Germline and somaticNF1 gene mutation spectrum in NF1-associated malignant peripheral nerve sheath tumors (MPNSTs)

Abstract

About 10% of neurofibromatosis type 1 (NF1) patients develop malignant peripheral nerve sheath tumors (MPNSTs) and represent considerable patient morbidity and mortality. Elucidation of the genetic mechanisms by which inherited and acquired NF1 disease gene variants lead to MPNST development is important. A study was undertaken to identify the constitutional and somatic NF1 mutations in 34 MPNSTs from 27 NF1 patients. The NF1 germline mutations identified in 22 lymphocytes DNA from these patients included seven novel mutations and a large 1.4-Mb deletion. The NF1 germline mutation spectrum was similar to that previously identified in adult NF1 patients without MPNST. Somatic NF1 mutations were identified in tumor DNA from 31 out of 34 MPNSTs, of which 28 were large genomic deletions. The high prevalence (>90%) of such deletions in MPNST contrast with the =or<20% found in benign neurofibromas and is indicative of the involvement of different mutational mechanisms in these tumors. Coinactivation of the TP53 gene by deletion, or by point mutation along with NF1 gene inactivation, is known to exacerbate disease symptoms in NF1, therefore TP53 gene inactivation was screened. DNA from 20 tumors showed evidence for loss of heterozygosity (LOH) across the TP53 region in 11 samples, with novel TP53 point mutations in four tumors.

Exploring the somatic NF1 mutational spectrum associated with NF1 cutaneous neurofibromas

“…17,18 Indeed, three of the somatic NF1 mutations characterised here (p.R816X, p.R304X, p.L1569X) have previously been identified as somatic lesions (two of these three mutations are CpG located and therefore compatible with a mechanism of methylation-mediated deamination of 5-methylcytosine) in both benign and malignant tumours. [41][42][43][44][45][46] A total of seven novel somatic NF1 missense mutations were identified during the course of this study.…”

“…47 In our study, MLPA analysis succeeded in identifying only a single intragenic deletion in one neurofibroma, indicating that mitotic recombination was the likely mechanism for LOH in the remaining 24 neurofibromas. Our previous studies found significantly higher levels (approximately 70 and 90%, respectively) of NF1-associated LOH in both PNFs and MPNSTs, 17,18 an indication that NF1-LOH may be less prominent in benign neurofibromas than in PNFs and malignant tumours. One potential confounding factor here is cellular heterogeneity, but we do not consider that this would have substantially hampered the detection of intragenic deletions and duplications by MLPA in this study.…”

“…10,11 Currently, our understanding of the biological mechanisms underlying NF1 tumourigenesis is rather limited, although recent studies in mouse have (i) confirmed a direct role for the tumour microenvironment and (ii) identified skin-derived precursor cells as the cell of origin for cutaneous neurofibromas. 12 In studies of NF1 patients, somatic mutations affecting a number of other tumour suppressor genes, including TP53, CDKN2A and RB1 (variously involved in cell cycle regulation, DNA synthesis and apoptosis), have also been identified in MPNSTs, [13][14][15][16][17] PNFs 18,19 and those cutaneous neurofibromas that have been removed from NF1 patients who carry a particularly high tumour burden. 20 It is currently unclear (i) why some types of neurofibroma are present from birth, whereas others develop only during adolescence, (ii) what initiates neurofibroma growth and (iii) what determines the number of tumours that develop in a given individual.…”

Neurofibromatosis type 1 molecular diagnosis: what can NGS do for you when you have a large gene with loss of function mutations?

“…This observation is in accordance with previous data showing a B90% identification rate of the two NF1 hits in MPNSTs. 37 One-third (8/28) of the NF1 hits were Figure 1 Mutation dilution sequencing using NGS and Sanger methods. NGS allowed the mutation detection in all dilutions and also presented a quantitative aspect, providing the number of mutated reads.…”

“…The high prevalence of such rearrangements in MPNST contrast with the 5-10% found in constitutional DNAs from NF1 patients and is in accordance with previously identified MPNST somatic NF1 mutation spectrum. 37 As molecular analysis of the NF1 gene is challenging, NF1 tumour mutation-spectrum may have been less studied than other genes with gain-of-function mutations. However, NF1 was recently identified as one of the most significantly somatic mutated genes in the Cancer Genome Atlas (TCGA) that provided molecular tumour maps using exome sequencing in more than 3000 tumours from 12 cancer types.…”