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Liang W, Zhao Y, Meng Q, Jiang W, Deng S, Xue J. The role of long non-coding RNA in hepatocellular carcinoma. Aging (Albany NY) 2024; 16:4052-4073. [PMID: 38334963 PMCID: PMC10929815 DOI: 10.18632/aging.205523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 12/12/2023] [Indexed: 02/10/2024]
Abstract
Hepatocellular carcinoma (HCC) is a prevalent liver malignancy with complex etiology and generally poor prognosis. Recently, long non-coding RNAs (lncRNAs), non-protein-coding RNA molecules exceeding 200 nucleotides, have emerged as pivotal players in HCC, influencing its initiation, progression, invasion, and metastasis. These lncRNAs modulate gene expression at epigenetic, transcriptional, and post-transcriptional levels, actively participating in the pathological and physiological processes of HCC. Understanding the intricate relationship between lncRNAs and HCC is important for improving prognosis and reducing mortality. This review summarizes advancements in elucidating the role of lncRNAs in HCC pathogenesis.
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Affiliation(s)
- Weizheng Liang
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou 075000, Hebei, China
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou 075000, Hebei, China
- Tumor Research Institute, The First Affiliated Hospital of Hebei North University, Zhangjiakou 075000, Hebei, China
| | - Yan Zhao
- Department of Mathematics and Computer Science, Free University Berlin, Berlin 14195, Germany
| | - Qingxue Meng
- Technology Department, The First Affiliated Hospital of Hebei North University, Zhangjiakou 075000, Hebei, China
| | - Wenjie Jiang
- Department of Artificial Intelligence and Data Science, Hebei University of Technology, Tianjin 300401, China
| | - Shoulong Deng
- National Health Commission of China (NHC) Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China
| | - Jun Xue
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou 075000, Hebei, China
- Tumor Research Institute, The First Affiliated Hospital of Hebei North University, Zhangjiakou 075000, Hebei, China
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2
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Ahangar Davoodi N, Najafi S, Naderi Ghale-Noie Z, Piranviseh A, Mollazadeh S, Ahmadi Asouri S, Asemi Z, Morshedi M, Tamehri Zadeh SS, Hamblin MR, Sheida A, Mirzaei H. Role of non-coding RNAs and exosomal non-coding RNAs in retinoblastoma progression. Front Cell Dev Biol 2022; 10:1065837. [PMID: 36619866 PMCID: PMC9816416 DOI: 10.3389/fcell.2022.1065837] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Retinoblastoma (RB) is a rare aggressive intraocular malignancy of childhood that has the potential to affect vision, and can even be fatal in some children. While the tumor can be controlled efficiently at early stages, metastatic tumors lead to high mortality. Non-coding RNAs (ncRNAs) are implicated in a number of physiological cellular process, including differentiation, proliferation, migration, and invasion, The deregulation of ncRNAs is correlated with several diseases, particularly cancer. ncRNAs are categorized into two main groups based on their length, i.e. short and long ncRNAs. Moreover, ncRNA deregulation has been demonstrated to play a role in the pathogenesis and development of RB. Several ncRNAs, such as miR-491-3p, miR-613,and SUSD2 have been found to act as tumor suppressor genes in RB, but other ncRNAs, such as circ-E2F3, NEAT1, and TUG1 act as tumor promoter genes. Understanding the regulatory mechanisms of ncRNAs can provide new opportunities for RB therapy. In the present review, we discuss the functional roles of the most important ncRNAs in RB, their interaction with the genes responsible for RB initiation and progression, and possible future clinical applications as diagnostic and prognostic tools or as therapeutic targets.
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Affiliation(s)
- Nasrin Ahangar Davoodi
- Eye Research Center, Rassoul Akram Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zari Naderi Ghale-Noie
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ashkan Piranviseh
- Brain and Spinal Cord Injury Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Samaneh Mollazadeh
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Sahar Ahmadi Asouri
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Mohammadamin Morshedi
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran,School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | | | - Michael R. Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, South Africa
| | - Amirhossein Sheida
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran,School of Medicine, Kashan University of Medical Sciences, Kashan, Iran,*Correspondence: Amirhossein Sheida, ; Hamed Mirzaei, ,
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran,*Correspondence: Amirhossein Sheida, ; Hamed Mirzaei, ,
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Ozkur M, Benlier N, Takan I, Vasileiou C, Georgakilas AG, Pavlopoulou A, Cetin Z, Saygili EI. Ginger for Healthy Ageing: A Systematic Review on Current Evidence of Its Antioxidant, Anti-Inflammatory, and Anticancer Properties. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:4748447. [PMID: 35585878 PMCID: PMC9110206 DOI: 10.1155/2022/4748447] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/11/2022] [Indexed: 12/24/2022]
Abstract
The world's population is ageing at an accelerated pace. Ageing is a natural, physiological but highly complex and multifactorial process that all species in the Tree of Life experience over time. Physical and mental disabilities, and age-related diseases, would increase along with the increasing life expectancy. Ginger (Zingiber officinale) is a plant that belongs to the Zingiberaceae family, native to Southeast Asia. For hundreds of years, ginger has been consumed in various ways by the natives of Asian countries, both as culinary and medicinal herb for the treatment of many diseases. Mounting evidence suggests that ginger can promote healthy ageing, reduce morbidity, and prolong healthy lifespan. Ginger, a well-known natural product, has been demonstrated to possess antioxidant, anti-inflammatory, anticancer, and antimicrobial properties, as well as an outstanding antiviral activity due to a high concentration of antiviral compounds. In this review, the current evidence on the potential role of ginger and its active compounds in the prevention of ageing is discussed.
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Affiliation(s)
- Mehtap Ozkur
- Department of Medical Pharmacology, Faculty of Medicine, SANKO University, Gaziantep, Turkey
| | - Necla Benlier
- Department of Medical Pharmacology, Faculty of Medicine, SANKO University, Gaziantep, Turkey
| | - Işıl Takan
- Izmir Biomedicine and Genome Center, Balcova, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, Izmir 35220, Turkey
| | - Christina Vasileiou
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, 157 80 Athens, Greece
| | - Alexandros G. Georgakilas
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, 157 80 Athens, Greece
| | - Athanasia Pavlopoulou
- Izmir Biomedicine and Genome Center, Balcova, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, Izmir 35220, Turkey
| | - Zafer Cetin
- Department of Medical Biology, School of Medicine, SANKO University, Gaziantep, Turkey
- Department of Biological and Biomedical Sciences, Graduate Education Institute, SANKO University, Gaziantep, Turkey
| | - Eyup Ilker Saygili
- Department of Medical Biochemistry, School of Medicine, SANKO University, Gaziantep, Turkey
- Department of Molecular Medicine, Graduate Education Institute, SANKO University, Gaziantep, Turkey
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4
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Wang H, Chen Y, Liu Y, Li Q, Luo J, Wang L, Chen Y, Sang C, Zhang W, Ge X, Yao Z, Miao L, Liu X. The lncRNA ZFAS1 regulates lipogenesis in colorectal cancer by binding polyadenylate-binding protein 2 to stabilize SREBP1 mRNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:363-374. [PMID: 35036050 PMCID: PMC8728310 DOI: 10.1016/j.omtn.2021.12.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 12/08/2021] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is the fourth leading cause of cancer-related mortality globally. Therefore, a better understanding of the early molecular events of this disease is needed. Long noncoding RNAs (lncRNAs) play a critical role in the regulation of tumorigenesis and cancer progression. In this study, we investigated the characteristics of ZFAS1 in CRC. We analyzed three independent microarray datasets of CRC tissues from GEO and found that ZFAS1 expression was remarkably upregulated in all three datasets. Moreover, we validated the overexpression of ZFAS1 in CRC tissues compared with normal tissues and found that ZFAS1 was positively correlated with tumor size and metastasis in CRC. Knockdown of ZFAS1 significantly suppressed the malignant phenotype and lipogenesis of CRC cells. Mechanistically, ZFAS1 binds polyadenylate-binding protein 2 (PABP2) to stabilize SREBP1 mRNA, thereby increasing the expression of SREBP1 and its target genes stearoyl-CoA desaturase (SCD1) and fatty acid synthase (FASN), thus promoting CRC lipid accumulation. These data demonstrated that ZFAS1 could act as an oncogene for CRC and that ZFAS1 reprograms lipid metabolism by binding with PABP2 to stabilize SREBP1 mRNA accumulation, implicating it as a novel and potent target for the treatment of CRC.
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Affiliation(s)
- Huishan Wang
- Department of Gastroenterology, Shanghai Songjiang District Central Hospital, Shanghai 210000, China
| | - Yuli Chen
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, China
| | - Yanwen Liu
- Department of Oncology, Zhongda Hospital, Medical School of Southeast University, Nanjing 210000, China
| | - Qiuhui Li
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, China
| | - Jing Luo
- Department of Cardiothoracic Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing 210011, China
| | - Li Wang
- Department of Oncology, The Third Medical School of Nanjing Medical University, Nanjing 210011, China
| | - Yuanyuan Chen
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, China
| | - Chen Sang
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow of University, Changzhou G 213003, China
| | - Wen Zhang
- Department of Oncology, Zhongda Hospital, Medical School of Southeast University, Nanjing 210000, China
| | - Xianxiu Ge
- Department of Gastroenterology, Shanghai Songjiang District Central Hospital, Shanghai 210000, China
| | - Zhifeng Yao
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow of University, Changzhou G 213003, China
| | - Lin Miao
- Medical Center for Digestive Diseases, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Xianghua Liu
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, China
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5
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Uboveja A, Satija YK, Siraj F, Saluja D. p73-regulated FER1L4 lncRNA sponges the oncogenic potential of miR-1273g-3p and aids in the suppression of colorectal cancer metastasis. iScience 2022; 25:103811. [PMID: 35198876 PMCID: PMC8844823 DOI: 10.1016/j.isci.2022.103811] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/01/2021] [Accepted: 01/20/2022] [Indexed: 02/07/2023] Open
Abstract
p73 belongs to the p53 tumor suppressor family and is involved in the suppression of metastasis. However, its specific mechanism of action remains to be elucidated. Long non-coding RNAs portray a crucial role in tumor suppression. We have identified lncRNA FER1L4 as a p73 transcriptional target. The binding of p73 to FER1L4 promoter was established by bioinformatics analysis, luciferase reporter, and ChIP assays. Both FER1L4 and p73 knockdown enhanced the migration and invasion rate of colorectal cancer cells. FER1L4 also plays a critical role in p73-mediated cell-cycle arrest and apoptosis. FER1L4 sponged the expression of miR-1273g-3p, which, in turn, increased PTEN expression, leading to cell-cycle arrest. RNA in situ hybridization revealed the down-regulation of both p73 and FER1L4 expression in a metastatic colon cancer tissue as compared with non-metastatic tissue. Collectively, we impart conclusive proof that p73 exerts its anti-metastatic properties by inducing lncRNA FER1L4 in response to genotoxic stress. Long non-coding RNA FER1L4 functions as a direct transcriptional target of p73 FER1L4 plays a pivotal role in p73-mediated cell-cycle arrest and apoptosis FER1L4kd augments colorectal cancer cell proliferation in a p73-dependent manner p73-FER1L4 axis sponges miR-1273g-3p and inhibits its oncogenic role
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Affiliation(s)
- Apoorva Uboveja
- Dr.B.R. Ambedkar Centre for Biomedical Research and Delhi School of Public Health, University of Delhi, New Delhi 110007, India
| | - Yatendra Kumar Satija
- Dr.B.R. Ambedkar Centre for Biomedical Research and Delhi School of Public Health, University of Delhi, New Delhi 110007, India
- Corresponding author
| | - Fouzia Siraj
- National Institute of Pathology (ICMR), Safdarjung Hospital Campus, New Delhi 110029, India
| | - Daman Saluja
- Dr.B.R. Ambedkar Centre for Biomedical Research and Delhi School of Public Health, University of Delhi, New Delhi 110007, India
- Corresponding author
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6
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Hobani YH. Focally amplified long non-coding RNA in epithelial cancer as a potential biomarker and therapeutic target. Biomark Med 2021; 15:1797-1808. [PMID: 34821156 DOI: 10.2217/bmm-2021-0455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Deregulation of long non-coding RNAs (lncRNAs) has been implicated in tumorigenesis. FALEC is a lncRNA upregulated in multiple cancer types. FALEC functions as an oncogene through various mechanisms, such as competitively binding miRNAs and regulation of PI3K/AKT, Tp53 and phosphatase and tensin homolog signaling pathways. Pertinent to clinical practice, the use of FALEC as a putative biomarker has been identified. These findings suggested that FALEC might play a pivotal role in human cancers. Further studies are warranted to examine the diagnostic and prognostic performance of FALEC as a noninvasive biomarker in liquid biopsy samples and promote its development to be a clinically utilizable prognostic cancer biomarker and molecular therapeutic target.
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Affiliation(s)
- Yahya H Hobani
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Jazan University, Jazan, 45142, Saudi Arabia
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7
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Chen H, Guan Q, Guo H, Miao L, Zhuo Z. The Genetic Changes of Hepatoblastoma. Front Oncol 2021; 11:690641. [PMID: 34367972 PMCID: PMC8335155 DOI: 10.3389/fonc.2021.690641] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/05/2021] [Indexed: 12/19/2022] Open
Abstract
Hepatoblastoma is the most common malignant liver cancer in childhood. The etiology of hepatoblastoma remains obscure. Hepatoblastoma is closely related to genetic syndromes, hinting that hepatoblastoma is a genetic predisposition disease. However, no precise exposures or genetic events are reported to hepatoblastoma occurrence. During the past decade, significant advances have been made in the understanding of etiology leading to hepatoblastoma, and several important genetic events that appear to be important for the development and progression of this tumor have been identified. Advances in our understanding of the genetic changes that underlie hepatoblastoma may translate into better patient outcomes. Single nucleotide polymorphisms (SNPs) have been generally applied in the research of etiology's exploration, disease treatment, and prognosis assessment. Here, we reviewed and discussed the molecular epidemiology, especially SNPs progresses in hepatoblastoma, to provide references for future studies and promote the study of hepatoblastoma's etiology.
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Affiliation(s)
- Huitong Chen
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qian Guan
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Huiqin Guo
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Lei Miao
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Zhenjian Zhuo
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
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Chen C, Zheng H. LncRNA LINC00944 Promotes Tumorigenesis but Suppresses Akt Phosphorylation in Renal Cell Carcinoma. Front Mol Biosci 2021; 8:697962. [PMID: 34291088 PMCID: PMC8287069 DOI: 10.3389/fmolb.2021.697962] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/25/2021] [Indexed: 11/23/2022] Open
Abstract
Long non-coding RNA (lncRNA) is a kind of RNA that possesses longer than 200 nucleotides and lacks protein coding function. It was recognized as a junk sequence for a long time. Recent studies have found that lncRNAs are actively functioning in almost every aspect of cell biology and involved in a variety of biological functions. LncRNAs are closely related to a variety of human diseases, especially tumors. Recently, lncRNAs are being increasingly reported in renal cancer. In our study, we identified the expression of lncRNA LINC00944 is significantly elevated in renal cell carcinoma (RCC) tissues and cell lines and high LINC00944 expression is significantly correlated with the tumor stage and prognosis of RCC. The knockdown of LINC00944 by CRISPR/dCas9-KRAB in higher expressing 786-O and 769-P RCC cells could significantly decrease proliferation and migration and also promote phosphorylation of Akt compared with the control group. Our study is the first to report the function of lncRNA LINC00944 in RCC. And we provide clinicopathological and experimental evidence that lncRNA LINC00944 acts as an oncogene in RCC, suggesting that targeting lncRNA LINC00944 expression might be a promising therapeutic strategy for the treatment of RCC.
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Affiliation(s)
- Chiheng Chen
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Hanxiong Zheng
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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Daulatabad SV, Srivastava R, Janga SC. Lantern: an integrative repository of functional annotations for lncRNAs in the human genome. BMC Bioinformatics 2021; 22:279. [PMID: 34039271 PMCID: PMC8157669 DOI: 10.1186/s12859-021-04207-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/18/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND With advancements in omics technologies, the range of biological processes where long non-coding RNAs (lncRNAs) are involved, is expanding extensively, thereby generating the need to develop lncRNA annotation resources. Although, there are a plethora of resources for annotating genes, despite the extensive corpus of lncRNA literature, the available resources with lncRNA ontology annotations are rare. RESULTS We present a lncRNA annotation extractor and repository (Lantern), developed using PubMed's abstract retrieval engine and NCBO's recommender annotation system. Lantern's annotations were benchmarked against lncRNAdb's manually curated free text. Benchmarking analysis suggested that Lantern has a recall of 0.62 against lncRNAdb for 182 lncRNAs and precision of 0.8. Additionally, we also annotated lncRNAs with multiple omics annotations, including predicted cis-regulatory TFs, interactions with RBPs, tissue-specific expression profiles, protein co-expression networks, coding potential, sub-cellular localization, and SNPs for ~ 11,000 lncRNAs in the human genome, providing a one-stop dynamic visualization platform. CONCLUSIONS Lantern integrates a novel, accurate semi-automatic ontology annotation engine derived annotations combined with a variety of multi-omics annotations for lncRNAs, to provide a central web resource for dissecting the functional dynamics of long non-coding RNAs and to facilitate future hypothesis-driven experiments. The annotation pipeline and a web resource with current annotations for human lncRNAs are freely available on sysbio.lab.iupui.edu/lantern.
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Affiliation(s)
- Swapna Vidhur Daulatabad
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Informatics and Communications Technology Complex, 535 W Michigan St., IT 475H, Indianapolis, IN, 46202, USA
| | - Rajneesh Srivastava
- Department of Surgery, Indiana Center for Regenerative Medicine and Engineering (ICRME), Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Sarath Chandra Janga
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Informatics and Communications Technology Complex, 535 W Michigan St., IT 475H, Indianapolis, IN, 46202, USA.
- Department of Medical and Molecular Genetics, Medical Research and Library Building, Indiana University School of Medicine, 975 West Walnut Street, Indianapolis, IN, 46202, USA.
- Centre for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN, 46202, USA.
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Li S, Mao L, Zhao F, Yan J, Song G, Luo Q, Li Z. C19orf10 promotes malignant behaviors of human bladder carcinoma cells via regulating the PI3K/AKT and Wnt/β-catenin pathways. J Cancer 2021; 12:4341-4354. [PMID: 34093834 PMCID: PMC8176426 DOI: 10.7150/jca.56993] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/21/2021] [Indexed: 12/16/2022] Open
Abstract
Background: Chromosome 19 open reading frame 10 (C19orf10) is a myocardial repair mediator overexpressed in hepatocellular carcinoma. However, its function and clinical value in bladder cancer (BC) have not been reported. This study aimed to investigate the role of C19orf10 in BC progression and explore underlying mechanisms. Methods: C19orf10 expression in BC tissues and human BC cell lines was assessed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and western blot analysis. The correlation between the C19orf10 protein levels determined by immunohistochemical staining and the clinicopathological characteristics of 192 BC patients was evaluated. BC cell lines SW780, J82 and UMUC-3 were transfected with small interfering RNA (siRNA) targeting C19orf10 or plasmids overexpressing C19orf10. Cell proliferation, migration and invasion were measured by Cell Counting Kit-8, Colony formation, EdU incorporation and Transwell assays. The effect of small hairpin RNA (shRNA)-mediated stable C19orf10 knockdown on tumor formation was assessed in a xenograft mouse model. The expressions of epithelial-mesenchymal transition (EMT) markers, PI3K/AKT and Wnt/β-catenin signaling pathways-related molecules were determined by western blot assay. Results: C19orf10 was significantly upregulated in the BC tissues and a panel of human BC cell lines. High expression of C19orf10 was positively associated with malignant behaviors in BC. C19orf10 knockdown inhibited cell proliferation, migration, and invasion in SW780 and J82 cells, while C19orf10 overexpression in UMUC-3 cells resulted in opposite effects. In addition, C19orf10 silence in SW780 cells suppressed tumor growth in xenograft mice. Moreover, C19orf10 promotes the malignant behaviors and EMT of human bladder carcinoma cells via regulating the PI3K/AKT and Wnt/β-catenin pathways. Conclusion: C19orf10 is overexpressed in BC and functions as an oncogenic driver that promotes cell proliferation and metastasis, and induces EMT of BC cells via mechanisms involving activation of the PI3K/AKT and Wnt/β-catenin pathways. This study provides valuable insight on targeting C19orf10 for BC treatment.
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Affiliation(s)
- Shi Li
- College of Bioengineering, Chongqing University, Chongqing 400030, P. R. China.,Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518000, P.R. China.,Shenzhen Key Laboratory of Genitourinary Tumor, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518000, P.R. China
| | - Longyi Mao
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518000, P.R. China.,Shenzhen Key Laboratory of Genitourinary Tumor, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518000, P.R. China
| | - Fangrong Zhao
- College of Chemical and Biological Engineering, Hunan University of Science and Engineering, Yongzhou, Hunan 425199, P.R. China
| | - Juan Yan
- College of Chemical and Biological Engineering, Hunan University of Science and Engineering, Yongzhou, Hunan 425199, P.R. China
| | - Guanbin Song
- College of Bioengineering, Chongqing University, Chongqing 400030, P. R. China
| | - Qing Luo
- College of Bioengineering, Chongqing University, Chongqing 400030, P. R. China
| | - Zesong Li
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518000, P.R. China.,Shenzhen Key Laboratory of Genitourinary Tumor, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518000, P.R. China
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11
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Liu X, Li X, Li J. Long Non-coding RNA FEZF1-AS1 Promotes Growth and Reduces Apoptosis Through Regulation of miR-363-3p/PAX6 Axis in Retinoblastoma. Biochem Genet 2021; 59:637-651. [PMID: 33432525 PMCID: PMC8096736 DOI: 10.1007/s10528-020-10026-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023]
Abstract
Retinoblastoma is the most common malignancy in children's eyes with high incidence. Long non-coding RNAs (lncRNAs) play important roles in the progression of retinoblastoma. LncRNA FEZF1 antisense RNA 1 (FEZF1-AS1) has been found to stimulate retinoblastoma. However, the mechanism of FEZF1-AS1 underlying progression of retinoblastoma is still unclear. In current study, FEZF1-AS1 was up-regulated in retinoblastoma tissues and cells. FEZF1-AS1 overexpression enhanced retinoblastoma cell viability, promoted cell cycle, and inhibited apoptosis. Conversely, FEZF1-AS1 knockdown reduced cell viability, cycle, and elevated apoptosis. The interaction between FEZF1-AS1 and microRNA-363-3p (miR-363-3p) was confirmed. FEZF1-AS1 down-regulated miR-363-3p and up-regulated PAX6. PAX6 was a target gene of miR-363-3p. EZF1-AS1 promoted retinoblastoma cell viability and suppressed apoptosis via PAX6. Further, we demonstrated that FEZF1-AS1 contribute to tumor formation in vivo. In conclusion, FEZF1-AS1 elevated growth and inhibited apoptosis by regulating miR-363-3p/PAX6 in retinoblastoma, which provide a new target for retinoblastoma treatment.
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Affiliation(s)
- Xiuming Liu
- Department of Ophthalmology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, No. 1, Huanghe Road, Huaiyin District, Huaian, 223300, Jiangsu, China.
| | - Xiaofeng Li
- Department of Ophthalmology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, No. 1, Huanghe Road, Huaiyin District, Huaian, 223300, Jiangsu, China
| | - Jianchang Li
- Department of Ophthalmology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, No. 1, Huanghe Road, Huaiyin District, Huaian, 223300, Jiangsu, China
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Huang J, Hou S, Xu J, Wu J, Yin J. Long non-coding RNA OIP5-AS1 promotes cell proliferation and aerobic glycolysis in gastric cancer through sponging miR-186. Arch Med Sci 2021; 17:1742-1751. [PMID: 34900056 PMCID: PMC8641525 DOI: 10.5114/aoms.2019.87213] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/09/2018] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION Long non-coding RNAs (lncRNAs) play vital roles in tumour initiation and progression. LncRNA OIP5-AS1 is a potential oncogene in many types of human malignancies, but its biological functions in gastric cancer (GC) remain to be further elucidated. MATERIAL AND METHODS The expression levels of OIP5-AS1 and miR-186 in GC tissues and cell lines were detected by RT-qPCR analysis. CCK-8 assay and colony formation assay were performed to investigate the proliferation of GC cells in vitro, and a nude mouse tumour model was established to validate the role of OIP5-AS1 in GC tumorigenesis in vivo. The glucose consumption and lactate production of GC cells were detected by ELISA assay. Interaction between OIP5-AS1 and miR-186 was determined using dual luciferase reporter assay. RESULTS The results demonstrated that OIP5-AS1 was upregulated in GC tissues and cell lines and that its high expression was notably correlated with aggressive clinicopathological features of GC patients. Functionally, knockdown of OIP5-AS1 inhibited GC cell proliferation and enhanced cell apoptosis in vitro, and inhibited GC xenograft growth in vivo. In addition, knockdown of OIP5-AS1 reduced the glucose consumption and lactate production in GC cells. In particular, OIP5-AS1 may function as a ceRNA for miR-186, and inhibition of miR-186 blocks the effects of OIP5-AS1 knockdown on aerobic glycolysis in GC cells. CONCLUSIONS Accordingly, our findings suggested that the OIP5-AS1/miR-186 axis might be considered as a potential therapeutic target for GC patients.
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Affiliation(s)
- Jiaobao Huang
- Department of General Surgery, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Shuangshuang Hou
- Department of General Surgery, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Jian Xu
- Department of General Surgery, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Ju Wu
- Department of General Surgery, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Jiajun Yin
- Department of General Surgery, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
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Shirvani Farsani Z, Zahirodin A, Ghaderian SMH, Shams J, Naghavi Gargari B. The role of long non-coding RNA MALAT1 in patients with bipolar disorder. Metab Brain Dis 2020; 35:1077-1083. [PMID: 32458337 DOI: 10.1007/s11011-020-00580-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/11/2020] [Indexed: 01/08/2023]
Abstract
Bipolar disorders are known as chronic, recurrent, and heterogenic diseases. Regarding, diagnosis and treatment of them are very complex. The molecular mechanism and pathophysiology of bipolar disorder are slightly known. Accordingly, long noncoding RNAs are considered as one of the main factors that are dysfunctional in many diseases such as the nervous system diseases. Hence, we aim to investigate the expression of two long non coding RNAs, MALAT1 and UCA1, in patients in bipolar disorder. The levels of MALAT1 and UCA1 lncRNA were evaluated in peripheral blood mononuclear cells (PBMCs) of 50 bipolar patients and 50 healthy controls with real-time PCR. Also, ROC curve analysis and correlation analysis were performed between the gene expression and some clinical features of bipolar individuals. The significant decline of MALAT1 expression level was found in the patients compared to controls; but no significant difference was observed in the UCA1 expression level between the patients and controls. Furthermore, computational analysis of CpG Islands and miRNAs binding sites on LncRNAs, MALAT1, and UCA1 was conducted. Also, The ROC curve area (AUC) of MALAT1 was 0.80. The current results suggest that the expression level of MALAT1 could serve as a potential diagnostic biomarker for bipolar patients.
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Affiliation(s)
- Zeinab Shirvani Farsani
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University G.C, Tehran, IR, Iran
| | - Alireza Zahirodin
- Behavioral Science Research Center, Shahid Beheshti University of Medical Sciences, Tehran, IR, Iran
| | | | - Jamal Shams
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, IR, Iran
| | - Bahar Naghavi Gargari
- Department of Basic Sciences, Faculty of Nursing & Midwifery, Shahid Beheshti University of Medical Sciences, IR, Tehran, Iran.
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lncRNA FEZF1‑AS1 promotes migration, invasion and epithelial‑mesenchymal transition of retinoblastoma cells by targeting miR‑1236‑3p. Mol Med Rep 2020; 22:3635-3644. [PMID: 32901841 PMCID: PMC7533456 DOI: 10.3892/mmr.2020.11478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/18/2020] [Indexed: 12/15/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) and microRNAs (miRs) have been reported to regulate disease progression in numerous types of disease, including retinoblastoma (Rb). Therefore, the present study aimed to investigate the effects of the lncRNA FEZ family zinc finger 1 antisense RNA 1 (FEZF1-AS1) on Rb and to determine its possible mechanism of action. Reverse transcription-quantitative PCR and western blot analysis were conducted to detect the gene or protein expression. Cell Counting Kit-8, wound healing and transwell invasion assays were performed to estimate the capabilities of cell viability, invasion and migration. The potential association between FEZF1-AS1 and miR-1236-3p in Y79 cells was measured via dual-luciferase reporter assay. The results of the present study revealed that the levels of FEZF1-AS1 were significantly upregulated in different Rb cell lines, with the most prominent upregulation observed in Y79 cells. In addition, the cell viability, invasive and migratory abilities, and the ability to undergo epithelial-mesenchymal transition (EMT), were significantly inhibited following the transfection of short hairpin RNA (shRNA)-FEZF1-AS1 into Y79 cells. Further experimental validation confirmed that miR-1236-3p may be a direct target of FEZF1-AS1. Notably, the miR-1236-3p inhibitor was discovered to reverse the inhibitory effects of shRNA-FEZF1-AS1 on cell viability, invasion, migration and EMT. In conclusion, the findings of the present study suggested that lncRNA-FEZF1-AS1 may promote the viability, migration, invasion and EMT of Rb cells by modulating miR-1236-3p.
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Wang L, Xing Q, Feng T, He M, Yu W, Chen H. SNP rs710886 A>G in long noncoding RNA PCAT1 is associated with the risk of endometriosis by modulating expression of multiple stemness‐related genes via microRNA‐145 signaling pathway. J Cell Biochem 2019; 121:1703-1715. [PMID: 31595574 DOI: 10.1002/jcb.29406] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/05/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Liming Wang
- Department of Gynecology, Hubei Provincial Maternal and Child Health Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Qi Xing
- Department of Gynecology, Hubei Provincial Maternal and Child Health Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Tongfu Feng
- Department of Gynecology, Hubei Provincial Maternal and Child Health Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Ming He
- Department of Gynecology, Hubei Provincial Maternal and Child Health Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Weixu Yu
- Department of Gynecology, Hubei Provincial Maternal and Child Health Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Hui Chen
- Department of Gynecology and Obstetrics, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
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Lyu K, Xu Y, Yue H, Li Y, Zhao J, Chen L, Wu J, Zhu X, Chai L, Li C, Wen W, Lei W. Long Noncoding RNA GAS5 Acts As A Tumor Suppressor In Laryngeal Squamous Cell Carcinoma Via miR-21. Cancer Manag Res 2019; 11:8487-8498. [PMID: 31572003 PMCID: PMC6756574 DOI: 10.2147/cmar.s213690] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 09/04/2019] [Indexed: 01/01/2023] Open
Abstract
Purpose Long noncoding RNAs (lncRNAs) have been identified as an important class of noncoding RNAs that are deeply involved in multiple biological processes in tumorigenesis. This study is to investigate the critical roles and biological function of lncRNA growth arrest-specific 5 (GAS5) in tumorigenesis of laryngeal squamous cell carcinoma (LSCC). Patients and methods A total of 59 samples of LSCC and paired adjacent tissue, as well as corresponding clinicopathological information were collected. GAS5 expression in both LSCC tissues and human SUN1076 and SNU899 cell lines were analyzed by Real-time quantitative RT-PCR method. Ectopic expression of GAS5 by vector transfection in LSCC cell lines and followed by in vitro experiments was to investigate the critical roles and function of GAS5 in LSCC. Cell Counting Kit 8 (CCK8) assay and PE/7AAD Annexin V Apoptosis analysis was to evaluate cell proliferation ability and cell apoptosis. Co-transfection of GAS5 and miR-21 was to explore the interaction between GAS5 and miR-21 in LSCC. BAX and CDK6 protein level were analyzed by western blot method. Results This study demonstrated that GAS5 was significantly downregulated in LSCC tissue and human LSCC cell lines. GAS5 levels were correlated with the clinicopathological features of LSCC patients. In addition, the ectopic expression of GAS5 significantly inhibited cell proliferation and promoted apoptosis. Co-expression analyses indicated that GAS5 is negatively correlated with miR-21 in LSCC tissues. Overexpression of miR-21 eliminated GAS5-mediated cell apoptosis and proliferation suppression. Furthermore, GAS5, which upregulated BAX mRNA expression and downregulated CDK6 mRNA expression, was reversed by ectopic expression of miR-21. Conclusion GAS5 suppresses LSCC progression through the negative regulation of miR-21 and its targets involved in cell proliferation and apoptosis, indicating that GAS5 may serve as a biomarker and potential target for LSCC therapy.
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Affiliation(s)
- Kexing Lyu
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Yang Xu
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Huijun Yue
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Yun Li
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Jing Zhao
- Department of Otolaryngology, The Third Hospital of Heibei Medical University, Shijiazhuang, People's Republic of China
| | - Lin Chen
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Jianhui Wu
- Department of Otolaryngology, Meizhou People's Hospital, Meizhou, People's Republic of China
| | - Xiaolin Zhu
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Liping Chai
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Chunwei Li
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Weiping Wen
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Wenbin Lei
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
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Siddique H, Al-Ghafari A, Choudhry H, AlTurki S, Alshaibi H, Al Doghaither H, Alsufiani H. Long Noncoding RNAs as Prognostic Markers for Colorectal Cancer in Saudi Patients. Genet Test Mol Biomarkers 2019; 23:509-514. [DOI: 10.1089/gtmb.2018.0308] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Halima Siddique
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ayat Al-Ghafari
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Experimental Biochemistry Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Cancer and Mutagenesis Unit, and King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hani Choudhry
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Cancer and Mutagenesis Unit, and King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Innovation in Personalized Medicine, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Suzan AlTurki
- University Medical Services Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Huda Alshaibi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Huda Al Doghaither
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hadeil Alsufiani
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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Vural H, Kaya M. Prediction of new potential associations between LncRNAs and environmental factors based on KATZ measure. Comput Biol Med 2018; 102:120-125. [PMID: 30268976 DOI: 10.1016/j.compbiomed.2018.09.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 09/24/2018] [Accepted: 09/24/2018] [Indexed: 12/19/2022]
Abstract
The associations between genetic and environmental factors (EFs) are significant to understand the development and progression of many complex human diseases. There have been many research studies concerning genetic factors (protein-coding genes, microRNAs) and EFs but limited research addressing the associations between long noncoding RNAs (lncRNAs) and EFs. LncRNAs of more than 200 nucleotides are an important class of non-coding transcripts and are effective in the organization of gene expressions and, therefore, on the formation of diseases. Environmental factors can alter the expression patterns of some lncRNAs, so a thorough understanding of the associations between lncRNAs and environmental factors will contribute to the understanding of the mechanisms of many complex diseases at the molecular level. In this study, we have developed a model based on the KATZ measure to find potential new associations between lncRNAs and EFs by using the DLREFD database, which contains proven associations between lncRNAs and EFs. The KATZ measure and Gaussian interaction profile kernel similarity were used to predict new potential associations between lncRNAs and EFs. The AUC results obtained by global leave-one-out cross-validation and 2-fold and 5-fold cross-validations were 0.855, 0.827, 0.838, respectively. These results show that our model can predict new potential associations between lncRNAs and EFs with high reliability. Also, the results obtained in case studies demonstrate the effectiveness of our model.
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Affiliation(s)
- Hüseyin Vural
- Department of Computer Technologies, Adıyaman University, Adıyaman, Turkey.
| | - Mehmet Kaya
- Department of Computer Engineering, Fırat University, Elazığ, Turkey.
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Liu Y, Liu H, Zhang D. Identification of novel long non-coding RNA in diffuse intrinsic pontine gliomas by expression profile analysis. Oncol Lett 2018; 16:6401-6406. [PMID: 30405776 PMCID: PMC6202498 DOI: 10.3892/ol.2018.9461] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 09/04/2018] [Indexed: 12/19/2022] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG) is one of the most devastating types of pediatric cancer. Accumulating evidence suggests that the dysregulated expression of long non-coding (lnc)-RNAs is associated with various pathologies of the CNS. However, the expression patterns and prognostic roles of lncRNAs in DIPG have not yet been systematically determined. In the present study, lncRNA expression profiles were obtained from the Gene Expression Omnibus (GEO) database using the lncRNA-mining approach and a differential expression analysis for lncRNAs was performed between DIPG and low-grade brainstem glioma and DIPG and normal pediatric brainstem tissue. Using a two-tailed t-test, 58 and 197 lncRNAs were found to be significantly deferentially expressed (Fold change >2 or <0.5, FDR adjusted P<0.05). To identify the prognostic value of these 255 differentially expressed lncRNAs, univariate and multivariate Cox proportional hazards regression analysis were performed and a 9-lncRNA signature as a potential biomarker for predicting the prognosis of DIPG was constructed. Kaplan-Meier curve analysis showed that patients in the high-risk group exhibited a reduced survival time compared with patients in the low-risk group (median survival of 230 vs. 460 days, log-rank test P<0.001). Moreover, this lncRNA-signature could be used as an independent prognostic marker for DIPG patient survival. The present study provided novel candidates for the investigation of potential diagnostic or prognostic biomarkers and/or therapeutic targets of DIPG, as well as a novel insight into the underlying mechanisms of DIPG.
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Affiliation(s)
- Yuehui Liu
- Department of Neurology, The Affiliated Hospital of Inner Mongolia University for The Nationalities, Tongliao, Inner Mongolia 028007, P.R. China
| | - Haiping Liu
- College of Life Science, Inner Mongolia University for The Nationalities, Tongliao, Inner Mongolia 028000, P.R. China
| | - Dongwei Zhang
- Department of Neurology, The Affiliated Hospital of Inner Mongolia University for The Nationalities, Tongliao, Inner Mongolia 028007, P.R. China
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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: 2.8] [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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Liu T, Han Z, Li H, Zhu Y, Sun Z, Zhu A. LncRNA DLEU1 contributes to colorectal cancer progression via activation of KPNA3. Mol Cancer 2018; 17:118. [PMID: 30098595 PMCID: PMC6087004 DOI: 10.1186/s12943-018-0873-2] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/02/2018] [Indexed: 01/05/2023] Open
Abstract
Background Accumulating evidences show that long noncoding RNAs (lncRNA) play essential roles in the development and progression of various malignancies. However, their functions remains poorly understood and many lncRNAs have not been defined in colorectal cancer (CRC). In this study, we investigated the role of DLEU1 in CRC. Methods Quantitative real-time PCR was used to detect the expression of DLEU1 and survival analysis was adopted to explore the association between DLEU1 expression and the prognosis of CRC patients. CRC cells were stably transfected with lentivirus approach and cell proliferation, migration, invasion and cell apoptosis, as well as tumorigenesis in nude mice were performed to assess the effects of DLEU1 in BCa. Biotin-coupled probe pull down assay, RNA immunoprecipitation and Fluorescence in situ hybridization assays were conducted to confirm the relationship between DLEU1 and SMARCA1. Results Here we revealed that DLEU1 was crucial for activation of KPNA3 by recruiting SMARCA1, an essential subunit of the NURF chromatin remodeling complex, in CRC. DLEU1 was indispensible for the deposition of SMARCA1 at the promoter of KPNA3 gene. Increased expression of DLEU1 and KPNA3 was observed in human CRC tissues. And higher expression of DLEU1 or KPNA3 in patients indicates lower survival rate and poorer prognosis. DLEU1 knockdown remarkably inhibited CRC cell proliferation, migration and invasion in vitro and in vivo while overexpressing KPNA3 in the meantime reversed it. Conclusions Our results identify DLEU1 as a key regulator by a novel DLEU1/SMARCA1/KPNA3 axis in CRC development and progression, which may provide a potential biomarker and therapeutic target for the management of CRC. Electronic supplementary material The online version of this article (10.1186/s12943-018-0873-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tianyou Liu
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, #23 Youzheng Street, Harbin, 150001, Heilongjiang Province, China.
| | - Zhiyang Han
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, #23 Youzheng Street, Harbin, 150001, Heilongjiang Province, China
| | - Huanyu Li
- Department of General Surgery, Mulan Country People's Hospital, Harbin, 150001, China
| | - Yuekun Zhu
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, #23 Youzheng Street, Harbin, 150001, Heilongjiang Province, China
| | - Ziquan Sun
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, #23 Youzheng Street, Harbin, 150001, Heilongjiang Province, China
| | - Anlong Zhu
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, #23 Youzheng Street, Harbin, 150001, Heilongjiang Province, China
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22
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Li Q, Liu R, Zhao H, Di R, Lu Z, Liu E, Wang Y, Chu M, Wei C. Identification and Characterization of Long Noncoding RNAs in Ovine Skeletal Muscle. Animals (Basel) 2018; 8:ani8070127. [PMID: 30041440 PMCID: PMC6071021 DOI: 10.3390/ani8070127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 01/06/2023] Open
Abstract
Simple Summary LncRNAs may play important role in many biological processes. The aims of this research were to identify potential lncRNAs active in skeletal muscle of the Texel and Ujumqin sheep and investigate their functions. Overall, 2002 lncRNA transcripts were found, some of which may be related to muscle development. The findings obtained here should promote understanding of the regulatory functions of lncRNAs in ovine muscle development and potentially also in other mammals. Abstract Long noncoding RNAs (lncRNAs) are increasingly being recognized as key regulators in many cellular processes. However, few reports of them in livestock have been published. Here, we describe the identification and characterization of lncRNAs in ovine skeletal muscle. Eight libraries were constructed from the gastrocnemius muscle of fetal (days 85 and 120), newborn and adult Texel and Ujumqin sheep. The 2002 identified transcripts shared some characteristics, such as their number of exons, length and distribution. We also identified some coding genes near these lncRNA transcripts, which are particularly associated with transcriptional regulation- and development-related processes, suggesting that the lncRNAs are associated with muscle development. In addition, in pairwise comparisons between the libraries of the same stage in different breeds, a total of 967 transcripts were differentially expressed but just 15 differentially expressed lncRNAs were common to all stages. Among them, we found that TCONS_00013201 exhibited higher expression in Ujumqin samples, while TCONS_00006187 and TCONS_00083104 were higher in Texel samples. Moreover, TCONS_00044801, TCONS_00008482 and TCONS_00102859 were almost completely absent from Ujumqin samples. Our results suggest that differences in the expression of these lncRNAs may be associated with the muscular differences observed between Texel and Ujumqin sheep breeds.
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Affiliation(s)
- Qing Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Ruizao Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Huijing Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Ran Di
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Zengkui Lu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- College of Animal Science and Technology, Gansu Agriculture University, Lanzhou 730070, China.
| | - Enmin Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Yuqin Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China.
| | - Mingxing Chu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Caihong Wei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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23
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Li H, Yang J, Jiang R, Wei X, Song C, Huang Y, Lan X, Lei C, Ma Y, Hu L, Chen H. Long Non-coding RNA Profiling Reveals an Abundant MDNCR that Promotes Differentiation of Myoblasts by Sponging miR-133a. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 12:610-625. [PMID: 30195797 PMCID: PMC6078111 DOI: 10.1016/j.omtn.2018.07.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/29/2018] [Accepted: 07/03/2018] [Indexed: 12/31/2022]
Abstract
Muscle development is regulated by a series of complicate processes, and non-coding RNAs (ncRNAs) such as lncRNA have been reported to play important roles in regulating skeletal myogenesis and diseases. Here we profile the expression of lncRNA in cattle skeletal muscle tissue from fetus and adult developmental stages and detect 13,580 lncRNA candidates. Many of these lncRNAs are differentially expressed between two developmental stages. We further characterize one abundant lncRNA with the highest expression level of all downregulated lncRNAs, which we named muscle differentiation-associated lncRNA (MDNCR). Via luciferase screening, RNA binding protein immunoprecipitation (RIP), and RNA pull-down assays, MDNCR was observed to directly bind to miR-133a with 32 potential binding sites. GosB was identified as a target of miR-133a by luciferase activity, quantitative real-time qPCR, and western blotting assays. Overexpression of MDNCR increased the expression of GosB, whereas this effect was abolished by miR-133a. We found that MDNCR promotes myoblast differentiation and inhibits cell proliferation by sponging miR-133a. These results demonstrate that MDNCR binding miR-133a promotes cell differentiation by targeting GosB in cattle primary myoblasts.
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Affiliation(s)
- Hui Li
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Jiameng Yang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Rui Jiang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Xuefeng Wei
- College of Life Sciences, Xinyang Normal University, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan 464000, China
| | - Chengchuang Song
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Yongzhen Huang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Xianyong Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Chuzhao Lei
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Yun Ma
- College of Life Sciences, Xinyang Normal University, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan 464000, China
| | - Linyong Hu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810001, China
| | - Hong Chen
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China.
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24
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Tian L, He Y, Zhang H, Wu Z, Li D, Zheng C. Comprehensive analysis of differentially expressed profiles of lncRNAs and mRNAs reveals ceRNA networks in the transformation of diffuse large B-cell lymphoma. Oncol Lett 2018; 16:882-890. [PMID: 29963159 PMCID: PMC6019896 DOI: 10.3892/ol.2018.8722] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 11/16/2017] [Indexed: 12/02/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is one of the malignancies with a high mortality rate. The molecular mechanisms involved in transformation of DLBCL remain unclear. Therefore, it is critically important to investigate the biological mechanisms of DLBCL. Accumulating evidence indicates that long non-coding RNAs (lncRNAs) serve key functions in tumorigenesis, cancer progression and metastasis. Compared with follicular lymphoma (FL), a total of 123 upregulated lncRNAs and 192 downregulated lncRNAs in DLBCL were identified. Subsequently, a specific DLBCL-associated competing endogenous RNA (ceRNA) network and a specific FL-associated ceRNA network was constructed. Gene Oncology and Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that differentially expressed lncRNAs served key functions in regulating signal transduction, transcription, cell adhesion, development and protein amino acid phosphorylation. Furthermore, the molecular functions of PRKCQ antisense RNA 1, HLA complex P5, OIP5 antisense RNA 1, growth arrest specific 5 and taurine upregulated 1 were investigated, and it was revealed that these lncRNAs served important functions in regulating a series of biological processes, including anti-apoptosis, cell cycle, DNA repair, response to oxidative stress and transcription. The present study may provide a potential novel therapeutic and prognostic target for the treatment of DLBCL.
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Affiliation(s)
- Lu Tian
- Department of Vascular Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Yangyan He
- Department of Vascular Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Hongkun Zhang
- Department of Vascular Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Ziheng Wu
- Department of Vascular Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Donglin Li
- Department of Vascular Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Chengfei Zheng
- Department of Vascular Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
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25
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Yang J, Li C, Zhang L, Wang X. Extracellular Vesicles as Carriers of Non-coding RNAs in Liver Diseases. Front Pharmacol 2018; 9:415. [PMID: 29740327 PMCID: PMC5928552 DOI: 10.3389/fphar.2018.00415] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/10/2018] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicles (EVs) are small membranous vesicles secreted from normal, diseased, and transformed cells in vitro and in vivo. EVs have been found to play a critical role in cell-to-cell communication by transferring non-coding RNAs (ncRNAs) including microRNAs (miRNAs), long ncRNAs (lncRNAs) and so on. Emerging evidence shows that transferring biological information through EVs to neighboring cells in intercellular communication not only keep physiological functions, but also participate in the pathogenesis of liver diseases. Liver diseases often promote release of EVs and/or in different cargo sorting into these EVs. Either of these modifications can promote disease pathogenesis. Given this fact, EV-associated ncRNAs, such as miR-192, miR-122 and lncRNA-ROR and so on, can serve as new diagnostic biomarkers and new therapeutic targets for liver disease, because altered EV-associated ncRNAs may reflect the underlying liver disease condition. In this review, we focus on understanding the emerging role of EV-associated ncRNAs in viral hepatitis, liver fibrosis, alcoholic hepatitis (AH), non-alcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC) and discuss their utility in biomarker discovery and therapeutics. A better understanding of this multifaceted pattern of communication between different type cells in liver may contribute to developing novel approaches for personalized diagnostics and therapeutics.
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Affiliation(s)
- Junfa Yang
- School of Pharmacy, Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Hefei, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Anhui Medical University, Hefei, China
| | - Changyao Li
- School of Pharmacy, Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Hefei, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Anhui Medical University, Hefei, China
| | - Lei Zhang
- School of Pharmacy, Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Hefei, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Anhui Medical University, Hefei, China
| | - Xiao Wang
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
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26
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Zhao NN, Wang C, Lai CC, Cheng SJ, Yan J, Hong ZX, Yu LX, Zhu ZY, Zhang PR, Wang ZH, Wang XL, Zhang SG, Yang PH. Downregulation of BRAF-activated non-protein coding RNA in patients with hepatitis B virus-associated hepatocellular carcinoma. Oncol Lett 2018; 15:7794-7798. [PMID: 29725471 PMCID: PMC5920385 DOI: 10.3892/ol.2018.8327] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 02/03/2017] [Indexed: 02/06/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been investigated as a novel class of regulators of cellular processes, including cell growth, apoptosis and carcinogenesis. lncRNA BRAF-activated non-protein coding RNA (BANCR) has recently been revealed to be involved in tumorigenesis of numerous types of cancer, including papillary thyroid carcinoma, melanoma, non-small cell lung cancer and colorectal cancer. However, the expression profiles and biological relevance of lncRNA BANCR in hepatocellular carcinoma (HCC) has not yet been reported. In the present study, the expression level of BANCR in tumor tissues and para-cancerous tissues was determined by reverse transcription-quantitative polymerase chain reaction in patients with hepatitis B virus (HBV)-associated HCC, and its association with clinicopathological characteristics of patients was analyzed. The results demonstrated that the expression level of BANCR was significantly reduced in tumor tissues in comparison with in para-cancerous tissues (P<0.001). Furthermore, the present study demonstrated that BANCR expression level was closely associated with serum α-fetoprotein levels (P<0.01) and HCC tumor number (P<0.05). To the best of our knowledge, these results revealed for the first time that BANCR downregulated in patients with HBV-associated HCC and BANCR expression level may be a potential valuable diagnosis and therapeutic biomarker in HCC.
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Affiliation(s)
- Na-Na Zhao
- Department of Hepatobiliary Surgery, Beijing 302 Hospital, Beijing 100039, P.R. China
| | - Cheng Wang
- Department of Orthopedics, Beijing 307 Hospital Affiliated to Academy of Medical Sciences, Beijing 100071, P.R. China
| | - Cheng-Cai Lai
- Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, P.R. China
| | - Si-Jie Cheng
- Department of Hepatobiliary Surgery, Beijing 302 Hospital, Beijing 100039, P.R. China
| | - Jin Yan
- Department of Hepatobiliary Surgery, Beijing 302 Hospital, Beijing 100039, P.R. China
| | - Zhi-Xian Hong
- Department of Hepatobiliary Surgery, Beijing 302 Hospital, Beijing 100039, P.R. China
| | - Lin-Xiang Yu
- Department of Hepatobiliary Surgery, Beijing 302 Hospital, Beijing 100039, P.R. China
| | - Zhen-Yu Zhu
- Department of Hepatobiliary Surgery, Beijing 302 Hospital, Beijing 100039, P.R. China
| | - Pei-Rui Zhang
- Department of Hepatobiliary Surgery, Beijing 302 Hospital, Beijing 100039, P.R. China
| | - Zhao-Hai Wang
- Department of Hepatobiliary Surgery, Beijing 302 Hospital, Beijing 100039, P.R. China
| | - Xi-Liang Wang
- Department of Orthopedics, Beijing 307 Hospital Affiliated to Academy of Medical Sciences, Beijing 100071, P.R. China
| | - Shao-Geng Zhang
- Department of Hepatobiliary Surgery, Beijing 302 Hospital, Beijing 100039, P.R. China
| | - Peng-Hui Yang
- Department of Hepatobiliary Surgery, Beijing 302 Hospital, Beijing 100039, P.R. China.,Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, P.R. China
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27
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Cipriano A, Ballarino M. The Ever-Evolving Concept of the Gene: The Use of RNA/Protein Experimental Techniques to Understand Genome Functions. Front Mol Biosci 2018; 5:20. [PMID: 29560353 PMCID: PMC5845540 DOI: 10.3389/fmolb.2018.00020] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 02/20/2018] [Indexed: 12/12/2022] Open
Abstract
The completion of the human genome sequence together with advances in sequencing technologies have shifted the paradigm of the genome, as composed of discrete and hereditable coding entities, and have shown the abundance of functional noncoding DNA. This part of the genome, previously dismissed as “junk” DNA, increases proportionally with organismal complexity and contributes to gene regulation beyond the boundaries of known protein-coding genes. Different classes of functionally relevant nonprotein-coding RNAs are transcribed from noncoding DNA sequences. Among them are the long noncoding RNAs (lncRNAs), which are thought to participate in the basal regulation of protein-coding genes at both transcriptional and post-transcriptional levels. Although knowledge of this field is still limited, the ability of lncRNAs to localize in different cellular compartments, to fold into specific secondary structures and to interact with different molecules (RNA or proteins) endows them with multiple regulatory mechanisms. It is becoming evident that lncRNAs may play a crucial role in most biological processes such as the control of development, differentiation and cell growth. This review places the evolution of the concept of the gene in its historical context, from Darwin's hypothetical mechanism of heredity to the post-genomic era. We discuss how the original idea of protein-coding genes as unique determinants of phenotypic traits has been reconsidered in light of the existence of noncoding RNAs. We summarize the technological developments which have been made in the genome-wide identification and study of lncRNAs and emphasize the methodologies that have aided our understanding of the complexity of lncRNA-protein interactions in recent years.
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Affiliation(s)
- Andrea Cipriano
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Monica Ballarino
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
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28
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Lian Y, Li Z, Fan Y, Huang Q, Chen J, Liu W, Xiao C, Xu H. The lncRNA-HOXA-AS2/EZH2/LSD1 oncogene complex promotes cell proliferation in pancreatic cancer. Am J Transl Res 2017; 9:5496-5506. [PMID: 29312501 PMCID: PMC5752899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 12/08/2017] [Indexed: 06/07/2023]
Abstract
Emerging evidence have indicated that long non-coding RNAs (lncRNAs) play crucial roles in cancer development and progression. Previous studies have suggested that lncRNA-HOXA cluster antisense RNA 2 (HOXA-AS2) is involved in tumorigenesis of several cancers. However, little is known about the alteration and biological functions of HOXA-AS2 in pancreatic cancer (PC). The purpose of this study is to identify the role of HOXA-AS2 in PC. Here, we provided evidence that lncRNA HOXA-AS2 was up-regulated in PC tissues. In addition, Loss-of-function experiments revealed that HOXA-AS2 knockdown effectively suppressed proliferation by blocking the cell cycle transition and caused apoptosis of PC cells in vitro and in vivo. Mechanistically, we found that HOXA-AS2 directly interacted with enhancer of zeste homolog 2 (EZH2) and lysine specific demethylase 1 (LSD1), which promoted PC cell growth ability. Collectively, our findings demonstrated that lncRNA-HOXA-AS2/EZH2/LSD1 complex may function as an oncogene in PC cell proliferation, and also provides a potential therapy target for PC.
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Affiliation(s)
- Yifan Lian
- Department of Gastroenterology, Zhongshan Hospital, Xiamen UniversityXiamen, People’s Republic of China
| | - Zhaohua Li
- Department of Gastroenterology, Zhongshan Hospital, Xiamen UniversityXiamen, People’s Republic of China
| | - Yanyun Fan
- Department of Gastroenterology, Zhongshan Hospital, Xiamen UniversityXiamen, People’s Republic of China
| | - Qingwen Huang
- Department of Gastroenterology, Zhongshan Hospital, Xiamen UniversityXiamen, People’s Republic of China
| | - Jianmin Chen
- Department of Gastroenterology, Zhongshan Hospital, Xiamen UniversityXiamen, People’s Republic of China
| | - Wenming Liu
- Department of Gastroenterology, Zhongshan Hospital, Xiamen UniversityXiamen, People’s Republic of China
| | - Chuanxing Xiao
- Department of Gastroenterology, Zhongshan Hospital, Xiamen UniversityXiamen, People’s Republic of China
- Institute for Microbial Ecology, Xiamen UniversityXiamen, People’s Republic of China
| | - Hongzhi Xu
- Department of Gastroenterology, Zhongshan Hospital, Xiamen UniversityXiamen, People’s Republic of China
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29
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Clinicopathological and Prognostic Role of Long Noncoding RNA Linc00152 in Various Human Neoplasms: Evidence from Meta-Analysis. BIOMED RESEARCH INTERNATIONAL 2017; 2017:6010721. [PMID: 29285514 PMCID: PMC5733223 DOI: 10.1155/2017/6010721] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 09/24/2017] [Accepted: 10/01/2017] [Indexed: 02/06/2023]
Abstract
Recent researches have demonstrated that long noncoding RNA linc00152 was aberrantly upregulated in multiple tumor types. High expression of linc00152 was associated with poor outcomes in cancer patients. Therefore, we conducted this meta-analysis to evaluate its potential value as a prognostic predictor in various human neoplasms. Eligible studies were searched through several electronic databases including PubMed, Embase, Web of Science, and the Cochrane Library. Eight original studies including 752 cancer patients were ultimately enrolled. Statistical analysis suggested that overexpression of linc00152 was significantly correlated with unfavorable overall survival (OS) (HR = 2.05, 95% CI: 1.59–2.64) and disease-free/progression-free survival (DFS/PFS) (HR = 3.52, 95% CI: 1.82–6.79) in cancer patients. In addition, a significant correlation was observed between aberrant linc000152 expression and lymph node metastasis (LNM) (OR = 2.49, 95% CI: 1.57–3.94) but not in vessel invasion (VI) (OR = 1.02, 95% CI: 0.54–1.93) and distant metastasis (DM) (OR = 0.600, 95% CI: 0.213–1.689). Our meta-analysis demonstrated that high linc00152 expression significantly predicted inferior OS and DFS/PFS in multiple neoplasms, as well as advanced LNM and VI. Linc00152 may serve as a potential indicator in predicting poor outcomes and metastases of diverse cancers.
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30
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余 淦, 欧 正, 陶 启, 万 国, 陆 宗, 郎 斌. [Role of lncRNA PTENP1 in tumorigenesis and progression of bladder cancer and the molecular mechanism]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2017; 37:1494-1500. [PMID: 29180330 PMCID: PMC6779653 DOI: 10.3969/j.issn.1673-4254.2017.11.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 06/07/2023]
Abstract
OBJECTIVE To explore the molecular mechanism underlying the biological function of lncRNA PTENP1 in bladder cancer. METHODS Expressions of PTENP1, PTEN and miR-17 were examined by quantitative reverse transcriptase PCR (qRT-PCR) in 12 bladder cancer tissues. The expression of PTEN was examined by Western blotting in bladder cancer cell lines T24 and 5637 overexpressing PTENP1. Luciferase reporter assay was performed to confirm the targeting of miR-17 to PTENP1 and PTEN. T24 and 5637 cell lines with stable overexpression of PTENP1 and mir-17 were used to investigate effect of PTNE and miR-17 on the function of PTENP1 in bladder cancer. RESULTS The expression of miR-17 was up-regulated and PTENP1 and PTEN were down-regulated in bladder cancer tissues, where a positive correlation was found between PTENP1 and PTEN expressions and a negative correlation between PTENP1 and miR-17 (P<0.05). Overexpression of PTENP1 in bladder cancer cell lines T24 and 5637 obviously enhanced the expression of PTEN protein. miR-17 was found to target both PTENP1 and PTEN and promote the growth of bladder cancer. miR-17 could partially restore the tumor-suppressing activity of PTENP1 in bladder cancer. CONCLUSION By binding with miR-17, lncRNA PTENP1 functions as a PTEN competing endogenous RNA (ceRNA) to suppress the progression of bladder cancer.
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Affiliation(s)
- 淦 余
- 华中科技大学同济医学院附属同济医院泌尿外科,湖北 武汉 430030Department of Urology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - 正岳 欧
- 澳门理工学院高等卫生学校,澳门 999078School of Health Sciences, Macao Polytechnic Institute, Macao 999078, China
| | - 启业 陶
- 澳门理工学院高等卫生学校,澳门 999078School of Health Sciences, Macao Polytechnic Institute, Macao 999078, China
| | - 国悦 万
- 澳门理工学院高等卫生学校,澳门 999078School of Health Sciences, Macao Polytechnic Institute, Macao 999078, China
| | - 宗浩 陆
- 澳门理工学院高等卫生学校,澳门 999078School of Health Sciences, Macao Polytechnic Institute, Macao 999078, China
| | - 斌 郎
- 澳门理工学院高等卫生学校,澳门 999078School of Health Sciences, Macao Polytechnic Institute, Macao 999078, China
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31
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余 淦, 欧 正, 陶 启, 万 国, 陆 宗, 郎 斌. [Role of lncRNA PTENP1 in tumorigenesis and progression of bladder cancer and the molecular mechanism]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2017; 37:1494-1500. [PMID: 29180330 PMCID: PMC6779653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 08/03/2024]
Abstract
OBJECTIVE To explore the molecular mechanism underlying the biological function of lncRNA PTENP1 in bladder cancer. METHODS Expressions of PTENP1, PTEN and miR-17 were examined by quantitative reverse transcriptase PCR (qRT-PCR) in 12 bladder cancer tissues. The expression of PTEN was examined by Western blotting in bladder cancer cell lines T24 and 5637 overexpressing PTENP1. Luciferase reporter assay was performed to confirm the targeting of miR-17 to PTENP1 and PTEN. T24 and 5637 cell lines with stable overexpression of PTENP1 and mir-17 were used to investigate effect of PTNE and miR-17 on the function of PTENP1 in bladder cancer. RESULTS The expression of miR-17 was up-regulated and PTENP1 and PTEN were down-regulated in bladder cancer tissues, where a positive correlation was found between PTENP1 and PTEN expressions and a negative correlation between PTENP1 and miR-17 (P<0.05). Overexpression of PTENP1 in bladder cancer cell lines T24 and 5637 obviously enhanced the expression of PTEN protein. miR-17 was found to target both PTENP1 and PTEN and promote the growth of bladder cancer. miR-17 could partially restore the tumor-suppressing activity of PTENP1 in bladder cancer. CONCLUSION By binding with miR-17, lncRNA PTENP1 functions as a PTEN competing endogenous RNA (ceRNA) to suppress the progression of bladder cancer.
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Affiliation(s)
- 淦 余
- 华中科技大学同济医学院附属同济医院泌尿外科,湖北 武汉 430030Department of Urology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - 正岳 欧
- 澳门理工学院高等卫生学校,澳门 999078School of Health Sciences, Macao Polytechnic Institute, Macao 999078, China
| | - 启业 陶
- 澳门理工学院高等卫生学校,澳门 999078School of Health Sciences, Macao Polytechnic Institute, Macao 999078, China
| | - 国悦 万
- 澳门理工学院高等卫生学校,澳门 999078School of Health Sciences, Macao Polytechnic Institute, Macao 999078, China
| | - 宗浩 陆
- 澳门理工学院高等卫生学校,澳门 999078School of Health Sciences, Macao Polytechnic Institute, Macao 999078, China
| | - 斌 郎
- 澳门理工学院高等卫生学校,澳门 999078School of Health Sciences, Macao Polytechnic Institute, Macao 999078, China
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32
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Zhong Y, Chen Z, Guo S, Liao X, Xie H, Zheng Y, Cai B, Huang P, Liu Y, Zhou Q, Liu Y, Huang W. TUG1, SPRY4-IT1, and HULC as valuable prognostic biomarkers of survival in cancer: A PRISMA-compliant meta-analysis. Medicine (Baltimore) 2017; 96:e8583. [PMID: 29145271 PMCID: PMC5704816 DOI: 10.1097/md.0000000000008583] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 10/12/2017] [Accepted: 10/19/2017] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Long noncoding RNAs (LncRNAs) are involved in the development and progression of various cancers. Accumulating evidences indicated that expression of lncRNAs was related to the prognosis of tumors. METHODS Here, 3 well-known lncRNAs associated with cancer were gathered to prove the potential role of lncRNAs as novel predictors of survival in human cancer. This meta-analysis collected all eligible studies about TUG1, SPRY4-IT1, and HULC and explored the relationship between lncRNAs expression and lymph node metastasis (LNM) or overall survival (OS). A comprehensive, computerized literature search was undertaken by using PubMed, EMBASE, Cochrane Library, and Web of Science (up to October 10, 2017). Strength of association between 3 lncRNAs and cancer prognosis was assessed by computing the hazard ratios (HR) with its corresponding 95% confidence interval (CI). According to the inclusion and exclusion criteria, respectively, 10, 9, and 7 studies of 3 lncRNAs were included in this meta-analysis. RESULTS In the current meta-analysis, it could be concluded that the expression of these 3 lncRNAs in tumor tissues is not a direct evidence of LNM. In general, there was a significant negative correlation between TUG1 levels and OS time (pooled HR 1.54, 95% CI 1.06-2.24), SPRY4-IT1 levels and OS time (pooled HR 2.12, 95% CI 1.58-2.86) and HULC levels and OS time (pooled HR 2.10, 95% CI 1.18-3.73). It could be revealed from the result that high level expression of these 3 lncRNAs might be correlated with a bad prognosis. CONCLUSIONS In conclusion, the current meta-analysis demonstrated that TUG1, SPRY4-IT1, and HULC might serve as a moderate predictor of survival in human cancer.
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Affiliation(s)
- Yucheng Zhong
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen
| | - Zhicong Chen
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen
- Department of Urology, Peking University First Hospital, The Institute of Urology, Peking University, National Urological Cancer Centre, Beijing
| | - Shuyuan Guo
- Shantou University Medical College, Shantou, China
| | - Xinhui Liao
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen
| | - Haibiao Xie
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen
| | - Yien Zheng
- Shantou University Medical College, Shantou, China
| | - Bin Cai
- Shantou University Medical College, Shantou, China
| | | | - Yuhan Liu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen
| | - Qun Zhou
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen
| | - Yuchen Liu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen
| | - Weiren Huang
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen
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Peng WX, Huang JG, Yang L, Gong AH, Mo YY. Linc-RoR promotes MAPK/ERK signaling and confers estrogen-independent growth of breast cancer. Mol Cancer 2017; 16:161. [PMID: 29041978 PMCID: PMC5645922 DOI: 10.1186/s12943-017-0727-3] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 09/28/2017] [Indexed: 11/25/2022] Open
Abstract
Background The conversion from estrogen-dependent to estrogen-independent state of ER+ breast cancer cells is the key step to promote resistance to endocrine therapies. Although the crucial role of MAPK/ERK signaling pathway in estrogen-independent breast cancer cell growth is well established, the underlying mechanism is not fully understood. Methods In this study, we profiled lncRNA expression against a focused group of lncRNAs selected from lncRNA database. CRISPR/Cas9 was employed to knockout (KO) linc-RoR in MCF-7 cells, while rescue experiments were carried out to re-express linc-RoR in KO cells. Colony formation and MTT assays were used to examine the role of linc-RoR in estrogen-independent growth and tamoxifen resistance. Western blot and qRT-PCR were used to determine the change of protein and lncRNA levels, respectively. The expression of DUSP7 in clinical specimens was downloaded from Oncomine (www.oncomine.org) and the dataset from Kaplan-Meier Plotter (http://kmplot.com) was used to analyze the clinical outcomes in relation to DUSP7. Results We identified that linc-RoR functions as an onco-lncRNA to promote estrogen-independent growth of ER+ breast cancer. Under estrogen deprivation, linc-RoR causes the upregulation of phosphorylated MAPK/ERK pathway which in turn activates ER signaling. Knockout of linc-RoR abrogates estrogen deprivation-induced ERK activation as well as ER phosphorylation, whereas re-expression of linc-RoR restores all above phenotypes. Moreover, we show that the ERK-specific phosphatase Dual Specificity Phosphatase 7 (DUSP7), also known as MKP-X, is involved in linc-RoR KO-induced repression of MAPK/ERK signaling. Interestingly, linc-RoR KO increases the protein stability of DUSP7, resulting in repression of ERK phosphorylation. Clinical data analysis reveal that DUSP7 expression is lower in ER+ breast cancer samples than that in ER- breast cancer. Moreover, downregulation of DUSP7 expression is associated with poor patient survival. Conclusion Taken together, these results suggest that linc-RoR promotes estrogen-independent growth and activation of MAPK/ERK pathway of breast cancer cells by regulating the ERK-specific phosphatase DUSP7. Thus, this study might help not only in establishing a role for linc-RoR in estrogen-independent and tamoxifen resistance of ER+ breast cancer, but also suggesting a link between linc-RoR and MAPK/ERK pathway. Electronic supplementary material The online version of this article (10.1186/s12943-017-0727-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wan-Xin Peng
- Department of Cell biology, School of Medicine, Jiangsu University, Zhenjiang, China.,Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jian-Guo Huang
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA.,Department of Biochemistry, University of Mississippi Medical Center, Jackson, MS, USA
| | - Liu Yang
- Department of Science & Research, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Ai-Hua Gong
- Department of Cell biology, School of Medicine, Jiangsu University, Zhenjiang, China.
| | - Yin-Yuan Mo
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA. .,Department of Pharmacology/Toxicology, University of Mississippi Medical Center, Jackson, MS, USA.
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34
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Zhou D, Du Q, Chen J, Wang Q, Zhang D. Identification and allelic dissection uncover roles of lncRNAs in secondary growth of Populus tomentosa. DNA Res 2017; 24:473-486. [PMID: 28453813 PMCID: PMC5737087 DOI: 10.1093/dnares/dsx018] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 04/04/2017] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) function in various biological processes. However, their roles in secondary growth of plants remain poorly understood. Here, 15,691 lncRNAs were identified from vascular cambium, developing xylem, and mature xylem of Populus tomentosa with high and low biomass using RNA-seq, including 1,994 lncRNAs that were differentially expressed (DE) among the six libraries. 3,569 cis-regulated and 3,297 trans-regulated protein-coding genes were predicted as potential target genes (PTGs) of the DE lncRNAs to participate in biological regulation. Then, 476 and 28 lncRNAs were identified as putative targets and endogenous target mimics (eTMs) of Populus known microRNAs (miRNAs), respectively. Genome re-sequencing of 435 individuals from a natural population of P. tomentosa found 34,015 single nucleotide polymorphisms (SNPs) within 178 lncRNA loci and 522 PTGs. Single-SNP associations analysis detected 2,993 associations with 10 growth and wood-property traits under additive and dominance model. Epistasis analysis identified 17,656 epistatic SNP pairs, providing evidence for potential regulatory interactions between lncRNAs and their PTGs. Furthermore, a reconstructed epistatic network, representing interactions of 8 lncRNAs and 15 PTGs, might enrich regulation roles of genes in the phenylpropanoid pathway. These findings may enhance our understanding of non-coding genes in plants.
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MESH Headings
- Cambium/genetics
- Cambium/growth & development
- Cambium/metabolism
- Epistasis, Genetic
- Gene Expression Regulation, Plant
- Genetic Association Studies
- Polymorphism, Single Nucleotide
- Populus/genetics
- Populus/growth & development
- Populus/metabolism
- Quantitative Trait, Heritable
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/physiology
- RNA, Plant/genetics
- RNA, Plant/physiology
- Sequence Analysis, DNA
- Sequence Analysis, RNA
- Transcriptome
- Xylem/genetics
- Xylem/growth & development
- Xylem/metabolism
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Affiliation(s)
- Daling Zhou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P. R. China
| | - Qingzhang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P. R. China
| | - Jinhui Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P. R. China
| | - Qingshi Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P. R. China
| | - Deqiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P. R. China
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35
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Jin S, Chen S, Ma Y, Yang B, Liu Y. LincRNA FEZF1-AS1 contributes to the proliferation of LAD cells by silencing p57 expression. Oncotarget 2017; 8:103004-103013. [PMID: 29262540 PMCID: PMC5732706 DOI: 10.18632/oncotarget.21265] [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: 05/23/2017] [Accepted: 09/05/2017] [Indexed: 01/08/2023] Open
Abstract
LincRNA FEZF1-AS1 has been identified to exert oncogenic functions in various biological processes of tumorigenesis. However, the function of FEZF1-AS1 in lung adenocarcinoma still remains unclear. Our findings revealed that FEZF1-AS1 was increased in lung adenocarcinoma tissues and cell lines and high level of FEZF1-AS1 was associated with poor prognosis of lung adenocarcinoma. Functional experiments and mechanistic investigations demonstrated that knockdown of FEZF1-AS1 significantly repressed proliferation through influencing the distribution of cell cycle. Besides, we also uncovered that FEZF1-AS1 could suppress p57 expression through recruiting EZH2 and LSD1 to the promoter of p57, thus influenced the cell cycle and proliferation. Collectively, our results suggested that FEZF1-AS1 was involved in the progression of lung adenocarcinoma and might be as a potential therapy target for human lung adenocarcinoma.
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Affiliation(s)
- Shuai Jin
- Department of Thoracic surgery, PLA General Hospital, Beijing, 100853 China
| | - Siyu Chen
- Department of Thoracic surgery, PLA General Hospital, Beijing, 100853 China
| | - Yongfu Ma
- Department of Thoracic surgery, PLA General Hospital, Beijing, 100853 China
| | - Bo Yang
- Department of Thoracic surgery, PLA General Hospital, Beijing, 100853 China
| | - Yang Liu
- Department of Thoracic surgery, PLA General Hospital, Beijing, 100853 China
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Identifying Novel Glioma-Associated Noncoding RNAs by Their Expression Profiles. Int J Genomics 2017; 2017:2312318. [PMID: 29138748 PMCID: PMC5613369 DOI: 10.1155/2017/2312318] [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: 05/12/2017] [Accepted: 07/20/2017] [Indexed: 12/14/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) play a significant role in cancer development as regulators of protein-coding genes. Their dysregulation was in some extent already associated with glioma, the most aggressive primary brain tumours in adults. The correct diagnosis and treatment selection due to high tumour heterogeneity might be difficult and inadequate, resulting in poor prognosis. Studies of expression patterns of noncoding RNAs (ncRNAs) could provide useful insight in glioma molecular development. We used the qPCR approach to screen and investigate the expression of lncRNAs that were previously deregulated in other cancer types. The study showed altered expression levels for numerous lncRNAs across histologically different glioma samples. Validation of few lncRNAs showed association of expression levels with histological subtype and/or malignancy grade. We also observed deregulated and subtype-distinctive expression for four lncRNA-associated miRNAs. Expression of few lncRNAs and miRNA was also associated with patients' survival, showing potential prognostic value. Several ncRNAs, some already related to glioma and some, to the best of our knowledge, investigated for the first time, might be of greater importance in glioma molecular development and progression. Finding the subtype-specific lncRNA and/or miRNA expression patterns may contribute additional information for a more objective classification.
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37
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Zhang CH, Wang J, Zhang LX, Lu YH, Ji TH, Xu L, Ling LJ. Shikonin reduces tamoxifen resistance through long non-coding RNA uc.57. Oncotarget 2017; 8:88658-88669. [PMID: 29179465 PMCID: PMC5687635 DOI: 10.18632/oncotarget.20809] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/23/2017] [Indexed: 02/07/2023] Open
Abstract
Tamoxifen resistance is a serious problem in the endocrine therapy of breast cancer. Long non-coding RNAs play important roles in tumor development. In this study, we revealed the involvement of lncRNA uc.57 and its downstream gene BCL11A in TAM resistance. Tamoxifen-resistant MCF-7R cells showed lower expression of uc.57 and higher expression of BCL11A mRNA and protein than the parental MCF-7 cells. Moreover, levels of uc.57 mRNA were lower and BCL11A mRNA were higher in breast cancer tissues than in precancerous breast tissues. Shikonin treatment reduced tamoxifen resistance in MCF-7R cells both in vitro and in vivo, targeting uc.57/BCL11A. Fluorescence in situ hybridization and RNA immunoprecipitation analyses showed that uc.57 binds to BCL11A. Uc.57 overexpression downregulated BCL11A and reduced tamoxifen resistance in MCF-7R cells both in vitro and in vivo. BCL11A knockdown also reduced tamoxifen resistance by inhibiting PI3K/AKT and MAPK signaling pathways. It thus appears shikonin reduces tamoxifen resistance of MCF-7R breast cancer cells by inducing uc.57, which downregulates BCL11A to inhibit PI3K/AKT and MAPK signaling pathways.
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Affiliation(s)
- Chen-Han Zhang
- Breast disease division, First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Jue Wang
- Breast disease division, First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Lin-Xin Zhang
- Breast disease division, First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Yi-Han Lu
- Breast disease division, First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Tian-Hao Ji
- Breast disease division, First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Lu Xu
- Breast disease division, First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Li-Jun Ling
- Breast disease division, First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu Province, China
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38
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Xu C, Qi R, Ping Y, Li J, Zhao H, Wang L, Du MY, Xiao Y, Li X. Systemically identifying and prioritizing risk lncRNAs through integration of pan-cancer phenotype associations. Oncotarget 2017; 8:12041-12051. [PMID: 28076842 PMCID: PMC5355324 DOI: 10.18632/oncotarget.14510] [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: 07/15/2016] [Accepted: 12/12/2016] [Indexed: 02/01/2023] Open
Abstract
LncRNAs have emerged as a major class of regulatory molecules involved in normal cellular physiology and disease, our knowledge of lncRNAs is very limited and it has become a major research challenge in discovering novel disease-related lncRNAs in cancers. Based on the assumption that diverse diseases with similar phenotype associations show similar molecular mechanisms, we presented a pan-cancer network-based prioritization approach to systematically identify disease-specific risk lncRNAs by integrating disease phenotype associations. We applied this strategy to approximately 2800 tumor samples from 14 cancer types for prioritizing disease risk lncRNAs. Our approach yielded an average area under the ROC curve (AUC) of 80.66%, with the highest AUC (98.14%) for medulloblastoma. When evaluated using leave-one-out cross-validation (LOOCV) for prioritization of disease candidate genes, the average AUC score of 97.16% was achieved. Moreover, we demonstrated the robustness as well as the integrative importance of this approach, including disease phenotype associations, known disease genes and the numbers of cancer types. Taking glioblastoma multiforme as a case study, we identified a candidate lncRNA gene SNHG1 as a novel disease risk factor for disease diagnosis and prognosis. In summary, we provided a novel lncRNA prioritization approach by integrating pan-cancer phenotype associations that could help researchers better understand the important roles of lncRNAs in human cancers.
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Affiliation(s)
- Chaohan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Rui Qi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Jie Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Hongying Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Li Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | | | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
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39
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Zhu H, Yu J, Zhu H, Guo Y, Feng S. Identification of key lncRNAs in colorectal cancer progression based on associated protein-protein interaction analysis. World J Surg Oncol 2017; 15:153. [PMID: 28797257 PMCID: PMC5553992 DOI: 10.1186/s12957-017-1211-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 07/22/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) was one of the most commonly diagnosed malignancies. The molecular mechanisms involved in the progression of CRC remain unclear. Accumulating evidences showed that long noncoding RNAs (lncRNAs) played key roles in tumorigenesis, cancer progression, and metastasis. Therefore, we aimed to explore the roles of lncRNAs in the progression of CRC. METHODS In this study, we aimed to identify differentially expressed lncRNAs and messenger RNAs (mRNAs) in CRC by analyzing a cohort of previously published datasets: GSE64857. GO and KEGG pathway analyses were applied to give us insight in the functions of those lncRNAs and mRNAs in CRC. RESULTS Totally, 46 lncRNAs were identified as differentially expressed between stage II and stage III CRC for the first time screening by microarray. GO and KEGG pathway analyses showed that differentially expressed lncRNAs were involved in regulating signal transduction, cell adhesion, cell differentiation, focal adhesion, and cell adhesion molecules. CONCLUSIONS We found three lncRNAs (LOC100129973, PGM5-AS1, and TTTY10) widely co-expressed with differentially expressed mRNAs. We also constructed lncRNA-associated PPI in CRC and found that these lncRNAs may be associated with CRC progression. Moreover, we found that high PGM5-AS1 expression levels were associated with worse overall survival in CRC cancer. We believe that this study would provide novel potential therapeutic and prognostic targets for CRC.
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Affiliation(s)
- Haishan Zhu
- The First Hospital of ZhaoQing, Guangdong, China
| | - Jiajing Yu
- Huashan Hospital, Fudan University, Shanghai, China
| | - Haifeng Zhu
- The First Hospital of ZhaoQing, Guangdong, China
| | - Yusheng Guo
- Huashan Hospital, Fudan University, Shanghai, China
| | - Shengjie Feng
- Huashan Hospital, Fudan University, Shanghai, China.
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40
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Liu YW, Xia R, Lu K, Xie M, Yang F, Sun M, De W, Wang C, Ji G. LincRNAFEZF1-AS1 represses p21 expression to promote gastric cancer proliferation through LSD1-Mediated H3K4me2 demethylation. Mol Cancer 2017; 16:39. [PMID: 28209170 PMCID: PMC5314465 DOI: 10.1186/s12943-017-0588-9] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 01/13/2017] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Although the prognosis of gastric cancer patients have a favorable progression, there are some patients with unusual patterns of locoregional and systemic recurrence. Therefore, a better understanding of early molecular events of the disease is needed. Current evidences demonstrate that long noncoding RNAs (lncRNAs) may be an important class of functional regulators involved in human gastric cancers development. Our previous studies suggest that HOTAIR contributes to gastric cancer development, and the overexpression of HOTAIR predicts a poor prognosis. In this study, we investigated the characteristic of the LncRNA FEZF1-AS1 in gastric cancer. METHODS QRT-PCR was used to detect the expression of FEZF1-AS1 in gastric cancer tissues and cells. MTT assays, clonogenic survival assays and nude mouse xenograft model were used to examine the tumorigenesis function of FEZF1-AS1 in vitro and in vivo. Bioinformatics analysis were used to select downstream target genes of FEZF1-AS1. Cell cycle analysis, ChIP, RIP,RNA Pulldown assays were examined to dissect molecular mechanisms. RESULTS In this study, we reported that FEZF1-AS1, a 2564 bp RNA, was overexpressed in gastric cancer, and upregulated FEZF1-AS1 expression indicated larger tumor size and higher clinical stage; additional higher expression of FEZF1-AS1 predicted poor prognosis. Further experiments revealed that knockdown FEZF1-AS1 significantly inhibited gastric cancer cells proliferation by inducing G1 arrest and apoptosis, whereas endogenous expression FEZF1-AS1 promoted cell growth. Additionally, RIP assay and RNA-pulldown assay evidenced that FEZF1-AS1 could epigenetically repress the expression of P21 via binding with LSD1, the first discovered demethylase. ChIP assays demonstrated that LSD1 could directly bind to the promoter of P21, inducing H3K4me2 demethylation. CONCLUSION In summary, these data demonstrated that FEZF1-AS1 could act as an "oncogene" for gastric cancer partly through suppressing P21 expression; FEZF1-AS1 may be served as a candidate prognostic biomarker and target for new therapies of gastric cancer patients.
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Affiliation(s)
- Yan-Wen Liu
- Department of Oncology, Zhongda Hospital, Medical School, Southeast University, Nanjing, Jiangsu, People's Republic of China
| | - Rui Xia
- Department of Laboratory, Affiliated Chest Hospital of southeast University, Nanjing, Jiangsu, People's Republic of China
| | - Kai Lu
- Department of surgery, Affiliated the second hospital of Bengbu Medical College, Lianyungang, jiangsu, People's Republic of China
| | - Min Xie
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Fen Yang
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Ming Sun
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Wei De
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China.
| | - Cailian Wang
- Department of Oncology, Zhongda Hospital, Medical School, Southeast University, Nanjing, Jiangsu, People's Republic of China.
| | - Guozhong Ji
- Department of Gastroenterology Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China.
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Conte F, Fiscon G, Chiara M, Colombo T, Farina L, Paci P. Role of the long non-coding RNA PVT1 in the dysregulation of the ceRNA-ceRNA network in human breast cancer. PLoS One 2017; 12:e0171661. [PMID: 28187158 PMCID: PMC5302781 DOI: 10.1371/journal.pone.0171661] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 01/24/2017] [Indexed: 12/14/2022] Open
Abstract
Recent findings have identified competing endogenous RNAs (ceRNAs) as the drivers in many disease conditions, including cancers. The ceRNAs indirectly regulate each other by reducing the amount of microRNAs (miRNAs) available to target messenger RNAs (mRNAs). The ceRNA interactions mediated by miRNAs are modulated by a titration mechanism, i.e. large changes in the ceRNA expression levels either overcome, or relieve, the miRNA repression on competing RNAs; similarly, a very large miRNA overexpression may abolish competition. The ceRNAs are also called miRNA "decoys" or miRNA "sponges" and encompass different RNAs competing with each other to attract miRNAs for interactions: mRNA, long non-coding RNAs (lncRNAs), pseudogenes, or circular RNAs. Recently, we developed a computational method for identifying ceRNA-ceRNA interactions in breast invasive carcinoma. We were interested in unveiling which lncRNAs could exert the ceRNA activity. We found a drastic rewiring in the cross-talks between ceRNAs from the physiological to the pathological condition. The main actor of this dysregulated lncRNA-associated ceRNA network was the lncRNA PVT1, which revealed a net biding preference towards the miR-200 family members in normal breast tissues. Despite its up-regulation in breast cancer tissues, mimicked by the miR-200 family members, PVT1 stops working as ceRNA in the cancerous state. The specific conditions required for a ceRNA landscape to occur are still far from being determined. Here, we emphasized the importance of the relative concentration of the ceRNAs, and their related miRNAs. In particular, we focused on the withdrawal in breast cancer tissues of the PVT1 ceRNA activity and performed a gene expression and sequence analysis of its multiple isoforms. We found that the PVT1 isoform harbouring the binding site for a representative miRNA of the miR-200 family shows a drastic decrease in its relative concentration with respect to the miRNA abundance in breast cancer tissues, providing a plausibility argument to the breakdown of the sponge program orchestrated by the oncogene PVT1.
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Affiliation(s)
- Federica Conte
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Rome, Italy
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Rome, Italy
| | - Matteo Chiara
- Department of Biosciences, University of Milan, Milan, Italy
| | - Teresa Colombo
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Rome, Italy
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, “Sapienza” University, Rome, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Rome, Italy
- * E-mail:
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42
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Gao Q, Xie H, Zhan H, Li J, Liu Y, Huang W. Prognostic Values of Long Noncoding RNA GAS5 in Various Carcinomas: An Updated Systematic Review and Meta-Analysis. Front Physiol 2017; 8:814. [PMID: 29163187 PMCID: PMC5673644 DOI: 10.3389/fphys.2017.00814] [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: 07/19/2017] [Accepted: 10/03/2017] [Indexed: 02/05/2023] Open
Abstract
The growth arrest-specific transcript 5 (GAS5) is a long noncoding RNA with low expression in multiple cancers. This meta-analysis aims to explore the association between GAS5 expression levels and cancer patients' prognosis. We collected all the relevant literatures about GAS5 expression levels associated with overall survival (OS), lymph node metastasis (LNM) and high tumor stage (II/III/IV) (HTS) from the PubMed and Web of Science. The hazard ratio (HR) and the corresponding 95% confidence interval (CI) were calculated to evaluate the link strength between GAS5 and cancer prognosis. A total of 934 patients from 14 studies were included to the present meta-analysis, according to the inclusion and exclusion criteria. The results demonstrated that low expression of GAS5 could predict poor OS in cancer patients (HR = 1.955, 95% CI: 1.551-2.465, P < 0.001). Meanwhile we also analyzed the following cancers independently: hepatocellular carcinoma (HR = 1.893, 95% CI: 1.103-3.249, P = 0.021) and urothelial carcinoma (HR = 1.653, 95% CI: 1.185-2.306, P = 0.003). Compared to the high GAS5 expression group, additionally, patients with low GAS5 expression in tumor tissues were more prone to lymph node metastasis (OR = 0.234, 95%CI: 0.153-0.358, P < 0.001) and high tumor stage (OR = 0.185, 95% CI:0.102-0.333, P < 0.001). In conclusion, this meta-analysis showed that GAS5 might be served as a novel biomarker for predicting prognosis in various types of cancers.
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Affiliation(s)
- Qunjun Gao
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Graduate School of Guangzhou Medical University, Shenzhen, China
- Guangzhou Medical University, Guangzhou, China
| | - Haibiao Xie
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Graduate School of Guangzhou Medical University, Shenzhen, China
- Shantou University Medical College, Shantou, China
| | - Hengji Zhan
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Graduate School of Guangzhou Medical University, Shenzhen, China
- Shenzhen University, Shenzhen, China
| | - Jianfa Li
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Graduate School of Guangzhou Medical University, Shenzhen, China
| | - Yuchen Liu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Graduate School of Guangzhou Medical University, Shenzhen, China
- *Correspondence: Yuchen Liu
| | - Weiren Huang
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Graduate School of Guangzhou Medical University, Shenzhen, China
- Weiren Huang
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Yang ZY, Yang F, Zhang YL, Liu B, Wang M, Hong X, Yu Y, Zhou YH, Zeng H. LncRNA-ANCR down-regulation suppresses invasion and migration of colorectal cancer cells by regulating EZH2 expression. Cancer Biomark 2017; 18:95-104. [PMID: 27983539 DOI: 10.3233/cbm-161715] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Our study aimed to explore the effects of long noncoding RNA (lncRNA)-ANCR on the invasion and migration of colorectal cancer (CRC) cells by regulating enhancer of zeste homolog 2 (EZH2) expression. CRC tissues and adjacent normal tissues were collected and CRC SW620 cells line and normal human intestinal epithelial cells (HIECs) were incubated. CRC SW620 cells line was transfected with ANCR-siRNA. The expressions of ANCR and EZH2 mRNA were measured by real-time quantitative polymerase chain reaction (RT-qPCR). EZH2 and trimethylation of H3K27 (H3K27me3) protein expressions were detected using Western blotting. The relationship between ANCR and EZH2 was determined through RNA pull-down and co-immunoprecipitation (co-IP) assays. Cell invasion and migration were determined by Trans-well and cell scratch assays. ANCR, EZH2 and H3K27me3 expressions were up-regulated in CRC tissues and SW620 cells (all P < 0.05). After transfected with ANCR-siRNA, SW620 cells showed decreased ANCR expression and EZH2 mRNA and protein expressions (all P < 0.05). According to the results of RNA pull-down and co-IP assays, ANCR could specifically bind to EZH2. The results of Trans-well and cell scratch tests showed that when ANCR expression was decreased, the invasion and migration abilities of SW620 cells significantly declined (both P < 0.05). In conclusion, these results suggest that lncRNA-ANCR could influence the invasion and migration of CRC cells by specifically binding to EZH2.
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Affiliation(s)
- Zhao-Yang Yang
- Department of First Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Fang Yang
- Department of First Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Ying-Li Zhang
- Department of Internal Medicine, Harbin Red Cross Central Hospital, Harbin, Heilongjiang, China
| | - Bao Liu
- Department of First Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Meng Wang
- Department of First Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Xuan Hong
- Department of First Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Yan Yu
- Department of Sixth Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Yao-Hui Zhou
- Department of Internal Medicine, The First Hospital of Harbin, Harbin, Heilongjiang, China
| | - Hai Zeng
- Department of Internal Medicine, The First Hospital of Harbin, Harbin, Heilongjiang, China
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Zhao ZH, Hao W, Meng QT, Du XB, Lei SQ, Xia ZY. Long non-coding RNA MALAT1 functions as a mediator in cardioprotective effects of fentanyl in myocardial ischemia-reperfusion injury. Cell Biol Int 2017; 41:62-70. [PMID: 27862640 DOI: 10.1002/cbin.10701] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/05/2016] [Indexed: 12/18/2022]
Abstract
Long non-coding (lncRNA) MALAT1 can be increased by hypoxia or ischemic limbs. Also, downregulation of MALAT1 contributes to reduction of cardiomyocyte apoptosis. However, the functional involvement of MALAT1 in myocardial ischemia-reperfusion (I/R) injury has not been defined. This study investigated the functional involvement of lncRNA-MALAT1 in cardioprotective effects of fentanyl. HL-1, a cardiac muscle cell line from the AT-1 mouse atrial cardiomyocyte tumor lineage was pre-treated with fentanyl and generated cell model of hypoxia-reoxygenation (H/R). Relative expression of MALAT1, miR-145, and Bnip3 mRNA in cells was determined by quantitative real-time PCR. Cardiomyocyte H/R injury was indicated by lactate dehydrogenase (LDH) release and cell apoptosis. The results showed that fentanyl abrogates expression of responsive gene for H/R and induces downregulation of MALAT1 and Bnip3 and upregulation of miR-145. We found that miR-145/Bnip3 pathway was negatively regulated by MALAT1 in H/R-HL-1 cell with or without fentanyl treatment. Moreover, both MALAT1 overexpression and miR-145 knockdown reverse cardioprotective effects of fentanyl, as indicated by increase in LDH release and cell apoptosis. The reversal effect of MALAT1 for fentanyl is confirmed in cardiac ischemia/reperfusion (I/R) mice. In summary, lncRNA-MALAT1 is sensitive to H/R injury and abrogates cardioprotective effects of Fentanyl by negatively regulating miR-145/Bnip3 pathway.
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Affiliation(s)
- Zhi-Hui Zhao
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Hubei Zhang Road, Wu chang District No. 99 Jie fang Road 238, 430060, Wuhan, China
| | - Wei Hao
- Department of Anesthesiology, Inner Mongolia Autonomous Region People's Hospital, Zhao Wu Da Road, No.20, Sai Han District, 010017, Huhhot, Inner Mongolia Autonomous Region, China
| | - Qing-Tao Meng
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Hubei Zhang Road, Wu chang District No. 99 Jie fang Road 238, 430060, Wuhan, China
| | - Xiao-Bing Du
- Department of Anesthesiology, Inner Mongolia Autonomous Region People's Hospital, Zhao Wu Da Road, No.20, Sai Han District, 010017, Huhhot, Inner Mongolia Autonomous Region, China
| | - Shao-Qing Lei
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Hubei Zhang Road, Wu chang District No. 99 Jie fang Road 238, 430060, Wuhan, China
| | - Zhong-Yuan Xia
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Hubei Zhang Road, Wu chang District No. 99 Jie fang Road 238, 430060, Wuhan, China
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Abstract
The advent of next-generation sequencing has demonstrated that eukaryotic genomes are extremely complex than what were previously thought. Recent studies revealed that in addition to protein-coding genes, nonprotein-coding genes have allocated a large fraction of the genome. Long noncoding RNA (lncRNA) genes are classified as nonprotein-coding genes, serving as a molecular signal, decoy, guide and scaffold. They were suggested to play important roles in chromatin states, epigenetic and posttranscriptional regulation of genes. Aberrant expression of lncRNAs and changes in their structure are associated with a wide spectrum of diseases ranging from different types of cancer and neurodegeneration to ?-thalassaemia. The purpose of this study was to summarize the current progress in understanding the genomic bases and origin of lncRNAs. Moreover, this study focusses on the diverse functions of lncRNAs in normal cells as well as various types of disease to illustrate the potential impacts of lncRNAs on diverse biological processes and their therapeutic significance.
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Zhan S, Dong Y, Zhao W, Guo J, Zhong T, Wang L, Li L, Zhang H. Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat. BMC Genomics 2016; 17:666. [PMID: 27550073 PMCID: PMC4994410 DOI: 10.1186/s12864-016-3009-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/10/2016] [Indexed: 01/23/2023] Open
Abstract
Background Long non-coding RNAs (lncRNAs) have been studied extensively over the past few years. Large numbers of lncRNAs have been identified in mouse, rat, and human, and some of them have been shown to play important roles in muscle development and myogenesis. However, there are few reports on the characterization of lncRNAs covering all the development stages of skeletal muscle in livestock. Results RNA libraries constructed from developing longissimus dorsi muscle of fetal (45, 60, and 105 days of gestation) and postnatal (3 days after birth) goat (Capra hircus) were sequenced. A total of 1,034,049,894 clean reads were generated. Among them, 3981 lncRNA transcripts corresponding to 2739 lncRNA genes were identified, including 3515 intergenic lncRNAs and 466 anti-sense lncRNAs. Notably, in pairwise comparisons between the libraries of skeletal muscle at the different development stages, a total of 577 transcripts were differentially expressed (P < 0.05) which were validated by qPCR using randomly selected six lncRNA genes. The identified goat lncRNAs shared some characteristics, such as fewer exons and shorter length, with the lncRNAs in other mammals. We also found 1153 lncRNAs genes were neighbored 1455 protein-coding genes (<10 kb upstream and downstream) and functionally enriched in transcriptional regulation and development-related processes, indicating they may be in cis-regulatory relationships. Additionally, Pearson’s correlation coefficients of co-expression levels suggested 1737 lncRNAs and 19,422 mRNAs were possibly in trans-regulatory relationships (r > 0.95 or r < −0.95). These co-expressed mRNAs were enriched in development-related biological processes such as muscle system processes, regulation of cell growth, muscle cell development, regulation of transcription, and embryonic morphogenesis. Conclusions This study provides a catalog of goat muscle-related lncRNAs, and will contribute to a fuller understanding of the molecular mechanism underpinning muscle development in mammals. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3009-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Siyuan Zhan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yao Dong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiazhong Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tao Zhong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linjie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Hongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
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Sun Y, Zheng ZP, Li H, Zhang HQ, Ma FQ. ANRIL is associated with the survival rate of patients with colorectal cancer, and affects cell migration and invasion in vitro. Mol Med Rep 2016; 14:1714-20. [PMID: 27314206 DOI: 10.3892/mmr.2016.5409] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 05/20/2016] [Indexed: 01/16/2023] Open
Abstract
Antisense noncoding RNA in the INK4 locus (ANRIL) has been reported to be upregulated in various types of human cancer, and is also highly expressed in normal human tissue. The aim of the present study was to identify whether ANRIL may be a possible target for colorectal cancer (CRC) therapy. Reverse transcription‑quantitative polymerase chain reaction was used to quantify the expression levels of the long noncoding RNA (lncRNA) ANRIL in 97 paired CRC and adjacent non‑neoplastic tissue samples. In addition, the HT29 and RKO human CRC cell lines underwent ANRIL RNA interference, and knockdown efficiency was evaluated by western blotting. Cell viability, and migratory and invasive ability were subsequently assessed. The CRC tissues were revealed to express higher levels of ANRIL lncRNA compared with the adjacent non‑neoplastic tissues (P<0.05). Furthermore, high ANRIL expression was significantly associated with reduced survival rate (P<0.05). ANRIL gene expression was successfully silenced in human CRC cells. ANRIL knockdown decreased proliferation, inhibited migration and invasion, and reduced the colony‑forming ability of the cells. These data indicated that the lncRNA ANRIL is upregulated in CRC tissues, and is associated with CRC cell pathogenesis. Furthermore, the underlying mechanisms of these effects may be exploited for therapeutic benefit.
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Affiliation(s)
- Yi Sun
- Department of Oncology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Zhao-Peng Zheng
- Department of Oncology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Hang Li
- Department of Oncology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Han-Qun Zhang
- Department of Oncology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Fa-Qiang Ma
- Department of Oncology, The Second Affiliated Hospital of Guizhou Medical University, Kaili, Guizhou 556000, P.R. China
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Tian J, Song Y, Du Q, Yang X, Ci D, Chen J, Xie J, Li B, Zhang D. Population genomic analysis of gibberellin-responsive long non-coding RNAs in Populus. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2467-82. [PMID: 26912799 DOI: 10.1093/jxb/erw057] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Long non-coding RNAs (lncRNAs) participate in a wide range of biological processes, but lncRNAs in plants remain largely unknown; in particular, we lack a systematic identification of plant lncRNAs involved in hormone responses. Moreover, allelic variation in lncRNAs remains poorly characterized at a large scale. Here, we conducted high-throughput RNA-sequencing of leaves from control and gibberellin (GA)-treated Populus tomentosa and identified 7655 reliably expressed lncRNAs. Among the 7655 lncRNAs, the levels of 410 lncRNAs changed in response to GA. Seven GA-responsive lncRNAs were predicted to be putative targets of 18 miRNAs, and one GA-responsive lncRNA (TCONS_00264314) was predicted to be a target mimic of ptc-miR6459b. Computational analysis predicted 939 potential cis-regulated target genes and 965 potential trans-regulated target genes for GA-responsive lncRNAs. Functional annotation of these potential target genes showed that they participate in many different biological processes, including auxin signal transduction and synthesis of cellulose and pectin, indicating that GA-responsive lncRNAs may influence growth and wood properties. Finally, single nucleotide polymorphism (SNP)-based association analysis showed that 112 SNPs from 52 GA-responsive lncRNAs and 1014 SNPs from 296 potential target genes were significantly associated with growth and wood properties. Epistasis analysis also provided evidence for interactions between lncRNAs and their potential target genes. Our study provides a comprehensive view of P. tomentosa lncRNAs and offers insights into the potential functions and regulatory interactions of GA-responsive lncRNAs, thus forming the foundation for future functional analysis of GA-responsive lncRNAs in P. tomentosa.
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Affiliation(s)
- Jiaxing Tian
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China
| | - Yuepeng Song
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China
| | - Qingzhang Du
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China
| | - Xiaohui Yang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China
| | - Dong Ci
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China
| | - Jinhui Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China
| | - Jianbo Xie
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China
| | - Bailian Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China. Department of Forestry, North Carolina State University, Raleigh, NC 27695-8203, USA
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, PR China.
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Snijders AM, Mao JH. Co-Expression Network Analysis of Fbxw7-Associated LncRNAs Reveals Their Functions in Radiation-Induced Thymic Lymphoma. INSIGHTS IN CANCER RESEARCH 2016; 1:1-5. [PMID: 27376155 PMCID: PMC4926873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
FBXW7, an E3-ubiquitin protein ligase in SCFs (SKP1-cullin-F-box) complex, is a major human tumor suppressor gene, and understanding mechanisms by which FBXW7 contributes to tumorigenesis is critical for the treatment of human cancers with FBXW7 deficiency. Long non-coding RNAs (lncRNAs) have emerged as key regulators of various biological processes. Here we have identified a set of lncRNAs that are associated with Fbxw7 deficiency. The correlation network and functional annotation analysis revealed that Fbxw7-associated lncRNAs regulate genes involved in cell cycle, DNA repair, metabolic process, and cell communication and adhesion. The number of coding genes that correlated with individual lncRNAs varied largely. A lncRNA on chromosome 15 (A_30_P01032978), which was upregulated in tumors from Fbxw7 deficient mice was positively correlated with 15 coding genes. High expression of this 15-gene signature was associated with poor prognosis in two independent human breast cancer studies. Our results open possible new avenues to understand mechanisms by which Fbxw7 deficiency increases tumor susceptibility via the alteration of lncRNAs.
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Affiliation(s)
| | - Jian-Hua Mao
- Corresponding authors: Antoine M Snijders and Jian-Hua Mao, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA, and
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Dang Y, Lan F, Ouyang X, Wang K, Lin Y, Yu Y, Wang L, Wang Y, Huang Q. Expression and clinical significance of long non-coding RNA HNF1A-AS1 in human gastric cancer. World J Surg Oncol 2015; 13:302. [PMID: 26472090 PMCID: PMC4608159 DOI: 10.1186/s12957-015-0706-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/22/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Increasing evidence has demonstrated that long non-coding RNAs (lncRNAs) play essential roles in the occurrence and development of human cancers, including gastric cancer (GC). However, the functional and clinical significance of lncRNAs are still poorly understood. METHODS In this study, the expression of LncRNA HNF1A antisense RNA 1 (HNF1A-AS1) was first examined by lncRNAs microarray analysis in 6 GC tissues, and was then further verified by real-time quantitative reverse transcription PCR (qRT-PCR) both in 3 GC cell lines and 161 cases of GC tissues. We also evaluated the association between HNF1A-AS1 expression and clinicopathological features of patients with GC. RESULTS LncRNAs microarray analysis results exhibited that HNF1A-AS1 was downregulated in GCs tissues (mean fold change 2.06, p < 0.05), which was further confirmed by qRT-PCR. The results from qRT-PCR showed that the expression of HNF1A-AS1 was not only downregulated in three GC cell lines (AGS, BGC-823, and MKN-45) relative to that in a normal gastric mucosal epithelial cell line (GES-1), but also decreased in GC tissues relative to that in paired adjacent non-neoplastic tissues (low expression, 94 of 161; low expression rate, 58.38%). Furthermore, low HNF1A-AS1 expression was associated with tumor size/diameter (p = 0.005, multivariate analysis), levels of serum carcinoembryonic antigen (CEA), and carbohydrate antigen 19-9 (CA19-9), and RRM1 expression in tissue samples (p = 0.028, p = 0.009, and p = 0.006, respectively). CONCLUSIONS Taken together, our data indicate that lncRNA HNF1A-AS1 may be a regulator of GC, and thus, it may have potential as a novel biomarker and treatment target for this type of cancer.
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Affiliation(s)
- Yuan Dang
- Department of Experimental Medicine, Fuzhou General Hospital (Dongfang Hospital), 156 North Xi-er Huan Road, Fuzhou City, Fujian Province, 350025, China.
| | - Fenghua Lan
- Department of Experimental Medicine, Fuzhou General Hospital (Dongfang Hospital), 156 North Xi-er Huan Road, Fuzhou City, Fujian Province, 350025, China.
| | - Xiaojuan Ouyang
- Department of Experimental Medicine, Fuzhou General Hospital (Dongfang Hospital), 156 North Xi-er Huan Road, Fuzhou City, Fujian Province, 350025, China.
| | - Kai Wang
- Department of Experimental Medicine, Fuzhou General Hospital (Dongfang Hospital), 156 North Xi-er Huan Road, Fuzhou City, Fujian Province, 350025, China.
| | - Youdong Lin
- Department of Experimental Medicine, Fuzhou General Hospital (Dongfang Hospital), 156 North Xi-er Huan Road, Fuzhou City, Fujian Province, 350025, China.
| | - Yinghao Yu
- Department of Pathology, Fuzhou General Hospital (Dongfang Hospital), 156 North Xi-er Huan Road, Fuzhou City, Fujian Province, 350025, China.
| | - Lie Wang
- Department of General Surgery, Fuzhou General Hospital (Dongfang Hospital), 156 North Xi-er Huan Road, Fuzhou City, Fujian Province, 350025, China.
| | - Yu Wang
- Department of General Surgery, Fuzhou General Hospital (Dongfang Hospital), 156 North Xi-er Huan Road, Fuzhou City, Fujian Province, 350025, China.
| | - Qiaojia Huang
- Department of Experimental Medicine, Fuzhou General Hospital (Dongfang Hospital), 156 North Xi-er Huan Road, Fuzhou City, Fujian Province, 350025, China.
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