Introduction: Genome-wide association studies (GWASs) have contributed to the study of neuroblastoma (NB) genetics by identifying common risk variants that activate cancer-related processes associated with NB susceptibility.
Aim: This study aims to functionally characterize the 11p11.2 predisposition locus identified in our GWAS on 2101 cases and 4202 controls, evaluating how the regulatory variant and its target gene can influence NB development.
Methods: To identify functional variants, we annotated 72 candidate SNPs with functional data from public NB databases and validated the functional SNP’s regulatory activity vialuciferase assays in NB cells. The candidate SNP was predicted to map inside a GATA3 binding motif and differential GATA3 allele binding was evaluated using ChIP-qPCR. eQTL analysis and CRISPR/Cas9 genome editing allowed us to identify the target gene of the functional SNP. To evaluate its role in NB tumorigenesis, we correlated gene expression with clinical features using RNA-seq data from 498 tumors and performed MTT and invasion assays after gene silencing in NB cells. Targeted lipidomic assays were performed to study the involvement of the target gene in lipid metabolism.
Results: rs2863002T>C represents the candidate functional SNP of the risk locus. The rs2863002-C allele correlated with high expression levels of its target gene HSD17B12 and showed a lower binding affinity for the transcription factor GATA3 in NB cells, suggesting that it may alter the GATA3 binding motif. High HSD17B12 expression levels correlated with poor prognosis and survival in NB tumors, and gene silencing in NB cells reduced proliferation and invasiveness, supporting the oncogenic role of HSD17B12 in NB. Lipidomic results showed that HSD17B12 silencing in NB cells altered lipid metabolism, affecting lipid molecules related to energy production and cellular membrane chemical—physical properties.
Conclusions: This study highlights the importance of the post-GWAS functional characterization of risk loci to identify new susceptibility genes and new biological mechanisms underlying NB predisposition.
