Probing the role of somatic X-chromosome alterations in shaping cancer sex differences

项目摘要 癌症是一个主要的全球公共卫生问题，也是美国的第二大死亡原因。许多 癌症类型显示出性别之间发病率的差异，这些差异只是部分原因。 可由非遗传因素解释，如激素差异，致癌物质暴露，生活方式和获得 保健到目前为止，我们对遗传因素--特别是那些编码在性别上的遗传因素--的理解， 染色体-有助于癌症发病机制的性别特异性差异仍然不完整。一 男性和女性之间的基本遗传差异在于X染色体的组成和调节， 染色体（chrX）;相对于雄性体细胞，雌性体细胞具有额外的chrX。大多数基因 在雌性中的chrX的一个拷贝上通过X染色体失活（XCI）过程被表观遗传学沉默， 导致一个活性（chrXa）和一个非活性（chrXi）染色体X。另外，我们最近发现 XIST -启动XCI的长非编码RNA-可以在一个男性亚群中体细胞表达， 癌的因此，我们假设X染色体的体细胞改变可能会扰乱XCI在这两个 女性和男性，导致致癌或有害的基因表达变化。在这个项目中，我们将 通过两个目的研究男性和女性背景下体细胞chrX改变在癌症中的作用。目标1： 将锚我们的研究在易位肾细胞癌（tRCC），一个亚型的肾癌通常驱动 通过涉及chrX上TFE 3基因的致癌重排。其他肾癌患者都是男性- tRCC占主导地位，在发病率方面显示出约2：1的女性偏倚，提示了以下假设： 女性中chrX的额外拷贝使致癌TFE 3融合的风险增加一倍。这意味着TFE 3 在雌性中，chrXi可以引起重排，这将需要XCI的破坏和重新激活。 通常沉默的基因。我们将开发单倍型特异性生物信息学方法来区分 chrXa和chrXi，并将这些方法部署在一系列基因组数据集上，以了解转录水平。 tRCC中每个chrX同源物重排的后果。我们还将使用以下模型对TFE 3融合进行建模： CRISPR/Cas9探索TFE 3重排的差异转录和功能影响 包括chrXa和chrXi。在目标2中，我们将扩展我们令人惊讶的观察结果，即一些男性癌症可以 体细胞激活XIST表达。我们将确定在何种程度上XIST的体细胞激活在男性 与在雌性XCI中观察到的稳定chrX沉默的特征相关。我们还将确定 男性中的XIST激活赋予可能代表性别特异性癌症的选择性遗传脆弱性 个依赖项该项目将利用创新的基因组和功能遗传学方法来探索 关于chrX上的体细胞改变如何有助于癌症发病机制的基本问题。更广泛地说， 这项工作旨在建立一个新的范式，为我们理解的遗传因素，驱动性别偏见， 癌症的发生和发展，并确定以性别特异性方式靶向肿瘤的新策略。

PROJECT SUMMARY Cancer is a major global public health problem and the second leading cause of death in the United States. Many cancer types display differences in incidence between the sexes, and these differences are only partially explainable by non-genetic factors, such as hormonal differences, carcinogen exposure, lifestyle, and access to health care. To date, our understanding of how genetic factors – particularly those encoded on the sex chromosomes – contribute to sex-specific differences in cancer pathogenesis has remained incomplete. A fundamental genetic difference between males and females is in the composition and regulation of the X- chromosome (chrX); relative to male somatic cells, female somatic cells have an extra chrX. Most of the genes on one copy of chrX in females are epigenetically silenced via the process of X-chromosome inactivation (XCI), resulting in one active (chrXa) and one inactive (chrXi) chromosome X. Additionally, we have recently discovered that XIST – the long non-coding RNA that initiates XCI – can be somatically expressed in a subset of male cancers. We therefore hypothesize that somatic alterations of the X chromosome may perturb XCI in both females and males, leading to either oncogenic or deleterious gene expression changes. In this project, we will study the role of somatic chrX alterations in cancer in both male and female contexts via two aims. In Aim 1, we will anchor our studies in translocation renal cell carcinoma (tRCC), a subtype of kidney cancer usually driven by oncogenic rearrangements involving the TFE3 gene on chrX. While all other kidney cancers are male- predominant, tRCC displays a ~2:1 female bias in incidence, prompting the hypothesis that the presence of an extra copy of chrX in females doubles the risk for developing oncogenic TFE3 fusions. This implies that TFE3 rearrangements can arise from chrXi in females, which would necessitate a disruption of XCI and the reactivation of ordinarily silenced genes. We will develop haplotype-specific bioinformatic methods to distinguish between chrXa and chrXi and deploy these methods across a range of genomic datasets to understand the transcriptional consequences of rearrangements on each of the chrX homologs in tRCC. We will also model TFE3 fusions using CRISPR/Cas9 to explore the differential transcriptional and functional implications of TFE3 rearrangements involving chrXa vs chrXi. In Aim 2, we will expand upon our surprising observation that some male cancers can somatically activate XIST expression. We will determine to what extent somatic activation of XIST in males is associated with the features of stable chrX silencing seen in female XCI. We will also determine whether somatic XIST activation in males confers selective genetic vulnerabilities that may represent sex-specific cancer dependencies. This project will leverage innovative genomic and functional genetic approaches to explore fundamental questions about how somatic alterations on chrX contribute to cancer pathogenesis. More broadly, this work seeks to establish a new paradigm for our understanding of the genetic factors that drive sex bias in cancer initiation and progression and to identify novel strategies to target tumors in a sex-specific fashion.