Bilateral BBSRC-SFI: Understanding the impact of divergent Sin3A/HDAC1 complex assemblies in gene regulation

双边 BBSRC-SFI：了解不同的 Sin3A/HDAC1 复合体组装对基因调控的影响

• 批准号: BB/P021689/1
• 负责人: Shaun Cowley
• 金额: $ 51.84万
• 依托单位: University of Leicester
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2017
• 资助国家: 英国
• 起止时间: 2017 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FP021689%2F1
• 关键词: Bilateral; BBSRC; SFI; Understanding; impact

'Histone deacetylase' (HDAC) enzymes, the class of enzymes which catalyse the removal of the acetyl group from acetylated lysines, have been implicated in almost all cellular processes, including cell cycle, DNA synthesis, DNA repair and gene expression. There are 18 HDACs in mammals, which can be categorized initially as having either a Zn2+-dependent (Class I, II and IV) or NAD+ dependent (Class III - Sirtuins) catalytic domain; and then further by the presence of additional N-terminal domains and a tissue specific expression pattern (Class II and IV) or a short C-terminal tail and ubiquitous expression (Class I). Classically, class I HDACs (HDAC1, 2 and 3) are thought to be involved in the process of gene repression as the catalytic core of canonical co-repressor complexes, such as Sin3A, NuRD and CoREST. The Sin3a complex is thought to be recruited to chromatin by a combination of transcription factors and Sin3-associated proteins (SAPs) where it then mediates histone deacetylation and consequent chromatin compaction. Clinically, generic HDAC inhibitors (HDACi) are used to treat both depression (Valproic acid) and subcutaneous T-cell lymphoma (SAHA). Despite this clinical importance, almost nothing is known about their mode of action. Furthermore, the use of these generic HDACi, is associated with a number of debilitating side-effects including, fatigue, diarrhoea, low platelet counts (thrombocytopaenia), and hyperammonemia, which can lead to brain damage. Therefore, given the positive therapeutic value of HDAC inhibition in numerous disease states, and the appalling side-effects of generic HDACi, the logical way forward is to disrupt individual HDAC complexes. The Sin3A/HDAC1 complex for instance, has been shown to play a critical role in cell cycle regulation, therefore inhibition of additional HDAC1/2 complexes (NuRD, CoREST and MiDAC) may be unnecessary to arrest the growth of cancer cells. A key challenge to specifically inhibiting individual HDAC complexes will be to understand how they are assembled, and which co-factors are essential for their function. To date, most major proteomics studies of the Sin3A complex in mammals have used cancer cell lines. In this proposal, we aim to identify all essential co-factors and substrates (including non-histones) of the Sin3A complex in an array of primary cell types. To achieve this, we will employ state of the art proteomic and transcriptomic approaches, developed in the Cowley and Bracken labs. The specific aims we will pursue are the following: i) assess the requirement for the stem cell specific SAPs, Fam60a and Tet1, to the function of Sin3A in cells, ii) test whether the composition of Sin3A is the same in different types of primary cells, and iii) ask what fraction of the aceytlome (around 4,000 site of Lys-ac in most cell types) is regulated specifically by the Sin3A complex. By using Sin3A as an exemplar of a class I HDAC complex, we expect to extend our understanding of HDAC complexes in a cellular context. By understanding the molecular basis for how HDAC complexes function we can use that knowledge to design new drugs to treat a variety of diseases including, epilepsy, bipolar disorder, Alzheimer's disease, and cancer.

“组蛋白去乙酰化酶”（HDAC）酶是一类催化乙酰化赖氨酸中乙酰基的去除的酶，几乎涉及所有的细胞过程，包括细胞周期、DNA合成、DNA修复和基因表达。哺乳动物中有18种hdac，最初可分为Zn2+依赖（I、II和IV类）或NAD+依赖（III类- Sirtuins）催化结构域；然后进一步通过存在额外的n端结构域和组织特异性表达模式（II类和IV类）或短c端尾部和普遍表达（I类）。传统上，I类hdac （HDAC1、2和3）被认为是典型的协同抑制因子复合物（如Sin3A、NuRD和CoREST）的催化核心，参与基因抑制过程。Sin3a复合体被认为是通过转录因子和sin3相关蛋白（SAPs）的组合募集到染色质上的，然后它介导组蛋白去乙酰化和随后的染色质压实。临床上，通用HDAC抑制剂（HDACi）用于治疗抑郁症（丙戊酸）和皮下t细胞淋巴瘤（SAHA）。尽管具有临床重要性，但人们对它们的作用方式几乎一无所知。此外，这些通用HDACi的使用与许多使人衰弱的副作用有关，包括疲劳、腹泻、血小板计数低（血小板减少症）和高氨血症，这可能导致脑损伤。因此，鉴于抑制HDAC在许多疾病状态中的积极治疗价值，以及通用HDAC的可怕副作用，合乎逻辑的前进道路是破坏单个HDAC复合物。例如，Sin3A/HDAC1复合物已被证明在细胞周期调节中起关键作用，因此抑制额外的HDAC1/2复合物（NuRD， CoREST和MiDAC）可能不需要阻止癌细胞的生长。特异性抑制单个HDAC复合物的一个关键挑战将是了解它们是如何组装的，以及哪些辅助因子对它们的功能至关重要。迄今为止，大多数主要的哺乳动物Sin3A复合体蛋白质组学研究都使用了癌细胞系。在本提案中，我们的目标是鉴定一系列原代细胞类型中Sin3A复合体的所有必需辅因子和底物（包括非组蛋白）。为了实现这一目标，我们将采用最先进的蛋白质组学和转录组学方法，这些方法是在考利和布雷肯实验室开发的。我们将追求的具体目标如下：i)评估干细胞特异性sap， Fam60a和Tet1对细胞中Sin3A功能的需求，ii)测试Sin3A的组成在不同类型的原代细胞中是否相同，以及iii)询问哪些比例的乙酰基组（在大多数细胞类型中约有4,000个Lys-ac位点）是由Sin3A复合物特异性调节的。通过使用Sin3A作为一类HDAC复合物的范例，我们希望扩展我们对细胞背景下HDAC复合物的理解。通过了解HDAC复合物如何发挥作用的分子基础，我们可以利用这些知识设计新药来治疗各种疾病，包括癫痫、双相情感障碍、阿尔茨海默病和癌症。

项目成果

Comprehensive Transcriptomic Analysis of Novel Class I HDAC Proteolysis Targeting Chimeras (PROTACs).

• DOI: 10.1021/acs.biochem.2c00288
• 发表时间: 2023-02-07
• 期刊: BIOCHEMISTRY
• 影响因子: 2.9
• 作者: Baker, India M.;Smalley, Joshua P.;Sabat, Khadija A.;Hodgkinson, James T.;Cowley, Shaun M.
• 通讯作者: Cowley, Shaun M.

A 'click' chemistry approach to novel entinostat (MS-275) based class I histone deacetylase proteolysis targeting chimeras.

• DOI: 10.1039/d2md00199c
• 发表时间: 2022-12-14
• 期刊: RSC medicinal chemistry
• 影响因子: 4.1

Proximity-dependent biotin identification (BioID) reveals a dynamic LSD1-CoREST interactome during embryonic stem cell differentiation.

• DOI: 10.1039/d1mo00236h
• 发表时间: 2022-01-17
• 期刊: Molecular omics
• 影响因子: 2.9
• 作者: Barnes CE;English DM;Broderick M;Collins MO;Cowley SM
• 通讯作者: Cowley SM

Histone deacetylase (HDAC) 1 and 2 complexes regulate both histone acetylation and crotonylation in vivo.

• DOI: 10.1038/s41598-018-32927-9
• 发表时间: 2018-10-02
• 期刊: Scientific reports
• 影响因子: 4.6
• 作者: Kelly RDW;Chandru A;Watson PJ;Song Y;Blades M;Robertson NS;Jamieson AG;Schwabe JWR;Cowley SM
• 通讯作者: Cowley SM

Sin3A recruits Tet1 to the PAH1 domain via a highly conserved Sin3-Interaction Domain.

• DOI: 10.1038/s41598-018-32942-w
• 发表时间: 2018-10-02
• 期刊: Scientific reports
• 影响因子: 4.6
• 作者: Chandru A;Bate N;Vuister GW;Cowley SM
• 通讯作者: Cowley SM