Common Genetic Variants in NEFL Influence Gene Expression and Neuroblastoma Risk

Abstract

The genetic etiology of sporadic neuroblastoma is still largely obscure. In a genome-wide association study, we identified single nucleotide polymorphisms (SNP) associated with neuroblastoma at the LINC00340, BARD1, LMO1, DUSP12, HSD17B12, HACE1 and LIN28B gene loci, but these explain only a small fraction of neuroblastoma heritability. Other neuroblastoma susceptibility genes are likely hidden among signals discarded by the multiple testing corrections. In this study, we evaluated 8 additional genes selected as candidates for further study based on proven involvement in neuroblastoma differentiation. SNP at these candidate genes were tested for association with disease susceptibility in 2101 cases and 4202 controls, with the associations found replicated in an independent cohort of 459 cases and 809 controls. Replicated associations were further studied for cis-effect using gene expression, transient overexpression, silencing and cellular differentiation assays. The neurofilament gene NEFL harbored three SNP associated with neuroblastoma (rs11994014; Pcombined=0.0050; OR=0.88, rs2979704; Pcombined=0.0072; OR=0.87, rs105911; Pcombined=0.0049; OR=0.86). The protective allele of rs1059111 correlated with increased NEFL expression. Biological investigations showed that ectopic overexpression of NEFL inhibited cell growth specifically in neuroblastoma cells carrying the protective allele. NEFL overexpression also enhanced differentiation and impaired the proliferation and anchorage-independent growth of cells with protective allele and basal NEFL expression, while impairing invasiveness and proliferation of cells homozygous for the risk genotype. Clinically, high levels of NEFL expression in primary neuroblastoma specimens was associated with better overall survival (P=0.03; HR=0.68). Our results show that common variants of NEFL influence neuroblastoma susceptibility and they establish that NEFL expression influences disease initiation and progression.

Genetic susceptibility to neuroblastoma

“…[89] This original GWAS has been expanded and replicated as additional patient samples have been accrued, leading to the identification of DNA alleles significantly associated with high-risk and low-risk neuroblastoma predisposition, including CASC15, BARD1, LMO1, LIN28B, HACE1, DUSP12, DDX4, IL31RA, HSD17B12, NEFL, TP53, AND NBPF23 (Table 1). [72, 74, 75, 79, 81, 88, 89, 102–104, 107] The discovery of these susceptibility loci demonstrates the utility of interrogating GWAS signals for clues into the underlying biology driving neuroblastoma genesis.…”

“…[102] Overexpression of NEFL in cells with a protective allele caused cells to adopt a more differentiated phenotype and to have reduced proliferative capacity. The authors suggested that decreased expression of NEFL alters the differentiation state of sympathetic neurons and may predispose neuroblastoma.…”

miR-204 mediates post-transcriptional down-regulation of PHOX2B gene expression in neuroblastoma cells

“…In particular, consistent with a putative effect of the variant T-allele on weakening the mRNA secondary structure, we did show that miR-204 is able, by means of a still undisclosed mechanism, to decrease the stability of the PHOX2B mRNA, at a larger extent in the presence of the T allele than in the presence of the A allele. This suggests a putative role of SNP rs1063611 as susceptibility locus for neuroblastoma, thus making highly probable an association between this SNP and neuroblastoma which might deserve to be tested in a large case-control study [38,39]. Our result also suggests a genotype-dependent effect of miR-204 which should be therefore considered when reasoning about possible therapeutic interventions and personalized medicine.…”

Lack of Associations betweenXPCGene Polymorphisms and Neuroblastoma Susceptibility in a Chinese Population

“…Several gene polymorphisms are significantly associated with the risk of neuroblastoma, such as LIN28B [10], HACE1 [10], BARD1 [11], LMO1 [12], HSD17B12 [13], DDX4 [13], IL31RA [13], and DUSP12 [13], which have been discovered by means of GWAS. Besides, several genes, such as FAS [14], FASL [14], NEFL [15], and TGFBR3L [16], have been discovered by candidate gene approach.…”