Characterizing the genomic architecture and molecular mechanisms driving the form

描述（由申请人提供）：脑膜瘤是最常见的原发性脑肿瘤，在美国发病率为17万，起源于包裹中枢神经系统的三层膜中的蛛网膜细胞。虽然在80%的病例中组织学上是良性的，但它们可以通过包围和压迫关键的神经血管结构而导致神经功能缺损，由于缺乏成熟的药物或化疗方法，因此需要积极地进行手术或放射治疗。在2013年1月之前，已知脑膜瘤形成的唯一主要遗传因素是神经纤维蛋白2 (NF2)，在约50%的肿瘤中，该基因因22号染色体的突变或缺失而中断。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300名被研究的患者中，80%的患者脑膜瘤形成的基础是5个基因突变和/或22号染色体缺失。3个基因（NF2、AKT1和SMO）的突变已在其他肿瘤类型中报道，2个基因（KLF4和TRAF7）未发生与肿瘤相关的突变。KLF4是一种转录因子，是四种能够诱导多能状态的基因之一，其表达在几种癌症中减少，K409残基与DNA直接接触。TRAF7是一种促凋亡的E3泛素连接酶，在C端有7个WD40重复序列。大约四分之一的脑膜瘤携带TRAF7突变，通常与复发性AKT1E17K或复发性KLF4K409Q突变共同发生，但总是与NF2突变相互排斥。激活Hedgehog信号的SMO突变在大约3%的脑膜瘤中被发现。突变谱预测染色体不稳定性、恶性进展、组织学亚型和解剖位置。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：研究计划包含两个具体目标。第一个目标将建立在我们初步脑膜瘤分类的基础上，并使用全外显子组测序来识别其他脑膜瘤驱动基因。为了丰富新脑膜瘤基因的发现，只对已知驱动基因（NF2、TRAF7、AKT1、KLF4、SMO）没有突变或22号染色体缺失的肿瘤进行测序。第二个目标是通过ChIP-seq分析表征复发性KLF4K409Q突变对DNA结合的影响，并评估该突变对KLF4诱导多能性效率的影响。这两个目标将同时取得进展。

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.