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Cui T, Guo J, Sun Z. A computational prognostic model of lncRNA signature for clear cell renal cell carcinoma with genome instability. Expert Rev Mol Diagn 2021; 22:213-222. [PMID: 34871123 DOI: 10.1080/14737159.2021.1979960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Long non-coding RNAs (lncRNAs) play a critical role in genomic instability and prognosis of cancer patients, but the methods to identify genomic instability-related lncRNAs have yet to be established. In the present study, to assess the prognostic value of lncRNAs associated with genomic instability in clear cell renal cell carcinoma (ccRCC).A computational framework was established based on the mutation hypothesis and combined lncRNA expression and somatic mutation profiles of the ccRCC genome. Furthermore, a prognostic model was developed using the genome instability-derived lncRNA signature GILncSig based on three lncRNA genes (LINC02471, LINC01234, and LINC00460) and verified using multiple independent patient cohorts.This study established an effective computational method to study the role of lncRNAs in genomic instability, with potential applications in identifying new genomic instability-related cancer biomarkers.
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Affiliation(s)
- Tingting Cui
- Department of Ultrasound, China-Japan Union Hospital of Jilin University, Changchun, Jilin Province, China
| | - Jiantao Guo
- Department of Cardiac Surgery, The First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Zhixia Sun
- Department of Ultrasound, China-Japan Union Hospital of Jilin University, Changchun, Jilin Province, China
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Li Y, Zou J, Li B, Du J. Anticancer effects of melatonin via regulating lncRNA JPX-Wnt/β-catenin signalling pathway in human osteosarcoma cells. J Cell Mol Med 2021; 25:9543-9556. [PMID: 34547170 PMCID: PMC8505851 DOI: 10.1111/jcmm.16894] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 12/17/2022] Open
Abstract
Osteosarcoma (OS) is a type of malignant primary bone cancer, which is highly aggressive and occurs more commonly in children and adolescents. Thus, novel potential drugs and therapeutic methods are urgently needed. In the present study, we aimed to elucidate the effects and mechanism of melatonin on OS cells to provide a potential treatment strategy for OS. The cell survival rate, cell viability, proliferation, migration, invasion and metastasis were examined by trypan blue assay, MTT, colony formation, wound healing, transwell invasion and attachment/detachment assay, respectively. The expression of relevant lncRNAs in OS cells was determined by real-time qPCR analysis. The functional roles of lncRNA JPX in OS cells were further examined by gain and loss of function assays. The protein expression was measured by western blot assay. Melatonin inhibited the cell viability, proliferation, migration, invasion and metastasis of OS cells (Saos-2, MG63 and U2OS) in a dose-dependent manner. Melatonin treatment significantly downregulated the expression of lncRNA JPX in Saos-2, MG63 and U2OS cells. Overexpression of lncRNA JPX into OS cell lines elevated the cell viability and proliferation, which was accompanied by the increased metastasis. We also found that melatonin inhibited the OS progression by suppressing the expression of lncRNA JPX via regulating the Wnt/β-catenin pathway. Our results suggested that melatonin inhibited the biological functions of OS cells by repressing the expression of lncRNA JPX through regulating the Wnt/β-catenin signalling pathway, which indicated that melatonin might be applied as a potentially useful and effective natural agent in the treatment of OS.
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Affiliation(s)
- Yuan Li
- Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Suzhou Research Institute, Shandong University, Suzhou, Jiangsu, China
| | - Jilong Zou
- Department of Orthopedics, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Bo Li
- Department of Orthopedics, Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Jianyang Du
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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3
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Zhang Y, Tao Y, Liao Q. Long noncoding RNA: a crosslink in biological regulatory network. Brief Bioinform 2019; 19:930-945. [PMID: 28449042 DOI: 10.1093/bib/bbx042] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Indexed: 01/17/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) had been defined as a novel class of functional RNAs longer than 200 nucleotides around a decade ago. It is widely acknowledged that lncRNAs play a significant role in regulation of gene expression, but the biological and molecular mechanisms are diverse and complex, and remain to be determined. Especially, the regulatory network of lncRNAs associated with other biological molecules is still a controversial matter, thus becoming a new frontier of the studies on transcriptome. Recent advance in high-throughput sequencing technologies and bioinformatics approaches may be an accelerator to lift the mysterious veil. In this review, we will outline well-known associations between lncRNAs and other biological molecules, demonstrate the diverse bioinformatics approaches applied in prediction and analysis of lncRNA interaction and perform a case study for lncRNA linc00460 to concretely decipher the lncRNA regulatory network.
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Affiliation(s)
- Yuwei Zhang
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
| | - Yang Tao
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
| | - Qi Liao
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
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Carmona S, Lin B, Chou T, Arroyo K, Sun S. LncRNA Jpx induces Xist expression in mice using both trans and cis mechanisms. PLoS Genet 2018; 14:e1007378. [PMID: 29734339 PMCID: PMC5957434 DOI: 10.1371/journal.pgen.1007378] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 05/17/2018] [Accepted: 04/24/2018] [Indexed: 11/30/2022] Open
Abstract
Mammalian X chromosome dosage compensation balances X-linked gene products between sexes and is coordinated by the long noncoding RNA (lncRNA) Xist. Multiple cis and trans-acting factors modulate Xist expression; however, the primary competence factor responsible for activating Xist remains a subject of dispute. The lncRNA Jpx is a proposed competence factor, yet it remains unknown if Jpx is sufficient to activate Xist expression in mice. Here, we utilize a novel transgenic mouse system to demonstrate a dose-dependent relationship between Jpx copy number and ensuing Jpx and Xist expression. By localizing transcripts of Jpx and Xist using RNA Fluorescence in situ Hybridization (FISH) in mouse embryonic cells, we provide evidence of Jpx acting in both trans and cis to activate Xist. Our data contribute functional and mechanistic insight for lncRNA activity in mice, and argue that Jpx is a competence factor for Xist activation in vivo. Long noncoding RNA (lncRNA) have been identified in all eukaryotes but mechanisms of lncRNA function remain challenging to study in vivo. A classic model of lncRNA function and mechanism is X-Chromosome Inactivation (XCI): an essential process which balances X-linked gene expression between male and female mammals. The “master regulator” of XCI is lncRNA Xist, which is responsible for silencing one of the two X chromosomes in females. Another lncRNA, Jpx, has been proposed to activate Xist gene expression in mouse embryonic stem cells; however, no mouse models exist to address Jpx function in vivo. In this study, we developed a novel transgenic mouse system to demonstrate the regulatory mechanisms of lncRNA Jpx. We observed a dose-dependent relationship between Jpx copy number and Xist expression in transgenic mice, suggesting that Jpx is sufficient to activate Xist expression in vivo. In addition, we analyzed Jpx’s allelic origin and have provided evidence for Jpx inducing Xist transcription using both trans and cis mechanisms. Our work provides a framework for lncRNA functional studies in mice, which will help us understand how lncRNA regulate eukaryotic gene expression.
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Affiliation(s)
- Sarah Carmona
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, Irvine, CA, United States of America
| | - Benjamin Lin
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, Irvine, CA, United States of America
| | - Tristan Chou
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, Irvine, CA, United States of America
| | - Katti Arroyo
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, Irvine, CA, United States of America
| | - Sha Sun
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, Irvine, CA, United States of America
- * E-mail:
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The metabolic role of LncZBTB39-1:2 in the trophoblast mobility of preeclampsia. Genes Dis 2018; 5:235-244. [PMID: 30320188 PMCID: PMC6176159 DOI: 10.1016/j.gendis.2018.04.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 04/10/2018] [Indexed: 12/15/2022] Open
Abstract
Preeclampsia is characterized by new onset of hypertension and proteinuria after 20 weeks' gestation and is a leading cause of maternal and neonatal morbidity and mortality. The pathogenesis of preeclampsia is often associated with aberrant trophoblast function that leads to shallow placental implantation. However, the exact underlying mechanisms remain unclear. Placental LncZBTB39-1:2 expression level was investigated in 20 healthy placentae and 20 placentae with preeclampsia using qRT-PCR, and the metabolic profile of trophoblasts overexpressing LncZBTB39-1:2 in vitro was analysed using gas chromatography-mass spectrometry (GC-MS). In this study, we found that the expression of LncZBTB39-1:2 was significantly higher in preeclamptic placentae than in healthy placentae. Our metabolomics results have shown that tricarboxylic acid cycle intermediates and metabolites related to carbohydrate metabolism were decreased with the overexpression of LncZBTB39-1:2 in HTR8/SVneo cells. These findings were validated by detecting a lower level of intracellular ATP in HTR8/Vneo cells. Furthermore, the migration of HTR8/SVneo cells was compromised when cells were transfected with a plasmid encompassing LncZBTB39-1:2 overexpression. From these results, we conclude that abnormal levels of LncZBTB39-1:2 expression might lead to aberrant conditions in HTR-8/SVneo trophoblast cells. Aberrant conditions might be associated with dysregulated trophoblast migration and subsequent failure of uterine spiral artery remodelling, a pathogenesis recognised as a contributing factor in the aetiology of preeclampsia.
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Abstract
Recent discoveries on the delivery of small- and large-size molecules and organelles to the oocytes/eggs from external sources, such as surrounding somatic cells, body fluids, and sperm, change our understanding of female germ cells' (oocytes and eggs) self-containment and individuality. In this chapter, we will summarize present-day knowledge on sources and presumptive functions of different types of exogenous molecules and organelles delivered to the animal oocytes and eggs.
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Affiliation(s)
- Malgorzata Kloc
- The Houston Methodist Research Institute, Houston, TX, USA. .,Department of Surgery, The Houston Methodist Hospital, 6550 Fannin St., Houston, TX, 77030, USA.
| | - Jacek Z Kubiak
- CNRS UMR 6290, Cell Cycle Group, Institute of Genetics and Development of Rennes, Rennes, France.,University of Rennes 1, Faculty of Medicine, Rennes, France.,Department of Regenerative Medicine, Military Institute of Hygiene and Epidemiology (WIHE), Warsaw, Poland
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