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Gupta M, Kannappan S, Jain M, Douglass D, Shah R, Bose P, Narendran A. Development and validation of a 21-gene prognostic signature in neuroblastoma. Sci Rep 2023; 13:12526. [PMID: 37532697 PMCID: PMC10397261 DOI: 10.1038/s41598-023-37714-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 06/26/2023] [Indexed: 08/04/2023] Open
Abstract
Survival outcomes for patients with neuroblastoma vary markedly and reliable prognostic markers and risk stratification tools are lacking. We sought to identify and validate a transcriptomic signature capable of predicting risk of mortality in patients with neuroblastoma. The TARGET NBL dataset (n = 243) was used to develop the model and two independent cohorts, E-MTAB-179 (n = 478) and GSE85047 (n = 240) were used as validation sets. EFS was the primary outcome and OS was the secondary outcome of interest for all analysis. We identified a 21-gene signature capable of stratifying neuroblastoma patients into high and low risk groups in the E-MTAB-179 (HR 5.87 [3.83-9.01], p < 0.0001, 5 year AUC 0.827) and GSE85047 (HR 3.74 [2.36-5.92], p < 0.0001, 5 year AUC 0.815) validation cohorts. Moreover, the signature remained independent of known clinicopathological variables, and remained prognostic within clinically important subgroups. Further, the signature was effectively incorporated into a risk model with clinicopathological variables to improve prognostic performance across validation cohorts (Pooled Validation HR 6.93 [4.89-9.83], p < 0.0001, 5 year AUC 0.839). Similar prognostic utility was also demonstrated with OS. The identified signature is a robust independent predictor of EFS and OS outcomes in neuroblastoma patients and can be combined with clinically utilized clinicopathological variables to improve prognostic performance.
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Affiliation(s)
- Mehul Gupta
- Department of Pediatrics and Oncology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Sunand Kannappan
- Department of Pediatrics and Oncology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Mohit Jain
- Department of Pediatrics and Oncology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - David Douglass
- Department of Pediatrics, Hematology/Oncology Section, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, AR, 72202, USA
| | - Ravi Shah
- Department of Pediatrics and Oncology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Pinaki Bose
- Departments of Oncology and Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada.
- Cumming School of Medicine, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada.
| | - Aru Narendran
- Department of Pediatrics and Oncology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada.
- Departments of Oncology and Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada.
- Cumming School of Medicine, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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Liu X, Chen J, Zhang S, Liu X, Long X, Lan J, Zhou M, Zheng L, Zhou J. LINC00839 promotes colorectal cancer progression by recruiting RUVBL1/Tip60 complexes to activate NRF1. EMBO Rep 2022; 23:e54128. [PMID: 35876654 PMCID: PMC9442307 DOI: 10.15252/embr.202154128] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 06/28/2022] [Accepted: 07/06/2022] [Indexed: 11/09/2022] Open
Abstract
The long noncoding RNA LINC00839 has been shown to be involved in the progression of some cancer types, such as bladder cancer, prostate cancer, breast cancer, and neuroblastoma. However, if LINC00839 has roles in colorectal cancer (CRC), it has not been elucidated so far. Here, we focus on the biological role and involved mechanisms of LINC00839 in CRC. We show that LINC00839 is selectively upregulated in CRC and locates to the nucleus. High expression of LINC00839 is associated with poor outcomes in CRC patients. Functional experiments show that LINC00839 promotes CRC proliferation, invasion, and metastasis in vitro and in vivo. Mechanistically, LINC00839 recruits Ruvb1 to the Tip60 complex and increases its acetylase activity. LINC00839 guides the complex to the NRF1 promoter and promotes acetylation of lysines 5 and 8 of histones H4, thereby upregulating the expression of NRF1. Subsequently, NRF1 activates mitochondrial metabolism and biogenesis, thereby promoting CRC progression. In summary, our study reports on a mechanism by which LINC00839 positively regulates NRF1, thus promoting mitochondrial metabolism and biogenesis, as well as CRC progression.
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Affiliation(s)
- Xiaoting Liu
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jianxiong Chen
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Sijing Zhang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xunhua Liu
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiaoli Long
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jiawen Lan
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Miao Zhou
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lin Zheng
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jun Zhou
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
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Li J, Wei S, Zhang Y, Lu S, Zhang X, Wang Q, Yan J, Yang S, Chen L, Liu Y, Huang Z. Comprehensive Analyses of Mutation-Derived Long-Chain Noncoding RNA Signatures of Genome Instability in Kidney Renal Papillary Cell Carcinoma. Front Genet 2022; 13:874673. [PMID: 35547247 PMCID: PMC9082950 DOI: 10.3389/fgene.2022.874673] [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: 02/12/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The role of long-chain noncoding RNA (lncRNA) in genomic instability has been demonstrated to be increasingly importance. Therefore, in this study, lncRNAs associated with genomic instability were identified and kidney renal papillary cell carcinoma (KIRP)-associated predictive features were analysed to classify high-risk patients and improve individualised treatment. Methods: The training (n = 142) and test (n = 144) sets were created using raw RNA-seq and patient’s clinical data of KIRP obtained from The Cancer Genome Atlas (TCGA).There are 27 long-chain noncoding RNAs (lncRNAs) that are connected with genomic instability, these lncRNAs were identified using the ‘limma’ R package based on the numbers of somatic mutations and lncRNA expression profiles acquired from KIRP TCGA cohort. Furthermore, Cox regression analysis was carried out to develop a genome instability-derived lncRNA-based gene signature (GILncSig), whose prognostic value was confirmed in the test cohort as well as across the entire KIRP TCGA dataset. Results: A GILncSig derived from three lncRNAs (BOLA3-AS1, AC004870, and LINC00839), which were related with poor KIRP survival, was identified, which was split up into high- and low-risk groups. Additionally, the GILncSig was found to be an independent prognostic predictive index in KIRP using univariate and multivariate Cox analysis. Furthermore, the prognostic significance and characteristics of GilncSig were confirmed in the training test and TCGA sets. GilncSig also showed better predictive performance than other prognostic lncRNA features. Conclusion: The function of lncRNAs in genomic instability and the genetic diversity of KIRP were elucidated in this work. Moreover, three lncRNAs were screened for prediction of the outcome of KIRP survival and novel insights into identifying cancer biomarkers related to genomic instability were discussed.
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Affiliation(s)
- Jian Li
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Shimei Wei
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yan Zhang
- Department of Pediatrics, Shanxi Children's Hospital, Taiyuan, China
| | - Shuangshuang Lu
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Xiaoxu Zhang
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Qiong Wang
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Jiawei Yan
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Sanju Yang
- Graduate School of Youjiang Medical University for Nationalities, Baise, China
| | - Liying Chen
- Graduate School of Youjiang Medical University for Nationalities, Baise, China
| | - Yunguang Liu
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Zhijing Huang
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
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Jahangiri L, Pucci P, Ishola T, Pereira J, Cavanagh ML, Turner SD. Deep analysis of neuroblastoma core regulatory circuitries using online databases and integrated bioinformatics shows their pan-cancer roles as prognostic predictors. Discov Oncol 2021; 12:56. [PMID: 35201514 PMCID: PMC8777518 DOI: 10.1007/s12672-021-00452-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/16/2021] [Indexed: 12/29/2022] Open
Abstract
AIM Neuroblastoma is a heterogeneous childhood cancer derived from the neural crest. The dual cell identities of neuroblastoma include Mesenchymal (MES) and Adrenergic (ADRN). These identities are conferred by a small set of tightly-regulated transcription factors (TFs) binding super enhancers, collectively forming core regulatory circuitries (CRCs). The purpose of this study was to gain a deep understanding of the role of MES and ADRN TFs in neuroblastoma and other cancers as potential indicators of disease prognosis, progression, and relapse. METHODS To that end, we first investigated the expression and mutational profile of MES and ADRN TFs in neuroblastoma. Moreover, we established their correlation with neuroblastoma risk groups and overall survival while establishing their extended networks with long non-coding RNAs (lncRNAs). Furthermore, we analysed the pan-cancer expression and mutational profile of these TFs and their correlation with patient survival and finally their network connectivity, using a panel of bioinformatic tools including GEPIA2, human pathology atlas, TIMER2, Omicsnet, and Cytoscape. RESULTS We show the association of multiple MES and ADRN TFs with neuroblastoma risk groups and overall survival and find significantly higher expression of various MES and ADRN TFs compared to normal tissues and their association with overall survival and disease-free survival in multiple cancers. Moreover, we report the strong correlation of the expression of these TFs with the infiltration of stromal and immune cells in the tumour microenvironment and with stemness and metastasis-related genes. Furthermore, we reveal extended pan-cancer networks comprising these TFs that influence the tumour microenvironment and metastasis and may be useful indicators of cancer prognosis and patient survival. CONCLUSION Our meta-analysis shows the significance of MES and ADRN TFs as indicators of patient prognosis and the putative utility of these TFs as potential novel biomarkers.
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Affiliation(s)
- Leila Jahangiri
- Department of Life Sciences, Birmingham City University, Birmingham, UK
- School of Science & Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS UK
- Division of Cellular and Molecular Pathology, Addenbrooke’s Hospital, University of Cambridge, Cambridge, UK
| | - Perla Pucci
- Division of Cellular and Molecular Pathology, Addenbrooke’s Hospital, University of Cambridge, Cambridge, UK
| | - Tala Ishola
- Department of Life Sciences, Birmingham City University, Birmingham, UK
| | - Joao Pereira
- Department of Neurology, Massachusetts General Hospital, Boston, MA USA
| | - Megan L. Cavanagh
- Department of Life Sciences, Birmingham City University, Birmingham, UK
| | - Suzanne D. Turner
- Division of Cellular and Molecular Pathology, Addenbrooke’s Hospital, University of Cambridge, Cambridge, UK
- CEITEC, Masaryk University, Brno, Czech Republic
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MIAT Is an Upstream Regulator of NMYC and the Disruption of the MIAT/NMYC Axis Induces Cell Death in NMYC Amplified Neuroblastoma Cell Lines. Int J Mol Sci 2021; 22:ijms22073393. [PMID: 33806217 PMCID: PMC8038079 DOI: 10.3390/ijms22073393] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 12/29/2022] Open
Abstract
Neuroblastoma (NBL) is the most common extracranial childhood malignant tumor and represents a major cause of cancer-related deaths in infants. NMYC amplification or overexpression is associated with the malignant behavior of NBL tumors. In the present study, we revealed an association between long non-coding RNA (lncRNA) myocardial infarction associated transcript (MIAT) and NMYC amplification in NBL cell lines and MIAT expression in NBL tissue samples. MIAT silencing induces cell death only in cells with NMYC amplification, but in NBL cells without NMYC amplification it decreases only the proliferation. MIAT downregulation markedly reduces the NMYC expression in NMYC-amplified NBL cell lines and c-Myc expression in NMYC non-amplified NBL cell lines, but the ectopic overexpression or downregulation of NMYC did not affect the expression of MIAT. Moreover, MIAT downregulation results in decreased ornithine decarboxylase 1 (ODC1), a known transcriptional target of MYC oncogenes, and decreases the glycolytic metabolism and respiratory function. These results indicate that MIAT is an upstream regulator of NMYC and that MIAT/NMYC axis disruption induces cell death in NMYC-amplified NBL cell lines. These findings reveal a novel mechanism for the regulation of NMYC in NBL, suggesting that MIAT might be a potential therapeutic target, especially for those with NMYC amplification.
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Yang L, Pei L, Yi J. LINC00839 Regulates Proliferation, Migration, Invasion, Apoptosis and Glycolysis in Neuroblastoma Cells Through miR-338-3p/GLUT1 Axis. Neuropsychiatr Dis Treat 2021; 17:2027-2040. [PMID: 34188473 PMCID: PMC8232867 DOI: 10.2147/ndt.s309467] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/27/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are related to the development and treatment of neuroblastoma. The lncRNA LINC00839 is dysregulated in neuroblastoma, while its function and mechanism in neuroblastoma development remain largely unclear. METHODS The tumor and adjacent noncancerous tissues were collected from 48 neuroblastoma patients. LINC00839, glucose transporter 1 (GLUT1) and microRNA-338-3p (miR-338-3p) abundances were examined via quantitative reverse transcription polymerase chain reaction or Western blot. Cell proliferation, apoptosis, migration, invasion and glycolysis were assessed via Cell Counting Kit-8, colony formation, flow cytometry, wound healing, transwell, glucose uptake and lactate production. The target relationship of miR-338-3p and LINC00839 or GLUT1 was tested via dual-luciferase reporter analysis and RNA immunoprecipitation. The function of LINC00839 on neuroblastoma cell growth in vivo was tested via a xenograft model. RESULTS LINC00839 and GLUT1 abundances were increased in neuroblastoma tissues and cell lines. The high expression of LINC00839 and GLUT1 indicated the lower overall survival. LINC00839 interference constrained neuroblastoma cell proliferation, migration, invasion and glycolysis, and facilitated apoptosis. GLUT1 overexpression or miR-338-3p knockdown could mitigate the influence of LINC00839 silence on neuroblastoma cell processes. LINC00839 could regulate GLUT1 expression via miR-338-3p. LINC00839 knockdown reduced neuroblastoma cell growth in xenograft model. CONCLUSION LINC00839 silence repressed neuroblastoma cell proliferation, migration, invasion and glycolysis and promoted apoptosis via regulating miR-338-3p/GLUT1 axis.
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Affiliation(s)
- Lixia Yang
- Department of Neurology, The First People's Hospital of Jingmen Affiliated to Hubei Minzu University, Jingmen, 434000, People's Republic of China
| | - Liangyan Pei
- Department of Neurology, The First People's Hospital of Jingmen Affiliated to Hubei Minzu University, Jingmen, 434000, People's Republic of China
| | - Jilong Yi
- Department of Neurology, The First People's Hospital of Jingmen Affiliated to Hubei Minzu University, Jingmen, 434000, People's Republic of China
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7
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Ge S, Mi Y, Zhao X, Hu Q, Guo Y, Zhong F, Zhang Y, Xia G, Sun C. Characterization and validation of long noncoding RNAs as new candidates in prostate cancer. Cancer Cell Int 2020; 20:531. [PMID: 33292248 PMCID: PMC7603695 DOI: 10.1186/s12935-020-01615-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/20/2020] [Indexed: 12/19/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) have been proved to be an important regulator in gene expression. In almost all kinds of cancers, lncRNAs participated in the process of pathogenesis, invasion, and metastasis. Meanwhile, compared with the large amounts of patients, there is rare knowledge about the role of lncRNAs in prostate cancer (PCa). Material/Method In this study, lncRNA expression profiles of prostate cancer were detected by Agilent microarray chip, 5 pairs of case and control specimens were involved in. Differentially expressed lncRNAs were screened out by volcano plot for constructing lncRNA-miRNA-mRNA central network. Then, the top ten up-regulated and down-regulated lncRNAs were validated by qRT-PCR in another 5 tumor specimens and 7 para-cancerous/benign contrasts. Furthermore, we searched for the survival curve of the top 10 upregulated and downregulated lncRNAs. Results A total of 817 differentially expressed lncRNAs were filtered out by the criteria of fold change (FC) and t-test p < 0.05. Among them, 422 were upregulated, whereas 395 were downregulated in PCa tissues. Gene ontology and KEGG pathway analyses showed that many lncRNAs were implicated in carcinogenesis. lnc-MYL2-4:1 (FC = 0.00141, p = 0.01909) and NR_125857 (FC = 59.27658, p = 0.00128) had the highest magnitude of change. The subsequent qPCR confirmed the expression of NR_125857 was in accordance with the clinical samples. High expression of PCA3, PCAT14 and AP001610.9 led to high hazard ratio while low expression of RP11-279F6.2 led to high hazard ratio. Conclusions Our study detected a relatively novel complicated map of lncRNAs in PCa, which may have the potential to investigate for diagnosis, treatment and follow-up in PCa. Our study revealed the expression of NR_125857 in human PCa tissues was most up-regulated. Further studies are needed to investigate to figure out the mechanisms in PCa.
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Affiliation(s)
- Shengyang Ge
- Department of Urology, Huashan Hospital, Fudan University, 12 Central Urumqi Rd, Shanghai, 200040, P. R. China
| | - Yuanyuan Mi
- Department of Urology, Affiliated Hospital of Jiangnan University, Hefeng Rd, Wuxi, 214000, PR China
| | - Xiaojun Zhao
- Department of Clinical Immunology, Shanghai Center for Clinical Laboratory, 528 Hongshan Rd, Shanghai, 200126, P. R. China
| | - Qingfeng Hu
- Department of Urology, Huashan Hospital, Fudan University, 12 Central Urumqi Rd, Shanghai, 200040, P. R. China
| | - Yijun Guo
- Department of Urology, Jing'an District Central Hospital, Fudan University, 259 Xikang Rd, Shanghai, 200040, P. R. China
| | - Fan Zhong
- Department of Systems Biology for Medicine, and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, 130 Dongan Rd, Shanghai, P. R. China
| | - Yang Zhang
- Department of Systems Biology for Medicine, and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, 130 Dongan Rd, Shanghai, P. R. China
| | - Guowei Xia
- Department of Urology, Huashan Hospital, Fudan University, 12 Central Urumqi Rd, Shanghai, 200040, P. R. China.
| | - Chuanyu Sun
- Department of Urology, Huashan Hospital, Fudan University, 12 Central Urumqi Rd, Shanghai, 200040, P. R. China.
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Hu Y, Sun H, Hu J, Zhang X. LncRNA DLX6-AS1 Promotes the Progression of Neuroblastoma by Activating STAT2 via Targeting miR-506-3p. Cancer Manag Res 2020; 12:7451-7463. [PMID: 32904436 PMCID: PMC7455600 DOI: 10.2147/cmar.s252521] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
Background Neuroblastoma (NB) is a common malignant tumor of the sympathetic nervous system, mainly disturbing children. Long non-coding RNAs (lncRNAs) serving as promising cancer biomarkers have been well recognized. Our study intends to explore the functions of lncRNA X–inactive specific transcript (DLX6-AS1) in NB and provide a potential action mechanism. Methods The expression of DLX6-AS1, miR-506-3p and signal transducer and activator of transcription 2 (STAT2) was measured by quantitative real-time polymerase chain reaction (qRT-PCR). Cell proliferation was assessed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and colony formation assay. Cell cycle distribution was determined by flow cytometry assay. The protein level of cell cycle-related markers and STAT2 was detected by Western blot. Glycolysis progress was evaluated according to glucose consumption, lactate production and ATP level. The target genes were predicted by the online database Starbase3.0 and verified by dual-luciferase reporter assay. Results DLX6-AS1 expression was highly elevated in NB tissues and cells. DLX6-AS1 deficiency inhibited NB cell proliferation, cell cycle and glycolysis in vitro. MiR-506-3p was a target of DLX6-AS1, and miR-506-3p absence partly reversed the effects of DLX6-AS1 deficiency. Besides, STAT2 was targeted by miR-506-3p, and its expression was regulated by DLX6-AS1 through miR-506-3p. MiR-506-3p restoration also inhibited NB cell malignant behaviors, and STAT2 overexpression partially abolished the role of miR-506-3p restoration. Moreover, DLX6-AS1 deficiency weakened tumor growth in vivo. Conclusion DLX6-AS1 regulated cell proliferation, cell cycle and glycolysis in vitro and tumor growth in vivo to promote the development of NB by upregulating STAT2 via targeting miR-506-3p.
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Affiliation(s)
- Yanping Hu
- Department of Pediatrics, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan 471009, People's Republic of China
| | - Huifang Sun
- Department of Pediatrics, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan 471009, People's Republic of China
| | - Jiting Hu
- Department of Pediatrics, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan 471009, People's Republic of China
| | - Xiaomin Zhang
- Department of Pediatrics, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan 471009, People's Republic of China
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Meng X, Fang E, Zhao X, Feng J. Identification of prognostic long noncoding RNAs associated with spontaneous regression of neuroblastoma. Cancer Med 2020; 9:3800-3815. [PMID: 32216054 PMCID: PMC7286466 DOI: 10.1002/cam4.3022] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/25/2020] [Accepted: 03/12/2020] [Indexed: 12/13/2022] Open
Abstract
Background The association between long noncoding RNAs (lncRNAs) and spontaneous regression of neuroblastoma (NB) has rarely been investigated and remains unknown. Objective To identify prognostic lncRNAs involved in the spontaneous regression of NB. Methods Differential expression analyses were performed between those samples with an outcome of death in stage 4 NB group and those samples with an outcome of survival in stage 4S NB group in two independent public datasets, respectively. Univariate Cox proportional hazard regression survival analysis was performed in each of the entire cohort to identify those lncRNAs significantly associated with overall survival (OS). Those lncRNAs independently associated with OS were then identified by multivariate Cox survival analysis and used to construct an lncRNA risk score. Results A total of 20 differentially expressed and survival‐related lncRNAs were identified sharing between the two independent cohorts. The expression of each of these 20 lncRNAs was significantly correlated with the expression of NTRK1, which is a well‐known factor involved in NB spontaneous regression. Four lncRNAs (LNC00839, FIRRE, LOC283177, and LOC101928100) were identified to be significantly associated with survival independent with each other and a four‐lncRNA signature risk score was constructed. Patients with high lncRNA signature risk score had a significantly poorer OS and event‐free survival than those with low lncRNA signature risk score. The four‐lncRNA signature has a good performance in predicting survival independent with MYCN amplification (nonamplified vs amplified), age status (<18 months vs ≥18 months), risk status (low risk vs high risk), and International Neuroblastoma Staging System (INSS) stage (INSS 1/2/3/4S vs INSS 4). Conclusions We identified 20 survival‐related lncRNAs that might be associated with the spontaneous regression of NB and developed a four‐lncRNA signature risk score. The four‐lncRNA signature is an independent prognostic factor for survival of NB patients.
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Affiliation(s)
- Xinyao Meng
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Erhu Fang
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiang Zhao
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiexiong Feng
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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10
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Zhou JG, Liang B, Jin SH, Liao HL, Du GB, Cheng L, Ma H, Gaipl US. Development and Validation of an RNA-Seq-Based Prognostic Signature in Neuroblastoma. Front Oncol 2019; 9:1361. [PMID: 31867276 PMCID: PMC6904333 DOI: 10.3389/fonc.2019.01361] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 11/18/2019] [Indexed: 12/25/2022] Open
Abstract
Objective: The stratification of neuroblastoma (NBL) prognosis remains difficult. RNA-based signatures might be able to predict prognosis, but independent cross-platform validation is still rare. Methods: RNA-Seq-based profiles from NBL patients were acquired and then analyzed. The RNA-Seq prognostic index (RPI) and the clinically adjusted RPI (RCPI) were successively established in the training cohort (TARGET-NBL) and then verified in the validation cohort (GSE62564). Survival prediction was assessed using a time-dependent receiver operating characteristic (ROC) curve and area under the ROC curve (AUC). Functional enrichment analysis of the genes was conducted using bioinformatics methods. Results: In the training cohort, 10 gene pairs were eventually integrated into the RPI. In both cohorts, the high-risk group had poor overall survival (OS) (P < 0.001 and P < 0.001, respectively) and favorable event-free survival (EFS) (P = 0.00032 and P = 0.06, respectively). ROC curve analysis also showed that the RPI predicted OS (60 month AUC values of 0.718 and 0.593, respectively) and EFS (60 month AUC values of 0.627 and 0.852, respectively) well in both the training and validation cohorts. Clinicopathological indicators associated with prognosis in the univariate and multivariate regression analyses were identified and added to the RPI to form the RCPI. The RCPI was also used to divide populations into different risk groups, and the high-risk group had poor OS (P < 0.001 and P < 0.001, respectively) and EFS (P < 0.05 and P < 0.05, respectively). Finally, the RCPI had higher accuracy than the RPI for the prediction of OS (60 month AUC values of 0.730 and 0.852, respectively) and EFS (60 month AUC values of 0.663 and 0.763, respectively) in both the training and validation cohorts. Moreover, these differentially expressed genes may be involved in certain NBL-related events. Conclusions: The RCPI could reliably categorize NBL patients based on different risks of death.
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Affiliation(s)
- Jian-Guo Zhou
- Department of Oncology, Affiliated Hospital of Zunyi Medical University, Zunyi, China.,Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Bo Liang
- Affiliated Nanjing Hospital of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Su-Han Jin
- Department of Orthodontics, Affiliated Stemmatological Hospital of Zunyi Medical University, Zunyi, China
| | - Hui-Ling Liao
- College of Integrated Traditional Chinese and Western Medicine, Southwest Medical University, Luzhou, China
| | - Guo-Bo Du
- Department of Oncology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Long Cheng
- Department of Oncology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Hu Ma
- Department of Oncology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Udo S Gaipl
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany
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11
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Smith CM, Catchpoole D, Hutvagner G. Non-Coding RNAs in Pediatric Solid Tumors. Front Genet 2019; 10:798. [PMID: 31616462 PMCID: PMC6764412 DOI: 10.3389/fgene.2019.00798] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 07/30/2019] [Indexed: 12/15/2022] Open
Abstract
Pediatric solid tumors are a diverse group of extracranial solid tumors representing approximately 40% of childhood cancers. Pediatric solid tumors are believed to arise as a result of disruptions in the developmental process of precursor cells which lead them to accumulate cancerous phenotypes. In contrast to many adult tumors, pediatric tumors typically feature a low number of genetic mutations in protein-coding genes which could explain the emergence of these phenotypes. It is likely that oncogenesis occurs after a failure at many different levels of regulation. Non-coding RNAs (ncRNAs) comprise a group of functional RNA molecules that lack protein coding potential but are essential in the regulation and maintenance of many epigenetic and post-translational mechanisms. Indeed, research has accumulated a large body of evidence implicating many ncRNAs in the regulation of well-established oncogenic networks. In this review we cover a range of extracranial solid tumors which represent some of the rarer and enigmatic childhood cancers known. We focus on two major classes of ncRNAs, microRNAs and long non-coding RNAs, which are likely to play a key role in the development of these cancers and emphasize their functional contributions and molecular interactions during tumor formation.
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Affiliation(s)
- Christopher M Smith
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Daniel Catchpoole
- School of Software, University of Technology Sydney, Sydney, Australia.,The Tumour Bank-CCRU, Kids Research, The Children's Hospital at Westmead, Sydney, Australia
| | - Gyorgy Hutvagner
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
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12
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Yerukala Sathipati S, Sahu D, Huang HC, Lin Y, Ho SY. Identification and characterization of the lncRNA signature associated with overall survival in patients with neuroblastoma. Sci Rep 2019; 9:5125. [PMID: 30914706 PMCID: PMC6435792 DOI: 10.1038/s41598-019-41553-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/05/2019] [Indexed: 01/16/2023] Open
Abstract
Neuroblastoma (NB) is a commonly occurring cancer among infants and young children. Recently, long non-coding RNAs (lncRNAs) have been using as prognostic biomarkers for therapeutics and interventions in various cancers. Considering the poor survival of NB, the lncRNA-based therapeutic strategies must be improved. This work proposes an overall survival time estimator called SVR-NB to identify the lncRNA signature that is associated with the overall survival of patients with NB. SVR-NB is an optimized support vector regression (SVR)-based method that uses an inheritable bi-objective combinatorial genetic algorithm for feature selection. The dataset of 231 NB patients that contains overall survival information and expression profiles of 783 lncRNAs was used to design and evaluate SVR-NB from the database of gene expression omnibus accession GSE62564. SVR-NB identified a signature of 35 lncRNAs and achieved a mean squared correlation coefficient of 0.85 and a mean absolute error of 0.56 year between the actual and estimated overall survival time using 10-fold cross-validation. Further, we ranked and characterized the 35 lncRNAs according to their contribution towards the estimation accuracy. Functional annotations and co-expression gene analysis of LOC440896, LINC00632, and IGF2-AS revealed the association of co-expressed genes in Kyoto Encyclopedia of Genes and Genomes pathways.
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Grants
- This work was funded by Ministry of Science and Technology ROC under the contract numbers MOST 106-2634-F-075-001-, 106-2218-E-009-031-, 107-2221-E-009-154-, 107-2218-E-029-001-, and 107-2314-B-039-025-. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
- This work was funded by Ministry of Science and Technology ROC under the contract numbers MOST 107-2221-E-009 -154 &#x2013;, 107-2634-F-075 -001 &#x2013;, 107-2218-E-009 -005 &#x2013;, 107-2218-E-029 -001 &#x2013;, and 107-2319-B-400 -001 &#x2013;, and was financially supported by the &#x201C;Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B)&#x201D; from The Featured Areas Research Center Program within the framework of the Higher Education Sprout Project by the Ministry of Education (MOE) in Taiwan. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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Affiliation(s)
| | - Divya Sahu
- Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei, Taiwan
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Yenching Lin
- Interdisciplinary Neuroscience Ph.D. Program, National Chiao Tung University, Hsinchu, Taiwan
| | - Shinn-Ying Ho
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan.
- Interdisciplinary Neuroscience Ph.D. Program, National Chiao Tung University, Hsinchu, Taiwan.
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.
- Center For Intelligent Drug Systems and Smart Bio-devices (IDSB), National Chiao Tung University, Hsinchu, Taiwan.
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