Role of Transcription Factor ADP-ribosylation in Breast Cancer Biology

项目总结/摘要 癌症的分子异质性对治疗和药物发现工作构成了主要障碍。 以前的研究通过描述特定癌症的不同分子亚型来解决这一挑战 (e.g.,乳腺癌），基于基因表达的细胞类型特异性模式。去审问那些 癌症亚型的基础，克劳斯实验室已经开发出一个强大的和多方面的计算 整合来自各种基因组测定的数据以定义增强子的总功能评分的流水线 元素（TFSEE）。这种方法的一个结果是识别癌症亚型- 富集的转录因子（TF）促进亚型特异性增强子形成并驱动下游 转录结果。在乳腺癌中，几种TFSEI鉴定的亚型特异性TF是唯一的 所需的同源乳腺癌亚型的生长，但不影响增殖或生存力， 其他亚型。最近的研究还表明，ADP-核糖基化（ADPR化），一种翻译后修饰， 蛋白质的修饰，在乳腺癌的不同亚型中变化很大。ADPR化是 由多聚（ADP-核糖）聚合酶（PARP）家族的酶介导，包括PARP-1，一种核酶 这是FDA批准的PARP抑制剂药物的靶点。PARP在DNA修复中的作用是众所周知的， 但最近的研究表明，BRCA 1/2在转录调控中也有重要的非依赖性作用。在 通过初步分析，我们已经鉴定了一组在乳腺癌中ADPR化的癌症相关TF。 这些研究的长期目标是更好地了解分子和 乳腺癌亚型特异性转录因子通过ADPR化调控的生化机制， 以及不同乳腺癌亚型对PARP抑制剂的反应。我们的假设是， 亚型特异性转录因子决定了它们的功能，并可能影响乳腺癌细胞对PARP的反应 抑制剂的我们已经提出了一个项目，将使用一套完整的生化，分子，细胞为基础， 小鼠为基础的，基因组和蛋白质组学测定，以测试我们的总体和具体的机制假设。 具体来说，我们将：（1）确定乳腺癌中ADPR化的TF（目标1），（2）确定如何在乳腺癌中表达ADPR化的TF（目标1），（3）确定乳腺癌中ADPR化的TF（目标1），（4）确定乳腺癌中ADPR化的TF（目标1），（5）确定乳腺癌中ADPR化的TF（目标1），（6）确定乳腺癌中ADPR化的TF（目标1），（7）确定乳腺癌中ADPR化的TF（目标2），（8）确定乳腺癌中ADPR化的TF（目标1），（9）确定乳腺癌中ADPR化的TF（目标2），（9）确定乳腺癌中ADPR化的TF（目标1），（10）确定乳腺癌中ADPR化的TF（目标2）。 TF的ADPR化影响它们的分子和生化功能（目的2），和（3）确定 TF ADPR化对乳腺癌细胞对临床使用的PARP抑制剂的反应的影响（目的3）。这些研究 将利用PI实验室在PARP、ADPR化、增强子功能和基因方面的专业知识， 癌症的调控。虽然最初的重点是乳腺癌，但我们的研究结果应该广泛适用于 多种癌症类型。我们使用“组学”和功能测定的综合方法将提供新的见解 研究乳腺癌中TF ADP-核糖基化的调节，这将作为如何探索PARP的模型。 功能和ADP-核糖基化。使用基于小鼠的模型和患者样本将允许 我们探索我们的机械结果的临床相关性。我们预计，我们的研究将提出新的 PARP抑制剂在DNA修复途径以外的癌症中的治疗潜力的途径。

Project Summary/Abstract The molecular heterogeneity of cancers poses a major hurdle for treatment and drug discovery efforts. Previous studies have addressed this challenge by characterizing distinct molecular subtypes of specific cancers (e.g., breast cancers), based on cell type-specific patterns of gene expression. To interrogate the molecular underpinnings of cancer subtypes, the Kraus Lab has developed a robust and multi-faceted computational pipeline that integrates data from various genomic assays to define a Total Functional Score of Enhancer Elements (TFSEE) for each subtype. One outcome of this method is the identification of cancer subtype- enriched transcription factors (TFs) that promote subtype-specific enhancer formation and drive downstream transcriptional outcomes. In breast cancers, several TFSEE-identified subtype-specific TFs are uniquely required for the growth of the cognate breast cancer subtype, but do not affect the proliferation or viability of other subtypes. Recent studies have also shown that ADP-ribosylation (ADPRylation), a post-translational modification of proteins, varies dramatically across the different subtypes of breast cancers. ADPRylation is mediated by the Poly(ADP-ribose) polymerase (PARP) family of enzymes, including PARP-1, a nuclear enzyme which is the target of FDA-approved PARP inhibitor drugs. PARPs are well known for the roles in DNA repair, but recent studies suggest an important BRCA1/2-independent role in transcriptional regulation as well. In preliminary analyses, we have identified a cohort of cancer-related TFs that are ADPRylated in breast cancers. The long-term objective of these studies is to achieve a better understanding of the molecular and biochemical mechanisms underlying the regulation of breast cancer subtype-specific TFs by ADPRylation, as well as the responses of distinct breast cancer subtypes to PARP inhibitors. Our hypothesis is that ADPRylation of subtype-specific TFs dictates their function and may influence the response of breast cancer cells to PARP inhibitors. We have proposed a project that will use an integrated set of biochemical, molecular, cell-based, mouse-based, genomic, and proteomic assays to test our overarching and specific mechanistic hypotheses. Specifically, we will: (1) Identify TFs that are ADPRylated in breast cancers (Aim 1), (2) Determine how ADPRylation of TFs affects their molecular and biochemical functions (Aim 2), and (3) Determine the effects of TF ADPRylation on the responses of breast cancer cells to clinically used PARP inhibitors (Aim 3). These studies will take advantage of the expertise of the PI’s lab in PARPs, ADPRylation, enhancer function, and gene regulation in cancer. Although focused initially on breast cancers, our results should be broadly applicable across a variety of cancer types. Our integrative approach using ‘omics’ and functional assays will provide new insights into the regulation of TF ADP-ribosylation in breast cancers that will serve as a model for how to explore PARP function and ADP-ribosylation in cancer cells. The use of mouse-based models and patient samples will allow us to explore the clinical relevance of our mechanistic results. We anticipate that our studies will suggest new avenues for the therapeutic potential of PARP inhibitors in cancers beyond DNA repair pathways.