Whole Exome Sequencing Reveals the Order of Genetic Changes during Malignant Transformation and Metastasis in a Single Patient with NF1-plexiform Neurofibroma

Abstract

Purpose Malignant peripheral nerve sheath tumors (MPNSTs) occur at increased frequency in individuals with neurofibromatosis type 1 (NF1), where they likely arise from benign plexiform neurofibroma precursors. While previous studies have employed a variety of discovery approaches to discover genes associated with MPNST pathogenesis, it is currently unclear what molecular events are associated with the evolution of MPNST from plexiform neurofibroma. Experimental Design Whole exome sequencing was performed on biopsy materials representing plexiform neurofibroma (n=3), MPNST, and metastasis from a single individual with NF1 over a 14-year period. Additional validation cases were used to assess candidate genes involved in malignant progression, while a murine MPNST model was employed for functional analysis. Results There was an increasing proportion of cells with a somatic NF1 gene mutation as the tumors progressed from benign to malignant, suggesting a clonal process in MPNST development. Copy number variations, including loss of one copy of the TP53 gene, were identified in the primary tumor and the metastatic lesion, but not in benign precursor lesions. A limited number of genes with non-synonymous somatic mutations (βIII-spectrin and ZNF208) were discovered, several of which were validated in additional primary and metastatic MPNST samples. Lastly, increased βIII-spectrin expression was observed in the majority of MPNSTs, and shRNA-mediated knockdown reduced murine MPNST growth in vivo. Conclusion Collectively, the ability to track the molecular evolution of MPNST in a single individual with NF1 offers new insights into the sequence of genetic events important for disease pathogenesis and progression for future mechanistic study.

Analysis of intratumor heterogeneity in Neurofibromatosis type 1 plexiform neurofibromas and neurofibromas with atypical features: Correlating histological and genomic findings

“…The analysis revealed NF1 point mutations in different PNFs (1PNF, 4PNF, 4PNF2, 6PNF) as the cause of somatic NF1 inactivation (Figure A). The analysis of the somatic mutations affecting the NF1 gene in the different parts analyzed from each tumor (regardless of mutation type/mechanism) revealed invariably that all parts from the same PNF or ANF shared the same somatic NF1 mutation (Figure A), consistent with recent findings analyzing three parts of a single PNF (Hirbe et al., ). This result strongly indicated the clonal origin of the whole tumor mass studied in all cases, although not all parts contained the same percentage of cells bearing the NF1 somatic mutation (Table ).…”

Genomic MET amplification occurs early in NF1-related malignant peripheral nerve sheath tumor (MPNST) progression and is a potent therapeutic target

“…In our analysis, we identify in the pre-treatment specimen hemizygous microdeletions in the NF1 and TP53 loci, with concomitantly observed amplifications of MET, HGF, and EGFR. It is not surprising that a TP53 variant was present in the pre-treatment MPNST given the prevalence of P53 mutations in clinical samples (47), and the known driver effects of P53 in the context of As discussed previously, we observed a heterogeneous treatment response to capmatinib in the NF1-P53 and NF1 tumor groups. One explanation for this partial response is that MPNSTs maintain a fundamental plasticity for reprogramming of RAS effector kinase signaling in the setting of MET inhibition similar to what is observed in breast, lung, and gastric cancers (62)(63)(64)(65)(66).…”

Loss of H3K27 tri-methylation is a diagnostic marker for malignant peripheral nerve sheath tumors and an indicator for an inferior survival

“…Therefore, in the past, many efforts have been undertaken to identify additional molecular markers that could differentiate between these tumors. (17;18) For example, expression profiling in matched malignant peripheral nerve sheath tumors and neurofibroma samples did identify more than 500 kinase genes that are differentially expressed between both entities, with mitotic regulators BUB1B , PBK and NEK2 being overexpressed in malignant peripheral nerve sheath tumors. (19) However, the patterns of these changes turned out to be complex and heterogeneous, without a single unifying alteration that could be used as a diagnostic marker.…”