The complete spectrum of somatic mutations of the most aggressive forms of neuroblastoma is still to be defined. Here we sought to identify additional potential cancer drivers in high-risk and ultra-high-risk (high-risk patients with any adverse event within 36 months from diagnosis) neuroblastoma.
Whole exome sequencing was performed for 17 ultra-high-risk germline and tumor pairs to identify somatic mutations and deep targeted sequencing of 134 genes selected from the initial screening in an additional set of 48 germline and tumor pairs (62.5% were ultra-high-risk and high-risk), 17 ultra-high-risk tumors and 17 human-derived neuroblastoma cell lines.
Combining both cohorts we found 22 significantly mutated genes, many of which implicated in cancer progression processes. Of these, fifteen (68.2%) were highly expressed in neuroblastoma supporting the biological rationale for their involvement in this malignancy. CHD9, annotated as cancer driver in public databases, was the most significantly altered gene (4.0% of cases) after ALK. Other genes (PTK2, NAV3, NAV1, LRRC17, PXDN, FZD1, ARHGEF10L and ATRX) expressed in neuroblastoma and involved in cell invasiveness and migration were mutated at frequencies between 4% and 2%. Pathways implicated in cell survival, proliferation and motility (focal adhesion and regulation of actin cytoskeleton) were the most frequently disrupted affecting 14.1% of cases, suggesting potential novel therapeutic strategies to prevent disease progression. Rare potentially pathogenic germline variants were significantly enriched in BARD1, CHEK2 and AXIN2.
To conclude, the combination of whole exome and deep targeted sequencing in a discovery and validation cohort experimental design, identified novel cancer genes in clinically aggressive neuroblastomas. Our analyses demonstrate that infrequently mutated genes may have pathway-level implications in leading tumor progression and suggests possible novel strategies for therapeutic interventions in aggressive forms of neuroblastoma.