Chemical Genetic Approaches to Study Chromatin Complexes

研究染色质复合物的化学遗传学方法

基本信息

批准号：
10656923
负责人：
Brian Liau
金额：
$ 57.89万
依托单位：
HARVARD UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-05-03 至 2028-04-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10656923
关键词：
Active Sites Address Agreement Alleles Automobile Driving Binding Biochemical Biological Assay Biology Cellular biology ChIP-seq Chemicals Childhood Brain Neoplasm Chromatin Complex DNA Binding Data Development Disease Drug Modelings Drug Modulation Drug Targeting Drug usage Enhancers Epigenetic Process Feedback GFI1B gene Gene Expression Genetic Engineering Genetic Transcription Genome Genomic approach Glues Goals Growth HDAC1 gene Induced Mutation Knowledge Link Lysine Lysine Degradation Pathway Malignant Neoplasms Maps Mediating Modality Modeling Molecular Molecular Biology Mutate Mutation Oncogenes Oncology Pathway interactions Pharmaceutical Preparations Phenocopy Process Recurrence Regulation Reporting Resolution Role Site Structure Testing Therapeutic Up-Regulation Work anti-cancer therapeutic base editing biophysical analysis cancer therapy chemical genetics drug action drug discovery drug mechanism epigenome epigenomics functional genomics genetic approach genetic corepressor genome-wide histone demethylase human disease inhibitor innovation insight interdisciplinary approach interest live cell microscopy medulloblastoma medulloblastoma cell line mouse model mutant neoplastic cell novel therapeutic intervention overexpression pharmacologic protein degradation reconstitution resistance allele small molecule structural biology therapeutic target transcription factor transcriptome sequencing tumor tumorigenesis ubiquitin-protein ligase

项目摘要

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.

表观基因组包含控制基因表达和基因组功能的关键层。突变通常会改变染色质复合物的功能，经常导致异常的表观基因组景观确定控制染色质复合物及其相互作用的机制将在肿瘤细胞中观察到。我们对表观基因组进展过程的理解，它们在癌症中如何被破坏，以及它们如何被破坏经过药理学调节以进行药物发现测试，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。研究赖氨酸特异性组蛋白去甲基化酶-1 (LSD1)，这是一种转录辅阻遏物，是 LSD1 与各种辅阻遏物和转录因子 (TF) 形成复合物，包括 GFI1B、它们与多种肿瘤类型的发展密切相关并涉及耐药性。从化学抑制子筛选中获得的等位基因，我们之前的工作表明 LSD1 活性位点抑制剂发挥通过破坏 LSD1-GFI1B 复合物、修改先前的药物机制模型来发挥抗增殖作用值得注意的是，GFI1B 在第 3 组和第 4 组中经常因增强子劫持突变而过度表达。髓母细胞瘤 (MB) 和 LSD1 抑制剂对 GFI1B 驱动的 MB 小鼠模型有效。 E3 泛素连接酶 KBTBD4 在 3/4 MB 组中也经常发生突变，最近有报道称其介导 CoREST（LSD1 的专性复杂伙伴）的降解这些观察结果表明了一种可能的机制。 GFI1B 和 KBTBD4 之间的连接位于 3/4 MB 组中，通过 LSD1-CoREST 介导。 LSD1-CoREST、GFI1B 和 KBTBD4 之间的分子相互作用和相互作用仍不清楚且存在为了解决这些差距，第一个具体目标是研究结构，通过多学科方法研究 LSD1-GFI1B 复合物的动力学和相互作用，其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。小分子通过增强 KBTBD4 活性降解 LSD1-CoREST 的机制，提供关键的深入了解通过新出现的方式靶向 LSD1 复合物的策略。 KBTBD4 MB 突变促进 LSD1-CoREST 降解及其对 LSD1- 的下游影响 GFI1B 和 MB 癌症表观基因组在这些目标中，LSD1 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，该方法利用药物抑制等位基因预计这些研究的结果将阐明细胞、分子和结构生物学。控制染色质复合物功能和相互作用的生化原理和高级策略药理学靶向它们用于治疗应用。