Genomic Evolution of Breast Cancer

描述（由申请人提供）：我们体内的每个细胞都通过有丝分裂与其他细胞相关，我们每个体细胞的历史都是一个分叉的细胞谱系树，其根是受精卵。我们将使用这一概念来建立100例her2阳性乳腺癌病例中肿瘤病变和癌之间的谱系关系。我们将通过对每个病例的几个不同组织样本（正常、肿瘤、癌）进行基因组测序并进行表达谱分析来实现这一目标。我们将识别的体细胞变异（单核苷酸变异、结构变异和非整倍体）将用于构建谱系树，作为路线图，以确定在进化过程中基因组驱动事件（HER2过表达和/或扩增、非整倍体和关键癌症基因突变）和基因表达变化发生的时间。另外几个肿瘤样本太小，无法进行全基因组测序，将通过靶向PCR和测序对每个病例中192个已确定的体细胞突变进行鉴定和分型。这些额外的样本将大大拓宽系统发育树，并有助于更精细地分辨肿瘤进化过程中哪些类型的突变和其他基因组变化首先发生。它们还将使我们能够确定在同一病例中是否存在复发的突变。值得注意的是，在我们之前的工作中，我们已经表明，基于这种树分析，PIK3CA中的H1047R在几个患者中多次出现。如果存在的话，我们将发现更多这样的突变。我们提出的工作与其他肿瘤进化研究不同，

DESCRIPTION (provided by applicant): Every cell present in our bodies is related to every other cell by mitotic division, and the history of each of our somas is a bifurcating cell lineage tree whose root is the zygote. We will use this concept to establish lineage relationships among neoplastic lesions and carcinomas from each of 100 HER2-positive breast cancer cases. We will accomplish this by sequencing the genomes of several distinct tissue samples (normal, neoplastic, carcinoma) from each case and by performing expression profiling. The somatic variation we will identify (single nucleotide variants, structural variants, and aneuploidies) willbe used to build lineage trees that serve as roadmaps to determine when during evolution genomic driver events (HER2 overexpression and/or amplification, aneuploidies, and mutations in key cancer genes) and gene expression changes occurred. Several additional neoplastic samples that are too small for whole-genome sequencing will be identified and typed by targeted PCR and sequencing, for 192 of the identified somatic mutations from each case. These additional samples will substantially broaden the phylogenetic tree and facilitate finer resolution as to which types of mutations and other genomic changes happen first during neoplastic evolution. They will also allow us to determine if there are mutations that recur within the same case. Remarkably, in our previous work we have shown, on the basis of such tree analyses, that H1047R in PIK3CA has arisen multiple times within several patients. We will identify additional such mutations, if they exist. Our proposed work is distinct from other studies of tumor evolution, which have so far focused exclusively on within-tumor subclone evolution or metastatic changes, and which cannot order the earliest driver changes. Our study will distinguish drivers of the initial proliferative phenotype from those that cause a full-blown carcinoma. This can only be done by comparative analyses of early neoplasias with normal tissue and with carcinomas. We note that this concept is well-established in species phylogenetics and evolution, where past events are routinely inferred by comparison among extant species, and which have broadly facilitated insight into both gene function and evolutionary mechanisms. Just like evolving species, cells in our somas are governed by inheritance, change, and divergence, and our understanding of the origins and evolution of neoplasias towards tumors will benefit from a phylogenetic and evolutionary perspective. Our proposed study is one of the first that is dedicated to examining cancer in the light of evolution. We believe that a fuller understanding of mutational mechanisms, the order of driver changes during progression, and the role of hypermutable sites, will be essential for improving diagnostics, prediction, and drug development of this fundamentally evolutionary disease.