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Abdi E, Latifi-Navid S, Panahi A. Long noncoding RNA polymorphisms in gynecological cancers. Per Med 2024; 21:59-68. [PMID: 38095072 DOI: 10.2217/pme-2023-0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Gynecological malignancies are one of the main causes of cancer-induced mortality. Despite remarkable recent therapeutic advances, current therapeutic options are not sufficient. Regarding the effect of long noncoding RNAs (lncRNAs) on cell differentiation, proliferation and apoptosis, variations in their expression cause different anomalies, such as tumorigenesis. SNPs influence lncRNA function and expression. LncRNA polymorphisms can predict cancer risk and are effective for early diagnosis and customized therapy. In this literature review, we comprehensively investigate the effect of lncRNA polymorphisms on gynecological cancers. LncRNA-related variants are proposed to evaluate cancer incidence, early detection and management of personalized therapy. Nonetheless, more studies are required to validate the consistency of current findings in numerous samples and across various ethnic groups.
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Affiliation(s)
- Esmat Abdi
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil, 5619911367, Iran
| | - Saeid Latifi-Navid
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil, 5619911367, Iran
| | - Alireza Panahi
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil, 5619911367, Iran
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2
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Mukhopadhyay A, Deshpande SN, Bhatia T, Thelma BK. Significance of an altered lncRNA landscape in schizophrenia and cognition: clues from a case-control association study. Eur Arch Psychiatry Clin Neurosci 2023; 273:1677-1691. [PMID: 37009928 DOI: 10.1007/s00406-023-01596-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/20/2023] [Indexed: 04/04/2023]
Abstract
Genetic etiology of schizophrenia is poorly understood despite large genome-wide association data. Long non-coding RNAs (lncRNAs) with a probable regulatory role are emerging as important players in neuro-psychiatric disorders including schizophrenia. Prioritising important lncRNAs and analyses of their holistic interaction with their target genes may provide insights into disease biology/etiology. Of the 3843 lncRNA SNPs reported in schizophrenia GWASs extracted using lincSNP 2.0, we prioritised n = 247 based on association strength, minor allele frequency and regulatory potential and mapped them to lncRNAs. lncRNAs were then prioritised based on their expression in brain using lncRBase, epigenetic role using 3D SNP and functional relevance to schizophrenia etiology. 18 SNPs were finally tested for association with schizophrenia (n = 930) and its endophenotypes-tardive dyskinesia (n = 176) and cognition (n = 565) using a case-control approach. Associated SNPs were characterised by ChIP seq, eQTL, and transcription factor binding site (TFBS) data using FeatSNP. Of the eight SNPs significantly associated, rs2072806 in lncRNA hsaLB_IO39983 with regulatory effect on BTN3A2 was associated with schizophrenia (p = 0.006); rs2710323 in hsaLB_IO_2331 with role in dysregulation of ITIH1 with tardive dyskinesia (p < 0.05); and four SNPs with significant cognition score reduction (p < 0.05) in cases. Two of these with two additional variants in eQTL were observed among controls (p < 0.05), acting likely as enhancer SNPs and/or altering TFBS of eQTL mapped downstream genes. This study highlights important lncRNAs in schizophrenia and provides a proof of concept of novel interactions of lncRNAs with protein-coding genes to elicit alterations in immune/inflammatory pathways of schizophrenia.
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Affiliation(s)
- Anirban Mukhopadhyay
- Department of Genetics, University of Delhi South Campus, Benito Juarez Marg, New Delhi, 110021, India
| | - Smita N Deshpande
- Department of Psychiatry, Postgraduate Institute of Medical Education and Research-Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Triptish Bhatia
- Department of Psychiatry, Postgraduate Institute of Medical Education and Research-Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Marg, New Delhi, 110021, India.
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3
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Huang J, Ji X. Never a dull enzyme, RNA polymerase II. Transcription 2023; 14:49-67. [PMID: 37132022 PMCID: PMC10353340 DOI: 10.1080/21541264.2023.2208023] [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: 02/10/2023] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/04/2023] Open
Abstract
RNA polymerase II (Pol II) is composed of 12 subunits that collaborate to synthesize mRNA within the nucleus. Pol II is widely recognized as a passive holoenzyme, with the molecular functions of its subunits largely ignored. Recent studies employing auxin-inducible degron (AID) and multi-omics techniques have revealed that the functional diversity of Pol II is achieved through the differential contributions of its subunits to various transcriptional and post-transcriptional processes. By regulating these processes in a coordinated manner through its subunits, Pol II can optimize its activity for diverse biological functions. Here, we review recent progress in understanding Pol II subunits and their dysregulation in diseases, Pol II heterogeneity, Pol II clusters and the regulatory roles of RNA polymerases.
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Affiliation(s)
- Jie Huang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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4
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Yang Z, Zhu J, Yang T, Tang W, Zheng X, Ji S, Ren Z, Lu F. Comprehensive analysis of the lncRNAs-related immune gene signatures and their correlation with immunotherapy in lung adenocarcinoma. Br J Cancer 2023; 129:1397-1408. [PMID: 37543671 PMCID: PMC10628174 DOI: 10.1038/s41416-023-02379-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 07/06/2023] [Accepted: 07/25/2023] [Indexed: 08/07/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs)-related immune genes (lrRIGs) play a crucial role in the development and progression of lung adenocarcinoma (LUAD). However, reliable prognostic signatures based on lrRIGs have not yet been identified. METHODS We screened lrRIGs associated with the prognosis of LUAD using The Cancer Genome Atlas (TCGA) database and then established a novel prognostic nine-gene signature composed of CD79A, INHA, SHC3, LIFR, TNFRSF11A, GPI, F2RL1, SEMA7A and WFDC2 through bioinformatic approaches. A risk score derived from this gene signature was used to divide LUAD patients into the low- and high-risk groups. The latter was confirmed to have markedly worse overall survival (O.S.). A nomogram was developed using the risk score and other independent prognostic elements, demonstrating excellent performance in predicting the O.S. rate of LUAD patients. RESULTS We observed that the infiltration of diverse immune cell subtypes and response to immunotherapy and chemotherapy significantly differed between the low- and high-risk groups. CONCLUSIONS Overall, stratification based on this gene signature could be used to guide better therapeutic management and improve outcomes for LUAD patients.
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Affiliation(s)
- Zhengyan Yang
- Joint National Laboratory for Antibody Drug Engineering, the First Affiliated Hospital, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Jianling Zhu
- Joint National Laboratory for Antibody Drug Engineering, the First Affiliated Hospital, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Department of Immunology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Tiantian Yang
- Joint National Laboratory for Antibody Drug Engineering, the First Affiliated Hospital, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Department of Immunology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Wenjun Tang
- Joint National Laboratory for Antibody Drug Engineering, the First Affiliated Hospital, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Department of Immunology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Xiaowei Zheng
- Department of Clinical Laboratory, Puyang Hospital of Traditional Chinese Medicine, Puyang, China
| | - Shaoping Ji
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Zhiguang Ren
- Joint National Laboratory for Antibody Drug Engineering, the First Affiliated Hospital, School of Basic Medical Sciences, Henan University, Kaifeng, China.
- Institute of Traditional Chinese Medicine, Henan University, Kaifeng, China.
| | - Feng Lu
- Joint National Laboratory for Antibody Drug Engineering, the First Affiliated Hospital, School of Basic Medical Sciences, Henan University, Kaifeng, China.
- Department of Immunology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
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5
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Najeeb N, Murukan AB, Renjitha A, Jayaram M, Jabbar AA, Haridasan H, Prijikumar A, Baiju S, Nixon AA, Krishnan PA, Rodriguez S, Kumar S, Polipalli SK, Singh KK, Nair BG, Ghate SD, Rao RSP, Kishor PBK, Aloor A, Suravajhala R, Chaubey G, Suravajhala P. Inferring Recombination Events in SARS-CoV-2 Variants In Silico. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1412:253-270. [PMID: 37378772 DOI: 10.1007/978-3-031-28012-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Over the last 34 months, at least 10 severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) distinct variants have evolved. Among these, some were more infectious while others were not. These variants may serve as candidates for identification of the signature sequences linked to infectivity and viral transgressions. Based on our previous hijacking and transgression hypothesis, we aimed to investigate whether SARS-CoV-2 sequences associated with infectivity and trespassing of long noncoding RNAs (lncRNAs) provide a possible recombination mechanism to drive the formation of new variants. This work involved a sequence and structure-based approach to screen SARS-CoV-2 variants in silico, taking into account effects of glycosylation and links to known lncRNAs. Taken together, the findings suggest that transgressions involving lncRNAs may be linked with changes in SARS-CoV-2-host interactions driven by glycosylation events.
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Affiliation(s)
- Nihal Najeeb
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Aparna B Murukan
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Anagha Renjitha
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Malavika Jayaram
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Ayisha A Jabbar
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Haripriya Haridasan
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Akshara Prijikumar
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Sneha Baiju
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Adrial Ann Nixon
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | | | - Sunu Rodriguez
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Somesh Kumar
- Genome Sequencing Lab, Lok Nayak Hospital, Delhi, India
| | | | - Keshav K Singh
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Kaul Genetics Building, Birmingham, AL, USA
| | - Bipin G Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Sudeep D Ghate
- Center for Bioinformatics, NITTE University, Mangaluru, India
| | | | | | - Arya Aloor
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Renuka Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India.
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LncPheDB: a genome-wide lncRNAs regulated phenotypes database in plants. ABIOTECH 2022; 3:169-177. [PMID: 36304839 PMCID: PMC9590470 DOI: 10.1007/s42994-022-00084-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/12/2022] [Indexed: 11/01/2022]
Abstract
LncPheDB (https://www.lncphedb.com/) is a systematic resource of genome-wide long non-coding RNAs (lncRNAs)-phenotypes associations for multiple species. It was established to display the genome-wide lncRNA annotations, target genes prediction, variant-trait associations, gene-phenotype correlations, lncRNA-phenotype correlations, and the similar non-coding regions of the queried sequence in multiple species. LncPheDB sorted out a total of 203,391 lncRNA sequences, 2000 phenotypes, and 120,271 variants of nine species (Zea mays L., Gossypium barbadense L., Triticum aestivum L., Lycopersicon esculentum Mille, Oryza sativa L., Hordeum vulgare L., Sorghum bicolor L., Glycine max L., and Cucumis sativus L.). By exploring the relationship between lncRNAs and the genomic position of variants in genome-wide association analysis, a total of 68,862 lncRNAs were found to be related to the diversity of agronomic traits. More importantly, to facilitate the study of the functions of lncRNAs, we analyzed the possible target genes of lncRNAs, constructed a blast tool for performing similar fragmentation studies in all species, linked the pages of phenotypic studies related to lncRNAs that possess similar fragments and constructed their regulatory networks. In addition, LncPheDB also provides a user-friendly interface, a genome visualization platform, and multi-level and multi-modal convenient data search engine. We believe that LncPheDB plays a crucial role in mining lncRNA-related plant data. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-022-00084-3.
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Abdi E, Latifi-Navid S. LncRNA polymorphisms and urologic cancer risk. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2022; 63:190-203. [PMID: 35178782 DOI: 10.1002/em.22472] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/11/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Urologic cancers involve nearly one-quarter of all cancers and include the prostate, bladder, and kidney cancers. Long non-coding RNAs (LncRNAs) are expressed in a tissue-specific manner and affect cell proliferation, apoptosis, and differentiation. LncRNAs expression is misregulated in urologic cancers, as their aberrant expression may make them capable of being utilized in the diagnosis, prognosis, and treatment of cancers. LncRNAs polymorphisms can affect their structure, expression, and function by interfering with the associated target mRNAs. As a result, lncRNA polymorphisms may be linked to the mechanism driving cancer susceptibility. Therefore, SNPs in lncRNAs may be a beneficial biomarker for early diagnosis and prognosis of cancers, as they affect lncRNA role in tumorigenesis and cancer progression. Moreover, the genetic heredity of lncRNA SNPs affects the personal therapeutic response to drugs. In this study, the lncRNAs polymorphism is summarized in relation to urologic cancers. It is proposed that lncRNA-related polymorphisms, as an individual or combined genotypes, can predict urologic cancer risk, even clinical and prognostic outcomes. However, large-scale population-based prospective studies and comprehensive meta-analyses should be conducted to validate and use these lncRNAs SNPs as the indicators of urologic cancers. Future research should examine the function of these SNPs to explain their associations with urologic cancers.
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Affiliation(s)
- Esmat Abdi
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Saeid Latifi-Navid
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil, Iran
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8
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Zhong X, Guo Q, Zhao J, Li Y, Li X, Ren M, Shu M. Diagnostic significance of long non-coding RNAs expression in tuberculosis patients: A systematic review and meta-analysis. Medicine (Baltimore) 2022; 101:e28879. [PMID: 35363201 PMCID: PMC9282113 DOI: 10.1097/md.0000000000028879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 01/28/2021] [Indexed: 01/04/2023] Open
Abstract
OBJECTIVES It is crucial to identify effective diagnostic biosignatures of tuberculosis (TB) to optimize its treatment. Herein, we conducted a systematic review to elucidate the diagnostic efficacy of long noncoding RNA (lncRNAs) as TB biomarkers. METHODS We searched Medline, Web of Science, Embase, Cochrane Library, CNKI, Wanfang, VIP, and China Biology Medicine disc databases up to February 18, 2020. These studies focusing on lncRNAs as diagnosis markers of TB were collected. STATA 12.0 and Meta-disc1.4 software were used to analyze the data extracted from eligible studies. RESULTS We included 8 articles with 1058 TB patients, and 1896 healthy controls in our study. The values of pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio were 0.63, 0.86, 4.48, 0.43, and 10.31, respectively. Additionally, we plotted the summary receiver operating characteristic curve to evaluate the diagnostic accuracy, and the area under the curve was 0.80. CONCLUSION The present study is the first meta-analysis to assess the diagnostic accuracy of lncRNAs in TB patients. We found that lncRNAs might constitute potential biomarkers for the diagnosis of TB patients. More population-based high-quality research should be conducted to validate the efficacy lncRNAs in TB patients.
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Affiliation(s)
- Xiaoling Zhong
- Department of Infectious Pediatrics, West China Second Hospital, Sichuan University/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Qin Guo
- Department of Infectious Pediatrics, West China Second Hospital, Sichuan University/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Jing Zhao
- Emergency Department, Lanzhou University Second Hospital, Lanzhou 730030, China
| | - Yinyue Li
- Department of Infectious Pediatrics, West China Second Hospital, Sichuan University/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xue Li
- Department of Infectious Pediatrics, West China Second Hospital, Sichuan University/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Min Ren
- Department of Infectious Pediatrics, West China Second Hospital, Sichuan University/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Min Shu
- Department of Infectious Pediatrics, West China Second Hospital, Sichuan University/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
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9
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Long Non-Coding RNAs at the Chromosomal Risk Loci Identified by Prostate and Breast Cancer GWAS. Genes (Basel) 2021; 12:genes12122028. [PMID: 34946977 PMCID: PMC8701176 DOI: 10.3390/genes12122028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/20/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as key players in a variety of cellular processes. Deregulation of the lncRNAs has been implicated in prostate and breast cancers. Recently, germline genetic variations associated with cancer risk have been correlated with lncRNA expression and/or function. In addition, single nucleotide polymorphisms (SNPs) at well-characterized cancer-associated lncRNAs have been analyzed for their association with cancer risk. These SNPs may occur within the lncRNA transcripts or spanning regions that may alter the structure, function, and expression of these lncRNA molecules and contribute to cancer progression and may have potential as therapeutic targets for cancer treatment. Additionally, some of these lncRNA have a tissue-specific expression profile, suggesting them as biomarkers for specific cancers. In this review, we highlight some of the cancer risk-associated SNPs that modulated lncRNAs with a potential role in prostate and breast cancers and speculate on how these lncRNAs may contribute to cancer development.
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Salimi S, Sargazi S, Heidari Nia M, Mirani Sargazi F, Ghasemi M. Genetic variants of HOTAIR are associated with susceptibility to recurrent spontaneous abortion: A preliminary case-control study. J Obstet Gynaecol Res 2021; 47:3767-3778. [PMID: 34396639 DOI: 10.1111/jog.14977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/26/2021] [Accepted: 07/29/2021] [Indexed: 11/30/2022]
Abstract
AIM To investigate the association between Hox transcript antisenses RNA (HOTAIR) polymorphisms, rs12826786 C/T, rs920778 T/C, rs4759314 A/G, and rs1899663 G/T, with recurrent spontaneous abortion (RSA) susceptibility in the Iranian women. METHODS We enrolled 161 patients diagnosed with RSA and 177 healthy women with at least one live birth without a history of abortion. Genotyping of HOTAIR polymorphisms was carried out using both restriction fragment length polymorphism-polymerase chain reaction and amplification refractory mutation system-polymerase chain reaction methods. Odds ratios (ORs) with 95% confidence intervals (CIs) were assessed to estimate the strength of association. RESULTS Different inheritance models of rs12826786 C/T, rs920778 T/C, and rs1899663 G/T polymorphisms significantly enhanced the risk of RSA (p < 0.05), whereas the rs4759314 A/G polymorphism was correlated with diminished risk of developing RSA under recessive AA versus GA + GG (OR 0.42 [95% CI = 0.19-0.91]), log-additive GG versus GA vs. GG (OR 0.67 [95% CI = 0.48-0.93]), and allelic A versus G (OR 0.65 [95% CI = 0.47-0.92]) models. Moreover, the TGTC, TTCT, TTTC, CGTC, CGTT, CTCC, CTCT, CTTC, and CTTT haplotypes of rs920778/rs1899663/rs12826786/ significantly increased the risk of RSA. The studied variants were not in strong linkage disequilibrium. CONCLUSIONS Our results indicated that variations in the HOTAIR gene might serve as beneficial biomarkers for determining susceptibility to RSA. To confirm these findings, replication studies with a larger population and different races are needed.
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Affiliation(s)
- Saeedeh Salimi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran.,Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Saman Sargazi
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Milad Heidari Nia
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Fariba Mirani Sargazi
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Marzieh Ghasemi
- Pregnancy Health Research Center, Zahedan University of Medical Sciences, Zahedan, Iran.,Moloud Infertility Center, Ali Ibn Abitaleb Hospital, Zahedan University of Medical Sciences, Zahedan, Iran
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11
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Wang X, Song B, Zang M, Ji H, Yang H, Jiang S, Yang X. LOC100996425 acts as a promoter in prostate cancer by mediating hepatocyte nuclear factor 4A and the AMPK/mTOR pathway. J Cell Mol Med 2021; 25:8174-8186. [PMID: 34309216 PMCID: PMC8419185 DOI: 10.1111/jcmm.16657] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 04/23/2021] [Accepted: 05/01/2021] [Indexed: 12/11/2022] Open
Abstract
The involvement of long non-coding RNAs (lncRNAs), differentially expressed genes and signals in prostate cancer (PCa) continues to be a subject of investigation. This study determined effects of LOC100996425 on human PCa by targeting hepatocyte nuclear factor 4A (HNF4A) via the AMPK/mTOR pathway. PCa and adjacent normal tissues were obtained to characterize expression pattern of LOC100996425, HNF4A and the AMPK/mTOR pathway-related genes. Then, the target gene of LOC100996425 was determined with lncRNA target prediction website and further verification was obtained through luciferase assay and ribonucleoprotein immunoprecipitation. After that, PCa cells were introduced with LOC100996425, HNF4A, siLOC100996425 or siHNF4A to explore the specific significance of LOC100996425 and HNF4A in PCa. The mechanism associated with AMPK/mTOR pathway was investigated using AMPK inhibitor or activator. LOC100996425 was up-regulated, while HNF4A was down-regulated in the PCa tissues. HNF4A was a target gene of LOC100996425. PCa cells transfected with either siLOC100996425 or HNF4A displayed reduced rates of PCa cell proliferation and migration while elevating cell apoptosis. HNF4A overexpression reversed the promotive effect of LOC100996425 overexpression on PCa. The activation of AMPK pathway involved in the cancer progression mediated by LOC100996425. Down-regulation of LOC100996425 retards progression of PCa through HNF4A-mediated AMPK/mTOR pathway.
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Affiliation(s)
- Xiuyan Wang
- Department of Urology, The Second Hospital of Jilin University, Changchun, China
| | - Bin Song
- Department of Neurosurgery, The Second Hospital of Jilin University, Changchun, China
| | - Mingcui Zang
- Department of Hepatobiliary and Pancreatic Surgery I, The First Hospital of Jilin University, Changchun, China
| | - He Ji
- Department of Gynaecology, The Second Hospital of Jilin University, Changchun, China
| | - He Yang
- Department of Urology, The Second Hospital of Jilin University, Changchun, China
| | - Shuang Jiang
- Department of Urology, The Second Hospital of Jilin University, Changchun, China
| | - Xiao Yang
- Department of Urology, The Second Hospital of Jilin University, Changchun, China
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Yang Y, Liu S, He C, Chen Z, Lyu T, Zeng L, Wang L, Zhang F, Chen H, Zhao RC. Long Non-coding RNA Regulation of Mesenchymal Stem Cell Homeostasis and Differentiation: Advances, Challenges, and Perspectives. Front Cell Dev Biol 2021; 9:711005. [PMID: 34368161 PMCID: PMC8339964 DOI: 10.3389/fcell.2021.711005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/21/2021] [Indexed: 12/25/2022] Open
Abstract
Given the self-renewal, multi-differentiation, immunoregulatory, and tissue maintenance properties, mesenchymal stem cells (MSCs) are promising candidates for stem cell-based therapies. Breakthroughs have been made in uncovering MSCs as key contributors to homeostasis and the regenerative repair of tissues and organs derived from three germ layers. MSC differentiation into specialized cell types is sophisticatedly regulated, and accumulating evidence suggests long non-coding RNAs (lncRNAs) as the master regulators of various biological processes including the maintenance of homeostasis and multi-differentiation functions through epigenetic, transcriptional, and post-translational mechanisms. LncRNAs are ubiquitous and generally referred to as non-coding transcripts longer than 200 bp. Most lncRNAs are evolutionary conserved and species-specific; however, the weak conservation of their sequences across species does not affect their diverse biological functions. Although numerous lncRNAs have been annotated and studied, they are nevertheless only the tip of the iceberg; the rest remain to be discovered. In this review, we characterize MSC functions in homeostasis and highlight recent advances on the functions and mechanisms of lncRNAs in regulating MSC homeostasis and differentiation. We also discuss the current challenges and perspectives for understanding the roles of lncRNAs in MSC functions in homeostasis, which could help develop promising targets for MSC-based therapies.
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Affiliation(s)
- Yanlei Yang
- Key Laboratory of the Ministry of Education, Department of Rheumatology and Clinical Immunology, Clinical Immunology Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Beijing Key Laboratory (No. BZO381), School of Basic Medicine, Center of Excellence in Tissue Engineering, Peking Union Medical College Hospital, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Suying Liu
- Key Laboratory of the Ministry of Education, Department of Rheumatology and Clinical Immunology, Clinical Immunology Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Chengmei He
- Key Laboratory of the Ministry of Education, Department of Rheumatology and Clinical Immunology, Clinical Immunology Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhilei Chen
- Key Laboratory of the Ministry of Education, Department of Rheumatology and Clinical Immunology, Clinical Immunology Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Taibiao Lyu
- Key Laboratory of the Ministry of Education, Department of Rheumatology and Clinical Immunology, Clinical Immunology Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Liuting Zeng
- Key Laboratory of the Ministry of Education, Department of Rheumatology and Clinical Immunology, Clinical Immunology Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Li Wang
- Key Laboratory of the Ministry of Education, Department of Rheumatology and Clinical Immunology, Clinical Immunology Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Fengchun Zhang
- Key Laboratory of the Ministry of Education, Department of Rheumatology and Clinical Immunology, Clinical Immunology Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Hua Chen
- Key Laboratory of the Ministry of Education, Department of Rheumatology and Clinical Immunology, Clinical Immunology Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Robert Chunhua Zhao
- Beijing Key Laboratory (No. BZO381), School of Basic Medicine, Center of Excellence in Tissue Engineering, Peking Union Medical College Hospital, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,School of Life Sciences, Shanghai University, Shanghai, China
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13
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Subtype specific expression and survival prediction of pivotal lncRNAs in muscle invasive bladder cancer. Sci Rep 2020; 10:20472. [PMID: 33235218 PMCID: PMC7687888 DOI: 10.1038/s41598-020-77252-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/26/2020] [Indexed: 11/08/2022] Open
Abstract
Comprehensive transcriptome expression analyses of bladder cancer revealed distinct lncRNA clusters with differential molecular and clinical characteristics. In this study, pivotal lncRNAs were assessed for their impact on survival and their differential expression between the molecular bladder cancer subtypes. FFPE samples from chemotherapy-naïve patients with muscle invasive bladder cancer (MIBC) were analyzed on the Nanostring nCounter platform for absolute quantification. An established 36-gene panel was used for molecular subtype classification into basal, luminal and infiltrated MIBC. In a second step, 14 pivotal lncRNAs were assessed for their molecular subtype attribution, and their predictive value in disease-specific survival. In silico validation was performed on a total of 487 MIBC patients (MDA, TGCA and Chungbuk cohort). Several pivotal lncRNAs showed a distinct molecular subtype attribution: e.g. MALAT1 showed a downregulation in the basal subtype (p = 0.009), TUG1 and CBR3AS1 showed an upregulation in the luminal subtype (p ≤ 0.001). High transcript levels of SNHG16, CBR3AS1 and H19 appeared to be predictive for a shorter disease-specific survival. Patients overexpressing putative oncogenes MALAT1 and TUG1 in MIBC tissue presented prolonged survival, suggesting tumor suppressive effects of both lncRNAs. The Nanostring nCounter proved to be a valid platform for the quantification of low-abundance transcripts including lncRNAs.
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14
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Wu M, Fu P, Qu L, Liu J, Lin A. Long Noncoding RNAs, New Critical Regulators in Cancer Immunity. Front Oncol 2020; 10:550987. [PMID: 33194608 PMCID: PMC7662117 DOI: 10.3389/fonc.2020.550987] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) play crucial roles in various aspects of cellular functions. Recent studies have revealed that lncRNAs are critical players in the immune system by modulating immune cell differentiation and functions, particularly in cancer immunity. Here we systematically summarize how lncRNAs are involved in different processes of the cancer immunity cycle, including immune cell differentiation, proliferation, trafficking, and infiltration. Moreover, the limitations of the current understanding of lncRNA’s functions in cancer immunity are described, such as the complexity of the cancer immunity system, the inclusive functions of lncRNAs in this system, and the associated immune response. In sum, the comprehensive investigation of the roles of lncRNAs in cancer immunity aids in cancer diagnosis and therapies.
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Affiliation(s)
- Minjie Wu
- Breast Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Peifen Fu
- Breast Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lei Qu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jian Liu
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Aifu Lin
- Breast Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
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15
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Li W, Xu C, Guo J, Liu K, Hu Y, Wu D, Fang H, Zou Y, Wei Z, Wang Z, Zhou Y, Li Q. Cis- and Trans-Acting Expression Quantitative Trait Loci of Long Non-Coding RNA in 2,549 Cancers With Potential Clinical and Therapeutic Implications. Front Oncol 2020; 10:602104. [PMID: 33194770 PMCID: PMC7604522 DOI: 10.3389/fonc.2020.602104] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 09/28/2020] [Indexed: 11/13/2022] Open
Abstract
Many cancer risk loci act as expression quantitative trait loci (eQTLs) of transcripts including non-coding RNA. Long non-coding RNAs (lncRNAs) are implicated in various human cancers. However, the pathological and clinical impacts of the genetic determinants of lncRNAs in cancers remain largely unknown. In this study, we performed eQTL mapping of lncRNA expression (elncRNA) in 11 TCGA cancer types and characterized the biological processes of elncRNAs in the setting of genomic location, cancer treatment responses, and immune microenvironment. As a result, 10.86% of the cis-eQTLs and 1.67% of the trans-eQTLs of lncRNA were related to known genome-wide association studies (GWAS) cancer risk loci. The elncRNAs are significantly enriched for those which are previously annotated as predictive of drug sensitivities in cancer cell lines. We further revealed the downstream transcriptomic effectors of eQTL-elncRNA pairs. Our data specifically suggested that the genes affected by eQTL-elncRNA associations are enriched in the immune system processes and eQTL-elncRNA associations influence the constitution of tumor infiltrating lymphocytes. In ovarian cancer, the "rs34631313-AC092580.4" pair was associated with increased fraction of CD8+ T cells and M1 Macrophage; whereas in KIRC, the "rs9546285-LINC00426" pair was associated with increased fraction of CD8+ T cells and a decreased fraction of M2 macrophages. Our findings provide a systematic view of the transcriptomic impacts of the eQTL landscape of lncRNA in human cancers and suggest its strong potential relevance to cancer immunity and treatment.
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Affiliation(s)
- Wenzhi Li
- Department of Urology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chaoqun Xu
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Jintao Guo
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Ke Liu
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Yudi Hu
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Dan Wu
- Department of Oncology, Xiamen the Fifth Hospital, Xiamen, China
| | - Hongkun Fang
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Yun Zou
- Department of Urology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ziwei Wei
- Department of Urology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhong Wang
- Department of Urology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Zhou
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Qiyuan Li
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
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16
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Jia Z, Li W, Bian P, Liu H, Pan D, Dou Z. LncRNA MCM3AP-AS1 Promotes Cell Proliferation and Invasion Through Regulating miR-543-3p/SLC39A10/PTEN Axis in Prostate Cancer. Onco Targets Ther 2020; 13:9365-9376. [PMID: 33061424 PMCID: PMC7519818 DOI: 10.2147/ott.s245537] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 07/24/2020] [Indexed: 12/11/2022] Open
Abstract
Objective Long-chain noncoding RNAs (lncRNAs) are key players in a wide range of biological processes, especially the pathogenesis and development of tumors. LncRNA MCM3AP-AS1 has been demonstrated to be involved in the invasion of various tumors including prostate cancer (PCa). However, its functions in PCa have not been fully elucidated. Methods qRT-PCR was conducted to measure the expression levels of lncRNA MCM3AP-AS1 and miR-543-3p in PCa tissue samples and cell lines. The expression levels of E-cadherin and SLC39A10 proteins were detected by Western blots. CCK-8 test, cell scratch test and trans-well test were used to evaluate the proliferation, invasion and migration abilities of PCa cells, respectively. Annexin V-FITC/PI experiments were carried out to determine the status of apoptosis. Bioinformatics analysis and Luciferase assay were used to explore the relationship between lncRNA MCM3AP-AS1, miR-543-3p and SLC39A10. Results In PCa tissue samples and cell lines, lncRNA MCM3AP-AS1 was up-regulated while miR-543-3p was down-regulated. Over-expression of MCM3AP-AS1 could promote the proliferation and invasion of PCa cells. Correlation analysis showed that the expression of MCM3AP-AS1 and miR-543-3p was significantly and inversely correlated. We further verified that miR-543-3p inhibitor was able to reverse si-MCM3AP-AS1-mediated inhibitory effects on the PCa cell proliferation, migration and invasion through regulating the downstream protein axis SLC39A10/PTEN/Akt. Finally, in vivo experiments indicated that knocking down of MCM3AP-AS1 could largely reduce tumor volumes, and decreased the ratio of Ki67-positive cells and the expression of SLC39A10 in tumor samples. Conclusion LncRNA MCM3AP-AS1 can promote the proliferation, migration and invasion abilities of PCa cells through regulating the miR-543-3p/SLC39A10/PTEN axis, which suggests that lncRNA MCM3AP-AS1 might be a potential target for prostate cancer therapy.
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Affiliation(s)
- Zhaohui Jia
- Department of Urology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, Henan 471003, People's Republic of China
| | - Wensheng Li
- Department of Urology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, Henan 471003, People's Republic of China
| | - Pan Bian
- Department of Urology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, Henan 471003, People's Republic of China
| | - Hui Liu
- Department of Urology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, Henan 471003, People's Republic of China
| | - Dong Pan
- Department of Urology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, Henan 471003, People's Republic of China
| | - Zhongling Dou
- Department of Urology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, Henan 471003, People's Republic of China
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17
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The LGMN pseudogene promotes tumor progression by acting as a miR-495-3p sponge in glioblastoma. Cancer Lett 2020; 490:111-123. [PMID: 32711096 DOI: 10.1016/j.canlet.2020.07.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 12/19/2022]
Abstract
Pseudogenes, which are long noncoding RNAs that originate from protein-coding genes, have been suggested to play important roles in disease. Although studies have revealed high expression of legumain (LGMN) in many types of tumors, the regulation of LGMN remains largely unknown. Here, we found that a novel LGMN pseudogene (LGMNP1) was upregulated in glioblastoma (GBM) tissues and high LGMNP1 expression in GBM cells enhanced proliferation and invasion. Biochemical analysis showed that cytoplasmic LGMNP1 functionally targeted miR-495-3p in a manner involving an RNA-induced silencing complex. Dual-luciferase reporter assays demonstrated that LGMN was a target of miR-495-3p, and LGMN was upregulated and positively correlated with LGMNP1 in GBM. Moreover, miR-495-3p was downregulated and negatively correlated with LGMNP1 in GBM tissues. Notably, the tumor-promoting effects of LGMNP1 upregulation could be alleviated by miR-495-3p mimics. Furthermore, GBM cells overexpressing LGMNP1 exhibited more aggressive tumor progression and elevated LGMN expression in vivo. Thus, our data illustrate that LGMNP1 exerts its oncogenic activity, at least in part, as a competitive endogenous RNA (ceRNA) that elevates LGMN expression by sponging miR-495-3p. CeRNA-mediated miRNA sequestration might be a novel therapeutic strategy in GBM.
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18
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Wu Z, Huang W, Chen Y, Chen B, Liu R, Bai P, Xing J. LINC01638 lncRNA promotes the proliferation, migration and invasion of prostate carcinoma cells by interacting with Notch1. Cancer Biomark 2019; 25:161-168. [PMID: 31104008 DOI: 10.3233/cbm-182137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
LINC01638 lncRNA is known as an oncogenic lncRNA in triple negative breast cancer. However, the role of LINC01638 lncRNA in other diseases is unknown. In the present study we observed that plasma levels of LINC01638 lncRNA and Notch1 were upregulated in prostate carcinoma patients comparing with healthy controls. LINC01638 lncRNA and Notch1 were positively correlated in prostate carcinoma patients but not in healthy controls. Upregulation of LINC01638 lncRNA distinguished prostate carcinoma patients from healthy controls. LINC01638 lncRNA overexpression in prostate carcinoma cells led to upregulated Notch1 expression. Notch1 overexpression also led to increased expression level of LINC01638 lncRNA. Both LINC01638 lncRNA and Notch1 overexpression promoted the proliferation, migration and invasion of prostate carcinoma cells. We concluded that LINC01638 lncRNA might promote the proliferation, migration and invasion of prostate carcinoma cells by interacting with Notch1.
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19
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Jiang D, Jin M, Ye D, Li Y, Jing F, Zhang X, Li Q, Chen K. Polymorphisms of a novel long non-coding RNA RP11-108K3.2 with colorectal cancer susceptibility and their effects on its expression. Int J Biol Markers 2019; 35:3-9. [PMID: 31789575 DOI: 10.1177/1724600819888512] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND RP11-108K3.2 was recently identified as a novel long non-coding RNA (lncRNA) transcript, and several single nucleotide polymorphisms (SNPs) have been identified in its coding region. This study aimed to explore the associations of tagSNPs in RP11-108K3.2 with the risk of colorectal cancer and their effects on its expression. METHODS A total of 821 colorectal cancer cases and 857 healthy controls were enrolled into this two-stage case-control study. Demographic characteristics and lifestyle information were collected by a validated questionnaire. Six tagSNPs were genotyped by using Sequenom MassARRAY platform. A total of 71 additional colorectal cancer cases were recruited, of which the genotypes of potential polymorphisms and the RP11-108K3.2 expression levels were determined. RESULTS In the discovery set, only the rs2470151 C/T polymorphism was found to have a promising association with the risk of colorectal cancer, and this polymorphism was further replicated in the validation set with a significantly decreased risk of colorectal cancer (adjusted odds ratio 0.73; 95% confidence interval 0.55, 0.97). Combined discovery set and validation set together, this negative association was found both in the heterozygote codominant model and the dominant model. Furthermore, colorectal cancer patients carrying rs2470151 CT/TT genotypes had a marginally lower RNA expression of RP11-108K3.2 than those carrying the CC genotype. Stratified analyses showed the association between rs2470151 and the risk of colorectal cancer were influenced by family history of cancer, smoking, alcohol consumption, and tea drinking. CONCLUSIONS These findings suggest that RP11-108K3.2 rs2470151 had a significant association with the risk of colorectal cancer; this may help to predict the susceptibility of colorectal cancer in Chinese populations.
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Affiliation(s)
- Danjie Jiang
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, Hangzhou, Zhejiang, China
| | - Mingjuan Jin
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, Hangzhou, Zhejiang, China
| | - Ding Ye
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, Hangzhou, Zhejiang, China.,Department of Epidemiology and Biostatistics, Zhejiang Chinese Medicine University, Hangzhou, Zhejiang, China
| | - Yingjun Li
- Department of Public Health, Hangzhou Medical School, Hangzhou, Zhejiang, China
| | - Fangyuan Jing
- Department of Public Health, Hangzhou Medical School, Hangzhou, Zhejiang, China
| | - Xiaocong Zhang
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, Hangzhou, Zhejiang, China
| | - Qilong Li
- Jiashan Institute of Cancer Prevention and Treatment, Jiaxing, Zhejiang, China
| | - Kun Chen
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, Hangzhou, Zhejiang, China.,Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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20
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Qi J, Du L, Deng J, Qin Y, Su G, Hou S, Lv M, Zhang Q, Kijlstra A, Yang P. Replication of Genome-Wide Association Analysis Identifies New Susceptibility Loci at Long Noncoding RNA Regions for Vogt-Koyanagi-Harada Disease. ACTA ACUST UNITED AC 2019; 60:4820-4829. [PMID: 31747682 DOI: 10.1167/iovs.19-27708] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Jian Qi
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing, The People's Republic of China
| | - Liping Du
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing, The People's Republic of China
| | - Jing Deng
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing, The People's Republic of China
| | - Yang Qin
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing, The People's Republic of China
| | - Guannan Su
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing, The People's Republic of China
| | - Shengping Hou
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing, The People's Republic of China
| | - Meng Lv
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing, The People's Republic of China
| | - Qi Zhang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing, The People's Republic of China
| | - Aize Kijlstra
- University Eye Clinic Maastricht, Maastricht, The Netherlands
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing, The People's Republic of China
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21
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Zuo Y, Liang Y, Zhang J, Hao Y, Li M, Wen Z, Zhao Y. Transcriptome Analysis Identifies Piwi-Interacting RNAs as Prognostic Markers for Recurrence of Prostate Cancer. Front Genet 2019; 10:1018. [PMID: 31695724 PMCID: PMC6817565 DOI: 10.3389/fgene.2019.01018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 09/24/2019] [Indexed: 12/11/2022] Open
Abstract
Prostate cancer remains the second leading cause of male cancer death, and there is an unmet need for biomarkers to identify patients with such aggressive disease. Piwi-inteacting RNAs (piRNAs) have been classified as transcriptional and posttranscriptional regulators in somatic cells. In this study, we discovered three piRNAs as novel prognostic markers and their association with prostate cancer biochemical recurrence was confirmed in validation data set. To obtain a better understanding of piRNA expression patterns in prostate cancer and to find gene coexpression with piRNAs, we performed weighted gene coexpression network analysis. Target genes of three piRNAs have also been predicted based on base complementarity and expression correlativity. Functional analysis revealed the relationships between target genes and prostate cancer. Our work also identified differential expression of piRNAs between Gleason stage 3 + 4 and 4 + 3 prostate cancer. Overall, this study may explain the roles and demonstrate the potential clinical utility of piRNAs in prostate cancer in a way.
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Affiliation(s)
- Yuanli Zuo
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yu Liang
- College of Chemistry, Sichuan University, Chengdu, China
| | - Jiting Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yingyi Hao
- College of Chemistry, Sichuan University, Chengdu, China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, China
| | - Zhining Wen
- College of Chemistry, Sichuan University, Chengdu, China.,Medical Big Data Center, Sichuan University, Chengdu, China
| | - Yun Zhao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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22
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Luo X, He S, Hu Y, Liu J, Chen X. Sp1-induced LncRNA CTBP1-AS2 is a novel regulator in cardiomyocyte hypertrophy by interacting with FUS to stabilize TLR4. Cardiovasc Pathol 2019; 42:21-29. [PMID: 31220774 DOI: 10.1016/j.carpath.2019.04.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/19/2019] [Accepted: 04/30/2019] [Indexed: 02/05/2023] Open
Abstract
Cardiomyocyte hypertrophy is a heart response adapting to increasing cardiac load. Prolonged cardiomyocyte hypertrophy indicates a higher risk of heart failure or even cardiac death. Long noncoding RNAs have been largely reported to modulate human diseases. CTPB1-AS2 is a newly discovered lncRNA reported as an oncogene in papillary thyroid cancer, but its function in cardiomyocyte hypertrophy has never been probed. Toll-like receptor 4 (TLR4) is recognized to play important roles in cardiomyocyte hypertrophy. The present study aimed to investigate the role of CTBP1-AS2 in cardiomyocyte hypertrophy. First, we discovered the low expression of CTBP1-AS2 in normal heart tissues in GETx database. Then, we established cardiomyocyte hypertrophy models on mice and cardiomyocytes through transverse aortic constriction surgery and Ang II treatment. We revealed the up-regulation of CTBP1-AS2 and TLR4 in cardiomyocyte hypertrophy models. Also, we confirmed the positive correlation between CTBP1-AS2 and TLR4 expressions in cardiomyocyte hypertrophy tissues. Loss-of-function assays confirmed that inhibiting CTBP1-AS2 attenuated the Ang II-induced cardiomyocyte hypertrophy. Mechanism research showed that CTBP1-AS2 stabilized TLR4 mRNA by recruiting FUS. Rescue assays certified that CTBP1-AS2 regulated cardiomyocyte hypertrophy through TLR4. Finally, we found Sp1 as an upstream activator for CTBP1-AS2 expression. In conclusion, our study uncovered CTBP1-AS2 as a novel regulator of cardiomyocyte hypertrophy through regulating TLR4, providing a new potential treatment target for cardiomyocyte hypertrophy.
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Affiliation(s)
- Xiaojia Luo
- Department of Cardiovascular Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Department of Cardiovascular Medicine, Chengdu Second People's Hospital, Chengdu, Sichuan, 610017, China
| | - Sen He
- Department of Cardiovascular Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yongmei Hu
- Department of Cardiovascular Medicine, Chengdu Second People's Hospital, Chengdu, Sichuan, 610017, China
| | - Jianxiong Liu
- Department of Cardiovascular Medicine, Chengdu Second People's Hospital, Chengdu, Sichuan, 610017, China
| | - Xiaoping Chen
- Department of Cardiovascular Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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23
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Ramnarine VR, Kobelev M, Gibb EA, Nouri M, Lin D, Wang Y, Buttyan R, Davicioni E, Zoubeidi A, Collins CC. The evolution of long noncoding RNA acceptance in prostate cancer initiation, progression, and its clinical utility in disease management. Eur Urol 2019; 76:546-559. [PMID: 31445843 DOI: 10.1016/j.eururo.2019.07.040] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 07/26/2019] [Indexed: 02/07/2023]
Abstract
CONTEXT It is increasingly evident that non-protein-coding regions of the genome can give rise to transcripts that form functional layers of the cancer genome. One of most abundant classes in these regions is long noncoding RNAs (lncRNAs). They have gained increasing attention in prostate cancer (PCa) and paved the way for a greater understanding of these cryptic regulators in cancer. OBJECTIVE To review current research exploring the functional biology of lncRNAs in PCa over the past three decades. EVIDENCE ACQUISITION A systematic review was performed using PubMed to search for reports with terms "long noncoding RNA", "prostate", and "cancer" over the past 30 yr (1988-2018). EVIDENCE SYNTHESIS We comprehensively surveyed the literature collected and summarise experiments leading to the characterisation of lncRNAs in PCa. A historical timeline of lncRNA identification is described, where each lncRNA is categorised mechanistically and within the primary areas of carcinogenesis: tumour risk and initiation, tumour promotion, tumour suppression, and tumour treatment resistance. We describe select lncRNAs that exemplify these areas. We also review whether these lncRNAs have a clinical utility in PCa diagnosis, prognosis, and prediction, and as therapeutic targets. CONCLUSIONS The biology of lncRNA is multifaceted, demonstrating a complex array of molecular and cellular functions. These studies reveal that lncRNAs are involved in every stage of PCa. Their clinical utility for diagnosis, prognosis, and prediction of PCa is well supported, but further evaluation for their therapeutic candidacy is needed. We provide a detailed resource and view inside the lncRNA landscape for other cancer biologists, oncologists, and clinicians. PATIENT SUMMARY In this study, we review current knowledge of the non-protein-coding genome in prostate cancer (PCa). We conclude that many of these regions are functional and a source of accurate biomarkers in PCa. With a strong research foundation, they hold promise as future therapeutic targets, yet clinical trials are necessary to determine their intrinsic value to PCa disease management.
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Affiliation(s)
- Varune Rohan Ramnarine
- Vancouver Prostate Centre, Vancouver, BC, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Maxim Kobelev
- Vancouver Prostate Centre, Vancouver, BC, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ewan A Gibb
- Decipher Biosciences Inc., Vancouver, BC, Canada
| | - Mannan Nouri
- Vancouver Prostate Centre, Vancouver, BC, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Dong Lin
- Vancouver Prostate Centre, Vancouver, BC, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada; Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, Canada
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Vancouver, BC, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada; Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, Canada
| | - Ralph Buttyan
- Vancouver Prostate Centre, Vancouver, BC, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | - Amina Zoubeidi
- Vancouver Prostate Centre, Vancouver, BC, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Colin C Collins
- Vancouver Prostate Centre, Vancouver, BC, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.
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24
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Adetula AA, Azmal SA, Sun C, Elokil A, Li S. Association of single nucleotide polymorphism at long non-coding RNA 8138.1 with duration of fertility in egg-laying hens. PeerJ 2019; 7:e7282. [PMID: 31338259 PMCID: PMC6628881 DOI: 10.7717/peerj.7282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 06/04/2019] [Indexed: 11/20/2022] Open
Abstract
A previous genome-wide transcriptional analysis identified long non-coding RNA 8138.1 (lncRNA8138.1) as a candidate gene related to hen duration of the fertility (DF) trait. LncRNA8138.1 gene response to growth factor and reproductive system development suggests it has a vital role in reproduction. In this study, we investigated the lncRNA8138.1 gene sequence in a population of egg-laying hens. The sequence analysis of the lncRNA8138.1 gene containing about 1.6 k nucleotides (nt) was observed with four single nucleotide polymorphisms (SNPs) and 7 nt indel including r.4937159A > G; r.4937219T > C; r.4937258G > C; r.4937318C > G and g.4937319_4937325delinsTGTGTGG. Next, the genomic DNAs from laying hen populations were subjected to polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) to detect a region of 457 bp carrying lncRNA8138.1 r.4937159A > G substitution. Further inspection of the region containing r.4937159A > G mutation revealed three genotypes viz., AA, AG, and GG were observed with respective frequencies of 0.106, 0.607, and 0.287 in laying hen population 1 (P1) (n = 1, 042) and respective frequencies of 0.176, 0.708, and 0.116 in laying hen population 2 (P2) (n = 826). Moreover, to further examining the frequencies of r.4937159A > G genotypes in P1 and P2, and their additive and dominance effects; r.4937159A > G locus was significantly associated with DF-trait in both P1 and P2 (EN: the number of eggs, FN: the number of fertile eggs after a single AI), and DN (the number of days post-insemination until last fertile egg). In testing for additive and dominance effects, additive effect was significant (P < 0.05) in both P1 and P2 for DF-trait, and the dominance effect was significant (P < 0.05) for EN and FN traits, suggesting that r.4937159A > G polymorphism is a potential biomarker for DF-trait. However, the identified novel r.4937159A > G mutation and others require further investigation to confirm phenotypic causality and potential genetic relationships with reproductive traits. Overall, our findings suggest the significance of genetic variation in long non-coding RNAs may assist in future breeding programs to improve selection for prolonged DF-trait.
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Affiliation(s)
- Adeyinka Abiola Adetula
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Syed Ali Azmal
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei, China.,Department of Livestock Services (DLS), Under the Ministry of Fisheries and Livestock (MOFL), Dhaka, Bangladesh
| | - Chenghao Sun
- Huadu Yukou Poultry Industry Co. Ltd, Beijing, Hubei, China
| | - Abdelmotaleb Elokil
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei, China.,Department of Animal Production, Faculty of Agriculture, Benha University, Moshtohor, Egypt
| | - Shijun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei, China
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25
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Hong JH, Jin EH, Kang H, Chang IA, Lee SI, Sung JK. Correlations between Genetic Polymorphisms in Long Non-Coding RNA PRNCR1 and Gastric Cancer Risk in a Korean Population. Int J Mol Sci 2019; 20:ijms20133355. [PMID: 31288430 PMCID: PMC6650882 DOI: 10.3390/ijms20133355] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/28/2019] [Accepted: 07/05/2019] [Indexed: 12/13/2022] Open
Abstract
We evaluated the association between prostate cancer non-coding RNA 1 (PRNCR1) polymorphisms and the risk of developing gastric cancer (GC) and GC subgroups in Korea. A case-control study was conducted with 437 GC patients and 357 healthy controls using a TaqMan genotyping assay. A chi-squared test, binary logistic regression, and genetic models were used to explore the association between five PRNCR1 polymorphisms and GC risk. After adjusting for gender and age, overall analyses using the recessive model indicated that the rs13252298 GG genotype was significantly associated with increased risk of intestinal-type gastric cancer (IGC). In the stratification analyses, the recessive model indicated that the rs1016343 TT genotype was significantly associated with decreased GC risk in individuals aged <60 years showing lymph node metastasis (LNM)-negative results. The rs13252298 GG genotype in the recessive model showed increased GC risk in subjects aged ≥60 years showing LNM-positive results and those aged ≥60 years in tumor stage III. In the dominant model, the rs16901946 combined genotype (AG/GG) was significantly associated with increased GC risk in subjects aged <60 years with tumor stage III. In the recessive model, the rs16901946 GG genotype was associated with decreased risk of GC and IGC in males aged ≥60 years. Thus, genetic variations in PRNCR1 may contribute to susceptibility to GC.
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Affiliation(s)
- Jang Hee Hong
- Clinical Trials Center, Chungnam National University Hospital, Daejeon 35015, Korea
- Department of Pharmacology, Chungnam National University College of Medicine, Daejeon 35015, Korea
| | - Eun-Heui Jin
- Research Institute for Medical Sciences, Chungnam National University College of Medicine, Daejeon 35015, Korea
| | - Hyojin Kang
- Department of Pharmacology, Chungnam National University College of Medicine, Daejeon 35015, Korea
| | - In Ae Chang
- Department of Pharmacology, Chungnam National University College of Medicine, Daejeon 35015, Korea
| | - Sang-Il Lee
- Department of Surgery, Chungnam National University Hospital, Chungnam National University College of Medicine, Daejeon 35015, Korea.
| | - Jae Kyu Sung
- Department of Internal Medicine, Chungnam National University Hospital, Chungnam National University College of Medicine, Daejeon 35015, Korea.
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26
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Li Z, Liu H, Ju W, Xing Y, Zhang X, Yang J. LncRNA GASL1 inhibits growth and promotes expression of apoptosis-associated proteins in prostate carcinoma cells through GLUT-1. Oncol Lett 2019; 17:5327-5334. [PMID: 31186749 PMCID: PMC6507392 DOI: 10.3892/ol.2019.10244] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 01/07/2019] [Indexed: 12/29/2022] Open
Abstract
Growth-arrest-associated long non-coding (lnc)RNA 1 (GASL1) is as newly identified lncRNA that is associated with liver cancer. The present study aimed to investigate the role of GASL1 in prostate carcinoma (PC). Expression levels of GASL1 in prostate tissues and sera from patients with PC and from healthy subjects were detected by reverse transcription-quantitative polymerase chain reaction. Receiver operating characteristic and survival curve analyses were performed to evaluate the diagnostic and prognostic values of GASL1 for patients with PC. A GASL1 expression vector was transfected into PC cells prior to assessment of cell proliferation and expression of B cell lymphoma 2 (Bcl-2) and glucose transporter 1 (GLUT-1) by Cell Counting Kit-8 and western blotting, respectively. The results demonstrated that GASL1 was significantly downregulated in the tissue and serum of patients with PC compared to those of healthy subjects. In addition, GASL1 was used to distinguish patients with PC from healthy controls, and low expression levels of GASL1 were associated with short survival time. Expression levels of GASL1 were significantly associated with tumor size. GASL1 overexpression inhibited PC cell growth. Overexpression of GASL1 upregulated Bcl-2 expression and downregulated GLUT-1 expression. In conclusion, these data suggested that lncRNA GASL1 may inhibit PC cell proliferation by targeting GLUT-1.
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Affiliation(s)
- Zhiqin Li
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Hong Liu
- Department of Critical Care Medicine, Institute of Anesthesiology and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Wen Ju
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Yifei Xing
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Xiaoping Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Jun Yang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
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27
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The POLR2E rs3787016 polymorphism is strongly associated with the risk of female breast and cervical cancer. Pathol Res Pract 2019; 215:1061-1065. [PMID: 30846411 DOI: 10.1016/j.prp.2019.02.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 02/01/2019] [Accepted: 02/26/2019] [Indexed: 02/08/2023]
Abstract
The rs3787016 polymorphism, in polymerase II polypeptide E (POLR2E), was previously identified as being associated with the risk for prostate cancer, esophageal cancer, breast cancer, papillary thyroid carcinoma and liver cancer, suggesting that rs3787016 may server as a common genetic factor to affect individual susceptibility to cancer. To prove the hypothesis, we here performed a case-control study to explore the association between rs3787016 and cervical cancer risk, and to confirm the association between rs3787016 and breast cancer in a central Chinese population, which was followed by a meta-analysis to precisely estimate the association between rs3787016 and risk of female breast and cervical cancer. The genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and confirmed by sequencing. Our results indicated that rs3787016 was associated with the risk of both breast cancer and cervical cancer, and stratified analysis indicated that the association remained particularly for ≤60 years old females who smoke and drink. Moreover, after grouping breast cancer and cervical cancer together, our meta-analysis demonstrated that rs3787016 was associated with overall cancer risk and breast cancer risk. Collectively, the POLR2E rs3787016 polymorphism may be a valuable biomarker for female breast and cervical cancer predisposition.
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28
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Shao G, Wang M, Fan X, Zhong L, Wang Z, Zhang P, Ji S. lncRNA CASC9 positively regulates CHK1 to promote breast cancer cell proliferation and survival through sponging the miR‑195/497 cluster. Int J Oncol 2019; 54:1665-1675. [PMID: 30816435 PMCID: PMC6438439 DOI: 10.3892/ijo.2019.4734] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 08/07/2018] [Indexed: 12/16/2022] Open
Abstract
Accumulating evidence has demonstrated that long non-coding RNAs (lncRNAs) play important roles in the pathogenesis and development of diverse types of human disorders. Cancer susceptibility candidate 9 (CASC9), a gene encoding a lncRNA, has frequently been reported to be dysregulated and has been implicated in multiple types of human malignancies. However, the biological role of lncRNA CASC9 in breast cancer (BC) remains largely unknown. The present study aimed to investigate the role of lncRNA CASC9 in BC and to elucidate the potential molecular mechanisms involved. In the present study, lncRNA CASC9 was found to be significantly upregulated in both BC tissues and cell lines. Furthermore, functional analyses revealed that lncRNA CASC9 accelerated BC cell proliferation, promoted cell cycle progression and suppressed cell apoptosis. Moreover, mechanical experiments demonstrated that lncRNA CASC9 positively regulated checkpoint kinase 1 (CHK1) by competitively binding to the miR-195/497 cluster in BC cells. Additionally, the knockdown of lncRNA CASC9 was observed to suppress breast tumor growth in vivo. Taken together, the results of this study indicate that lncRNA CASC9 plays an oncogenic role in BC through sponging the miR-195/497 cluster, and that lncRNA CASC9 may be used as a novel therapeutic target and as a potential diagnostic marker for BC.
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Affiliation(s)
- Guoli Shao
- Specialized Medical Service Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510282, P.R. China
| | - Mengchuan Wang
- Department of General Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510282, P.R. China
| | - Xulong Fan
- Maternity and Children's Healthcare Hospital of Foshan, Foshan, Guangdong 52800, P.R. China
| | - Lin Zhong
- Specialized Medical Service Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510282, P.R. China
| | - Zixiang Wang
- Department of General Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510282, P.R. China
| | - Pusheng Zhang
- Department of General Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510282, P.R. China
| | - Shufeng Ji
- Specialized Medical Service Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510282, P.R. China
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29
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Sattarifard H, Hashemi M, Hassanzarei S, Basiri A, Narouie B, Ghavami S. Long non-coding RNA POLR2E gene polymorphisms increased the risk of prostate cancer in a sample of the Iranian population. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2018; 38:1-11. [PMID: 30587086 DOI: 10.1080/15257770.2017.1391394] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The current study aimed to examine the impact of POLR2E rs1046040 and rs3787016 polymorphisms on prostate cancer (PCa) risk in a sample of southeast Iranian population. The present case-control study was performed on 178 patients with PCa and 180 benign prostatic hyperplasia (BPH). Genotyping of the variants was done by mismatch PCR-RFLP. The findings showed that the rs3787016 C > T variant significantly increased the risk of PCa in codominant (OR = 1.84, 95% CI = 1.12-3.03, P = 0.018, CT vs CC), dominant (OR = 1.88, 95% CI = 1.63-3.05, P = 0.011, CT + TT vas CC) and allele (OR = 1.77, 95% CI = 1.52-2.72, P = 0.010, T vs C) inheritance model. Regarding rs1046040 C > T polymorphism, the findings revealed that the CT genotype significantly increased the risk of PCa compared to the CC genotype (OR = 1.60, 95% CI = 1.03-2.49, P = 0.043). Furthermore, rs3787016 CT/rs1046040 CC as well as rs3787016 CT/rs1046040 CT increased the risk of PCa compared to the CC/CC genotype (p = 0.029 and p = 0.014, respectively). Haplotype analysis proposed that rs3787016 T/rs1046040 C significantly increased the risk of PCa compared to C/C (p = 0.037). No significant association was observed between POLR2E variants and clinicopathological characteristics of PCa patients. In conclusion, the findings propose that POLR2E variants may be a risk factor for susceptibility to PCa in a sample of Iranian population.
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Affiliation(s)
- Hedieh Sattarifard
- a Cellular and Molecular Research Center , Zahedan University of Medical Sciences , Zahedan , Iran.,b Department of Clinical Biochemistry, School of Medicine , Zahedan University of Medical Sciences , Zahedan , Iran
| | - Mohammad Hashemi
- a Cellular and Molecular Research Center , Zahedan University of Medical Sciences , Zahedan , Iran.,b Department of Clinical Biochemistry, School of Medicine , Zahedan University of Medical Sciences , Zahedan , Iran
| | - Shekoufeh Hassanzarei
- b Department of Clinical Biochemistry, School of Medicine , Zahedan University of Medical Sciences , Zahedan , Iran
| | - Abbas Basiri
- c Department of Urology, Urology and Nephrology Research Center, Shahid Labbafinejad Medical Center , Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Behzad Narouie
- c Department of Urology, Urology and Nephrology Research Center, Shahid Labbafinejad Medical Center , Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Saeid Ghavami
- d Department of Human Anatomy and Cell Science, Faculty of Health Sciences, College of Medicine , University of Manitoba , Winnipeg , Canada.,e Health Policy Research Center , Shiraz University of Medical Sciences , Shiraz , Iran
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30
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Chen B, Wang S, Ma G, Han J, Zhang J, Gu X, Feng X. The association of POLR2E rs3787016 polymorphism and cancer risk: a Chinese case-control study and meta-analysis. Biosci Rep 2018; 38:BSR20180853. [PMID: 30291213 PMCID: PMC6239260 DOI: 10.1042/bsr20180853] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/13/2018] [Accepted: 10/03/2018] [Indexed: 12/15/2022] Open
Abstract
How single nucleotide polymorphisms in long non-coding RNAs are involved in cancer susceptibility remains poorly understood. We hypothesized that polymerase II polypeptide E (POLR2E) rs3787016 polymorphism, identified in a genome-wide association study of prostate cancer, might be a common genetic risk factor for cancer risk. To address this issue, we here conducted a case-control study to investigate the association of POLR2E rs3787016 polymorphism with risk of liver and lung cancer (including 800 normal controls, 480 liver cancer patients, and 550 lung cancer patients), followed by a meta-analysis. The genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism and confirmed by sequencing. Although no significant association was found for rs3787016 with risk of liver or lung cancer, the further stratified analysis identified that rs3787016 contributed to liver cancer risk particularly for over than 60 years individuals who drink. Moreover, the meta-analysis demonstrated that rs3787016 was associated with overall cancer risk and prostate cancer risk. Collectively, the POLR2E rs3787016 polymorphism may be a valuable biomarker for cancer predisposition.
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Affiliation(s)
- Bifeng Chen
- Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Shang Wang
- Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Guangxin Ma
- Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Jin Han
- Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Jingli Zhang
- Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Xiuli Gu
- Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Reproductive Genetics, Wuhan Tongji Reproductive Medicine Hospital, Wuhan, China
| | - Xianhong Feng
- Clinical Laboratory, Wuhan Xinzhou District People's Hospital, Wuhan, China
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31
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Cardoso C, Serafim RB, Kawakami A, Gonçalves Pereira C, Roszik J, Valente V, Vazquez VL, Fisher DE, Espreafico EM. The lncRNA RMEL3 protects immortalized cells from serum withdrawal-induced growth arrest and promotes melanoma cell proliferation and tumor growth. Pigment Cell Melanoma Res 2018; 32:303-314. [PMID: 30457212 DOI: 10.1111/pcmr.12751] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 12/12/2022]
Abstract
RMEL3 is a recently identified lncRNA associated with BRAFV600E mutation and melanoma cell survival. Here, we demonstrate strong and moderate RMEL3 upregulation in BRAF and NRAS mutant melanoma cells, respectively, compared to melanocytes. High expression is also more frequent in cutaneous than in acral/mucosal melanomas, and analysis of an ICGC melanoma dataset showed that mutations in RMEL3 locus are preponderantly C > T substitutions at dipyrimidine sites including CC > TT, typical of UV signature. RMEL3 mutation does not correlate with RMEL3 levels, but does with poor patient survival, in TCGA melanoma dataset. Accordingly, RMEL3 lncRNA levels were significantly reduced in BRAFV600E melanoma cells upon treatment with BRAF or MEK inhibitors, supporting the notion that BRAF-MEK-ERK pathway plays a role to activate RMEL3 gene transcription. RMEL3 overexpression, in immortalized fibroblasts and melanoma cells, increased proliferation and survival under serum starvation, clonogenic ability, and xenografted melanoma tumor growth. Although future studies will be needed to elucidate the mechanistic activities of RMEL3, our data demonstrate that its overexpression bypasses the need of mitogen activation to sustain proliferation/survival of non-transformed cells and suggest an oncogenic role for RMEL3.
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Affiliation(s)
- Cibele Cardoso
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil.,Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Rodolfo B Serafim
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Akinori Kawakami
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Cristiano Gonçalves Pereira
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Valeria Valente
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil.,School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil.,Center for Cell-Based Therapy CEPID/FAPESP, Ribeirão Preto, Brazil
| | - Vinicius L Vazquez
- Molecular Oncology Research Center (CPOM) and Melanoma/Sarcoma Surgery Department, Barretos Cancer Hospital, Barretos, Brazil
| | - David E Fisher
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Enilza M Espreafico
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
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32
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Wang F, Liang S, Liu X, Han L, Wang J, Du Q. LINC00460 modulates KDM2A to promote cell proliferation and migration by targeting miR-342-3p in gastric cancer. Onco Targets Ther 2018; 11:6383-6394. [PMID: 30323616 PMCID: PMC6174301 DOI: 10.2147/ott.s169307] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background Increasing evidence has shown that long non-coding RNAs (lncRNAs) play important roles in the occurrence and development of human cancers. LINC00460, a novel tumor-related lncRNA, has been reported to be involved in several types of human malignancies. However, the role of LINC00460 in gastric cancer (GC) is still unclear. The present study aimed at exploring the biological role of LINC00460 in GC and illuminating the potential molecular mechanisms. Methods In this study, qRT-PCR, western blotting, MTT assay, and Transwell invasion assay were used to conduct relevant experimental analysis. Results Here, we found that LINC00460 was highly expressed in GC tissues and cell lines. Moreover, LINC00460 overexpression was found to promote GC cell proliferation, migration and invasion, whereas LINC00460 down-regulation significantly inhibited these processes. Notably, we confirmed that LINC00460 could up-regulate KDM2A expression by competitively binding to miR-342-3p in GC cells. Furthermore, the suppressive effects of LINC00460 down-regulation on GC cell proliferation, migration and invasion were partially reversed by a miR-342-3p inhibitor. Conclusion In summary, our findings provide evidence for LINC00460 as a potential therapeutic target in GC.
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Affiliation(s)
- Fang Wang
- Department of Oncology, Affiliated Hospital of Jining Medical College, Jining 272029, China,
| | - Shaobo Liang
- Department of Gastroenterology, Central Hospital of Shanxian County, Heze, 274399, China
| | - Xiaowei Liu
- Department of Oncology, Affiliated Hospital of Jining Medical College, Jining 272029, China,
| | - Lei Han
- Department of Oncology, Affiliated Hospital of Jining Medical College, Jining 272029, China,
| | - Junye Wang
- Department of Oncology, Affiliated Hospital of Jining Medical College, Jining 272029, China,
| | - Qin Du
- Department of Oncology, Affiliated Hospital of Jining Medical College, Jining 272029, China,
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33
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Zeng Q, Wu KH, Liu K, Hu Y, Chen XD, Zhang L, Shen H, Tian Q, Zhao LJ, Deng HW, Tan LJ. Genome-wide association study of lncRNA polymorphisms with bone mineral density. Ann Hum Genet 2018; 82:244-253. [PMID: 29663307 PMCID: PMC6298226 DOI: 10.1111/ahg.12247] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 11/30/2017] [Accepted: 01/25/2018] [Indexed: 01/10/2023]
Abstract
Recent studies suggested that long noncoding RNAs (lncRNAs) were widely transcribed in the genome, but their potential roles in the genetic complexity of human disorders required further exploration. The purpose of the present study was to explore genetic polymorphisms of lncRNAs associated with bone mineral density (BMD) and its potential value. Based on the lncRNASNP database, 55,906 lncSNPs were selected to conduct a genome-wide association study meta-analysis among 11,140 individuals of seven independent studies for BMDs at femoral neck (FN), lumbar spine, and total hip (HIP). Promising results were replicated in Genetic Factors for Osteoporosis Consortium (GEFOS Sequencing, n = 32,965). We found two lncRNA loci that were significantly associated with BMD. MEF2C antisense RNA 1 (MEF2C-AS1) located at 5q14.3 was significantly associated with FN-BMD after Bonferroni correction, and the strongest association signal was detected at rs6894139 (P = 3.03 × 10-9 ). LOC100506136 rs6465531 located at 7q21.3 showed significant association with HIP-BMD (P = 7.43 × 10-7 ). MEF2C-AS1 rs6894139 was replicated in GEFOS Sequencing with P-value of 1.43 × 10-23 . Our results illustrated the important role of polymorphisms in lncRNAs in determining variations of BMD and provided justification and evidence for subsequent functional studies.
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Affiliation(s)
- Qin Zeng
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Ke-Hao Wu
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Kun Liu
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Yuan Hu
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Xiang-Ding Chen
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Lei Zhang
- Center of Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, PR, China
| | - Hui Shen
- Center of Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Qin Tian
- Center of Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Lan-Juan Zhao
- Center of Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Hong-Wen Deng
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
- Center of Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Li-Jun Tan
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
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van Dam S, Võsa U, van der Graaf A, Franke L, de Magalhães JP. Gene co-expression analysis for functional classification and gene-disease predictions. Brief Bioinform 2018; 19:575-592. [PMID: 28077403 PMCID: PMC6054162 DOI: 10.1093/bib/bbw139] [Citation(s) in RCA: 422] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/01/2016] [Indexed: 01/06/2023] Open
Abstract
Gene co-expression networks can be used to associate genes of unknown function with biological processes, to prioritize candidate disease genes or to discern transcriptional regulatory programmes. With recent advances in transcriptomics and next-generation sequencing, co-expression networks constructed from RNA sequencing data also enable the inference of functions and disease associations for non-coding genes and splice variants. Although gene co-expression networks typically do not provide information about causality, emerging methods for differential co-expression analysis are enabling the identification of regulatory genes underlying various phenotypes. Here, we introduce and guide researchers through a (differential) co-expression analysis. We provide an overview of methods and tools used to create and analyse co-expression networks constructed from gene expression data, and we explain how these can be used to identify genes with a regulatory role in disease. Furthermore, we discuss the integration of other data types with co-expression networks and offer future perspectives of co-expression analysis.
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Affiliation(s)
- Sipko van Dam
- Department of Genetics, UMCG HPC CB50, RB Groningen, Netherlands
| | - Urmo Võsa
- Department of Genetics, UMCG HPC CB50, RB Groningen, Netherlands
| | | | - Lude Franke
- Department of Genetics, UMCG HPC CB50, RB Groningen, Netherlands
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Yan H, Yang X, Zhao X, Wang H. Identification of genes and pathways related with cerebral small vessel disease based on a long non-coding RNA-mediated, competitive endogenous RNA network. Exp Ther Med 2018; 16:121-126. [PMID: 29896231 PMCID: PMC5995035 DOI: 10.3892/etm.2018.6148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 04/18/2018] [Indexed: 11/13/2022] Open
Abstract
This study aimed to investigate the cerebral small vessel disease (SVD), an intrinsic disorder of the brain's perforating arterioles, which could cause serious cognitive decreasing and trigger dementia. In this study, we present a multi-step computational approach to construct a functional SVD long non-coding RNA (lncRNA)-mediated ceRNA network (LMCN) by integrating genome-wide lncRNA and mRNA expression profiles, miRNA-target interactions, and functional analyses. We used hypergeometric test to evaluate enrichment significance of miRNAs and we obtained the LMCN, which contained 27 lncRNAs, 7,229 mRNA, and 28,871 lncRNAs-mRNA interrelationship pairs. What's more, co-expression analysis was utilized to constructe a competitive endogenous RNAs (ceRNAs) interaction network which comprised of 21 lncRNAs, 129 mRNAs and 141 interaction pairs. We determined that metastasis-associated lung adenocarcinoma transcript 1 and MIR155 host gene acted synergistically to regulate mRNAs in a network module of the competitive LMCN. Moreover, 7 genes were obtained through Gene Ontology enrichment. In addition, 29 mRNA enriched pathways significantly associated with lncRNAs was obtained via Fisher test. In conclusion, we identified 7 potential lncRNAs and 29 possible lncRNA-mediated pathways associated with SVD. Thus, ceRNAs could accelerate biomarker discovery and therapeutic development in SVD.
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Affiliation(s)
- Hui Yan
- Department of Neurology, The People's Hospital of Yucheng, Yucheng, Dezhou, Shandong 251200, P.R. China
| | - Xiaoli Yang
- Department of Neurology, The People's Hospital of Yucheng, Yucheng, Dezhou, Shandong 251200, P.R. China
| | - Xueman Zhao
- Department of Neurology, The People's Hospital of Yucheng, Yucheng, Dezhou, Shandong 251200, P.R. China
| | - Huankun Wang
- Department of Neurology, The People's Hospital of Yucheng, Yucheng, Dezhou, Shandong 251200, P.R. China
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36
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Chen B, Li J, Yi C, Jiao Y, Gu X, Feng X. Long non-coding RNA POLR2E rs3787016 is associated with the risk of papillary thyroid carcinoma in Chinese population. Pathol Res Pract 2018; 214:1040-1044. [DOI: 10.1016/j.prp.2018.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 03/30/2018] [Accepted: 04/13/2018] [Indexed: 11/16/2022]
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Diamantopoulos MA, Tsiakanikas P, Scorilas A. Non-coding RNAs: the riddle of the transcriptome and their perspectives in cancer. ANNALS OF TRANSLATIONAL MEDICINE 2018; 6:241. [PMID: 30069443 DOI: 10.21037/atm.2018.06.10] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Non-coding RNAs (ncRNAs) constitute a heterogeneous group of RNA molecules in terms of biogenesis, biological function as well as length and structure. These biological molecules have gained attention recently as a potentially crucial layer of tumor cell progression or regulation. ncRNAs are expressed in a broad spectrum of tumors, and they play an important role not only in maintaining but also in promoting cancer development and progression. Recent discoveries have revealed that ncRNAs may act as key signal transduction mediators in tumor signaling pathways by interacting with RNA or proteins. These results reinforce the hypothesis, that ncRNAs constitute therapeutic targets, and point out their clinical potential as stratification markers. The major purpose of this review is to mention the emergence of the importance of ncRNAs, as molecules which are correlated with cancer, and to discuss their clinical implicit as prognostic diagnostic indicators, biomarkers, and therapeutic targets.
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Affiliation(s)
- Marios A Diamantopoulos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis Tsiakanikas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
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38
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Chu H, Chen Y, Yuan Q, Hua Q, Zhang X, Wang M, Tong N, Zhang W, Chen J, Zhang Z. The HOTAIR, PRNCR1 and POLR2E polymorphisms are associated with cancer risk: a meta-analysis. Oncotarget 2018; 8:43271-43283. [PMID: 28159929 PMCID: PMC5522144 DOI: 10.18632/oncotarget.14920] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/27/2016] [Indexed: 12/30/2022] Open
Abstract
Long non-coding RNAs (LncRNAs) have been widely studied and aberrant expression of lncRNAs are involved in diverse cancers. Genetic variation in lncRNAs can influence the lncRNAs expression and function. At present, there are many studies to investigate the association between lncRNAs polymorphisms and cancer susceptibility. However, it has no systematic study to evaluate the association. We performed a meta-analysis to summarize the results of common lncRNAs (HOTAIR, PRNCR1, POLR2E and H19) polymorphisms on cancer risk, by using the random-effect model to obtain the odds ratio (ORs) and 95% confidence interval (95%CI). We also applied the meta-regression and publication bias analysis to seek the source of heterogeneity and evaluate the stability of results, respectively. The summary results indicated that HOTAIR rs920778 increased the cancer risk in recessive model (OR = 1.61, 95% CI = 1.08-2.41, Pheterogeneity<0.001). For PRNCR1 (rs1016343, rs16901946) and POLR2E (rs3787016), we also found the significant association with incresed risk of cancer (all P<0.05). However, we did not observe any significant association between H19 rs2107425 and cancer risk. Our meta-analysis results revealed that these four lncRNAs polymorphisms (HOTAIR rs920778, PRNCR1 rs1016343 and rs16901946, POLR2E rs3787016) can contribute to cancer risk. Further studies should confirm these findings.
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Affiliation(s)
- Haiyan Chu
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Oncology, The Affiliated Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yaoyao Chen
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qinbo Yuan
- Department of Urology, Huaiyin Hospital of Huai'an City, Huai'an, China.,Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qiuhan Hua
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xu Zhang
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Na Tong
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wei Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jinfei Chen
- Department of Oncology, The Affiliated Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Zhengdong Zhang
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
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HUANG S, CUI H, LOU Z, WANG X, CHEN L, XIE Z, HEHIR M, YAO X, REN Y, CEN D, WENG G. Association of rs3787016 in Long Non-coding RNAs POLR2E and rs2910164 in MiRNA-146a with Prostate Cancer: A Systematic Review and Meta-analysis. IRANIAN JOURNAL OF PUBLIC HEALTH 2018; 47:623-632. [PMID: 29922603 PMCID: PMC6005969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND The aim of this study was to conduct a meta-analysis to estimate the association between the two SNPs and PCa risk. METHODS Medline, Embase, Scopus, PubMed, Web of Science, Wan Fang Database and Chinese Zhi Wang Database were searched for the association of the two SNPs with susceptibility to PCa. The effect size was pooled by odds ratios (ORs) and 95% confidence intervals (95% CIs). RESULTS Nine case-control studies, 5 on rs3787016 and 4 on rs2910164, were included. As regards rs3787016, an increased risk of PCa was identified in all genotype models (T versus C: OR = 1.18, 95% CI 1.11-1.25; CT versus CC: OR = 1.17, 95% CI 1.08-1.26; TT versus CC: OR = 1.41, 95% CI 1.22-1.63; TT + CT versus CC: OR = 1.20, 95% CI 1.12-1.30; TT versus CT + CC: OR = 1.32, 95% CI 1.15-1.52). However, no significant association was found between rs2910164 and PCa risk in any genetic models, in fact a trend of reduced risk could be seen (C versus G: OR = 0.91, 95% CI 0.79-1.05; GC versus GG: OR = 0.93, 95% CI 0.74-1.18; CC versus GG: OR = 0.70, 95% CI 0.47-1.02; CC + GC versus GG: OR = 0.90, 95% CI 0.73-1.12; CC versus GC + GG: OR = 0.78, 95% CI 0.56-1.08). Besides, in analysis of subgroups by source of controls, the decreased results were observed in studies using population-based controls. CONCLUSION lncRNA POLR2E polymorphism rs3787016 is associated with a significantly increased risk of PCa, while a trend of reduced risk appears with mir-146a polymorphism rs2910164.
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Affiliation(s)
- Shuaishuai HUANG
- Laboratory of Kidney Carcinoma, Urology and Nephrology Institute of Ningbo University, Ningbo Urology and Nephrology Hospital, Ningbo, Zhejiang 315000, China
| | - Hui CUI
- Laboratory of Kidney Carcinoma, Urology and Nephrology Institute of Ningbo University, Ningbo Urology and Nephrology Hospital, Ningbo, Zhejiang 315000, China
| | - Zhongguan LOU
- Laboratory of Kidney Carcinoma, Urology and Nephrology Institute of Ningbo University, Ningbo Urology and Nephrology Hospital, Ningbo, Zhejiang 315000, China
| | - Xue WANG
- Laboratory of Kidney Carcinoma, Urology and Nephrology Institute of Ningbo University, Ningbo Urology and Nephrology Hospital, Ningbo, Zhejiang 315000, China
| | - Liangliang CHEN
- Laboratory of Kidney Carcinoma, Urology and Nephrology Institute of Ningbo University, Ningbo Urology and Nephrology Hospital, Ningbo, Zhejiang 315000, China
| | - Zhenhua XIE
- Laboratory of Kidney Carcinoma, Urology and Nephrology Institute of Ningbo University, Ningbo Urology and Nephrology Hospital, Ningbo, Zhejiang 315000, China
| | - Michael HEHIR
- Dept. of Medical School, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Xuping YAO
- Laboratory of Kidney Carcinoma, Urology and Nephrology Institute of Ningbo University, Ningbo Urology and Nephrology Hospital, Ningbo, Zhejiang 315000, China
| | - Yu REN
- Laboratory of Kidney Carcinoma, Urology and Nephrology Institute of Ningbo University, Ningbo Urology and Nephrology Hospital, Ningbo, Zhejiang 315000, China
| | - Dong CEN
- Laboratory of Kidney Carcinoma, Urology and Nephrology Institute of Ningbo University, Ningbo Urology and Nephrology Hospital, Ningbo, Zhejiang 315000, China,Corresponding Authors: Emails: ,
| | - Guobin WENG
- Laboratory of Kidney Carcinoma, Urology and Nephrology Institute of Ningbo University, Ningbo Urology and Nephrology Hospital, Ningbo, Zhejiang 315000, China,Corresponding Authors: Emails: ,
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Yuan Q, Chu H, Ge Y, Ma G, Du M, Wang M, Zhang Z, Zhang W. LncRNA PCAT1 and its genetic variant rs1902432 are associated with prostate cancer risk. J Cancer 2018; 9:1414-1420. [PMID: 29721051 PMCID: PMC5929086 DOI: 10.7150/jca.23685] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/26/2018] [Indexed: 01/16/2023] Open
Abstract
Emerging evidence has showed that lncRNAs and trait-associated loci in lncRNAs play a crucial role in the progression of cancer including prostate cancer (PCa).This study aimed to investigate the molecular mechanisms of lncRNA PCAT1 involved in PCa development and its genetic variant associated with PCa risk. We applied cell proliferation and apoptosis assays to assess the effect of PCAT1 on PCa cell phenotypes. In addition, the genome-wide profiling of gene expression was assessed from three pairs of DU145 cells transfected with PCAT1 overexpression vector or negative control (NC) vector. Furthermore, a case-control study was conducted to explore the associations of four tagging single nucleotide polymorphisms (tagSNPs) and PCa risk in 850 PCa cases and 860 cancer-free controls. Our results showed that lncRNA PCAT1 promoted cell proliferation and inhibited cell apoptosis. Ingenuity pathway analysis (IPA) indicated that dysregulated mRNAs induced by overexpression of PCAT1 were primarily enriched in androgen-independent prostate tumor term and implicated in the disease and functions networks, such as cell death and survival, cell proliferation and gene expression. Besides, rs1902432 in PCAT1 was significantly associated with increased risk of PCa (Additive model: OR = 1.19, P = 0.014; Co-dominant model: CC vs. TT, OR = 1.45, P =0.012; Recessive model: CC vs. TT/CT, OR= 1.34, P = 0.027). This study suggests that PCAT1 may act as an oncogene through promoting cell proliferation and suppressing cell apoptosis in PCa development, and genetic variant in PCAT1 contributes to the susceptibility to PCa.
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Affiliation(s)
- Qinbo Yuan
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Urology, Huaiyin Hospital of Huai'an City, Huai'an, China.,Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Haiyan Chu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuqiu Ge
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Gaoxiang Ma
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mulong Du
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wei Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Li Q, Zhang J, Zhou J, Yang B, Liu P, Cao L, Jing L, Liu H. lncRNAs are novel biomarkers for differentiating between cisplatin-resistant and cisplatin-sensitive ovarian cancer. Oncol Lett 2018; 15:8363-8370. [PMID: 29805570 PMCID: PMC5950027 DOI: 10.3892/ol.2018.8433] [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: 03/01/2017] [Accepted: 12/05/2017] [Indexed: 12/16/2022] Open
Abstract
Cisplatin-resistant ovarian cancer occurs in patients with ovarian cancer treated with cisplatin-based chemotherapy, which results in tumor progression during treatment, or recurrence of the tumor within 6 months of the treatment. It is vital that a novel biomarker for diagnosis, or an efficient therapeutic target of cisplatin-resistant ovarian is identified. Long non-coding (lnc)RNAs were determined to serve critical functions in a variety of distinct types of cancer, including ovarian cancer; however, there is limited knowledge regarding the differential expression levels of lncRNAs in cisplatin-resistant and cisplatin-sensitive ovarian cancer. Therefore, in the present study, the expression levels were determined for these cancer types. The lncRNA expression profile in cisplatin-resistant ovarian cancer was analyzed and compared with the results for cisplatin-sensitive ovarian cancer; gene ontology and pathway analysis demonstrated that the dysregulated lncRNAs participated in important biological processes. Subsequently, it was identified that these dysregulated lncRNAs were present in other ovarian cancer tissues and in SKOV3 ovarian cancer cells, as well as its cisplatin-resistant clone, SKOV3/CDDP. In addition, it was revealed that 8 lncRNAs (Enst0000435726, Enst00000585612, Enst00000566734, Enst00000453783, NR_023915, RP11_697E22.2, uc010jub.1 and tcons_00008505) were associated with cisplatin-resistant ovarian cancer. The present study may assist in improving understanding of the initiation and developmental mechanisms underlying cisplatin-resistant ovarian cancer, which could aid future studies in discovering potential biomarkers for diagnosis or therapeutic targets that may be used in clinical treatment.
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Affiliation(s)
- Qing Li
- Department of Pathology, Shanghai Pudong New Area People's Hospital, Shanghai 201299, P.R. China
| | - Juan Zhang
- Department of Pathology, Affiliated Nanjing Maternal and Child Health Hospital, Nanjing Medical University, Nanjing, Jiangsu 210004, P.R. China
| | - Juan Zhou
- Department of Pathology, Shanghai Pudong New Area People's Hospital, Shanghai 201299, P.R. China
| | - Binglie Yang
- Department of Gynecology and Obstetrics, Shanghai Pudong New Area People's Hospital, Shanghai 201299, P.R. China
| | - Pingping Liu
- Department of Gynecology and Obstetrics, Shanghai Pudong New Area People's Hospital, Shanghai 201299, P.R. China
| | - Lei Cao
- Department of Pathology, Shanghai Pudong New Area People's Hospital, Shanghai 201299, P.R. China
| | - Lei Jing
- Department of Pathology, Shanghai Pudong New Area People's Hospital, Shanghai 201299, P.R. China
| | - Hua Liu
- Department of Pathology, Shanghai Pudong New Area People's Hospital, Shanghai 201299, P.R. China
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Lin C, Yang L. Long Noncoding RNA in Cancer: Wiring Signaling Circuitry. Trends Cell Biol 2018; 28:287-301. [PMID: 29274663 PMCID: PMC5869122 DOI: 10.1016/j.tcb.2017.11.008] [Citation(s) in RCA: 386] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/27/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022]
Abstract
Long noncoding RNAs (lncRNAs), which are encoded by a vast less explored region of the human genome, may hold missing drivers of cancer and have gained attention recently as a potentially crucial layer of cancer cell regulation. lncRNAs are aberrantly expressed in a broad spectrum of cancers, and they play key roles in promoting and maintaining tumor initiation and progression, demonstrating their clinical potential as biomarkers and therapeutic targets. Recent discoveries have revealed that lncRNAs act as key signal transduction mediators in cancer signaling pathways by interacting with proteins, RNA, and lipids. Here, we review the mechanisms by which lncRNAs regulate cellular responses to extracellular signals and discuss their clinical potential as diagnostic indicators, stratification markers, and therapeutic targets of combinatorial treatments.
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Affiliation(s)
- Chunru Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Wang Q, Wu Y, Li F, Zhu H, Zhou B, Qian Y, Ge C, Xu J, Chen L, Chu M, Jiang L, Peng J. Association of genetic polymorphisms in immune-related lncRNA with osteoarthritis susceptibility in Chinese Han population. Per Med 2018; 15:103-110. [PMID: 29714128 DOI: 10.2217/pme-2017-0072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Aim: Immune-related lncRNA may influence osteoarthritis (OA) susceptibility. We conducted this study to assess whether the genetic variants in several immune-related lncRNA influence OA susceptibility. Methods: The current research genotyped four SNPs in 306 OA patients and 316 healthy controls, including PRNCR1 rs7463708, PRNCR1 rs1456315, PRNCR1 rs16901946 and KIF13B1 rs643472, to investigate their associations with OA susceptibility. Results: We identified that PRNCR1 rs1456315 was associated with OA susceptibility in Chinese Han population (recessive model: odds ratio = 2.24; 95% CI: 1.05–4.81; additive model: odds ratio = 1.36; 95% CI: 1.03–1.80). Conclusion: Individuals with PRNCR1 rs1456315 mutant G allele were more likely to suffer from OA in Chinese Han population.
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Affiliation(s)
- Qiang Wang
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Yinliang Wu
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Fanian Li
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Heping Zhu
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Bo Zhou
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Yuqiang Qian
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Chi Ge
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Jing Xu
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Liang Chen
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Miao Chu
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Long Jiang
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
| | - Jun Peng
- Department of Orthopedic, The Yixing People's Hospital, Yixing 214200, PR China
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Gao L, Zhang H, Zhang B, Wang C. A novel long non-coding RNATCONS_00001798 is downregulated and predicts survival in patients with non-small cell lung cancer. Oncol Lett 2018; 15:6015-6021. [PMID: 29564001 DOI: 10.3892/ol.2018.8080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 10/18/2017] [Indexed: 01/22/2023] Open
Abstract
The morbidity and mortality rates of patients with non-small cell lung cancer (NSCLC) are increasing worldwide. Previous studies have demonstrated that long non-coding RNAs (lncRNAs) may serve critical roles in oncogenesis and cancer progression. The present study aimed to investigate the expression of lncRNA TCONS_00001798 and the clinicopathological factors and prognosis of patients with NSCLC. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was used to measure the expression of TCONS_00001798 in 118 paired NSCLC and adjacent non-tumor tissues. The association between TCONS_00001798 expression and patient clinicopathological factors and survival rates was subsequently analyzed. The results demonstrated that the expression of TCONS_00001798 was significantly downregulated in NSCLC tissues compared with adjacent non-tumor tissues (P<0.001). Additionally, the expression of TCONS_00001798 was negatively associated with lymph node metastasis (P<0.001) and an advanced pathological stage (P=0.003). A Kaplan-Meier analysis demonstrated that decreased TCONS_00001798 expression was significantly associated with shorter overall survival (OS) and disease-free survival (DFS) rates (each P<0.001). Furthermore, the results of multivariate analyses revealed that TCONS_00001798 expression may serve as an independent predictor for OS and DFS rates (each P=0.001). Therefore, the present study demonstrated that TCONS_00001798 may be involved in the oncogenesis and progression of NSCLC and that TCONS_00001798 may be a potential diagnostic and therapeutic target in patients with NSCLC.
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Affiliation(s)
- Liuwei Gao
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, P.R. China.,National Clinical Research Centre for Cancer, Tianjin 300060, P.R. China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China.,Tianjin Lung Cancer Centre, Tianjin 300060, P.R. China
| | - Hua Zhang
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, P.R. China.,National Clinical Research Centre for Cancer, Tianjin 300060, P.R. China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China.,Tianjin Lung Cancer Centre, Tianjin 300060, P.R. China
| | - Bin Zhang
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, P.R. China.,National Clinical Research Centre for Cancer, Tianjin 300060, P.R. China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China.,Tianjin Lung Cancer Centre, Tianjin 300060, P.R. China
| | - Changli Wang
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, P.R. China.,National Clinical Research Centre for Cancer, Tianjin 300060, P.R. China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China.,Tianjin Lung Cancer Centre, Tianjin 300060, P.R. China
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45
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Murugan AK, Munirajan AK, Alzahrani AS. Long noncoding RNAs: emerging players in thyroid cancer pathogenesis. Endocr Relat Cancer 2018; 25:R59-R82. [PMID: 29146581 DOI: 10.1530/erc-17-0188] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 11/16/2017] [Indexed: 12/18/2022]
Abstract
Thyroid cancer continues to be the most common malignancy of endocrine glands. The incidence of thyroid cancer has risen significantly over the past 4 decades and has emerged as a major health issue. In recent years, significant progress has been achieved in our understanding of the molecular mechanisms of thyroid carcinogenesis, resulting in significant diagnostic, prognostic and therapeutic implications; yet, it has not reached a satisfactory level. Identifying novel molecular therapeutic targets and molecules for diagnosis and prognosis is expected to advance the overall management of this common malignancy. Long noncoding RNAs (lncRNAs) are implicated in the regulation of various key cellular genes involved in cell differentiation, proliferation, cell cycle, apoptosis, migration and invasion mainly through modulation of gene expression. Recent studies have established that lncRNAs are deregulated in thyroid cancer. In this review, we discuss extensively the tumor-suppressive (for example, LINC00271, MEG3, NAMA, PTCSC1/2/3, etc.) and oncogenic (for example, ANRIL, FAL1, H19, PVT1, etc.) roles of various lncRNAs and their possible disease associations implicated in thyroid carcinogenesis. We briefly summarize the strategies and mechanisms of lncRNA-targeting agents. We also describe the potential role of lncRNAs as prospective novel therapeutic targets, and diagnostic and prognostic markers in thyroid cancer.
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Affiliation(s)
- Avaniyapuram Kannan Murugan
- Division of Molecular EndocrinologyDepartment of Molecular Oncology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Arasambattu Kannan Munirajan
- Department of GeneticsDr ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, India
| | - Ali S Alzahrani
- Division of Molecular EndocrinologyDepartment of Molecular Oncology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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46
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Shukla CJ, McCorkindale AL, Gerhardinger C, Korthauer KD, Cabili MN, Shechner DM, Irizarry RA, Maass PG, Rinn JL. High-throughput identification of RNA nuclear enrichment sequences. EMBO J 2018; 37:embj.201798452. [PMID: 29335281 PMCID: PMC5852646 DOI: 10.15252/embj.201798452] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 11/21/2022] Open
Abstract
In the post‐genomic era, thousands of putative noncoding regulatory regions have been identified, such as enhancers, promoters, long noncoding RNAs (lncRNAs), and a cadre of small peptides. These ever‐growing catalogs require high‐throughput assays to test their functionality at scale. Massively parallel reporter assays have greatly enhanced the understanding of noncoding DNA elements en masse. Here, we present a massively parallel RNA assay (MPRNA) that can assay 10,000 or more RNA segments for RNA‐based functionality. We applied MPRNA to identify RNA‐based nuclear localization domains harbored in lncRNAs. We examined a pool of 11,969 oligos densely tiling 38 human lncRNAs that were fused to a cytosolic transcript. After cell fractionation and barcode sequencing, we identified 109 unique RNA regions that significantly enriched this cytosolic transcript in the nucleus including a cytosine‐rich motif. These nuclear enrichment sequences are highly conserved and over‐represented in global nuclear fractionation sequencing. Importantly, many of these regions were independently validated by single‐molecule RNA fluorescence in situ hybridization. Overall, we demonstrate the utility of MPRNA for future investigation of RNA‐based functionalities.
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Affiliation(s)
- Chinmay J Shukla
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Alexandra L McCorkindale
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Chiara Gerhardinger
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Keegan D Korthauer
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - David M Shechner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rafael A Irizarry
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Philipp G Maass
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
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47
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Fang S, Zhang L, Guo J, Niu Y, Wu Y, Li H, Zhao L, Li X, Teng X, Sun X, Sun L, Zhang MQ, Chen R, Zhao Y. NONCODEV5: a comprehensive annotation database for long non-coding RNAs. Nucleic Acids Res 2018; 46:D308-D314. [PMID: 29140524 PMCID: PMC5753287 DOI: 10.1093/nar/gkx1107] [Citation(s) in RCA: 338] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/14/2017] [Accepted: 10/25/2017] [Indexed: 02/05/2023] Open
Abstract
NONCODE (http://www.bioinfo.org/noncode/) is a systematic database that is dedicated to presenting the most complete collection and annotation of non-coding RNAs (ncRNAs), especially long non-coding RNAs (lncRNAs). Since NONCODE 2016 was released two years ago, the amount of novel identified ncRNAs has been enlarged by the reduced cost of next-generation sequencing, which has produced an explosion of newly identified data. The third-generation sequencing revolution has also offered longer and more accurate annotations. Moreover, accumulating evidence confirmed by biological experiments has provided more comprehensive knowledge of lncRNA functions. The ncRNA data set was expanded by collecting newly identified ncRNAs from literature published over the past two years and integration of the latest versions of RefSeq and Ensembl. Additionally, pig was included in the database for the first time, bringing the total number of species to 17. The number of lncRNAs in NONCODEv5 increased from 527 336 to 548 640. NONCODEv5 also introduced three important new features: (i) human lncRNA-disease relationships and single nucleotide polymorphism-lncRNA-disease relationships were constructed; (ii) human exosome lncRNA expression profiles were displayed; (iii) the RNA secondary structures of NONCODE human transcripts were predicted. NONCODEv5 is also accessible through http://www.noncode.org/.
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Affiliation(s)
- ShuangSang Fang
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - LiLi Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - JinCheng Guo
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
| | - YiWei Niu
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yang Wu
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Hui Li
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - LianHe Zhao
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - XiYuan Li
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - XueYi Teng
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - XianHui Sun
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Liang Sun
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Michael Q Zhang
- School of Medicine, MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - RunSheng Chen
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- To whom correspondence should be addressed. Tel: +86 10 6260 0822; Fax: +86 10 6260 1356; . Correspondence may also be addressed to RunSheng Chen. Tel: +86 10 6488 8543; Fax: +86 10 6487 7837;
| | - Yi Zhao
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- Chinese Academy of Sciences, LuoYang Branch of Institute of Computing Technology, Luoyang, China
- To whom correspondence should be addressed. Tel: +86 10 6260 0822; Fax: +86 10 6260 1356; . Correspondence may also be addressed to RunSheng Chen. Tel: +86 10 6488 8543; Fax: +86 10 6487 7837;
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48
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Genome-Wide Mapping of SNPs in Non-coding RNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1094:39-48. [DOI: 10.1007/978-981-13-0719-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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49
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Chen N, Guo D, Xu Q, Yang M, Wang D, Peng M, Ding Y, Wang S, Zhou J. Long non-coding RNA FEZF1-AS1 facilitates cell proliferation and migration in colorectal carcinoma. Oncotarget 2017; 7:11271-83. [PMID: 26848625 PMCID: PMC4905472 DOI: 10.18632/oncotarget.7168] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/21/2016] [Indexed: 12/26/2022] Open
Abstract
Long non-coding RNAs (lncRNA) have been shown to play important roles in the development and progression of cancer. Here, we discovered a novel long noncoding RNA (lncRNA) FEZF1 antisense RNA1 (FEZF1-AS1) is markedly upregulated in human primary colorectal carcinoma (CRC) and associated with CRC metastasis and poor prognosis. Moreover, the downregulation of FEZF1-AS1 expression significantly inhibited the CRC cells proliferation, migration and invasiveness, suppressed S-phase entry in vitro, and repressed tumor growth and metastasis in vivo. In contrast, overexpression of FEZF1-AS1 could promote the aggressive behaviors of CRC cells. We further discovered that the downregulation of FEZF1-AS1 reduced its sense-cognate gene FEZF1 mRNA and protein expression in CRC cells. There was a positive correlation between FEZF1-AS1 and FEZF1 expression in CRC. Moreover, FEZF1 knockdown also significantly suppressed CRC cell proliferation, migration, and invasion. Our findings indicate that the dysregulation of FEZF1-AS1 participates in colorectal tumorigenesis and progression, which might be achieved, at least in part, through FEZF1 induction.
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Affiliation(s)
- Na Chen
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Dan Guo
- Department of Pharmacy, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Qiong Xu
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Minhui Yang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Dan Wang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Man Peng
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yanqing Ding
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Shuang Wang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jun Zhou
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
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50
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Sá ACC, Sadee W, Johnson JA. Whole Transcriptome Profiling: An RNA-Seq Primer and Implications for Pharmacogenomics Research. Clin Transl Sci 2017; 11:153-161. [PMID: 28945944 PMCID: PMC5866981 DOI: 10.1111/cts.12511] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 09/03/2017] [Indexed: 12/16/2022] Open
Affiliation(s)
- Ana Caroline C Sá
- Center for Pharmacogenomics & Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida, USA.,Genetics & Genomic Graduate Program, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Wolfgang Sadee
- Center for Pharmacogenomics, Department of Cancer Biology and Genetic, College of Medicine, Ohio State University, Columbus, Ohio, USA
| | - Julie A Johnson
- Center for Pharmacogenomics & Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida, USA.,Genetics & Genomic Graduate Program, Genetics Institute, University of Florida, Gainesville, Florida, USA.,Division of Cardiovascular Medicine, Colleges of Pharmacy and Medicine, University of Florida, Gainesville, Florida, USA
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