Castro-Piedras Isabel, Vartak David, Sharma Monica, Pandey Somnath, Casas Laura, Molehin Deborah, Rasha Fahmida, Fokar Mohamed, Nichols Jacob, Almodovar Sharilyn, Rahman Rakhshanda Layeequr, Pruitt Kevin
Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States.
Center for Biotechnology & Genomics, Texas Tech University, Lubbock, TX, United States.
Front Oncol. 2020 Dec 10;10:576362. doi: 10.3389/fonc.2020.576362. eCollection 2020.
Abnormal regulation of DNA methylation and its readers has been associated with a wide range of cellular dysfunction. Disruption of the normal function of DNA methylation readers contributes to cancer progression, neurodevelopmental disorders, autoimmune disease and other pathologies. One reader of DNA methylation known to be especially important is MeCP2. It acts a bridge and connects DNA methylation with histone modifications and regulates many gene targets contributing to various diseases; however, much remains unknown about how it contributes to cancer malignancy. We and others previously described novel MeCP2 post-translational regulation. We set out to test the hypothesis that MeCP2 would regulate novel genes linked with tumorigenesis and that MeCP2 is subject to additional post-translational regulation not previously identified. Herein we report novel genes bound and regulated by MeCP2 through MeCP2 ChIP-seq and RNA-seq analyses in two breast cancer cell lines representing different breast cancer subtypes. Through genomics analyses, we localize MeCP2 to novel gene targets and further define the full range of gene targets within breast cancer cell lines. We also further examine the scope of clinical and pre-clinical lysine deacetylase inhibitors (KDACi) that regulate MeCP2 post-translationally. Through proteomics analyses, we identify many additional novel acetylation sites, nine of which are mutated in Rett Syndrome. Our study provides important new insight into downstream targets of MeCP2 and provide the first comprehensive map of novel sites of acetylation associated with both pre-clinical and FDA-approved KDACi used in the clinic. This report examines a critical reader of DNA methylation and has important implications for understanding MeCP2 regulation in cancer models and identifying novel molecular targets associated with epigenetic therapies.
DNA甲基化及其识别蛋白的异常调控与多种细胞功能障碍有关。DNA甲基化识别蛋白正常功能的破坏会促进癌症进展、神经发育障碍、自身免疫性疾病和其他病理状况。一种已知特别重要的DNA甲基化识别蛋白是MeCP2。它起到桥梁作用，将DNA甲基化与组蛋白修饰联系起来，并调控许多导致各种疾病的基因靶点；然而，关于它如何促进癌症恶性发展仍有许多未知之处。我们和其他人之前描述了MeCP2的新型翻译后调控。我们着手测试这样一个假设，即MeCP2会调控与肿瘤发生相关的新基因，并且MeCP2会受到此前未发现的额外翻译后调控。在此，我们通过对代表不同乳腺癌亚型的两种乳腺癌细胞系进行MeCP2染色质免疫沉淀测序（ChIP-seq）和RNA测序（RNA-seq）分析，报告了由MeCP2结合并调控的新基因。通过基因组学分析，我们将MeCP2定位到新的基因靶点，并进一步确定乳腺癌细胞系内基因靶点的完整范围。我们还进一步研究了在翻译后调控MeCP2的临床和临床前赖氨酸脱乙酰酶抑制剂（KDACi）的范围。通过蛋白质组学分析，我们鉴定出许多额外的新乙酰化位点，其中9个在雷特综合征中发生了突变。我们的研究为MeCP2的下游靶点提供了重要的新见解，并提供了与临床前和美国食品药品监督管理局（FDA）批准的用于临床的KDACi相关的新乙酰化位点的首张综合图谱。本报告研究了一种关键的DNA甲基化识别蛋白，对于理解癌症模型中MeCP2的调控以及识别与表观遗传疗法相关的新分子靶点具有重要意义。
