Global characterization of lysine acetylation in cancer by a proteomics approach

通过蛋白质组学方法对癌症中赖氨酸乙酰化进行整体​​表征

• 批准号: 8250391
• 负责人: YINGMING ZHAO
• 金额: $ 31.4万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-06-01 至 2013-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8250391
• 关键词: Acetylation; Address; Animals; Antibodies; Applications Grants; Area; Atlases; Bioinformatics; Biological; Biological Markers; Biological Process; Biology; Cataloging; Catalogs; Cell Culture Techniques; Cell Line; Cells; Chromatin; Clinical Trials; Communities; Critiques; DNA; Data Set; Databases; Development; Disease; EP300 gene; Enzymes; Fractionation; High Pressure Liquid Chromatography; Histone Deacetylase Inhibitor; Knowledge; Laboratories; Light; Lysine; Malignant Neoplasms; Mass Spectrum Analysis; Methodology; Methods; Modification; Molecular Biology; Molecular Genetics; Normal Cell; Pathway interactions; Peptides; Play; Post-Translational Protein Processing; Process; Protein Acetylation; Proteins; Proteomics; Regulation; Research; Research Design; Research Infrastructure; Research Methodology; Resistance; Resolution; Role; Safety; Site; Specific qualifier value; Therapeutic; Transformed Cell Line; Vorinostat; Work; antitumor drug; cancer cell; cancer diagnosis; clinical application; design; drug development; environment related cancer; histone-binding proteins; human tissue; improved; innovation; insight; knowledge of results; novel; p300/CBP-Associated Factor; protein S precursor; research study; response; stable cell line; tool; tumor; tumor progression

DESCRIPTION (provided by applicant): Lysine-acetylation (LysAc) and its regulatory enzymes are broadly associated with cancers. Consequently, HDAC inhibitors have been developed to modulate the LysAc status, and are currently undergoing more than 80 clinical trials as anti-tumor therapeutics. Molecular biology and genetics approaches have been attempted to characterize LysAc pathway and the anti-tumor effects of HDAC inhibitors. However, such research provides limited insight into the functions of LysAc sites and their dynamics. LysAc sites among some substrate proteins have been elegantly analyzed by a candidate approach using mass spectrometry, generating key information for downstream biological studies to establish its known functions. Nevertheless, a large number of LysAc substrate proteins and their LysAc dynamics have not been globally studied in cancer-related environments before. This knowledge gap needs to be filled to improve our understanding of LysAc in cancer and other diseases. We hypothesize that dysregulation of LysAc plays a key role in cancer progression. The long-term objective of this research plan is to comprehensively elucidate the dynamic changes of lysine acetylation in cancer, and to use this knowledge to gain a better understanding of its biological functions. We propose to study global LysAc dynamics in cancer cells by a novel, integrated proteomics approach, consisting of (i) high- resolution protein pre-fractionation, (ii) efficient purification of LysAc peptides with anti- LysAc antibodies, and (iii) identification and quantification of the LysAc peptides by SILAC combined with 1D- HPLC/MS/MS or 2D-HPLC/MS/MS. This study is anticipated to identify a large number of non-nuclear LysAc proteins and to reveal their dynamics in cancer progression, therefore challenging the current concept that regulation of DNA-templated process is the major function of the modification. Given the difficulty in identifying new LysAc substrates, the novel, comprehensive LysAc datasets established in this study will address a critical barrier in the LysAc biology field. Specific aims of this research are: (1) To define the aberrant changes in lysine acetylation in cancer cells. LysAc will be quantified between two sets of matched normal and cancer cells, with an emphasis on quantifying LysAc with the highest possible sensitivity. (2) To identify downstream protein targets of suberoylanilide hydroxamic acid (SAHA), the first HDAC inhibitor approved for clinical application. We will quantify LysAc, with or without SAHA, in both normal (SAHA-resistant cells) and matched cancer cells (SAHA-sensitive cells). (3) To identify the lysine-acetylation protein targets for p300 acetyltransferase. We will quantify LysAc proteins among transformed cell lines, with or without expression of the active p300 to generate an atlas of p300 substrates. And (4) to analyze and disseminate LysAc datasets to research community. The novel information from this study will be analyzed by bioinformatics tools and used to construct a LysAc database, providing an infrastructure to stimulate drug development and LysAc-biology research. Lysine acetylation, a post-translational modification in proteins, is dysregulated in cancer development. The proposed study aims to elucidate the dynamic changes of lysine acetylation in cancer progression. The resulting knowledge can be used to understand the biological functions of the modification, to assist development of novel biomarkers for diagnosis of cancer and development of novel anti-tumor drug with high potency and better safety profile.

描述（由申请人提供）：赖氨酸 - 乙酰化（LYSAC）及其调节酶与癌症广泛相关。因此，已经开发出HDAC抑制剂来调节LYSAC状态，目前正在接受80多次临床试验作为抗肿瘤治疗。分子生物学和遗传学方法已尝试表征Lysac途径和HDAC抑制剂的抗肿瘤作用。但是，这样的研究提供了对Lysac站点及其动态功能的有限见解。通过使用质谱法的候选方法对某些底物蛋白的LYSAC位点进行了优雅的分析，从而为下游生物学研究生成了关键信息，以确定其已知功能。然而，以前在与癌症相关的环境中尚未在全球研究大量的Lysac底物蛋白及其LysAC动力学。需要填补这种知识差距，以提高我们对癌症和其他疾病中的Lysac的理解。我们假设LYSAC的失调在癌症进展中起关键作用。该研究计划的长期目标是全面阐明癌症中赖氨酸乙酰化的动态变化，并利用这些知识来更好地了解其生物学功能。我们建议通过一种新型的综合蛋白质组学方法研究癌细胞中的全球LYSAC动力学，包括（i）高分辨率蛋白质前分级前的蛋白质，（ii）用抗溶质抗体抗体和（iii）用SILAC鉴定和定量用SILAC鉴定和定量的MSS/MS MSS/MSS/MS MSS/MSS/MSS/MSS/MS MSS/MS MSS/MSS MSS/MSS MSS/MSS MSS/MSS MSS鉴定和定量。预计这项研究将确定大量的非核Lysac蛋白，并揭示其在癌症进展中的动态，因此挑战当前的概念，即调节DNA-修复过程是修饰的主要功能。考虑到难以识别新的Lysac底物，本研究中建立的新型Lysac数据集将解决Lysac生物学领域的关键障碍。这项研究的具体目的是：（1）定义癌细胞中赖氨酸乙酰化的异常变化。 LYSAC将在两组匹配的正常和癌细胞之间进行量化，重点是量化具有最高敏感性的LYSAC。 （2）确定suberoylanilide羟氨酸（SAHA）的下游蛋白质靶标，这是第一个批准用于临床应用的HDAC抑制剂。我们将在正常（耐SAHA的细胞）和匹配的癌细胞（SAHA敏感细胞）中量化Lysac，无论有没有SAHA。 （3）确定P300乙酰转移酶的赖氨酸 - 乙酰化蛋白靶标。我们将在转化的细胞系中量化Lysac蛋白，在有或没有活性p300表达的情况下以生成P300底物的地图集。 （4）将LYSAC数据集分析和传播到研究社区。这项研究的新信息将通过生物信息学工具进行分析，并用于构建LYSAC数据库，提供基础设施来刺激药物开发和Lysac-biology研究。 赖氨酸乙酰化是蛋白质的翻译后修饰，在癌症发展中失调。拟议的研究旨在阐明癌症进展中赖氨酸乙酰化的动态变化。所产生的知识可用于了解修饰的生物学功能，以帮助开发新型的生物标志物来诊断癌症和开发具有高效力和更好安全性的新型抗肿瘤药物。

项目成果

Quantitative proteomic analysis of histone modifications.

• DOI: 10.1021/cr500491u
• 发表时间: 2015-03-25
• 期刊: Chemical reviews
• 影响因子: 62.1
• 作者: Huang H;Lin S;Garcia BA;Zhao Y
• 通讯作者: Zhao Y

MS/MS/MS reveals false positive identification of histone serine methylation.

MS/MS/MS 揭示了组蛋白丝氨酸甲基化的假阳性鉴定。

• DOI: 10.1021/pr900864s
• 发表时间: 2010
• 期刊: Journal of proteome research
• 影响因子: 4.4
• 作者: Zhang,Junmei;Chen,Yue;Zhang,Zhihong;Xing,Gang;Wysocka,Joanna;Zhao,Yingming
• 通讯作者: Zhao,Yingming

Identification of four novel types of in vitro protein modifications.

四种新型体外蛋白质修饰的鉴定。

• DOI: 10.1021/pr800456q
• 发表时间: 2008
• 期刊: Journal of proteome research
• 影响因子: 4.4
• 作者: Xing,Gang;Zhang,Junmei;Chen,Yue;Zhao,Yingming
• 通讯作者: Zhao,Yingming

Identification of lysine succinylation as a new post-translational modification.

• DOI: 10.1038/nchembio.495
• 发表时间: 2011-01
• 期刊: NATURE CHEMICAL BIOLOGY
• 影响因子: 14.8
• 作者: Zhang, Zhihong;Tan, Minjia;Xie, Zhongyu;Dai, Lunzhi;Chen, Yue;Zhao, Yingming
• 通讯作者: Zhao, Yingming

A direct HDAC4-MAP kinase crosstalk activates muscle atrophy program.

• DOI: 10.1016/j.molcel.2012.04.025
• 发表时间: 2012-07-13
• 期刊: MOLECULAR CELL
• 影响因子: 16
• 作者: Choi, Moon-Chang;Cohen, Todd J.;Barrientos, Tomasa;Wang, Bin;Li, Ming;Simmons, Bryan J.;Yang, Jeong Soo;Cox, Gregory A.;Zhao, Yingming;Yao, Tso-Pang
• 通讯作者: Yao, Tso-Pang