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

基本信息

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

项目摘要

'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.

“组蛋白脱乙酰酶”(HDAC) 是一类催化乙酰化赖氨酸中乙酰基去除的酶，与几乎所有细胞过程有关，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+ 依赖性（I、II 和 IV 类）或 NAD+ 依赖性（III 类 - Sirtuins）催化结构域；然后进一步通过额外的 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）的存在。传统上，I 类 HDAC（HDAC1、2 和 3）被认为作为经典共抑制复合物（例如 Sin3A、NuRD 和 CoREST）的催化核心参与基因抑制过程。 Sin3a 复合物被认为是通过转录因子和 Sin3 相关蛋白 (SAP) 的组合被募集到染色质，然后介导组蛋白脱乙酰化和随后的染色质压缩。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，但对其作用方式几乎一无所知。此外，使用这些通用 HDACi 会导致许多使人衰弱的副作用，包括疲劳、腹泻、血小板计数低（血小板减少症）和高氨血症，这些副作用可能导致脑损伤。因此，鉴于 HDAC 抑制在多种疾病状态中的积极治疗价值，以及通用 HDACi 的可怕副作用，合乎逻辑的前进方向是破坏单个 HDAC 复合物。例如，Sin3A/HDAC1 复合物已被证明在细胞周期调节中发挥着关键作用，因此抑制其他 HDAC1/2 复合物（NuRD、CoREST 和 MiDAC）可能不需要抑制癌细胞的生长。特异性抑制单个 HDAC 复合物的一个关键挑战是了解它们是如何组装的，以及哪些辅因子对其功能至关重要。迄今为止，哺乳动物 Sin3A 复合体的大多数主要蛋白质组学研究都使用癌细胞系。在本提案中，我们的目标是鉴定一系列原代细胞类型中 Sin3A 复合物的所有必需辅助因子和底物（包括非组蛋白）。为了实现这一目标，我们将采用考利和布雷肯实验室开发的最先进的蛋白质组学和转录组学方法。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 Sin3A 在细胞中的功能的要求，ii) 测试 Sin3A 的组成在不同类型的原代细胞中是否相同iii) 询问乙酰细胞组的哪一部分（大多数细胞类型中大约 4,000 个 Lys-ac 位点）受到 Sin3A 复合物的特异性调节。通过使用 Sin3A 作为 I 类 HDAC 复合物的范例，我们希望扩展我们对细胞环境中 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来设计新药来治疗多种疾病，包括癫痫、双相情感障碍、阿尔茨海默病和癌症。

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

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
作者：
通讯作者：

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.