Characterizing the genomic architecture and molecular mechanisms driving the form

描述(申请人提供)：脑膜瘤是最常见的原发脑瘤，美国发病率为17万，起源于包围中枢神经系统的三层膜中的蛛网膜细胞。虽然80%的病例在组织学上是良性的，但它们可通过包围和压迫关键的神经血管结构而导致神经功能障碍，并由于缺乏现有的药物或化疗方法而积极接受手术或放射治疗。在2013年1月之前，唯一已知的脑膜瘤形成的主要遗传因素是神经纤维素2(NF2)，在大约50%的肿瘤中，它被22号染色体突变或丢失所干扰。其余一半肿瘤的遗传驱动因素仍未被发现。我们在2013年3月的《科学》杂志上报道，在所研究的300名患者中，有80%是由5个基因突变和/或22号染色体缺失导致脑膜瘤形成的。3个基因(NF2、AKT1和SMO)的突变已经在其他类型的肿瘤中被报道，2个基因(KLF4和TRAF7)没有与肿瘤相关的突变。KLF4是一种转录因子，被认为是能够诱导多能状态的四个基因之一，在几种癌症中表达降低，K409残基与DNA直接接触。TRAF7是一种促凋亡的E3泛素连接酶，其C端有7个WD40重复序列。大约四分之一的脑膜瘤存在TRAF7突变，通常与复发的AKT1E17K或复发的KLF4K409Q突变共存，但总是与NF2突变互斥。激活Hedgehog信号的SMO突变在大约3%的脑膜瘤中被发现。突变谱可预测染色体不稳定、恶性进展、组织亚型和解剖位置。然而，驱动其余五分之一脑膜瘤形成的基因仍未确定。具体目标：研究提案包含两个具体目标。第一个目标将建立在我们的初步脑膜瘤分类的基础上，并使用全外显子组测序来识别更多的脑膜瘤驱动基因。为了丰富脑膜瘤新基因的发现，将只对没有已知驱动基因突变(NF2、TRAF7、AKT1、KLF4、SMO)或22号染色体丢失的肿瘤进行测序。第二个目的将通过CHIP-SEQ分析来表征KLF4K409Q重复突变对DNA结合的影响，并将评估该突变对KLF4诱导多能性的效率的影响。这两个目标的进展将同时进行。

DESCRIPTION (provided by applicant): Meningiomas, the most common primary brain tumors with a US prevalence of 170,000, arise from arachnoid cells in the three-layered membrane encompassing the central nervous system. Although histologically benign in 80% of cases, they can cause neurologic deficits by encircling and compressing critical neurovascular structures and are aggressively treated with surgery or radiation due to the lack of established medical or chemotherapies. Before January 2013, the only major known genetic contributor to meningioma formation was Neurofibromin 2 (NF2), which is disrupted by mutation or loss of chromosome 22 in about 50% of tumors. Genetic drivers for the remaining half of tumors remained undiscovered. We reported (Science, March 2013) that mutations in 5 genes and/or chromosome 22 loss underlie meningioma formation in 80% of the 300 patients studied. Mutations in 3 genes (NF2, AKT1, and SMO) have been reported in other tumor types, and 2 genes (KLF4 and TRAF7) have not had mutations associated with neoplasia. KLF4 is a transcription factor best known as one of four genes capable of inducing a pluripotent state and whose expression is decreased in several cancers, and the K409 residue makes direct DNA contact. TRAF7 is a pro- apoptotic E3 ubiquitin ligase with seven WD40 repeats in the C terminal. Approximately one-fourth of meningiomas harbor TRAF7 mutations, which commonly co-occur with recurrent AKT1E17K or recurrent KLF4K409Q mutations but are always mutually exclusive of NF2 mutations. SMO mutations, which activate Hedgehog signaling, were found in approximately 3% of meningiomas. Mutational profile predicted chromosomal instability, malignant progression, histological subtype, and anatomical location. However, the genes driving the formation of the remaining one-fifth of meningiomas remain unidentified. Specific Aims: The research proposal entails two specific aims. The first aim will build upon our preliminary meningioma classification, and use whole-exome sequencing to identify additional meningioma driver genes. To enrich for the discovery of novel meningioma genes, only tumors without mutations in known driver genes (NF2, TRAF7, AKT1, KLF4, SMO) or chromosome 22 loss will be sequenced. The second aim will characterize the impact of the recurrent KLF4K409Q mutation on DNA binding via ChIP-seq analysis and will assess the impact of this mutation on the efficiency of KLF4 to induce pluripotency. Progress on the two aims will occur simultaneously.