Chemical Genetic Approaches to Study Chromatin Complexes

表观基因组包括控制基因表达和基因组功能的关键层。癌 突变经常改变染色质复合物的功能，导致异常的表观基因组景观， 在肿瘤细胞中观察到。确定控制染色质复合物及其相互作用的机制将 推进我们对表观基因组过程的理解，它们如何在癌症中被破坏，以及它们如何在癌症中被破坏。 为药物发现而调制的。因此，我们的中心目标是阐明 染色质复合物的机制，并测试其作为治疗靶点的前景。在这种追求中，这种应用 研究了赖氨酸特异性组蛋白脱甲基酶-1（LSD 1），一种转录辅抑制因子，是药物靶点， 肿瘤学LSD 1与各种辅阻遏物和转录因子（TF）形成复合物，包括GFI 1B， 其在发展中起关键作用并涉及各种肿瘤类型。利用抗药性 从化学抑制筛选获得的等位基因，我们先前的工作表明，LSD 1活性位点抑制剂发挥作用， 通过破坏LSD 1-GFI 1B复合物，修正先前的药物机制模型， 的行动。值得注意的是，在第3组和第4组中，GFI 1B经常被增强子劫持突变过表达 髓母细胞瘤（MB）和LSD 1抑制剂在GFI 1B驱动的MB小鼠模型中有效。有趣的是， E3泛素连接酶KBTBD 4在3/4 MB组中也经常突变，最近报道其介导 LSD 1的专性复合物伴侣CoREST的降解。这些观察结果表明， 在第3/4 MB组中，通过LSD 1-CoREST介导GFI 1B和KBTBD 4之间的连接。但 LSD 1-CoREST、GFI 1B和KBTBD 4之间的分子相互作用和相互作用仍不清楚， 这是我们理解上的一个重大差距。为了解决这些差距，第一个具体目标调查了结构， 动力学和LSD 1-GFI 1B复合体的相互作用，通过多学科方法，目标是 揭示了染色质调节因子-TF复合物的前所未有的观点。第二个目的是阐明 小分子通过增强KBTBD 4活性降解LSD 1-CoREST的机制，提供了关键的 通过新出现的模式深入了解靶向LSD 1复合物的策略。最后一个目的是研究如何 KBTBD 4 MB突变促进LSD 1-CoREST降解及其对LSD 1-CoREST的下游影响 GFI 1B和MB癌症表观基因组。在这些目标中，LSD 1复合物的机制和相互作用 将通过使用创新的化学基因组方法来探索，这些方法利用药物抑制等位基因， 细胞、分子和结构生物学预计这些研究的结果将阐明 控制染色质复合体功能和相互作用的生化原理及先进策略 以它们为靶点进行治疗。

The epigenome comprises a critical layer for controlling gene expression and genome function. Cancer mutations often alter the function of chromatin complexes, leading to aberrant epigenomic landscapes frequently observed in tumor cells. Determining the mechanisms controlling chromatin complexes and their interactions will advance our understanding of epigenomic processes, how they are disrupted in cancer, and how they can be pharmacologically modulated for drug discovery. Consequently, our central goals are to elucidate the mechanisms of chromatin complexes and test their promise as therapeutic targets. In this pursuit, this application investigates lysine-specific histone demethylase-1 (LSD1), a transcriptional corepressor that is a drug target for oncology. LSD1 forms complexes with various corepressors and transcription factors (TF), including GFI1B, which are critically involved in development and implicated across various tumor types. Using drug-resistance alleles obtained from a chemical suppressor screen, our prior work showed that LSD1 active site inhibitors exert their anti-proliferative effects by disrupting the LSD1-GFI1B complex, revising prior models of drug mechanism of action. Notably, GFI1B is frequently overexpressed by enhancer hijacking mutations in group 3 and 4 medulloblastoma (MB), and LSD1 inhibitors are effective in GFI1B-driven MB mouse models. Intriguingly, the E3 ubiquitin ligase KBTBD4 is also frequently mutated in group 3/4 MB and was recently reported to mediate degradation of CoREST, LSD1’s obligate complex partner. These observations suggest a possible mechanistic connection between GFI1B and KBTBD4 in group 3/4 MB, mediated through LSD1-CoREST. However, the molecular interactions and interplay between LSD1-CoREST, GFI1B, and KBTBD4 remain unclear and present a major gap in our understanding. To address these gaps, the first specific aim investigates the structure, dynamics, and interactions of the LSD1-GFI1B complex through a multidisciplinary approach, with the goal of revealing an unprecedented view into a chromatin regulator-TF complex. The second aim seeks to elucidate the mechanism of small molecules that degrade LSD1-CoREST by potentiating KBTBD4 activity, providing critical insight into strategies to target LSD1 complexes through new emerging modalities. The last aim studies how KBTBD4 MB mutations promote LSD1-CoREST degradation and their downstream consequences on LSD1- GFI1B and the MB cancer epigenome. Across these aims, the mechanisms and interactions of LSD1 complexes will be explored by using innovative chemical genomic approaches that leverage drug suppressor alleles with cell, molecular, and structural biology. It is expected that the findings from these studies will illuminate biochemical principles governing the function and interactions of chromatin complexes and advance strategies to pharmacologically target them for therapeutic applications.