Pemov A, Li H, Patidar R, Hansen N F, Sindiri S, Hartley S W, Wei J S, Elkahloun A, Chandrasekharappa S C, Boland J F, Bass S, Mullikin J C, Khan J, Widemann B C, Wallace M R, Stewart D R
Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
Department of Molecular Genetics and Microbiology, UF Genetics Institute, UF Health Cancer Center, University of Florida, Gainesville, FL, USA.
Oncogene. 2017 Jun 1;36(22):3168-3177. doi: 10.1038/onc.2016.464. Epub 2017 Jan 9.
Neurofibromatosis type 1 (NF1) is a common tumor-predisposition disorder due to germline mutations in the tumor suppressor gene NF1. A virtually pathognomonic finding of NF1 is the plexiform neurofibroma (PN), a benign, likely congenital tumor that arises from bi-allelic inactivation of NF1. PN can undergo transformation to a malignant peripheral nerve sheath tumor, an aggressive soft-tissue sarcoma. To better understand the non-NF1 genetic contributions to PN pathogenesis, we performed whole-exome sequencing, RNASeq profiling and genome-wide copy-number determination for 23 low-passage Schwann cell cultures established from surgical PN material with matching germline DNA. All resected tumors were derived from routine debulking surgeries. None of the tumors were considered at risk for malignant transformation at the time; for example, there was no pain or rapid growth. Deep (~500X) NF1 exon sequencing was also conducted on tumor DNA. Non-NF1 somatic mutation verification was performed using the Ampliseq/IonTorrent platform. We identified 100% of the germline NF1 mutations and found somatic NF1 inactivation in 74% of the PN. One individual with three PNs had different NF1 somatic mutations in each tumor. The median number of somatic mutations per sample, including NF1, was one (range 0-8). NF1 was the only gene that was recurrently somatically inactivated in multiple tumors. Gene Set Enrichment Analysis of transcriptome-wide tumor RNA sequencing identified five significant (FDR<0.01) and seven trending (0.01⩽FDR<0.02) gene sets related to DNA replication, telomere maintenance and elongation, cell cycle progression, signal transduction and cell proliferation. We found no recurrent non-NF1 locus copy-number variation in PN. This is the first multi-sample whole-exome and whole-transcriptome sequencing study of NF1-associated PN. Taken together with concurrent copy-number data, our comprehensive genetic analysis reveals the primacy of NF1 loss as the driver of PN tumorigenesis.
1型神经纤维瘤病（NF1）是一种常见的肿瘤易感疾病，由肿瘤抑制基因NF1的种系突变引起。NF1的一个几乎具有诊断意义的发现是丛状神经纤维瘤（PN），这是一种良性的、可能先天性的肿瘤，由NF1的双等位基因失活引起。PN可转变为恶性外周神经鞘瘤，一种侵袭性软组织肉瘤。为了更好地理解非NF1基因对PN发病机制的贡献，我们对从手术切除的PN材料中建立的23个低传代雪旺细胞培养物进行了全外显子组测序、RNA测序分析和全基因组拷贝数测定，并匹配种系DNA。所有切除的肿瘤均来自常规减瘤手术。当时没有一个肿瘤被认为有恶性转化风险；例如，没有疼痛或快速生长。还对肿瘤DNA进行了深度（约500X）NF1外显子测序。使用Ampliseq/IonTorrent平台进行非NF1体细胞突变验证。我们鉴定出100%的种系NF1突变，并在74%的PN中发现体细胞NF1失活。一名患有三个PN的个体在每个肿瘤中都有不同的NF1体细胞突变。每个样本（包括NF1）的体细胞突变中位数为1（范围0-8）。NF1是唯一在多个肿瘤中反复发生体细胞失活的基因。对全转录组肿瘤RNA测序的基因集富集分析确定了五个显著（FDR<0.01）和七个趋势性（0.01⩽FDR<0.02）基因集，与DNA复制、端粒维持和延长、细胞周期进程、信号转导和细胞增殖有关。我们在PN中未发现反复出现的非NF1基因座拷贝数变异。这是第一项关于NF1相关PN的多样本全外显子组和全转录组测序研究。结合同时期的拷贝数数据，我们的综合基因分析揭示了NF1缺失作为PN肿瘤发生驱动因素的首要地位。
