Integrating Genomic and Epigenomic Alterations in Cancer and its Microenvironment

尽管知道微环境在肿瘤发展中的重要性，但迄今为止，对实体肿瘤的遗传学研究，无论是散发性的还是遗传性的，都将它们视为单一的无定形实体。乳腺癌的遗传学和表观遗传学分析也不例外。应用381个微卫星标记杂合性缺失(LOH)扫描技术，对135例不同类型的散发性浸润性乳腺癌进行检测，在15条上皮性LOH显著缺失的染色体上发现19个关键基因座，在19条间质LOH显著缺失的19条染色体上发现38个关键基因座(染色体模式)。因此，我们最初假设这些区域在缺失时将在乳腺癌进展中发挥作用；我们还假设这些区域作为基因的信号，当表观遗传修饰时，这些基因与结构缺失一起在乳腺癌进展中发挥一些作用，与上皮-间质相互作用密切相关。因此，我们认为肿瘤微环境，特别是间质在乳腺癌的发生中起着基本的，但在很大程度上未明确的作用。将实验生物学家和计算生物学家聚集在一起，项目2将使用滚动模型迭代、定向遗传和表观遗传学分析和验证以及信息学模型构建的综合方法来了解乳腺癌的进展。这将涉及假说的产生和检验，最初的假说是19个上皮基因座内的基因的LOH和/或表观遗传失活将发生在开始或更早的进展中，并且多个间质靶点将是 参与促进进展、侵袭和转移。我们将采用定向的基于SNP的LOH和基于高甲基化的策略来检测150例浸润性乳腺癌间质和上皮中的58个初始靶区，以寻找在进展过程中经历LOH和/或高甲基化的关键基因。这些实验数据将被用来建立模型，一个采用系统发育学类型的方法，另一个利用类似网络的方法来帮助在上皮和间质的背景下整合肿瘤进展中的遗传和表观遗传变化。模型的建立和实验将继续，直到得到一个模型(S)，该模型可以准确地预测两个间隔内的变化，因为它们与进展有关。在不久的将来，这些上皮和间质的体细胞遗传和表观遗传进展相关的改变将与临床结果相关。LOH和LOH的新区域的阐明 与间质间隔相关的高甲基化最终可能揭示预防和治疗的新靶点。

Despite knowing the importance of the role of the microenvironment in tumor development, genetic studies of solid tumors, whether sporadic or hereditary, to date, have treated them as single amorphous entities. Genetic and epigenetic analyses of breast carcinomas are no exception. Using 381-microsatellite marker loss-of-heterozygosity (LOH) scan in 135 distinct sporadic invasive breast cancers, we have identified 19 key loci on 15 chromosomes with significant LOH in the epithelium and 38 key loci on 19 chromosomes with significant LOH in the stroma (chromosome-wise modeling). We therefore initially hypothesize that these regions which when loss would play a role in breast cancer progression; we also hypothesize that these regions act as signposts for genes which when epigenetically modified which together with structural loss play some role in breast cancer progression as germane to epithelial-stromal interactions. We believe therefore that the tumor microenvironment, especially the stroma plays an essential, but largely undefined role, in breast carcinogenesis. Bringing together experimental and computational biologists, Project 2 will use a rolling model iterative, integrative approach of directed genetic and epigenetic analysis and validation as well as informatics model building to understand breast cancer progression. This will involve hypothesis generation and testing, with the initial hypothesis that LOH and/or epigenetic inactivation of genes within the 19 epithelial loci would occur in initiation or earlier in progression and the multiple stromal targets would be involved to facilitate progression, invasion and metastases. We will take a directed SNP-based LOH and hypermethylation-based strategy to examine the 58 initial target regions in stroma and epithelium of 150 invasive breast carcinomas for key genes undergoing LOH and/or hypermethylation during progression. These experimental data will be used for model building, one taking a phylogenetics-type approach and the other utilizing a network-like approach to help integrate genetic and epigenetic alterations in tumor progression in the context of the epithelium and stroma. Model building and experimentation will continue until a model(s) are derived that can accurately predict the alterations in the 2 compartments as they relate to progression. In the near future, these somatic genetic and epigenetic progression-related alterations in epithelium and stroma will be correlated with clinical outcomes. Elucidation of novel regions of LOH and hypermethylation relevant in the stromal compartment might ultimately reveal novel targets for prevention and therapy.