Whole-exome sequencing reveals genetic variants in low-risk and high-risk neuroblastoma

• Published in: Gene 2023-04, Vol.860, p.147233-147233, Article 147233
• Main Authors: Altun, Zekiye, Yuan, Hongling, Baran, Burçin, Aktaş, Safiye, Sönmez, Esra Esmeray, Küçük, Can, Olgun, Nur
• Format: Article
• Language: English
• Subjects: cBioportal; COSMIC; Exome Sequencing; Gene variations; Genomics; Humans; Neuroblastoma; Neuroblastoma - genetics; Neuroblastoma - pathology; Oncogenes; Risk Factors; Whole-exome sequencing
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2023.147233

•Genetic variations in low-risk and high-risk NB patients were examined by WES.•The genetic variations found and compared with previous NB whole-exome sequencing studies in the cBioportal database.•Variants in ARID1A and NCOR2, related to chromatin remodeling, were commonly mutated in cBioportal and high-risk patients.•Candidate gene variations associated with chromatin remodeling, RAS pathway, cell proliferation, and DNA repair mechanism. This study aimed to investigate the genetic aberrations in neuroblastoma (NB) by comparing high and low-risk NB patients by whole-exome sequencing (WES) and to reveal the heterogeneity and association between somatic variants and clinical features. Seven NB patients with available clinical data were included in the study (4 in the low-risk group and 3 in the high-risk group). WES was performed and somatic variants associated with NB genes in the COSMIC database were selected through bioinformatics pipeline analysis. Variants were determined using the Integrative Genomics Viewer (IGV). Some gene variations were found in both groups, including variations in oncogene and tumor suppressor genes. In general, candidate gene variations were associated with chromatin remodeling complexes, the RAS pathway, cell proliferation, and DNA repair mechanism. Some variations in CSF1R, MSH6, PTPN11, SOX9, RET, TSC1, and DNMT1 genes were detected only in high-risk patients, while EP300, TET2, MYCN, PRDM1, and ARID2 gene variations were detected only in low-risk patients. When high-risk gene variants were compared with the cBioportal cancer genomic database, two common gene variants (ARID1A and NCOR2) were identified. However, when low-risk gene variants were compared with the cBioportal cancer genomic database, no common genes were found. GO/KEGG enrichment analysis was performed to find relevant biological processes and molecular pathways related to gene variants, which will help to decipher the molecular mechanisms of NB tumorigenesis and the phenotypic differences between high-risk and low-risk patients.