Abstract
Neuroblastoma is the most common extracranial solid tumor in childhood. Patients in high-risk group often have poor outcomes with low survival rates despite several treatment options. This study aimed to identify a genetic signature from gene expression profiles that can serve as prognostic indicators of survival time in patients of high-risk neuroblastoma, and that could be potential therapeutic targets. RNA-seq count data was downloaded from UCSC Xena browser and samples grouped into Short Survival (SS) and Long Survival (LS) groups. Differential gene expression (DGE) analysis, enrichment analyses, regulatory network analysis and machine learning (ML) prediction of survival group were performed. Forty differentially expressed genes (DEGs) were identified including genes involved in molecular function activities essential for tumor proliferation. DEGs used as features for prediction of survival groups included EVX2, NHLH2, PRSS12, POU6F2, HOXD10, MAPK15, RTL1, LGR5, CYP17A1, OR10AB1P, MYH14, LRRTM3, GRIN3A, HS3ST5, CRYAB and NXPH3. An accuracy score of 82% was obtained by the ML classification models. SMIM28 was revealed to possibly have a role in tumor proliferation and aggressiveness. Our results indicate that these DEGs can serve as prognostic indicators of survival in high-risk neuroblastoma patients and will assist clinicians in making better therapeutic and patient management decisions.
Highlights
Neuroblastoma is the most common extracranial solid tumor in childhood accounting for approximately 15% of pediatric cancer death [1,2,3]
The Differential gene expression (DGE) analysis is a powerful technique for identifying Differentially Expressed Gene (DEG) in a studied condition
In this study, using DESeq2 we identified 40 DEGs between Short Survival (SS) and Long Survival (LS) neuroblastoma samples
Summary
Neuroblastoma is the most common extracranial solid tumor in childhood accounting for approximately 15% of pediatric cancer death [1,2,3]. It develops anywhere along the sympathetic nervous system with 60% of the tumors occurring in the abdomen, commonly in the adrenal gland [4, 5]. Patients classified in low-risk groups have good outcomes contrary to high-risk groups who present poor outcomes despite extensive therapies [4] and with a disproportionate number dying or suffering profound treatment related morbidities [7, 8]. Tumors in high-risk neuroblastoma patients are often metastatic, resulting in survival rates of less than 50% [1]
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