Identification and Characterization of the LncRNA Signature Associated with Overall Survival in Patients with Neuroblastoma

Overview

Journal Sci Rep

Specialty Science

Date 2019 Mar 28

PMID 30914706

Citations 18

Authors

Srinivasulu Yerukala Sathipati

Divya Sahu

Hsuan-Cheng Huang

Yenching Lin

Shinn-Ying Ho

Affiliations

Soon will be listed here.

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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References

Zhou M, Zhao H, Wang Z, Cheng L, Yang L, Shi H . Identification and validation of potential prognostic lncRNA biomarkers for predicting survival in patients with multiple myeloma. J Exp Clin Cancer Res. 2015; 34:102. PMC: 4567800. DOI: 10.1186/s13046-015-0219-5. View

Wei J, Greer B, Westermann F, Steinberg S, Son C, Chen Q . Prediction of clinical outcome using gene expression profiling and artificial neural networks for patients with neuroblastoma. Cancer Res. 2004; 64(19):6883-91. PMC: 1298184. DOI: 10.1158/0008-5472.CAN-04-0695. View

Yang J, Chen W, Liu Z, Luo Y, Liu W . Effects of insulin-like growth factors-IR and -IIR antisense gene transfection on the biological behaviors of SMMC-7721 human hepatoma cells. J Gastroenterol Hepatol. 2003; 18(3):296-301. DOI: 10.1046/j.1440-1746.2003.02961.x. View

Molenaar J, Koster J, Zwijnenburg D, van Sluis P, Valentijn L, van der Ploeg I . Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes. Nature. 2012; 483(7391):589-93. DOI: 10.1038/nature10910. View

Matthay K, Villablanca J, Seeger R, Stram D, Harris R, Ramsay N . Treatment of high-risk neuroblastoma with intensive chemotherapy, radiotherapy, autologous bone marrow transplantation, and 13-cis-retinoic acid. Children's Cancer Group. N Engl J Med. 1999; 341(16):1165-73. DOI: 10.1056/NEJM199910143411601. View

Prensner J, Chinnaiyan A . The emergence of lncRNAs in cancer biology. Cancer Discov. 2011; 1(5):391-407. PMC: 3215093. DOI: 10.1158/2159-8290.CD-11-0209. View

Zhang J, Liu J, Xu X, Li L . Curcumin suppresses cisplatin resistance development partly via modulating extracellular vesicle-mediated transfer of MEG3 and miR-214 in ovarian cancer. Cancer Chemother Pharmacol. 2017; 79(3):479-487. DOI: 10.1007/s00280-017-3238-4. View

Wang W, Zhao Z, Yang F, Wang H, Wu F, Liang T . An immune-related lncRNA signature for patients with anaplastic gliomas. J Neurooncol. 2017; 136(2):263-271. DOI: 10.1007/s11060-017-2667-6. View

Cui T, Zhang L, Huang Y, Yi Y, Tan P, Zhao Y . MNDR v2.0: an updated resource of ncRNA-disease associations in mammals. Nucleic Acids Res. 2017; 46(D1):D371-D374. PMC: 5753235. DOI: 10.1093/nar/gkx1025. View

10.

Sahu D, Hsu C, Lin C, Yang T, Hsu W, Ho S . Co-expression analysis identifies long noncoding RNA SNHG1 as a novel predictor for event-free survival in neuroblastoma. Oncotarget. 2016; 7(36):58022-58037. PMC: 5295409. DOI: 10.18632/oncotarget.11158. View

11.

Warrick J, Tomlins S, Carskadon S, Young A, Siddiqui J, Wei J . Evaluation of tissue PCA3 expression in prostate cancer by RNA in situ hybridization--a correlative study with urine PCA3 and TMPRSS2-ERG. Mod Pathol. 2013; 27(4):609-20. PMC: 3968238. DOI: 10.1038/modpathol.2013.169. View

12.

Mosse Y, Laudenslager M, Longo L, Cole K, Wood A, Attiyeh E . Identification of ALK as a major familial neuroblastoma predisposition gene. Nature. 2008; 455(7215):930-5. PMC: 2672043. DOI: 10.1038/nature07261. View

13.

Tu Z, He D, Deng X, Xiong M, Huang X, Li X . An eight-long non-coding RNA signature as a candidate prognostic biomarker for lung cancer. Oncol Rep. 2016; 36(1):215-22. DOI: 10.3892/or.2016.4817. View

14.

Fagerberg L, Hallstrom B, Oksvold P, Kampf C, Djureinovic D, Odeberg J . Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Mol Cell Proteomics. 2013; 13(2):397-406. PMC: 3916642. DOI: 10.1074/mcp.M113.035600. View

15.

Li A . Preclinical in vitro screening assays for drug-like properties. Drug Discov Today Technol. 2014; 2(2):179-85. DOI: 10.1016/j.ddtec.2005.05.024. View

16.

Khvorova A, Watts J . The chemical evolution of oligonucleotide therapies of clinical utility. Nat Biotechnol. 2017; 35(3):238-248. PMC: 5517098. DOI: 10.1038/nbt.3765. View

17.

Zhu G, Wang S, Chen J, Wang Z, Liang X, Wang X . Long noncoding RNA HAS2-AS1 mediates hypoxia-induced invasiveness of oral squamous cell carcinoma. Mol Carcinog. 2017; 56(10):2210-2222. DOI: 10.1002/mc.22674. View

18.

Jiang L, Huang J, Higgs B, Hu Z, Xiao Z, Yao X . Genomic Landscape Survey Identifies SRSF1 as a Key Oncodriver in Small Cell Lung Cancer. PLoS Genet. 2016; 12(4):e1005895. PMC: 4836692. DOI: 10.1371/journal.pgen.1005895. View

19.

Sareen D, ORourke J, Meera P, Muhammad A, Grant S, Simpkinson M . Targeting RNA foci in iPSC-derived motor neurons from ALS patients with a C9ORF72 repeat expansion. Sci Transl Med. 2013; 5(208):208ra149. PMC: 4090945. DOI: 10.1126/scitranslmed.3007529. View

20.

Hu Y, Chen H, Yu C, Xu J, Wang J, Qian J . A long non-coding RNA signature to improve prognosis prediction of colorectal cancer. Oncotarget. 2014; 5(8):2230-42. PMC: 4039159. DOI: 10.18632/oncotarget.1895. View