Genomic analysis-integrated whole-exome sequencing of neuroblastomas identifies genetic mutations in axon guidance pathway

Abstract

Neuroblastoma (NB) is a childhood solid malignant tumor originating from precursor cells of the peripheral nervous system. We have previously established a risk classification system based on DNA copy number profiles. To further explore the pathogenesis of NBs in distinct risk groups, we performed whole-exome sequencing analysis of 57 primary and 7 recurrent/metastatic tumors with unique chromosomal aberration profiles as categorized by our genomic sub-grouping system. Overall, a low frequency of somatic mutations was found. Besides ALK (4/64, 6.3%), SEMA6C, SLIT1 and NRAS, genes involved in the axon guidance pathway, were identified as recurrently mutated in 6 of 64 tumors (9.4%). Pathway enrichment analysis revealed enrichment of 25 mutated genes in the mitogen-activated protein kinase (MAPK) pathway, 13 genes in the Wnt pathway, and 12 genes in the axon guidance pathway. Genomic analyses demonstrated that primary and matched recurrent or metastatic tumors obtained from sporadic and monozygotic twin NBs were clonally related with variable extents of genetic heterogeneity. Monozygotic twin NBs displayed different evolutionary trajectories. These results indicate the involvement of the axon guidance, MAPK and Wnt pathways in NB and demonstrate genomic diversity with NB progression.

PPP3CB contributes to poor prognosis through activating nuclear factor of activated T‐cells signaling in neuroblastoma

“…Consistent with these studies, we identified a significantly smaller mutation spectrum with a very low frequency of recurrent somatic mutations in 56 paired primary NBs . Intriguingly, we discovered a nonsense mutation in the C‐terminal of PPP3CB, the catalytic subunit of calcineurin, in a NB case with MYCN amplification .…”

“…We have found a nonsense mutation in the C-terminal of PPP3CB in front of the autoinhibitory domain in a primary MYCN-amplified NB tumor. 7 As the catalytic subunit of calcineurin, the truncated mutant encodes a constitutively active PPP3CB protein, independent of the calcium/calmodulin-dependent activation ( Figure 1A).…”

“…Consistent with these studies, we identified a significantly smaller mutation spectrum with a very low frequency of recurrent somatic mutations in 56 paired primary NBs. 7 Intriguingly, we discovered a nonsense mutation in the C-terminal of PPP3CB, the catalytic subunit of calcineurin, in a NB case with MYCN amplification. 7 The mutation occurs at the R459 residue in front of the autoinhibitory domain and results in the expression of a constitutively active PPP3CB protein ( Figure 1A).…”

Wnt Signalling Drives Context-Dependent Differentiation or Proliferation in Neuroblastoma

“…Our transcriptomic and functional data, together with recent mutation analysis [20] , indicate that a canonical Wnt programme may be more active in lower stage neuroblastoma and decreased/suppressed in higher stage neuroblastomas. We therefore examined β-catenin protein expression at the cellular level in neuroblastoma tissue sections.…”

“…In neuroblastoma, mutations in Wnt pathway components have only been reported very recently [20] , and identified mutations predicted to have high functional impact in a Wnt geneset defined by the KEGG database, and included NFATC1, FBXW11, TP53, AXIN2, LRP5, CCND1, FZD9, DVL2, FOSL1, WNT7B, VANGL1, LEF1, and PPP3CB genes. Interestingly, the latter three gene mutations introduce premature termination, suggestive of a tumour suppressive role of Wnt signalling in neuroblastoma.…”