Whole Exome Sequencing Identifies TSC1/TSC2 Biallelic Loss as the Primary and Sufficient Driver Event for Renal Angiomyolipoma Development.
Whole Exome Sequencing Identifies TSC1/TSC2 Biallelic Loss as the Primary and Sufficient Driver Event for Renal Angiomyolipoma Development.
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DOI：
10.1371/journal.pgen.1006242
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发表时间：
2016-08
期刊：
影响因子：
4.5
通讯作者：
Kwiatkowski DJ
中科院分区：
文献类型：
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作者：
Giannikou K;Malinowska IA;Pugh TJ;Yan R;Tseng YY;Oh C;Kim J;Tyburczy ME;Chekaluk Y;Liu Y;Alesi N;Finlay GA;Wu CL;Signoretti S;Meyerson M;Getz G;Boehm JS;Henske EP;Kwiatkowski DJ
肾血管平滑肌脂肪瘤是血管周上皮样（PEComa）家族中的一种肾脏肿瘤，常见于结节性硬化症（TSC）和淋巴管平滑肌瘤病（LAM）患者，但很少零星发生。尽管组织学上呈良性，但肾血管平滑肌脂肪瘤可导致危及生命的出血和肾衰竭。血管平滑肌脂肪瘤和LAM都有TSC 2或TSC 1突变。然而，其他体细胞事件在肿瘤发展中的频率和贡献尚不清楚。我们在来自15名受试者的32个切除的肿瘤样品（n = 30个血管平滑肌脂肪瘤，n = 2个LAM）中进行了全外显子组测序，其中包括三名TSC患者。在TSC 2中鉴定出2个生殖系和22个体细胞失活突变，以及1个生殖系TSC 1突变。20/32（62%）的样本在TSC 2或TSC 1中显示拷贝中性洛（CN-洛），至少有8个不同的洛区域，30/32（94%）的样本具有TSC 2或TSC 1的双等位基因缺失。全外显子组测序鉴定出中位数为4个体细胞非同义编码区突变（除了TSC 2/TSC 1），突变率低于几乎所有其他癌症类型。有三个突变的基因是已知的癌症相关基因（BAP 1，ARHGAP 35和SPEN），但它们在单个样品中各自突变，并且是具有不确定功能效应的错义变体。对16例TSC受试者血管平滑肌脂肪瘤的分析显示，TSC 2中存在第二命中点突变和CN-LOH，其中许多突变是不同的，表明它们是独立的克隆起源。然而，三个肿瘤除了个体突变外还有两个共享突变，这表明肿瘤发展的分支进化模式始于TSC 2的丢失。我们的研究结果表明，TSC 2和不太常见的TSC 1改变是血管平滑肌脂肪瘤/LAM的主要基本驱动事件，而其他体细胞突变是罕见的，可能不会导致肿瘤的发展。我们对一种叫做血管平滑肌脂肪瘤的肾脏肿瘤进行了全面的基因组分析。已知这些肿瘤在大多数患有多发性硬化症（TSC）和散发性淋巴管平滑肌瘤病（LAM）的个体中发生，并且在一般人群中很少见到。在这些血管平滑肌脂肪瘤中，我们发现了已知引起TSC的TSC 2和TSC 1基因的一致参与，但在蛋白编码区的其他地方很少（平均<5）突变。这与其他成人实体瘤形成鲜明对比，这些实体瘤通常含有数百至数千个此类突变。我们的研究结果表明，TSC 2/TSC 1的遗传改变是肾血管平滑肌脂肪瘤发生和发展的主要和必要的驱动遗传事件。对一个病人的多个血管平滑肌脂肪瘤的分析显示，在大多数样本中存在明显的遗传畸变，表明大多数肿瘤是独立发展的。从观察到的三个肿瘤中，除了各自的突变之外，还共享2个突变，分支克隆进化是明显的。我们的研究结果表明，治疗血管平滑肌脂肪瘤患者的治疗方法应侧重于TSC 2/TSC 1丢失的后果，包括但不限于mTOR激活。
Renal angiomyolipoma is a kidney tumor in the perivascular epithelioid (PEComa) family that is common in patients with Tuberous Sclerosis Complex (TSC) and Lymphangioleiomyomatosis (LAM) but occurs rarely sporadically. Though histologically benign, renal angiomyolipoma can cause life-threatening hemorrhage and kidney failure. Both angiomyolipoma and LAM have mutations in TSC2 or TSC1. However, the frequency and contribution of other somatic events in tumor development is unknown. We performed whole exome sequencing in 32 resected tumor samples (n = 30 angiomyolipoma, n = 2 LAM) from 15 subjects, including three with TSC. Two germline and 22 somatic inactivating mutations in TSC2 were identified, and one germline TSC1 mutation. Twenty of 32 (62%) samples showed copy neutral LOH (CN-LOH) in TSC2 or TSC1 with at least 8 different LOH regions, and 30 of 32 (94%) had biallelic loss of either TSC2 or TSC1. Whole exome sequencing identified a median of 4 somatic non-synonymous coding region mutations (other than in TSC2/TSC1), a mutation rate lower than nearly all other cancer types. Three genes with mutations were known cancer associated genes (BAP1, ARHGAP35 and SPEN), but they were mutated in a single sample each, and were missense variants with uncertain functional effects. Analysis of sixteen angiomyolipomas from a TSC subject showed both second hit point mutations and CN-LOH in TSC2, many of which were distinct, indicating that they were of independent clonal origin. However, three tumors had two shared mutations in addition to private somatic mutations, suggesting a branching evolutionary pattern of tumor development following initiating loss of TSC2. Our results indicate that TSC2 and less commonly TSC1 alterations are the primary essential driver event in angiomyolipoma/LAM, whereas other somatic mutations are rare and likely do not contribute to tumor development. We performed comprehensive genome analysis of a kidney tumor called angiomyolipoma. These tumors are known to develop in most individuals who have Tuberous Sclerosis Complex (TSC) and those who have sporadic lymphangioleiomyomatosis (LAM), and are seen rarely in the general population. In these angiomyolipomas, we found consistent involvement of the TSC2 and TSC1 genes that are known to cause TSC, but very few (<5 on average) mutations elsewhere in the protein-coding regions. This is in stark contrast to other adult solid tumours that typically harbor hundreds to thousands of such mutations. Our results indicate that genetic alterations in TSC2/TSC1 are the primary and essential driver genetic events for development and progression of renal angiomyolipoma. Analysis of multiple angiomyolipomas from a single patient showed distinct genetic aberrations in the majority of samples, indicating that most of the tumors had developed independently. Branched clonal evolution was evident from the observation of three tumors that shared 2 mutations in addition to mutations private to each. Our results indicate that therapeutic approaches for treatment of patients with angiomyolipoma should focus on the consequences of TSC2/TSC1 loss, including but not limited to mTOR activation.