去泛素化酶在乳腺癌中的研究新进展

泛素-蛋白酶体系统(ubiquitin-proteasome-system,UPS)是控制蛋白质降解的主要系统,也是细胞基本活动的关键调节器。去泛素化酶(deubiquitinating enzymes,DUBs)是泛素-蛋白酶体系统的组成部分,主要参与调节蛋白质泛素化和去泛素化的动态平衡,对细胞增殖、信号转导、神经病变或肿瘤发生意义重大。不同的DUBs在乳腺癌中的作用不同,最新发现去泛素化酶BAP1、OTUD3、ATXN3L主要调节乳腺癌细胞增殖,某些DUBs小分子抑制剂可以间接诱导三阴性乳腺癌细胞凋亡。本文主要综述这三个DUBs及去泛素化酶抑制剂在乳腺癌中的研究新进展,为寻找新型的乳腺癌分子靶向药物提供理论依据。     

泛素连接酶和去泛素化酶在帕金森病中的作用

中脑黑质多巴胺能神经元特异性损伤和α突触核蛋白聚集的分子机制是帕金森病（Parkinson’s disease,PD）研究领域亟待解决的问题。蛋白质异常聚集很大程度上是由于泛素-蛋白酶体系统（ubiquitin-proteasome system,UPS）功能障碍引起的。蛋白质泛素化由一系列泛素化酶级联反应促进，并受去泛素化酶（deubiquitylases,DUBs）的反向调节。泛素化和去泛素化过程异常导致蛋白质异常聚集和包涵体形成，进而损伤神经元。近来研究报道，蛋白质的泛素化和去泛素化修饰在PD的发病机制中发挥重要作用。E3泛素连接酶促进蛋白质的泛素化，有利于α突触核蛋白的清除、促进多巴胺能神经元的存活、维持线粒体的功能等。DUBs可以去掉底物蛋白质的泛素化修饰，抑制α突触核蛋白的降解，调控线粒体的功能和神经元内铁的稳态。本文以E3泛素连接酶和DUBs为切入点，综述了蛋白质泛素化和去泛素化修饰参与多巴胺能神经元损伤机制的最新研究进展。     

去泛素化酶在肾细胞癌中的作用

肾细胞癌（renal cell carcinoma,RCC）是成人肾脏的原发性恶性肿瘤。泛素-蛋白酶体系统（ubiquitin-proteasome system,UPS）对控制蛋白质水平和调节生理病理过程至关重要。去泛素化酶（deubiquitinases,DUBs）是UPS的关键成分,特别是从靶蛋白中去除泛素链,通过严格调节正常生理学中泛素化和去泛素化之间的平衡,对蛋白质稳态和质量控制显示出至关重要的作用。越来越多的研究表明,功能异常的DUBs与RCC的进展和转移有关。根据底物的不同,一些DUB可能会抑制RCC,而另一些则促进。本文综述了RCC相关DUB的最新研究进展,描述了其分类、功能作用,总结了DUB在RCC中的作用和作用机制,并讨论了靶向DUBs用于癌症治疗。     

去泛素化酶与肿瘤

泛素化修饰(ubiquitination modification)广泛存在于真核生物,通过26S蛋白酶体降解途径或信号传递等,改变蛋白质稳定性、定位和活性等功能,参与细胞的周期、转录、炎症、肿瘤和免疫等各项功能,是一类复杂的动态调控系统.泛素化调节是一个可逆过程,被泛素连接酶(ubiquitin ligase,E3)...     

定量蛋白质组学揭示酵母去泛素化酶Ubp14生物学功能

泛素化是一种动态可逆的蛋白质翻译后修饰,泛素分子在泛素激活酶、泛素结合酶和泛素连接酶的级联酶促反应催化下共价连接到底物蛋白上。去泛素化酶将泛素分子从底物上移除,动态可逆地调控泛素化修饰,在成熟泛素的生成、泛素链的移除与修剪、游离泛素链的回收等过程中发挥着关键的调控作用。本文的研究对象是酵母中泛素特异性蛋白酶(ubiquitin specific protease, USP)家族成员Ubp14,负责回收细胞内游离的泛素链。本研究定量比较了酵母细胞中Ubp14缺失对全蛋白质组的影响,进而找出其潜在的调控通路和分子功能。首先,通过同源重组技术构建了ubp14?菌株,发现其生长速度低于野生型酵母。利用稳定同位素氨基酸代谢标记技术结合深度覆盖的蛋白质组学分析技术,系统比较了ubp14?菌株相对于野生型菌株的差异蛋白,共计鉴定3 685个蛋白,通过统计学分析筛选得到109个差异蛋白。基因本体论分析发现,Ubp14缺失引起的差异蛋白主要参与了包括氨基酸代谢、氧化还原和热应激等生物学过程。本研究为深入探究去泛素化酶Ubp14的生物学功能,进而深刻理解游离泛素的稳态平衡与生物学过程调控提供了高可信的蛋白...     

去泛素化酶活性的调控

泛素化是一种非常重要的蛋白质翻译后修饰方式,在细胞生命活动的各个方面发挥作用。泛素化修饰是可逆的过程,去泛素化酶通过催化去除底物蛋白质上的泛素从而逆转该过程。去泛素化酶是一类数量众多的蛋白水解酶家族,近年来不断有新的去泛素化酶被发现和报道。鉴于其在细胞功能中的重要作用,去泛素化酶活性受到严格的调控。目前的研究表明,影响去泛素化酶活性的因素很多。本文主要从转录水平的调控、翻译后修饰、蛋白质定位和蛋白质相互作用等调控方式进行论述,以期为研究和利用去泛素化酶治疗疾病提供新思路。     

去泛素化酶在卵巢癌发生发展中的作用CSCD

泛素-蛋白酶体途径是细胞内蛋白质降解的重要方式,调节蛋白质稳定性。去泛素化酶可以识别特定蛋白质的泛素化信号从而使底物蛋白质去泛素化,逆转蛋白质泛素化过程,进而调控细胞增殖、分化、凋亡和迁移等多种生物学功能。去泛素化酶家族的多个成员通过影响细胞增殖凋亡及对化疗药物的敏感性等,在卵巢癌的发生发展中发挥十分重要的作用。一些小分子抑制剂通过抑制去泛素化酶的活性从而起到抗肿瘤的作用,并且具有特异性强,细胞毒性较弱等优势。本综述对参与卵巢癌发生发展的去泛素化酶以及相关的小分子抑制剂做一个全面的总结,为卵巢癌的诊断和治疗提供一个新的方向。     

去泛素化酶USP11在细胞中的功能作用及其研究进展

Ubiquitin-specific protease 11(USP11)属于半胱氨酸蛋白酶,是去泛素化酶家族(deubiquitinating enzymes,DUBs)的重要成员之一。近年来研究表明USP11能调节细胞内众多蛋白底物的稳定性及功能,包括DNA修复蛋白、病毒RNA复制相关蛋白、TGFβ和NF-κB信号转导通路相关蛋白等,在疾病的发生发展中起着重要的作用。主要综述了USP11的结构、在细胞中的分子功能以及与肿瘤和病毒性疾病的关系,探讨了USP11作为治疗分子靶标的可能性。     

组蛋白的泛素化与去泛素化修饰

泛素在真核生物体内广泛存在,泛素化修饰是转录后的修饰方式之一;组蛋白是染色质的主要成分之一,与基因的表达有密切关系。组蛋白的泛素化修饰与经典的蛋白质的泛素调节途径不同,不会导致蛋白质的降解,但是能够招募核小体到染色体、参与X染色体的失活、影响组蛋白的甲基化和基因的转录。组蛋白的去泛素化修饰同样与染色质的结构及基因表达密切相关。组蛋白的泛素化和磷酸化、乙酰化、甲基化修饰之间还存在协同和级联效应。     

去泛素化酶USP29调控CBX6蛋白质稳定性

多梳家族(polycomb group,PcG)是一类控制细胞命运和胚胎发育的转录抑制因子,主要以转录抑制复合物(polycomb repressive complex,PRC)的形式发挥功能.染色体盒蛋白质同源物6(chromobox protein homolog 6,CBX6)是PRC1的核心蛋白质亚基之一,在基...     

生物质谱与蛋白质组学

蛋白质组学是后基因组学时代最受关注的研究领域之一,其核心的鉴定技术——生物质谱近年来在仪器设计以及鉴定通量、分辨率和灵敏度等各方面均有质的飞跃,促进了蛋白质表达谱作图、定量蛋白质组分析、亚细胞器蛋白质组作图、蛋白质翻译后修饰以及蛋白质相互作用等蛋白质组研究各个领域的飞速发展。本综述了生物质谱技术的最新进展,及其在蛋白质组学研究中的应用。     

蛋白质组学方法在昆虫学研究中的应用

蛋白质组学作为后基因组学时代研究的一个重要内容,已广泛深入到生命科学和医药学的各个领域,其理论和技术的发展完善也为昆虫学研究带来了新的思维方式和研究方向。文章就近年来蛋白质组学在昆虫研究中的应用加以综述。     

基于质谱技术的蛋白质组定量方法

对不同状态下的蛋白质在表达和修饰水平上进行精确定量,对于探索蛋白质的生物功能、发现疾病的生物标志物都具有重要意义,也是当前蛋白质组学的一个重要研究前沿。近年来,各种蛋白质组定量的新技术和新方法不断涌现,但仍面临着巨大挑战。本文就基于质谱技术的多种蛋白质组定量方法的基本原理、近几年的研究进展和应用进行评述。     

Surface plasmon resonance mass spectrometry in proteomics

Due to the enormous complexity of the proteome, focus in proteomics shifts more and more from the study of the complete proteome to the targeted analysis of part of the proteome. The isolation of this specific part of the proteome generally includes an affinity-based enrichment. Surface plasmon resonance (SPR), a label-free technique able to follow enrichment in real-time and in a semiquantitative manner, is an emerging tool for targeted affinity enrichment. Furthermore, in combination with mass spectrometry (MS), SPR can be used to both selectively enrich for and identify proteins from a complex sample. Here we illustrate the use of SPR-MS to solve proteomics-based research questions, describing applications that use very different types of immobilized components: such as small (drug or messenger) molecules, peptides, DNA and proteins. We evaluate the current possibilities and limitations and discuss the future developments of the SPR-MS technique.     

Ubiquitinomics: History,methods, and applications in basic research and drug discovery

The ubiquitin-proteasome system (UPS) was discovered about 40 years ago and is known to regulate a multitude of cellular processes including protein homeostasis. Ubiquitylated proteins are recognized by downstream effectors, resulting in alterations of protein abundance, activity, or localization. Not surprisingly, the ubiquitylation machinery is dysregulated in numerous diseases, including cancers and neurodegeneration. Mass spectrometry (MS)-based proteomics has emerged as a transformative technology for characterizing protein ubiquitylation in an unbiased fashion. Here, we provide an overview of the different MS-based approaches for studying protein ubiquitylation. We review various methods for enriching and quantifying ubiquitin modifications at the peptide or protein level, outline MS acquisition, and data processing approaches and discuss key challenges. Finally, we examine how MS-based ubiquitinomics can aid both basic biology and drug discovery research.     

Mass spectrometry is only one piece of the puzzle in clinical proteomics.

Biomarker discovery in clinical proteomics is being performed on relatively large patient cohorts by utilizing the high throughput of laser desorption/ionization mass spectrometry (MALDI- and SELDI-TOF-MS). Dealing directly with patient samples as opposed to working in cell or animal systems requires a host of considerations both before and after mass spectrometric analysis to obtain robust biomarker candidates. The challenges associated with the heterogeneity of typical samples are amplified by the ability to detect hundreds to thousands of proteins simultaneously. Adherence to protocols and consistency, however, can ensure optimal results. A study starts necessarily with a relevant clinical question and proceeds to a planning phase where sample availability, statistical test selection, logistics and bias reduction are key points. The physical analysis requires consistency and standardized protocols that are helped significantly through automation. Data analysis is broken into two stages, screening and final testing, which can detect either single candidates or a pattern of proteins. Biomarker identification can be performed at this point and will help significantly in the last stage, interpretation. Replication should be performed in an independent sample set in a separate study. The candidate biomarkers from an initial study give a wealth of information that can help to pinpoint patient subpopulations for a more exhaustive proteomic study using complementary platforms with limited capacity but extremely high information content. A clinical proteomics pilot project can also lead to better selection of model systems by providing a direct link with patient samples.     

Mass spectrometry technologies for proteomics.

In the late 1980s, the advent of soft ionization techniques capable of generating stable gas phase ions from thermally unstable biomolecules, namely matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI), laid the way for the development of a set of powerful alternatives to the traditional Edman chemistry for the structural characterization of peptides and proteins. The rapid protein identification capabilities that, coupled with two-dimensional gel electrophoresis, provided insights into all sorts of biological systems since the dawn of proteomics and have been exploited in the last few years for the development of more powerful and automatable gel-free strategies, mainly based on multidimensional chromatographic separations of peptides from proteolytic digests. In parallel to the evolution of ion sources, mass analysers and scan modes, the invention of new elegant biochemical strategies to fractionate or simplify highly complex mixtures, or to introduce isotopic labels in peptides in a variety of ways now makes also possible large-scale, high-coverage quantitative studies in a wide dynamic range. In this review, we provide the fundamental concepts of mass spectrometry (MS) and describe the technological progress of MS-based proteomics since its earliest days. Representative literature examples of their true power, either when employed as exploratory or as targeted techniques, is provided as well.     

Information management for proteomics: a perspective

Proteomics is a data-rich discipline that makes extensive use of separation tools, mass spectrometry and bioinformatics to analyze and interpret the features and dynamics of the proteome. A major challenge for the field is how proteomics data can be stored and managed, such that data become permanent and can be mined with current and future tools. This article details our experience in the development of a commercial proteomic information management system. We identify the challenges faced in data acquisition, workflow management, data permanence, security, data interpretation and analysis, as well as the solutions implemented to address these issues. We finally provide a perspective on data management in proteomics and the implications for academic and industry-based researchers working in this field.