A novel risk signature that combines 10 long noncoding RNAs to predict neuroblastoma prognosis

Abstract

Neuroblastoma (NBL) is the most frequently encountered extracranial solid neoplasm and impacts significantly on the survival of patients, especially in cases of advanced tumor stage or relapse. A long noncoding RNA (lncRNA) signature to predict the survival of patients with NBL is proposed in this paper. Differentially expressed lncRNA (DElncRNA) was selected using the Limma plus Voom package in R based on the RNA-sequencing data downloaded from the Therapeutically Applicable Research To Generate Effective Treatments database and Genotype-Tissue Expression database. Univariate cox regression analysis, least absolute shrinkage and selection operator regression analysis, and multivariate cox regression analysis were conducted to identify candidate DElncRNAs for the risk signature. Consequently, 10 DElncRNAs were designated as candidate DElncRNAs for the risk signature. Time-dependent receiver operating characteristic curves and Kapan-Meier survival curves confirmed the efficacy of the risk signature in predicting the survival of patients with NBL (area under the curve = 0.941; p ≤ .001). One of the DElncRNA constituent subparts (LINC01010) was significantly associated with the survival outcome of patients with NBL in GSE62564 (p = .004). Thus, a risk signature comprising 10 DElncRNAs was identified as effective for individual risk stratification and the survival prediction outcomes of patients with NBL.

Prognostic Signature of Immune Genes and Immune-Related LncRNAs in Neuroblastoma: A Study Based on GEO and TARGET Datasets

“…At present, NB treatment is mainly based on the INRG risk stratification system ( 3 ). Researchers have discovered some prognostic markers that may assist clinicians in choosing the optimal treatment regimen, but few patients benefit from these markers, especially those in subgroups ( 37 – 40 ). It has not yet been elucidated whether the prognosis of NB patients can be predicted by immune-related genes and immune-related lncRNAs and their correlations with clinicopathological characteristics.…”

“…Long non-coding RNAs (lncRNAs) participate in the pathological process of tumors including NB in a variety of ways ( 6 , 49 ), and lncRNAs may serve as the prognostic markers for various cancers ( 37 ). For example, NBAT1 is located on chromosome 6p22, regulates NB progression, and is correlated with the favorable outcome of NB ( 50 ).…”

“…In addition, LncNB1 plays an oncogenic role in NB tumorigenesis ( 51 ). Gao L constructed a risk signature comprised of 10 lncRNAs, with the AUC value of as high as 0.941 in predicting patients’ survival ( 37 ). However, its generalization performance was unsatisfactory and the signature was not further verified in more independent datasets.…”

“…It served as an independent prognostic factor for OS and EFS in GSE49710 and OS in GSE16476 and had the most significant p-value. Gao identified 10 lncRNAs through differentially expressed analysis and incorporate them in a prognostic signature ( 37 ). By contrast, the 11 lncRNAs identified in this study were not the same as the results of the study by Gao, which might be ascribed to the different dataset detection and screening methods.…”

Development of a Machine Learning-Based Autophagy-Related lncRNA Signature to Improve Prognosis Prediction in Osteosarcoma Patients

“…Therapeutically Applicable Research to Generate Effective Treatments (TARGET) 1 is an open database for childhood cancers. It seeks to use a comprehensive genomic approach to identify molecular changes in the occurrence and development of childhood cancers that are difficult to treat (Gao et al, 2020;Zhang et al, 2020). We obtained gene expression and clinical data of osteosarcoma patients from the TARGET database.…”