Shihezi 832000, China.
| | - Xinwen Bo
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Sciences, 221 Wu Yi Road, Shihezi 832000, China.
| | - Tao Li
- College of Animal Science and Technology, Shihezi University, 221 North Fourth Road, Shihezi 832000, China.
| | - Lipeng Ma
- College of Animal Science and Technology, Shihezi University, 221 North Fourth Road, Shihezi 832000, China.
| | - Tenjiao Zhai
- College of Animal Science and Technology, Shihezi University, 221 North Fourth Road, Shihezi 832000, China.
| | - Tao Huang
- College of Animal Science and Technology, Shihezi University, 221 North Fourth Road, Shihezi 832000, China.
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218
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Chang CC, Liu TY, Lee YT, Chen YC, Yeh KT, Lee CC, Chen YL, Lin PC, Chang YS, Chan WL, Liu TC, Chang JG. Genome-wide analysis of lncRNAs in 3'-untranslated regions: CR933609 acts as a decoy to protect the INO80D gene. Int J Oncol 2018; 53:417-433. [PMID: 29750421 DOI: 10.3892/ijo.2018.4398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/24/2018] [Indexed: 11/06/2022] Open
Abstract
Long non‑coding RNAs (lncRNAs) have various functions, including chromatin remodeling and the regulation of gene expression at the transcriptional and post-transcriptional levels. However, few lncRNAs have been investigated comprehensively, with the majority being uncharacterized. In the present study, a bioinformatics pipeline was established to identify novel lncRNA sequences similar to the 3'-untranslated regions (3'‑UTRs) of protein-coding genes. These pairs of lncRNAs and coding genes contained the same microRNA (miRNA) target sites; the lncRNA CR933609 matched the 3'‑UTR of INO80 complex subunit D (INO80D) mRNA. The expression levels of CR933609 and INO80D were significantly decreased in non‑small cell lung cancer (NSCLC) and other cancer tissues. The expression levels of CR933609 and INO80D were decreased in CR933609-knockdown NSCLC cells, but only expression levels of INO80D decreased in INO80D knockdown cells. It was shown that there are independent promoters in CR933609 and INO80D. It was also found that the expression levels of INO80D were downregulated by endogenous miRNA‑5096 in A549 cells, but not in CR933609-overexpressing A549 cells. Furthermore, the lncRNA CR933609 acted as a decoy to protect INO80D from downregulation by miRNA‑5096 in NSCLC cells. A protocol was established to identify novel lncRNAs in the 3'‑UTR and the existence of novel lncRNAs was confirmed.
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Affiliation(s)
- Chun-Chi Chang
- Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C
| | - Ting-Yuan Liu
- Center for Precision Medicine, China Medical University Hospital, Taichung 404, Taiwan, R.O.C
| | - Ya-Ting Lee
- Epigenome Research Center, China Medical University Hospital, Taichung 404, Taiwan, R.O.C
| | - Yu-Chia Chen
- Center for Precision Medicine, China Medical University Hospital, Taichung 404, Taiwan, R.O.C
| | - Kun-Tu Yeh
- Department of Pathology, Changhua Christian Hospital, Changhua 500, Taiwan, R.O.C
| | - Chien-Chin Lee
- Epigenome Research Center, China Medical University Hospital, Taichung 404, Taiwan, R.O.C
| | - Ya-Ling Chen
- Division of Chest Medicine, Department of Internal Medicine, Changhua Christian Hospital, Changhua 500, Taiwan, R.O.C
| | - Pei-Chin Lin
- Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C
| | - Ya-Sian Chang
- Department of Laboratory Medicine, China Medical University, Taichung 404, Taiwan, R.O.C
| | - Wen-Ling Chan
- Epigenome Research Center, China Medical University Hospital, Taichung 404, Taiwan, R.O.C
| | - Ta-Chih Liu
- Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C
| | - Jan-Gowth Chang
- Center for Precision Medicine, China Medical University Hospital, Taichung 404, Taiwan, R.O.C
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219
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Lu P, Gu Y, Li L, Wang F, Yang X, Yang Y. Long Noncoding RNA CAMTA1 Promotes Proliferation and Mobility of the Human Breast Cancer Cell Line MDA-MB-231 via Targeting miR-20b. Oncol Res 2018; 26:625-635. [PMID: 28550685 PMCID: PMC7844752 DOI: 10.3727/096504017x14953948675395] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Breast cancer is a serious threat to women's physical and psychological health. Long noncoding RNA CAMTA1 (lncCAMTA1) was believed to be related with tumor progression, but its role in breast cancer is not clear. The human breast cancer cell line MDA-MB-231 was used to investigate the effect of lncCAMTA1 on cell viability, migration/invasion, and apoptosis. The expression of lncCAMTA1, miR-20b, and VEGF in MDA-MB-231 were measured after corresponding transfections. Binding effects between lncCAMTA1 and miR-20b, miR-20b, and VEGF 3'-UTR were measured. The effects of miR-20b and VEGF on breast cancer cells were also assessed after transfections. The phosphorylation levels of the MAPK/ERK and JAK/STAT3 pathways were determined to assess the effect of VEGF. The results showed that lncCAMTA1 expression promoted cell viability and migration/invasion, while knockdown of lncCAMTA1 promoted cell apoptosis via binding with miR-20b. lncCAMTA1 negatively regulated miR-20b expression. VEGF was a target of miR-20b, leading to the modification of the phosphorylation levels of MAPK, ERK, JAK, STAT1, and STAT3. Our findings suggested that lncCAMTA1 might promote proliferation and mobility of human breast cancer cells via binding with miR-20b. VEGF was a direct target of miR-20b and regulated activation of the MAPK/ERK and JAK/STAT3 signaling pathways. Therefore lncCAMTA1 has potential as a novel cancer diagnostic marker and as a putative novel therapeutic target for breast cancer treatment.
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Affiliation(s)
- Pengwei Lu
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Yuanting Gu
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Lin Li
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Fang Wang
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Xue Yang
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Yunqing Yang
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
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220
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Yin DD, Li SS, Shu QY, Gu ZY, Wu Q, Feng CY, Xu WZ, Wang LS. Identification of microRNAs and long non-coding RNAs involved in fatty acid biosynthesis in tree peony seeds. Gene 2018; 666:72-82. [PMID: 29738839 DOI: 10.1016/j.gene.2018.05.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/20/2018] [Accepted: 05/02/2018] [Indexed: 12/27/2022]
Abstract
MicroRNAs (miRNAs) and long noncoding RNAs (lncRNAs) act as important molecular regulators in a wide range of biological processes during plant development and seed formation, including oil production. Tree peony seeds contain >90% unsaturated fatty acids (UFAs) and high proportions of α-linolenic acid (ALA, > 40%). To dissect the non-coding RNAs (ncRNAs) pathway involved in fatty acids synthesis in tree peony seeds, we construct six small RNA libraries and six transcriptome libraries from developing seeds of two cultivars (J and S) containing different content of fatty acid compositions. After deep sequencing the RNA libraries, the ncRNA expression profiles of tree peony seeds in two cultivars were systematically and comparatively analyzed. A total of 318 known and 153 new miRNAs and 22,430 lncRNAs were identified, among which 106 conserved and 9 novel miRNAs and 2785 lncRNAs were differentially expressed between the two cultivars. In addition, potential target genes of the microRNA and lncRNAs were also predicted and annotated. Among them, 9 miRNAs and 39 lncRNAs were predicted to target lipid related genes. Results showed that all of miR414, miR156b, miR2673b, miR7826, novel-m0027-5p, TR24651|c0_g1, TR24544|c0_g15, and TR27305|c0_g1 were up-regulated and expressed at a higher level in high-ALA cultivar J when compared to low-ALA cultivar S, suggesting that these ncRNAs and target genes are possibly involved in different fatty acid synthesis and lipid metabolism through post-transcriptional regulation. These results provide a better understanding of the roles of ncRNAs during fatty acid biosynthesis and metabolism in tree peony seeds.
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Affiliation(s)
- Dan-Dan Yin
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shan-Shan Li
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qing-Yan Shu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhao-Yu Gu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qian Wu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng-Yong Feng
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-Zhong Xu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Liang-Sheng Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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221
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Ren T, Li Z, Zhou Y, Liu X, Han R, Wang Y, Yan F, Sun G, Li H, Kang X. Sequencing and characterization of lncRNAs in the breast muscle of Gushi and Arbor Acres chickens. Genome 2018; 61:337-347. [DOI: 10.1139/gen-2017-0114] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Chicken muscle quality is one of the most important factors determining the economic value of poultry, and muscle development and growth are affected by genetics, environment, and nutrition. However, little is known about the molecular regulatory mechanisms of long non-coding RNAs (lncRNAs) in chicken skeletal muscle development. Our study aimed to better understand muscle development in chickens and thereby improve meat quality. In this study, Ribo-Zero RNA-Seq was used to investigate differences in the expression profiles of muscle development related genes and associated pathways between Gushi (GS) and Arbor Acres (AA) chickens. We identified two muscle tissue specific expression lncRNAs. In addition, the target genes of these lncRNAs were significantly enriched in certain biological processes and molecular functions, as demonstrated by Gene Ontology (GO) analysis, and these target genes participate in five signaling pathway, as revealed by an analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Taken together, these data suggest that different lncRNAs might be involved in regulating chicken muscle development and growth and provide new insight into the molecular mechanisms of lncRNAs.
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Affiliation(s)
- Tuanhui Ren
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Yu Zhou
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xuelian Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Yongcai Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - FengBin Yan
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - GuiRong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Hong Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
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222
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Liu FT, Dong Q, Gao H, Zhu ZM. The prognostic significance of UCA1 for predicting clinical outcome in patients with digestive system malignancies. Oncotarget 2018; 8:40620-40632. [PMID: 28380443 PMCID: PMC5522294 DOI: 10.18632/oncotarget.16534] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 02/28/2017] [Indexed: 01/27/2023] Open
Abstract
Background Urothelial Carcinoma Associated 1 (UCA1) was an originally identified lncRNA in bladder cancer. Previous studies have reported that UCA1 played a significant role in various types of cancer. This study aimed to clarify the prognostic value of UCA1 in digestive system cancers. Results The meta-analysis of 15 studies were included, comprising 1441 patients with digestive system cancers. The pooled results of 14 studies indicated that high expression of UCA1 was significantly associated with poorer OS in patients with digestive system cancers (HR: 1.89, 95 % CI: 1.52–2.26). In addition, UCA1 could be as an independent prognostic factor for predicting OS of patients (HR: 1.85, 95 % CI: 1.45–2.25). The pooled results of 3 studies indicated a significant association between UCA1 and DFS in patients with digestive system cancers (HR = 2.50; 95 % CI = 1.30–3.69). Statistical significance was also observed in subgroup meta-analysis. Furthermore, the clinicopathological values of UCA1 were discussed in esophageal cancer, colorectal cancer and pancreatic cancer. Materials and methods A comprehensive retrieval was performed to search studies evaluating the prognostic value of UCA1 in digestive system cancers. Many databases were involved, including PubMed, Web of Science, Embase and Chinese National Knowledge Infrastructure and Wanfang database. Quantitative meta-analysis was performed with standard statistical methods and the prognostic significance of UCA1 in digestive system cancers was qualified. Conclusions Elevated level of UCA1 indicated the poor clinical outcome for patients with digestive system cancers. It may serve as a new biomarker related to prognosis in digestive system cancers.
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Affiliation(s)
- Fang-Teng Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330000, Jiangxi Province, P.R. China.,Medical School of Nanchang University, Nanchang 330000, Jiangxi Province, P.R. China
| | - Qing Dong
- Medical School of Nanchang University, Nanchang 330000, Jiangxi Province, P.R. China.,The Third Radiotherapy Department, Tumor Hospital of Jiangxi Province, Nanchang 330029, Jiangxi Province, P.R. China
| | - Hui Gao
- The Children's Hospital of Zhejiang University School of Medicine, Hangzhou 310052, Zhejiang Province, P.R. China
| | - Zheng-Ming Zhu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330000, Jiangxi Province, P.R. China
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223
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Koufariotis LT, Chen YPP, Stothard P, Hayes BJ. Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits. BMC Genomics 2018; 19:237. [PMID: 29618315 PMCID: PMC5885354 DOI: 10.1186/s12864-018-4617-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 03/22/2018] [Indexed: 02/03/2023] Open
Abstract
Background There are an exceedingly large number of sequence variants discovered through whole genome sequencing in most populations, including cattle. Deciphering which of these affect complex traits is a major challenge. In this study we hypothesize that variants in some functional classes, such as splice site regions, coding regions, DNA methylated regions and long noncoding RNA will explain more variance in complex traits than others. Two variance component approaches were used to test this hypothesis – the first determines if variants in a functional class capture a greater proportion of the variance, than expected by chance, the second uses the proportion of variance explained when variants in all annotations are fitted simultaneously. Results Our data set consisted of 28.3 million imputed whole genome sequence variants in 16,581 dairy cattle with records for 6 complex trait phenotypes, including production and fertility. We found that sequence variants in splice site regions and synonymous classes captured the greatest proportion of the variance, explaining up to 50% of the variance across all traits. We also found sequence variants in target sites for DNA methylation (genomic regions that are found be highly methylated in bovine placentas), captured a significant proportion of the variance. Per sequence variant, splice site variants explain the highest proportion of variance in this study. The proportion of variance captured by the missense predicted deleterious (from SIFT) and missense tolerated classes was relatively small. Conclusion The results demonstrate using functional annotations to filter whole genome sequence variants into more informative subsets could be useful for prioritization of the variants that are more likely to be associated with complex traits. In addition to variants found in splice sites and protein coding genes regulatory variants and those found in DNA methylated regions, explained considerable variation in milk production and fertility traits. In our analysis synonymous variants captured a significant proportion of the variance, which raises the possible explanation that synonymous mutations might have some effects, or more likely that these variants are miss-annotated, or alternatively the results reflect imperfect imputation of the actual causative variants. Electronic supplementary material The online version of this article (10.1186/s12864-018-4617-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lambros T Koufariotis
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Building 80, 306 Carmody Road, Brisbane, St Lucia, QLD, 4072, Australia. .,Collage of Science, Health and Engineering, La Trobe University, Melbourne, VIC, 3086, Australia. .,Department of Economic Development, Jobs, Transport and Resources, AgriBio Building, 5 Ring Road, Bundoora, VIC, 3086, Australia. .,Dairy Bio, 5 Ring Road, Bundoora, VIC, 3086, Australia.
| | - Yi-Ping Phoebe Chen
- Collage of Science, Health and Engineering, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2C8, Canada
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Building 80, 306 Carmody Road, Brisbane, St Lucia, QLD, 4072, Australia.,Department of Economic Development, Jobs, Transport and Resources, AgriBio Building, 5 Ring Road, Bundoora, VIC, 3086, Australia.,Dairy Bio, 5 Ring Road, Bundoora, VIC, 3086, Australia
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224
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Li CY, Liang GY, Yao WZ, Sui J, Shen X, Zhang YQ, Ma SM, Ye YC, Zhang ZY, Zhang WH, Yin LH, Pu YP. Identification and functional characterization of long non-coding RNAs in human gastric cancer. Oncol Lett 2018; 15:8805-8815. [PMID: 29805620 DOI: 10.3892/ol.2018.8369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 03/17/2017] [Indexed: 02/06/2023] Open
Abstract
Abnormal regulation of long non-coding RNAs (lncRNAs) appears to be a primary feature of numerous types of human cancer. However, the association between the dysregulation of lncRNAs and functional alterations in gastric cancer (GC) remains unclear. In previous studies, we applied microarray and bioinformatics analyses to screen for key lncRNAs from the tumor tissues and matched adjacent non-tumor tissues of 10 patients with GC. There were seven key lncRNAs demonstrated to be significantly different between carcinoma tissues and adjacent non-tumor tissues. In the present study, the expression of these seven selected lncRNAs were validated in 82 patients with GC to further investigate the association between lncRNAs and GC clinical characterization. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) results demonstrated that RP5-919F19, MCPH1 antisense RNA 1 (CTD-2541M15) and urothelial carcinoma-associated 1 (UCA1) exhibited consistent upregulation in cancer compared with adjacent non-tumor tissues, whereas AP000459, LOC101928316, tumor suppressor candidate 8 (LINC01071) and maternally expressed 3 (MEG3) showed consistent downregulation. The results from the microarray and RT-qPCR experiments achieved 100% agreement. A correlation analysis indicated that RP5-919F19, LOC101928316 and MEG3 were significantly associated with tumor differentiation degree, RP5-919F19, UCA1 and MEG3 were significantly associated with lymph node metastasis, and RP5-919F19, CTD-2541M15 and UCA1 were significantly associated with tumor-node-metastasis stage (P<0.05). In addition, it was identified that the differential expression of LINC01071 and LOC101928316 significantly correlated with the age and gender of the GC patients, respectively (P<0.05). The results suggest that the lncRNAs RP5-919F19, LOC101928316, CTD-2541M15, UCA1 and MEG3 are closely associated with the invasion and metastasis of GC, which reveals these indicators as potential specificity biomarkers for the diagnosis, prognosis and classification of GC. Thus, these lncRNAs merit further study as novel candidate biomarkers for the clinical diagnosis of GC and as potential targets for therapy.
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Affiliation(s)
- Cheng-Yun Li
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Ge-Yu Liang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Wen-Zhuo Yao
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Jing Sui
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Xian Shen
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Yan-Qiu Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Shu-Mei Ma
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Yan-Cheng Ye
- Department of Cancer Epidemiology, Wuwei Cancer Registry, Gansu Wuwei Tumor Hospital, Wuwei, Gansu 733000, P.R. China
| | - Zhi-Yi Zhang
- Department of Cancer Epidemiology, Wuwei Cancer Registry, Gansu Wuwei Tumor Hospital, Wuwei, Gansu 733000, P.R. China
| | - Wen-Hua Zhang
- Department of Cancer Epidemiology, Wuwei Cancer Registry, Gansu Wuwei Tumor Hospital, Wuwei, Gansu 733000, P.R. China
| | - Li-Hong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Yue-Pu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, P.R. China
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225
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Liu L, Chen X, Zhang Y, Hu Y, Shen X, Zhu W. Long non-coding RNA TUG1 promotes endometrial cancer development via inhibiting miR-299 and miR-34a-5p. Oncotarget 2018; 8:31386-31394. [PMID: 28404901 PMCID: PMC5458215 DOI: 10.18632/oncotarget.15607] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/24/2017] [Indexed: 01/17/2023] Open
Abstract
It is generally known that the human genome makes a large amount of noncoding RNAs compared with coding genes. Long non-coding RNAs (lncRNAs) which composed of more than 200 nucleotides have been described as the largest subclass of the non-coding transcriptome in human noncoding RNAs. Existing research shows that lncRNAs exerted biological functions in various tumors via participating in both oncogenic and tumor suppressing pathways. The previous studies indicated that lncRNA taurine upregulated 1 (TUG1) play important roles in the initiation and progression of malignancies. In this study,based on previous research, we investigated the expression and biological role of the lncRNA-TUG1. We analyzed the relationship between lncRNA-TUG1and endometrial carcinoma (EC) in a total 104 EC carcinoma specimens, compared with that in normal tissues. We found that lncRNA-TUG1 expression in cancer tissues was significantly higher than that in adjacent tissues. Through a series of experiments, the results demonstrated that lncRNA-TUG1 enhances the evolution and progression of EC through inhibiting miR-299 and miR-34a-5p.
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Affiliation(s)
- Lifen Liu
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Soochow University, Suzhou 215004, Jiangsu, China
| | - Xin Chen
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Soochow University, Suzhou 215004, Jiangsu, China
| | - Ying Zhang
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Soochow University, Suzhou 215004, Jiangsu, China
| | - Yanrong Hu
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Soochow University, Suzhou 215004, Jiangsu, China
| | - Xiaoqing Shen
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Soochow University, Suzhou 215004, Jiangsu, China
| | - Weipei Zhu
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Soochow University, Suzhou 215004, Jiangsu, China
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226
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Lan W, Hou A, Lakshminarayanan R, Lim Y, Tong L. Linc‐9432 is a novel pterygium linc
RNA
which regulates differentiation of fibroblasts. FEBS Lett 2018. [DOI: 10.1002/1873-3468.13027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Wanwen Lan
- Ocular Surface Research Group Singapore Eye Research Institute Singapore
| | - Aihua Hou
- Ocular Surface Research Group Singapore Eye Research Institute Singapore
- Duke‐NUS Graduate Medical School Eye‐Academic Clinical Program Singapore Singapore
| | | | - Yoon‐Pin Lim
- Department of Biochemistry Yong Loo Lin School of Medicine National University of Singapore Singapore
| | - Louis Tong
- Ocular Surface Research Group Singapore Eye Research Institute Singapore
- Duke‐NUS Graduate Medical School Eye‐Academic Clinical Program Singapore Singapore
- Department of Cornea and External Eye Disease Singapore National Eye Center Singapore
- Department of Ophthalmology Yong Loo Lin School of Medicine National University of Singapore Singapore
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227
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Differential Expression Profiling of Long Noncoding RNA and mRNA during Osteoblast Differentiation in Mouse. Int J Genomics 2018; 2018:7691794. [PMID: 29765976 PMCID: PMC5885395 DOI: 10.1155/2018/7691794] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 12/22/2017] [Accepted: 01/17/2018] [Indexed: 12/20/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are emerging as an important controller affecting metabolic tissue development, signaling, and function. However, little is known about the function and profile of lncRNAs in osteoblastic differentiation in mice. Here, we analyzed the RNA-sequencing (RNA-Seq) datasets obtained for 18 days in two-day intervals from neonatal mouse calvarial pre-osteoblast-like cells. Over the course of osteoblast differentiation, 4058 mRNAs and 3948 lncRNAs were differentially expressed, and they were grouped into 12 clusters according to the expression pattern by fuzzy c-means clustering. Using weighted gene coexpression network analysis, we identified 9 modules related to the early differentiation stage (days 2–8) and 7 modules related to the late differentiation stage (days 10–18). Gene ontology and KEGG pathway enrichment analysis revealed that the mRNA and lncRNA upregulated in the late differentiation stage are highly associated with osteogenesis. We also identified 72 mRNA and 89 lncRNAs as potential markers including several novel markers for osteoblast differentiation and activation. Our findings provide a valuable resource for mouse lncRNA study and improves our understanding of the biology of osteoblastic differentiation in mice.
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228
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Zhang Y, Cheng X, Liang H, Jin Z. Long non-coding RNA HOTAIR and STAT3 synergistically regulate the cervical cancer cell migration and invasion. Chem Biol Interact 2018; 286:106-110. [PMID: 29572071 DOI: 10.1016/j.cbi.2018.03.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 02/25/2018] [Accepted: 03/19/2018] [Indexed: 10/17/2022]
Abstract
Homeobox (HOX) transcript antisense RNA (HOTAIR) is a long intergenic non-coding RNA (lncRNA) that has been reported to be highly upregulated in several types of cancers. However, the role of HOTAIR in human cervical cancer is still unclear. We therefore investigated the expression and probable function of HOTAIR in cervical cancer cells. The expression of HOTAIR was examined in (HeLa, CaSki, ME-180, HT-3) and Human Cervical Epithelial Cells (HCerEpiC) by qRT-PCR. Transfection of si-NC, si-HOTAIR or si-STAT3 was carried out with the help of Lipofectamine 2000. The cell viability was assessed by CCK-8 assay. The cell migration and invasion was examined by wound healing and Boyden chamber assays. Protein expression was determined by western blotting. Our results showed that expression of HOTAIR was significantly upregulated in cervical cancer cells and inhibition of the expression of HOTAIR in HeLa cervical cancer cells resulted in suppression of cell proliferation, migration and invasion. Further, analysis of the promoter of HOTAIR, revealed that STAT3 could potentially regulate the activity of the HOTAIR in cervical cancer cells and inhibition of STAT3 had similar effects on the proliferation, migration and invasion of the cervical cancer cells as that of HOTAIR. Further, the suppression of STAT3 expression was associated with concomitant downregulation of IncRNA HOTAIR as indicated by the qRT-PCR. To unveil if STAT3 and HOTAIR have synergistic effects on the cell migration and invasion, si-STAT3 and si-HOTAIR were co-transformed into cervical HeLa cancer cells and it was observed that STAT3 and HOTAIR could synergistically inhibit the proliferation, migration and invasion of the cervical cancer cells. Taken together we conclude that HOTAIR and STAT3 synergistically regulate the proliferation, migration and invasion of cervical cancer cells.
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Affiliation(s)
- Yan Zhang
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Xiaoling Cheng
- Institute of Biological Medicine, Wuhan University of Science and Technology, Wuhan, Hubei 430065, China
| | - Hua Liang
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Zhenzhen Jin
- Department of Reproductive Medicine, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272029, China.
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229
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Cheng H, Huang CM, Wang Y, Hu XX, Xu XQ, Song XM, Tang GS, Chen L, Yang JM. Microarray profiling and co-expression network analysis of the lncRNAs and mRNAs associated with acute leukemia in adults. MOLECULAR BIOSYSTEMS 2018; 13:1102-1108. [PMID: 28428987 DOI: 10.1039/c6mb00874g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) are common types of acute leukemia in adults and cause low survival rate and poor outcome after 5 years despite high rates of complete remission (CR) with modern chemotherapeutic regimens. To understand the distinct mechanisms in leukemogenesis for ALL and AML and to identify markers for diagnosis and treatment, lncRNA and mRNA expression profiles of AML and ALL patients and healthy controls were generated using microarray analysis. For comparison, the differentially expressed mRNA functions were annotated using gene ontology (GO) and pathway analysis. The microarray revealed that 1011 lncRNAs and 2656 mRNAs differed in AML patients and 6069 lncRNAs and 5338 mRNAs differed in ALL patients from those in healthy controls. The GO terms and KEGG pathway annotation data revealed that the olfactory receptor activity, G-protein coupled receptor activity and olfactory transduction-related genes were significantly associated with AML and ALL. Co-expression network analysis indicated that 108 lncRNAs and 85 mRNAs were included in the co-expression network. This study is the first to explore genome-wide lncRNA expression and co-expression with mRNA patterns in AML and ALL using microarray technology and could provide basic information for new biomarkers or treatment targets to alleviate AML and ALL.
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Affiliation(s)
- Hui Cheng
- Institute of Hematology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China.
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230
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Yang W, Li Y, Song X, Xu J, Xie J. Genome-wide analysis of long noncoding RNA and mRNA co-expression profile in intrahepatic cholangiocarcinoma tissue by RNA sequencing. Oncotarget 2018; 8:26591-26599. [PMID: 28427159 PMCID: PMC5432281 DOI: 10.18632/oncotarget.15721] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 02/13/2017] [Indexed: 01/17/2023] Open
Abstract
Long noncoding RNAs (lncRNAs), which are pervasively transcribed in the genome, are emerging in molecular biology as crucial regulators of cancer. RNA-seq data were downloaded from GEO of NCBI and further analyzed to identify novel targets in intrahepatic cholangiocarcinoma (iCCA). We investigated differences in lncRNA and mRNA profiles between 7 pairs of iCCA and adjacent normal tissues. 230 lncRNAs were differentially expressed more than four-fold change in iCCA tissues. Among these, 97 were upregulated and 133 downregulated relatively to normal tissues. Moreover, 169 lncRNAs and 597 mRNAs formed the lncRNA-mRNA co-expression network which consist 766 network nodes and 769 connection edges. Bioinformatics analysis identified these dysregulated lncRNAs were associated with cholesterol homeostasis, insoluble fraction and lipid binding activity and were enriched in complement and coagulation cascades and PPAR signaling pathway. These results uncovered the landscape of iCCA-associated lncRNAs and co-expression network, providing insightful information about dysregulated lncRNAs in iCCA.
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Affiliation(s)
- Wenhui Yang
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Province Cancer Hospital, Affiliated Cancer Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yuan Li
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xia Song
- Shanxi Province Cancer Hospital, Affiliated Cancer Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jun Xu
- Shanxi Province Cancer Hospital, Affiliated Cancer Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jun Xie
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, China
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231
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Zeng Z, Huang B, Huang S, Zhang R, Yan S, Yu X, Shu Y, Zhao C, Lei J, Zhang W, Yang C, Wu K, Wu Y, An L, Ji X, Gong C, Yuan C, Zhang L, Liu W, Feng Y, Zhang B, Dai Z, Shen Y, Wang X, Luo W, Haydon RC, Luu HH, Zhou L, Reid RR, He TC, Wu X. The development of a sensitive fluorescent protein-based transcript reporter for high throughput screening of negative modulators of lncRNAs. Genes Dis 2018; 5:62-74. [PMID: 30159383 PMCID: PMC6110536 DOI: 10.1016/j.gendis.2018.02.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 02/05/2018] [Indexed: 12/24/2022] Open
Abstract
While the human genome is pervasively transcribed, <2% of the human genome is transcribed into protein-coding mRNAs, leaving most of the transcripts as noncoding RNAs, such as microRNAs and long-noncoding RNAs (lncRNAs), which are critical components of epigenetic regulation. lncRNAs are emerging as critical regulators of gene expression and genomic stability. However, it remains largely unknown about how lncRNAs are regulated. Here, we develop a highly sensitive and dynamic reporter that allows us to identify and/or monitor negative modulators of lncRNA transcript levels in a high throughput fashion. Specifically, we engineer a fluorescent fusion protein by fusing three copies of the PEST destruction domain of mouse ornithine decarboxylase (MODC) to the C-terminal end of the codon-optimized bilirubin-inducible fluorescent protein, designated as dBiFP, and show that the dBiFP protein is highly destabilized, compared with the commonly-used eGFP protein. We further demonstrate that the dBiFP signal is effectively down-regulated when the dBiFP and mouse lncRNA H19 chimeric transcript is silenced by mouse H19-specific siRNAs. Therefore, our results strongly suggest that the dBiFP fusion protein may serve as a sensitive and dynamic transcript reporter to monitor the inhibition of lncRNAs by microRNAs, synthetic regulatory RNA molecules, RNA binding proteins, and/or small molecule inhibitors so that novel and efficacious inhibitors targeting the epigenetic circuit can be discovered to treat human diseases such as cancer and other chronic disorders.
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Affiliation(s)
- Zongyue Zeng
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Bo Huang
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Shifeng Huang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Ruyi Zhang
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Shujuan Yan
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Xinyi Yu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Yi Shu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- The Children's Hospital, Chongqing Medical University, Chongqing, 400014, China
| | - Chen Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Jiayan Lei
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Wenwen Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Laboratory Medicine and Clinical Diagnostics, The Affiliated Yantai Hospital, Binzhou Medical University, Yantai, 264100, China
| | - Chao Yang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- The Children's Hospital, Chongqing Medical University, Chongqing, 400014, China
| | - Ke Wu
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Ying Wu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Immunology and Microbiology, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Liping An
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Key Laboratory of Orthopaedic Surgery of Gansu Province and the Department of Orthopaedic Surgery, The Second Hospital of Lanzhou University, Lanzhou, 730030, China
| | - Xiaojuan Ji
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- The Children's Hospital, Chongqing Medical University, Chongqing, 400014, China
| | - Cheng Gong
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Surgery, The Affiliated Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Chengfu Yuan
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, China Three Gorges University School of Medicine, Yichang, 443002, China
| | - Linghuan Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- The Children's Hospital, Chongqing Medical University, Chongqing, 400014, China
| | - Wei Liu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Yixiao Feng
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Bo Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Key Laboratory of Orthopaedic Surgery of Gansu Province and the Department of Orthopaedic Surgery, The Second Hospital of Lanzhou University, Lanzhou, 730030, China
| | - Zhengyu Dai
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Orthopaedic Surgery, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, 400021, China
| | - Yi Shen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Orthopaedic Surgery, Xiangya Second Hospital of Central South University, Changsha, 410011, China
| | - Xi Wang
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Wenping Luo
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Chongqing Key Laboratory for Oral Diseases and Biomedical Sciences, Chongqing, 401147, China
- The Affiliated Hospital of Stomatology of Chongqing Medical University, Chongqing, 401147, China
| | - Rex C. Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Hue H. Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Lan Zhou
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Russell R. Reid
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Surgery, Laboratory of Craniofacial Biology and Development, Section of Plastic Surgery, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Tong-Chuan He
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Xingye Wu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
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232
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Yavropoulou MP, Yovos JG. The "dark matter" of DNA and the regulation of bone metabolism: The role of non-coding RNAs. JOURNAL OF MUSCULOSKELETAL & NEURONAL INTERACTIONS 2018; 18:18-31. [PMID: 29504575 PMCID: PMC5881125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Epigenetics, present a new discipline that attempts to explain significant differences in phenotypes among patients with the same disease. In contrast to the other epigenetic mechanisms that modulate gene transcription, non-coding RNAs act at the post-transcriptional level. They directly modulate the gene expression of mRNA genes leading to mRNA target cleavage and degradation and translation repression. Bioinformatic predictions indicate that non coding RNAs may be involved in the regulation of 60% of the coding genes and each non-coding RNA can have multiple target genes, and each gene may be regulated by more than one non-coding RNAs. In the last decade several studies have shown a significant role of non-coding RNAs in the regulation of bone metabolism and function of bone cells opening a new era in the understanding of bone biology in health and disease.
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Affiliation(s)
- Maria P. Yavropoulou
- Laboratory of Clinical and Molecular Endocrinology, 1st Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece,Corresponding author: Maria P. Yavropoulou, MD, MSc, PhD, Endocrinologist Consultant, 1st Department of Internal Medicine, AHEPA Univ. Hospital, 1 S. Kyriakidi street 54636, Thessaloniki, Greece E-mail:
| | - John G. Yovos
- Laboratory of Clinical and Molecular Endocrinology, 1st Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
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233
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Jiang Q, Shan K, Qun-Wang X, Zhou RM, Yang H, Liu C, Li YJ, Yao J, Li XM, Shen Y, Cheng H, Yuan J, Zhang YY, Yan B. Long non-coding RNA-MIAT promotes neurovascular remodeling in the eye and brain. Oncotarget 2018; 7:49688-49698. [PMID: 27391072 PMCID: PMC5226539 DOI: 10.18632/oncotarget.10434] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 06/06/2016] [Indexed: 11/25/2022] Open
Abstract
Although nervous and vascular systems are functionally different, they usually share similar mechanisms for function maintenance. Neurovascular dysfunction has became the pathogenesis of several vascular and nervous disorders. Here we show that long non-coding RNA-MIAT is aberrantly expressed under neurovascular dysfunction condition. MIAT is shown as a regulator of vascular dysfunction, including retinal angiogenesis, corneal angiogenesis, and vascular permeability. MIAT is also shown as a regulator of retinal neurodegeneration under diabetic condition. Mechanistically, MIAT regulates neural and vascular cell function via MIAT/miR-150-5p/VEGF network. The eye is a valuable model to study central nervous system (CNS) disorders. We show that MIAT knockdown leads to cerebral microvascular degeneration, progressive neuronal loss and neurodegeneration, and behavioral deficits in a CNS neurovascular disorder, Alzheimer's disease. MIAT may represent a pharmacological target for treating neurovascular-related disorders.
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Affiliation(s)
- Qin Jiang
- Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Kun Shan
- Eye Hospital, Nanjing Medical University, Nanjing, China.,Research Center, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiao Qun-Wang
- Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Rong-Mei Zhou
- Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Hong Yang
- Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Chang Liu
- Eye Hospital, Nanjing Medical University, Nanjing, China.,Research Center, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu-Jie Li
- Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Jin Yao
- Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Xiu-Miao Li
- Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Yi Shen
- Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Hong Cheng
- Department of Neurology, Jiangsu Province Hospital, Nanjing, China
| | - Jun Yuan
- Department of Neurology, Jiangsu Chinese Medicine Hospital, Nanjing, China
| | - Yang-Yang Zhang
- Department of Cardiac Surgery, The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Biao Yan
- Research Center, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China
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234
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Liu W, Yan J, Zhang Z, Pian H, Liu C, Li Z. Identification of a selective DNA ligase for accurate recognition and ultrasensitive quantification of N6-methyladenosine in RNA at one-nucleotide resolution. Chem Sci 2018; 9:3354-3359. [PMID: 29780465 PMCID: PMC5932600 DOI: 10.1039/c7sc05233b] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 02/15/2018] [Indexed: 11/29/2022] Open
Abstract
Here we establish an ultrasensitive quantitation assay for accurately determining N6-methyladenosine at one-nucleotide resolution in RNA.
N6-Methyladenosine (m6A) is the most frequent post-transcriptional modification in RNA, and it plays a critical role in biological processes. The functions of m6A remain largely unexplored due to a lack of highly sensitive methods to quantitatively determine the m6A modification fraction at a precise location. Here, we first reveal that T3 DNA ligase has significant selectivity towards the m6A modification. On the basis of the new finding, we establish an ultrasensitive quantitation assay for accurately determining m6A at one-nucleotide resolution in RNA. With the proposed assay, as low as 4 fM RNA containing m6A can be determined and the selectivity is up to 54.1-fold to discriminate m6A against unmodified adenosine (A). The sensitivity has been improved about 106-fold so the proposed method can be successfully employed to accurately determine m6A in real biological samples, even in low abundance RNA.
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Affiliation(s)
- Weiliang Liu
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Jingli Yan
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Zhenhao Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Hongru Pian
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Zhengping Li
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
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235
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Huang J, Liu T, Shang C, Zhao Y, Wang W, Liang Y, Guo L, Yao S. Identification of lncRNAs by microarray analysis reveals the potential role of lncRNAs in cervical cancer pathogenesis. Oncol Lett 2018; 15:5584-5592. [PMID: 29552195 PMCID: PMC5840699 DOI: 10.3892/ol.2018.8037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 04/24/2017] [Indexed: 12/19/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been acknowledged to serve a significant role in cancer biology and abnormal expression in tumors is frequently observed. However, their mechanisms in cervical cancer remain unclear. With a genome-wide analysis of lncRNA expression in cervical cancer tissues, the present study aimed to identify lncRNA targets for the further study of cervical cancer. To elucidate the specific role of lncRNAs in the pathogenesis of this type of cancer, 6 cervical cancer samples paired with normal cervical tissues were obtained. Expression profiles of lncRNAs and mRNAs were constructed through microarray analysis and confirmed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) methods. Gene Ontology and pathway enrichment analyses were performed with computational methods. On the basis of correlations between the differential expression levels of lncRNAs and mRNAs, a coding-non-coding gene co-expression network (CNC network) was established. The differential expression of 5,844 lncRNAs and 4,436 mRNAs were discovered in cervical cancer samples compared with normal cervical tissues. Among the differentially expressed lncRNAs, 14 were chosen at random and validated by RT-qPCR; the majority of the results measured were consistent with the microarray results. Furthermore, the lncRNA ENST00000551152 was found to be upregulated and TCO. NS_00001368 lncRNA was downregulated in cervical cancer cell lines. The CNC network included 592 network nodes and 934 associations between 12 lncRNAs and 580 protein-coding genes, indicating that one lncRNA could act on a maximum of 141 coding genes, and that one coding gene may corresponded with a maximum of 5 lncRNAs. Overall, the present study has provided a complete expression profile of lncRNAs and mRNAs in cervical cancer, which may now be used to establish a solid foundation for cervical cancer research. These results may provide significant information for improving the understanding of the pathogenesis of cervical cancer and indicate potential therapeutic targets.
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Affiliation(s)
- Jiaming Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510800, P.R. China
| | - Tianyu Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510800, P.R. China
| | - Chunliang Shang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510800, P.R. China
| | - Yunhe Zhao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510800, P.R. China
| | - Wei Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510800, P.R. China
| | - Yanchun Liang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510800, P.R. China
| | - Luyan Guo
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510800, P.R. China
| | - Shuzhong Yao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510800, P.R. China
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236
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Zhang F, Li J, Xiao H, Zou Y, Liu Y, Huang W. AFAP1-AS1: A novel oncogenic long non-coding RNA in human cancers. Cell Prolif 2018; 51:e12397. [PMID: 29057544 PMCID: PMC6528908 DOI: 10.1111/cpr.12397] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 09/24/2017] [Indexed: 02/05/2023] Open
Abstract
Long non-coding RNAs (lncRNAs), a group of non-protein-coding RNAs with more than 200 nucleotides in length, are involved in multiple biological processes, such as the proliferation, apoptosis, migration and invasion. Moreover, numerous studies have shown that lncRNAs play important roles as oncogenes or tumour suppressor genes in human cancers. In this paper, we concentrate on actin filament-associated protein 1-antisense RNA 1 (AFAP1-AS1), a well-known long non-coding RNA that is overexpressed in various tumour tissues and cell lines, including oesophageal cancer, pancreatic ductal adenocarcinoma, nasopharyngeal carcinoma, lung cancer, hepatocellular carcinoma, ovarian cancer, colorectal cancer, biliary tract cancer and gastric cancer. Moreover, high expression of AFAP1-AS1 was associated with the clinicopathological features and cancer progression. In this review, we sum up the current studies on the characteristics of AFAP1-AS1 in the biological function and mechanism of human cancers.
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Affiliation(s)
- Fuyou Zhang
- Key Laboratory of Medical Reprogramming TechnologyShenzhen Second People's HospitalFirst Affiliated Hospital of Shenzhen UniversityShenzhen518039Guangdong ProvinceChina
| | - Jianfa Li
- Key Laboratory of Medical Reprogramming TechnologyShenzhen Second People's HospitalFirst Affiliated Hospital of Shenzhen UniversityShenzhen518039Guangdong ProvinceChina
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and GeneticsInstitute of UrologyPeking University Shenzhen HospitalShenzhen PKU‐HKUST Medical CenterShenzhen518036China
| | - Huizhong Xiao
- Key Laboratory of Medical Reprogramming TechnologyShenzhen Second People's HospitalFirst Affiliated Hospital of Shenzhen UniversityShenzhen518039Guangdong ProvinceChina
- University of South ChinaHengyangHunan421001China
| | - Yifan Zou
- Key Laboratory of Medical Reprogramming TechnologyShenzhen Second People's HospitalFirst Affiliated Hospital of Shenzhen UniversityShenzhen518039Guangdong ProvinceChina
- Shantou University Medical CollegeShantou515041Guangdong ProvinceChina
| | - Yuchen Liu
- Key Laboratory of Medical Reprogramming TechnologyShenzhen Second People's HospitalFirst Affiliated Hospital of Shenzhen UniversityShenzhen518039Guangdong ProvinceChina
| | - Weiren Huang
- Key Laboratory of Medical Reprogramming TechnologyShenzhen Second People's HospitalFirst Affiliated Hospital of Shenzhen UniversityShenzhen518039Guangdong ProvinceChina
- University of South ChinaHengyangHunan421001China
- Shantou University Medical CollegeShantou515041Guangdong ProvinceChina
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237
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Long Non-Coding RNAs in Multiple Myeloma. Genes (Basel) 2018; 9:genes9020069. [PMID: 29389884 PMCID: PMC5852565 DOI: 10.3390/genes9020069] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/18/2018] [Accepted: 01/26/2018] [Indexed: 12/30/2022] Open
Abstract
Multiple myeloma (MM) is an incurable disease caused by the malignant proliferation of bone marrow plasma cells, whose pathogenesis remains largely unknown. Although a large fraction of the genome is actively transcribed, most of the transcripts do not serve as templates for proteins and are referred to as non-coding RNAs (ncRNAs), broadly divided into short and long transcripts on the basis of a 200-nucleotide threshold. Short ncRNAs, especially microRNAs, have crucial roles in virtually all types of cancer, including MM, and have gained importance in cancer diagnosis and prognosis, predicting the response to therapy and, notably, as innovative therapeutic targets. Long ncRNAs (lncRNAs) are a very heterogeneous group, involved in many physiological cellular and genomic processes as well as in carcinogenesis, cancer metastasis, and invasion. LncRNAs are aberrantly expressed in various types of cancers, including hematological malignancies, showing either oncogenic or tumor suppressive functions. However, the mechanisms of the related disease-causing events are not yet revealed in most cases. Besides emerging as key players in cancer initiation and progression, lncRNAs own many interesting features as biomarkers with diagnostic and prognostic importance and, possibly, for their utility in therapeutic terms as druggable molecules. This review focuses on the role of lncRNAs in the pathogenesis of MM and summarizes the recent literature.
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238
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Xi J, Sun Q, Ma L, Kang J. Long non-coding RNAs in glioma progression. Cancer Lett 2018; 419:203-209. [PMID: 29355660 DOI: 10.1016/j.canlet.2018.01.041] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/07/2018] [Accepted: 01/10/2018] [Indexed: 01/17/2023]
Abstract
Glioma is one of most malignant primary tumors of the brain. However, due to a lack of effective means for diagnosing and treating glioma, the prognosis of glioma patients remains poor. Therefore, understanding the molecular mechanism of glioma progression is essential for effective treatment. Long non-coding RNAs (lncRNAs) are novel regulators of gene expression at the transcriptional, post-transcriptional and epigenetic levels. Recent evidence indicates that lncRNAs may play important roles in regulating the progression of glioma. In this article, we review the expression profile of lncRNAs in glioma and discuss the functions and known mechanisms of several representative lncRNAs in detail, as well as the prospects of lncRNAs as diagnostic and prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Jiajie Xi
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, PR China
| | - Qiaoyi Sun
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, PR China
| | - Li Ma
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, PR China
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, PR China.
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239
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Nobili L, Lionetti M, Neri A. Long non-coding RNAs in normal and malignant hematopoiesis. Oncotarget 2018; 7:50666-50681. [PMID: 27177333 PMCID: PMC5226612 DOI: 10.18632/oncotarget.9308] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/01/2016] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are defined as ncRNAs of more than 200 nt in length. They are involved in a large spectrum of biological processes, such as maintenance of genome integrity, genomic imprinting, cell differentiation, and development by means of mechanisms that remain to be fully elucidated. Besides their role in normal cellular physiology, accumulating evidence has linked lncRNA expression and functions to cancer development and progression. In this review, we summarize and discuss what is known about their expression and roles in hematopoiesis with a particular focus on their cell-type speciï¬city, functional interactions, and involvement in the pathobiology of hematological malignancies.
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Affiliation(s)
- Lucia Nobili
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Hematology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Marta Lionetti
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Hematology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Antonino Neri
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Hematology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milano, Italy
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240
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Abstract
It is estimated that more than 90% of the mammalian genome is transcribed as non-coding RNAs. Recent evidences have established that these non-coding transcripts are not junk or just transcriptional noise, but they do serve important biological purpose. One of the rapidly expanding fields of this class of transcripts is the regulatory lncRNAs, which had been a major challenge in terms of their molecular functions and mechanisms of action. The emergence of high-throughput technologies and the development in various conventional approaches have led to the expansion of the lncRNA world. The combination of multidisciplinary approaches has proven to be essential to unravel the complexity of their regulatory networks and helped establish the importance of their existence. Here, we review the current methodologies available for discovering and investigating functions of long non-coding RNAs (lncRNAs) and focus on the powerful technological advancement available to specifically address their functional importance.
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241
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Mito M, Kadota M, Tanaka K, Furuta Y, Abe K, Iwasaki S, Nakagawa S. Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing. Sci Rep 2018; 8:1143. [PMID: 29348483 PMCID: PMC5773701 DOI: 10.1038/s41598-018-19494-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 01/02/2018] [Indexed: 12/17/2022] Open
Abstract
The nervous system of higher eukaryotes is composed of numerous types of neurons and glia that together orchestrate complex neuronal responses. However, this complex pool of cells typically poses analytical challenges in investigating gene expression profiles and their epigenetic basis for specific cell types. Here, we developed a novel method that enables cell type-specific analyses of epigenetic modifications using tandem chromatin immunoprecipitation sequencing (tChIP-Seq). FLAG-tagged histone H2B, a constitutive chromatin component, was first expressed in Camk2a-positive pyramidal cortical neurons and used to purify chromatin in a cell type-specific manner. Subsequent chromatin immunoprecipitation using antibodies against H3K4me3-a chromatin modification mainly associated with active promoters-allowed us to survey the histone modifications in Camk2a-positive neurons. Indeed, tChIP-Seq identified hundreds of H3K4me3 modifications in promoter regions located upstream of genes associated with neuronal functions and genes with unknown functions in cortical neurons. tChIP-Seq provides a versatile approach to investigating the epigenetic modifications of particular cell types in vivo.
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Affiliation(s)
- Mari Mito
- RNA Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan.,RNA Systems Biochemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan
| | - Mitsutaka Kadota
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-Minamimachi, Chuou-ku, Kobe, 650-0047, Japan
| | - Kaori Tanaka
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-Minamimachi, Chuou-ku, Kobe, 650-0047, Japan
| | - Yasuhide Furuta
- Animal Resource Development Unit and RIKEN Center for Life Science Technologies, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe, 650-0047, Japan.,Genetic Engineering Team, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe, 650-0047, Japan
| | - Kuniya Abe
- Technology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan. .,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 2-1 Hirosawa, Wako, 351-0198, Japan.
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan. .,RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan.
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242
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Weng SL, Wu WJ, Hsiao YH, Yang SF, Hsu CF, Wang PH. Significant association of long non-coding RNAs HOTAIR genetic polymorphisms with cancer recurrence and patient survival in patients with uterine cervical cancer. Int J Med Sci 2018; 15:1312-1319. [PMID: 30275757 PMCID: PMC6158665 DOI: 10.7150/ijms.27505] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 06/30/2018] [Indexed: 12/17/2022] Open
Abstract
Up to date, no study explores the relationship of single nucleotide polymorphisms (SNPs) of long non-coding RNAs HOTAIR (lncRNAs HOTAIR) with cancer recurrence and patient survival in uterine cervical cancer for Taiwanese women. We therefore designed this study to investigate the clinical roles of lncRNAs HOTAIR SNPs in cervical cancer. One hundred and sixteen patients with cervical invasive cancer and 96 patients with preinvasive lesions as well as 318 control women were consecutively recruited. LncRNAs HOTAIR SNPs rs920778, rs12427129, rs4759314 and rs1899663 were analyzed and their genotypic frequencies were examined by real-time polymerase chain reaction. The results indicated that there were no genotypic differences between patients with cervical neoplasia and normal controls as well as among patients with invasive and invasive cancer, and normal controls. However, genotype GG in lncRNAs HOTAIR SNP rs920778 was demonstrated to be a predictor for poorer cancer recurrence probability [p=0.001, hazard ratio (HR): 7.25, 95% CI: 2.19-23.96]. Furthermore, cervical cancer patients with genotype GG in lncRNAs HOTAIR rs920778 had worse overall survival (p =0.002, HR: 7.22, 95% CI: 2.09-24.92). No significant associations exhibited between lncRNAs HOTAIR SNP rs920778 and clinicopathological parameters. In conclusion, this studied lncRNAs HOTAIR SNPs are not associated with cervical carcinongensis. However, lncRNAs HOTAIR SNP rs920778 may be regarded as an independent predictor of cancer recurrence probability and overall survival in cervical cancer patients.
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Affiliation(s)
- Shun-Long Weng
- Department of Obstetrics and Gynaecology, Hsinchu Mackay Memorial Hospital, Hsinchu City, Taiwan.,Department of Medicine, Mackay Medical College, New Taipei City, Taiwan.,Mackay Junior College of Medicine, Nursing and Management College, Taipei, Taiwan
| | - Wen-Jun Wu
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Yi-Hsuan Hsiao
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Obstetrics and Gynecology, Changhua Christian Hospital, Changhua, Taiwan
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chun-Fang Hsu
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Po-Hui Wang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Obstetrics and Gynecology, Chung Shan Medical University Hospital, Taichung, Taiwan
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243
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Long non-coding RNA RMST silencing protects against middle cerebral artery occlusion (MCAO)-induced ischemic stroke. Biochem Biophys Res Commun 2018; 495:2602-2608. [DOI: 10.1016/j.bbrc.2017.12.087] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 12/15/2017] [Indexed: 01/05/2023]
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244
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Chen C, Xu G, Yuan K, Sun Y, Bao G, Xu D, Cui Z. Transcriptional analysis of long non-coding RNAs in facet joint osteoarthritis. RSC Adv 2018; 8:33695-33701. [PMID: 35548800 PMCID: PMC9086565 DOI: 10.1039/c8ra04809f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/18/2018] [Accepted: 09/24/2018] [Indexed: 11/21/2022] Open
Abstract
It is recognized that facet joint osteoarthritis (FJOA) is commonly induced by the degeneration of articular cartilage of the facet joint.
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Affiliation(s)
- Chu Chen
- Department of Spine Surgery
- The Second Affiliated Hospital of Nantong University
- Nantong
- China
| | - Guanhua Xu
- Department of Spine Surgery
- The Second Affiliated Hospital of Nantong University
- Nantong
- China
| | - Kun Yuan
- Department of Spine Surgery
- The Second Affiliated Hospital of Nantong University
- Nantong
- China
| | - Yuyu Sun
- Department of Spine Surgery
- The Second Affiliated Hospital of Nantong University
- Nantong
- China
| | - Guofeng Bao
- Department of Spine Surgery
- The Second Affiliated Hospital of Nantong University
- Nantong
- China
| | - Dawei Xu
- Department of Spine Surgery
- The Second Affiliated Hospital of Nantong University
- Nantong
- China
| | - Zhiming Cui
- Department of Spine Surgery
- The Second Affiliated Hospital of Nantong University
- Nantong
- China
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245
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Xiao H, Zhang F, Zou Y, Li J, Liu Y, Huang W. The Function and Mechanism of Long Non-coding RNA-ATB in Cancers. Front Physiol 2018; 9:321. [PMID: 29692736 PMCID: PMC5902489 DOI: 10.3389/fphys.2018.00321] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 03/15/2018] [Indexed: 02/05/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are a class of transcriptional RNA molecules with a length of greater than 200 nucleotides that function as regulatory factors in many human diseases. Studies have shown that lncRNAs are involved in multiple cellular processes, including proliferation, apoptosis, migration, and invasion. In this report, a long non-coding RNA-ATB that is overexpressed in various tumor tissues and cell lines was investigated. Recent evidence suggests that ATB is dysfunctional in a variety of cancers, including hepatocellular carcinoma, gastric cancer (GC), colorectal cancer (CRC), breast cancer (BC), prostate cancer, renal cell carcinoma, non-small cell lung cancer (NSCLC), pancreatic cancer, osteosarcoma, and glioma. The high expression of ATB is associated with clinicopathological features of cancer patients. In addition, overexpression of lncRNA-ATB can promote tumor proliferation, migration, and invasion. LncRNA-ATB induces epithelial-mesenchymal transition (EMT) by competitively binding to miRNAs, thus promoting tumor progression. Biological functions and mechanisms of ATB in human cancers are discussed here, concluding that lncRNA-ATB may provide a new biomarker for use in diagnosis and prognosis of cancer.
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Affiliation(s)
- Huizhong Xiao
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
- University of South China, Hengyang, China
| | - Fuyou Zhang
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Yifan Zou
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Shantou University Medical College, Shantou, China
| | - Jianfa Li
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen, PKU-HKUST Medical Center, Shenzhen, China
| | - Yuchen Liu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
- *Correspondence: Yuchen Liu
| | - Weiren Huang
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
- University of South China, Hengyang, China
- Shantou University Medical College, Shantou, China
- Weiren Huang
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246
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Hou X, Du Y, Liu X, Zhang H, Liu Y, Yan N, Zhang Z. Genome-Wide Analysis of Long Non-Coding RNAs in Potato and Their Potential Role in Tuber Sprouting Process. Int J Mol Sci 2017; 19:ijms19010101. [PMID: 29286332 PMCID: PMC5796051 DOI: 10.3390/ijms19010101] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 12/20/2017] [Accepted: 12/28/2017] [Indexed: 11/16/2022] Open
Abstract
Sprouting is a key factor affecting the quality of potato tubers. The present study aimed to compare the differential expression of long non-coding RNAs (lncRNAs) in the apical meristem during the dormancy release and sprouting stages by using lncRNA sequencing. Microscopic observations and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed the changes in the morphology and expression of lncRNAs in potato tubers during sprouting. Meristematic cells of potato tuber apical buds divided continuously and exhibited vegetative cone bulging and vascularisation. In all, 3175 lncRNAs were identified from the apical buds of potato tubers, among which 383 lncRNAs were up-regulated and 340 were down-regulated during sprouting. The GO enrichment analysis revealed that sprouting mainly influenced the expression of lncRNAs related to the cellular components of potato apical buds (e.g., cytoplasm and organelles) and cellular metabolic processes. The KEGG enrichment analysis also showed significant enrichment of specific metabolic pathways. In addition, 386 differentially expressed lncRNAs during sprouting were identified as putative targets of 235 potato miRNAs. Quantitative real-time polymerase chain reaction results agreed with the sequencing data. Our study provides the first systematic study of numerous lncRNAs involved in the potato tuber sprouting process and lays the foundation for further studies to elucidate their precise functions.
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Affiliation(s)
- Xiaodong Hou
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Yongmei Du
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Xinmin Liu
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Hongbo Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Yanhua Liu
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Ning Yan
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Zhongfeng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
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247
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Li J, Wu L, Guo W, Chen J, Hu X, Wang M, Zhao Z, Ying B. Clinical relevance of LINC00152 and its variants in western Chinese tuberculosis patients. Oncotarget 2017; 8:115456-115468. [PMID: 29383173 PMCID: PMC5777785 DOI: 10.18632/oncotarget.23297] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 12/03/2017] [Indexed: 02/05/2023] Open
Abstract
Recent studies indicate that the long intergenic non-coding RNA LINC00152 plays crucial roles in various human diseases. Here, we investigated whether levels of LINC00152 or its genetic variants correlate with the clinical features of tuberculosis (TB) in western Chinese patients. We genotyped the single nucleotide polymorphism LINC00152 rs80292941 in 476 TB patients and 475 healthy subjects using a custom-by-design 48-Plex SNPscan Kit, and measured relative levels of LINC00152 using RT-qPCR. We observed that LINC00152 levels were lower in TB patients than controls. Moreover, rs80292941 TT genotype carriers had the lowest LINC00152 levels among TB patients, and rs80292941 AA genotype carriers are more likely to suffer from hepatotoxicity induced by antituberculosis therapy [OR = 3.97, 95% = 1.53-10.13, p = 0.002]. Our findings strongly suggest that LINC00152 may promote TB progression and highlight rs80292941 single nucleotide polymorphism as a novel predisposition marker for antituberculosis drug-induced hepatotoxicity.
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Affiliation(s)
- Jing Li
- Department of Clinical Laboratory, Central Hospital of Panzhihua City, Panzhihua, Sichuan 617067, P. R. China
| | - Lijuan Wu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Weihua Guo
- Department of Clinical Laboratory, Central Hospital of Panzhihua City, Panzhihua, Sichuan 617067, P. R. China
| | - Juli Chen
- Department of Clinical Laboratory, Central Hospital of Panzhihua City, Panzhihua, Sichuan 617067, P. R. China
| | - Xuejiao Hu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Zhenzhen Zhao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
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248
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Jiang B, Liu J, Zhang YH, Shen D, Liu S, Lin F, Su J, Lin QF, Yan S, Li Y, Mao WD, Liu ZL. Long noncoding RNA LINC00961 inhibits cell invasion and metastasis in human non-small cell lung cancer. Biomed Pharmacother 2017; 97:1311-1318. [PMID: 29156520 DOI: 10.1016/j.biopha.2017.11.062] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 10/25/2017] [Accepted: 11/10/2017] [Indexed: 01/08/2023] Open
Abstract
Long noncoding RNAs (LncRNAs) expression has been found to be misregulated in multiple human cancers, and a growing number of studies have revealed that lncRNAs can function as important oncogenes or tumor suppressors. In this study, we identified a lncRNA-LINC00961, which was significantly down-regulated in human non-small cell lung cancer tissues. Decreased LINC00961 was associated with NSCLC patients advanced clinical stage, lymph node metastasis, and shorter survival time. Further experiments demonstrated that LSD1 could directly bind to LINC00961 promoter regions and epigenetically repress its transcription in NSCLC cells. Moreover, MTT assays showed that LINC00961 had no influence on NSCLC cell proliferation. Ectopic overexpression of LINC00961 inhibits NSCLC cell migration, invasion in vitro and metastasis in vivo. Finally, qRT-PCR and western blot assays revealed that LINC00961 could act as a tumor suppressor partially via affecting β-catenin expression. Collectively, decreased LINC00961 might play a key role in NSCLC progression, and may serve as a novel prognostic marker in human NSCLC.
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Affiliation(s)
- Bin Jiang
- Department of Urology, The Affiliated Jiangyin Hospital of Southeast University Medical College, Wuxi, People's Republic of China
| | - Jing Liu
- Department of Urology, The Affiliated Jiangyin Hospital of Southeast University Medical College, Wuxi, People's Republic of China; Department of Respirology, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Yu-Hong Zhang
- Department of Oncology, The Affiliated Jiangyin Hospital of Southeast University Medical College, Wuxi, People's Republic of China
| | - Dong Shen
- Department of Oncology, The Affiliated Jiangyin Hospital of Southeast University Medical College, Wuxi, People's Republic of China
| | - Shaoping Liu
- Department of Oncology, The Affiliated Jiangyin Hospital of Southeast University Medical College, Wuxi, People's Republic of China
| | - Feng Lin
- Department of Oncology, The Affiliated Jiangyin Hospital of Southeast University Medical College, Wuxi, People's Republic of China
| | - Jun Su
- Department of Oncology, The Affiliated Jiangyin Hospital of Southeast University Medical College, Wuxi, People's Republic of China
| | - Qing-Feng Lin
- Department of Oncology, The Affiliated Jiangyin Hospital of Southeast University Medical College, Wuxi, People's Republic of China
| | - Shuai Yan
- Department of Oncology, The Affiliated Jiangyin Hospital of Southeast University Medical College, Wuxi, People's Republic of China
| | - Yong Li
- Department of Respirology, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Wei-Dong Mao
- Department of Oncology, The Affiliated Jiangyin Hospital of Southeast University Medical College, Wuxi, People's Republic of China.
| | - Zhi-Li Liu
- Department of Oncology, The Affiliated Jiangyin Hospital of Southeast University Medical College, Wuxi, People's Republic of China.
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249
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Han D, Gao X, Wang M, Qiao Y, Xu Y, Yang J, Dong N, He J, Sun Q, Lv G, Xu C, Tao J, Ma N. Long noncoding RNA H19 indicates a poor prognosis of colorectal cancer and promotes tumor growth by recruiting and binding to eIF4A3. Oncotarget 2017; 7:22159-73. [PMID: 26989025 PMCID: PMC5008352 DOI: 10.18632/oncotarget.8063] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/23/2016] [Indexed: 02/06/2023] Open
Abstract
The overall biological role and clinical significance of long non-coding RNA H19 in colorectal cancer (CRC) remain largely unknown. Here, we firstly report that the lncRNA H19 recruits eIF4A3 and promotes the CRC cell proliferation. We observed higher expression of H19 was significantly correlated with tumor differentiation and advanced TNM stage in a cohort of 83 CRC patients. Multivariate analyses revealed that expression of H19 served as an independent predictor for overall survival and disease-free survival. Further experiments revealed that overexpression of H19 promoted the proliferation of CRC cells, while depletion of H19 inhibited cell viability and induced growth arrest. Moreover, expression profile data showed that H19 upregulated a series of cell-cycle genes. Using bioinformatics prediction and RNA immunoprecipitation assays, we identified eIF4A3 as an RNA-binding protein that binds to H19. We confirmed that combining eIF4A3 with H19 obstructed the recruitment of eIF4A3 to the cell-cycle gene mRNA. Our results suggest that H19, as a growth regulator, could serve as a candidate prognostic biomarker and target for new therapies in human CRC.
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Affiliation(s)
- Dong Han
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China.,Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Xu Gao
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China.,Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Meng Wang
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yu Qiao
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China.,Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Ya Xu
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China
| | - Jing Yang
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China
| | - Nazhen Dong
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China
| | - Jun He
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China
| | - Qian Sun
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China
| | - Guixiang Lv
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China
| | - Changqing Xu
- Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Ji Tao
- Department of Gastrointestinal Medical Oncology, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, China
| | - Ning Ma
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China.,Heilongjiang Academy of Medical Sciences, Harbin, China
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250
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Identification of long non-coding RNAs as novel biomarker and potential therapeutic target for atrial fibrillation in old adults. Oncotarget 2017; 7:10803-11. [PMID: 26908457 PMCID: PMC4905440 DOI: 10.18632/oncotarget.7514] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 02/05/2016] [Indexed: 01/04/2023] Open
Abstract
Atrial fibrillation (AF) is a highly prevalent cardiac arrhythmia disease, which widely leads to exacerbate heart failure and ischemic stroke in elder world. Recently, long non-coding RNAs (lncRNAs), a subclass of noncoding RNAs, have been reported to play critical roles in pathophysiology of cardiac heart. However, little is known of their role in cardiac arrhythmia. In the present study, we investigated the expression levels of lncRNAs of AF patients and healthy people with Agilent Human lncRNA array for the first time. 177 lncRNAs of 78243 and 153 mRNAs of 30215 tested were identified to be differentially expressed (≥ 2-fold change), indicating that the expression of many lncRNAs are upregulated or downregulated in AF. Among these, NONHSAT040387 and NONHSAT098586 were the most upregulated and downregulated lncRNAs. Real time quantitative PCR were employed to validate the microarray analysis findings, and the results confirmed the consistence. GO and KEGG pathway analysis were applied to explore the potential lncRNAs functions, some pathways including oxygen transporter activity and protein heterodimerization activity were speculated to be involved in AF pathogenesis. These results shed some light on lncRNAs' physiologic functions and provide useful information for exploring potential therapeutic treatments for heart rhythm disease.
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