蛋白质组学及其在肿瘤研究中的应用

简要介绍了蛋白质组学的概念、研究方法及其在肿瘤研究中的应用.蛋白质组学研究直接定位于蛋白质水平,从整体、动态、定量的角度去研究基因的功能,是后基因组计划的一个重要组成部分.恶性肿瘤是一种多基因参与的复杂疾病,从蛋白质整体水平上研究恶性肿瘤将有助于进一步揭示恶性肿瘤的发病机制,发现恶肿瘤特异性的标志物及其药物治疗的靶标.     

蛋白质组学的进展

蛋白质组学是在细胞的整体蛋白质水平上进行研究、从蛋白质整体活动的角度来认识生命活动规律的一门新学科.简要介绍蛋白质组学的科学背景及其最新发展.     

种子蛋白质与蛋白质组的研究

综述了种子蛋白质与蛋白质组的研究,主要介绍了种子发育与形成、种子休眠与萌发、种子保存与活力以及种子与环境相互作用的蛋白质与蛋白质组的研究.同时阐述了当今蛋白质组学在种子研究中的应用以及所取得的成果,并展望了种子蛋白质组学的发展方向,种子生物学的研究将从基因水平走向整体水平,因此环境因子与种子蛋白质的相互作用是研究的重点.运用蛋白质组学将能揭示蛋白质的功能并明晰种子的生命机制.     

种子蛋白质与蛋白质组的研究

综述了种子蛋白质与蛋白质组的研究, 主要介绍了种子发育与形成、种子休眠与萌发、种子保存与活力以及种子与环境相互作用的蛋白质与蛋白质组的研究。同时阐述了当今蛋白质组学在种子研究中的应用以及所取得的成果, 并展望了种子蛋白质组学的发展方向, 种子生物学的研究将从基因水平走向整体水平, 因此环境因子与种子蛋白质的相互作用是研究的重点。运用蛋白质组学将能揭示蛋白质的功能并明晰种子的生命机制。     

蛋白质组学的应用研究进展

蛋白质组学(Proteomics)是一门大规模、高通量、系统化的研究某一类型细胞、组织或体液中的所有蛋白质组成及其功能的新兴学科。虽然基因决定蛋白质的水平,但是基因表达的水平并不能代表细胞内活性蛋白的水平,蛋白质组学分析是对蛋白质翻译和修饰水平等研究的一种补充,是全面了解基因组表达的一种必不可少的手段。蛋白质组学相关技术的发展极大地推动了蛋白质组学的研究进展,使其在各研究领域得到了广泛的应用。对蛋白质组学相关技术及其在各领域的应用进行了综述,最后对蛋白质组学的发展趋势和应用前景作出展望。     

微生物蛋白质组学的定量分析

越来越多的微生物基因组序列数据为系统地研究基因的调节和功能创造了有利条件.由于蛋白质是具有生物功能的分子,蛋白质组学在微生物基因组的功能研究中异军突起、蓬勃发展.微生物蛋白质组学的基本原则是,用比较研究来阐明和理解不同微生物之间或不同生长条件下基因的表达水平.显而易见,定量分析技术是比较蛋白质组学中急需发展的核心技术.对蛋白质组学定量分析技术在微生物蛋白质组研究中的进展进行了综述.     

叶绿体的蛋白质组学研究进展

蛋白质组学是以基因组编码的所有蛋白为研究对象,高通量地从细胞及整体水平上研究蛋白质的组成及其功能的新兴学科。在后基因组时代的今天,蛋白质组学的研究正逐渐深入到生命科学的各个领域,21世纪蛋白质组学将成为生命科学中最热门的学科。蛋白质组分析已成为鉴定植物功能的有力工具之一,叶绿体作为比较重要的细胞器,在植物蛋白质组学中已有较多的研究,,随着双向电泳技术的改进和质谱法的出现,并与不断增多的拟南芥、水稻、玉米等植物的序列数据相结合,叶绿体蛋白质组可以被快速鉴定。本文主要介绍了植物蛋白质组学、叶绿体及其蛋白质组学研究技术和研究进展,并对蛋白质组学的研究趋势进行了展望。     

蛋白质组学在哺乳动物睾丸和精子发生中的应用

“蛋白质组学”一词由Wilkins在1994年提出,被称作后基因组时代一个新兴的研究手段.它从整体水平上对组织或者细胞的蛋白质表达、功能、相互作用进行研究,现在成为生命科学未来发展的主要分支之一.睾丸是哺乳动物雄性生殖系统中的一个重要的器官,由曲精小管和间质细胞组成.蛋白质组学在睾丸和精子发生研究上的应用及其技术手段的不断创新,对睾丸功能、生殖机理、生殖疾病的研究起到了极其重要的作用.所以,从蛋白质水平对睾丸和精子发生进行研究,为更好地理解雄性哺乳动物的生殖机理和疾病提供了一个新思路.     

蛋白质组学研究技术及其联合应用

蛋白质组学是研究细胞、组织和器官内所有蛋白质的组成及其动态变化的科学,是在蛋白质水平上定量的、动态的、整体的研究生物体。目前蛋白质组学技术分为样品制备、分离和鉴定3个方面,其新技术主要有激光捕捉显微解剖法、离心超滤法、双向凝胶电泳、同位素亲和标签技术、色谱技术以及质谱技术等。然而,任何一种蛋白质组学研究技术都有其缺陷。因此多种技术的联合应用能使蛋白质组研究更精确和完整,是蛋白质组学的发展趋势。     

蛋白质组学在附睾研究中的应用

蛋白质组学是在后基因组时代出现的一个新的研究领域,它从整体水平对蛋白质的表达和功能模式进行分析.附睾是精子成熟和贮存的场所,因其基因表达呈现出高度的区域特异性,可能成为蛋白质组学,尤其是差异蛋白质组学研究的一个理想模型.本文主要对不同物种的附睾蛋白质组以及附睾不同区域的差异表达蛋白的研究进展予以综述,期望为附睾功能研究及开发新型男性避孕药带来新的思路和方法.     

Proteomic analysis at the bedside: early detection of cancer

Proteomic technologies promise to accelerate rapidly a new era in molecular medicine, especially in the detection and discovery of disease-related biomarkers. These technologies have no bigger impact than in the field of human cancer research. Beyond lifestyle-associated prevention strategies, early detection of cancer has the most profound impact on the ultimate course of the disease: the earlier the cancer is detected, the better the prognosis. Today, new proteomic technologies are being used to discover new diagnostic and prognostic biomarkers for the early detection and treatment of cancer that will have important implications at the bedside.     

Application of proteomics in the study of tumor metastasis

Tumor metastasis is the dominant cause of death in cancer patients. However, the molecular and cellular mechanisms underlying tumor metastasis are still elusive.The identification of protein molecules with their expressions correlated to the metastatic process would help to understand the metastatic mechanisms and thus facilitate the development of strategies for the therapeutic interventions and clinical management of cancer. Proteomics is a systematic research approach aiming to provide the global characterization of protein expression and function under given conditions. Proteomic technology has been widely used in biomarker discovery and pathogenetic studies including tumor metastasis. This article provides a brief review of the application of proteomics in identifying molecular factors in tumor metastasis process. The combination of proteomics with other experimental approaches in biochemistry, cell biology, molecular genetics and chemistry, together with the development of new technologies and improvements in existing methodologies will continue to extend its application in studying cancer metastasis.     

The changing chromatome as a driver of disease: A panoramic view from different methodologies

Chromatin-bound proteins underlie several fundamental cellular functions, such as control of gene expression and the faithful transmission of genetic and epigenetic information. Components of the chromatin proteome (the “chromatome”) are essential in human life, and mutations in chromatin-bound proteins are frequently drivers of human diseases, such as cancer. Proteomic characterization of chromatin and de novo identification of chromatin interactors could, thus, reveal important and perhaps unexpected players implicated in human physiology and disease. Recently, intensive research efforts have focused on developing strategies to characterize the chromatome composition. In this review, we provide an overview of the dynamic composition of the chromatome, highlight the importance of its alterations as a driving force in human disease (and particularly in cancer), and discuss the different approaches to systematically characterize the chromatin-bound proteome in a global manner.     

Synergistic effect of trichostatin A and 5‐aza‐2′‐deoxycytidine on growth inhibition of pancreatic endocrine tumour cell lines: A proteomic study

Our research group recently reported that pancreatic endocrine cancer cell lines are sensitive to the HDAC inhibitor trichostatin A (TSA). In the present paper, we show that the combined treatment of pancreatic endocrine tumour cell lines with TSA and the DNA methyltransferase inhibitor 5‐aza‐2′‐deoxycytidine (DAC) determines a strong synergistic inhibition of proliferation mainly due to apoptotic cell death. Proteomic analysis demonstrates that the modulation of specific proteins correlates with the antiproliferative effect of the drugs. A schematic network clarifies the most important targets or pathways involved in pancreatic endocrine cancer growth inhibition by single or combined drug treatments, which include proteasome, mitochondrial apoptotic pathway and caspase related proteins, p53 and Ras related proteins. A comparison between the patterns of proteins regulated by TSA or DAC in endocrine and ductal pancreatic cancer cell lines is also presented.     

A reagent resource to identify proteins and peptides of interest for the cancer community: a workshop report

On the basis of discussions with representatives from all sectors of the cancer research community, the National Cancer Institute (NCI) recognizes the immense opportunities to apply proteomics technologies to further cancer research. Validated and well characterized affinity capture reagents (e.g. antibodies, aptamers, and affibodies) will play a key role in proteomics research platforms for the prevention, early detection, treatment, and monitoring of cancer. To discuss ways to develop new resources and optimize current opportunities in this area, the NCI convened the "Proteomic Technologies Reagents Resource Workshop" in Chicago, IL on December 12-13, 2005. The workshop brought together leading scientists in proteomics research to discuss model systems for evaluating and delivering resources for reagents to support MS and affinity capture platforms. Speakers discussed issues and identified action items related to an overall vision for and proposed models for a shared proteomics reagents resource, applications of affinity capture methods in cancer research, quality control and validation of affinity capture reagents, considerations for target selection, and construction of a reagents database. The meeting also featured presentations and discussion from leading private sector investigators on state-of-the-art technologies and capabilities to meet the user community's needs. This workshop was developed as a component of the NCI's Clinical Proteomics Technologies Initiative for Cancer, a coordinated initiative that includes the establishment of reagent resources for the scientific community. This workshop report explores various approaches to develop a framework that will most effectively fulfill the needs of the NCI and the cancer research community.     

A proteomics approach to identify changes in protein profiles in pre-cancerous colon

The development of colon cancer is characterised by alterations in multiple genetic and epigenetic pathways in colon tissue leading ultimately to deregulation of colon epithelial cells. Early detection is an important factor in decreasing colon cancer deaths. Proteomic techniques were used to identify potential early markers in colon tissue exhibiting pre-cancerous activity that may characterise pathological changes in a chemically induced colon cancer rat model. Protein profiles were assessed in soluble and insoluble fractions prepared from distal colon of rats treated with the colonotropic carcinogen, dimethylhydrazine. Alterations in protein profiles were associated with the presence of aberrant crypt foci, hyperplasia and dysplasia, microanatomical changes, and metabolic changes in rat colon. These changes may have a potential role in the identification of pre-pathological features preceding colon tumorigenesis.     

Optimizing Size Exclusion Chromatography for Extracellular Vesicle Enrichment and Proteomic Analysis from Clinically Relevant Samples

The field of extracellular vesicle (EV) research has rapidly expanded in recent years, with particular interest in their potential as circulating biomarkers. Proteomic analysis of EVs from clinical samples is complicated by the low abundance of EV proteins relative to highly abundant circulating proteins such as albumin and apolipoproteins. To overcome this, size exclusion chromatography (SEC) has been proposed as a method to enrich EVs whilst depleting protein contaminants; however, the optimal SEC parameters for EV proteomics have not been thoroughly investigated. Here, quantitative evaluation and optimization of SEC are reported for separating EVs from contaminating proteins. Using a synthetic model system followed by cell line‐derived EVs, it is found that a 10 mL Sepharose 4B column in PBS produces optimal resolution of EVs from background protein. By spiking‐in cancer cell‐derived EVs to healthy plasma, it is shown that some cancer EV‐associated proteins are detectable by nano‐LC‐MS/MS when as little as 1% of the total plasma EV number are derived from a cancer cell line. These results suggest that an optimized SEC and nanoLC‐MS/MS workflow may be sufficiently sensitive for disease EV protein biomarker discovery from patient‐derived clinical samples.     

Establishment and proteomic characterization of a novel cell line,NCC-UPS2-C1, derived from a patient with undifferentiated pleomorphic sarcoma

Undifferentiated pleomorphic sarcoma (UPS) is an aggressive mesenchymal malignancy requiring novel therapeutic approaches to improve clinical outcome. Patient-derived cancer cell lines are an essential tool for investigating molecular mechanisms underlying cancer initiation and development; however, there is a lack of patient-derived cell lines of UPS available for research. The objective of this study was to develop a patient-derived cell model of UPS. A cell line designated NCC-UPS2-C1 was established from the primary tumor tissue of an 84-yr-old female patient with UPS. The short tandem repeat pattern of NCC-UPS2-C1 cells was identical to that of the original tumor and distinct from that of any other cell lines deposited in public cell banks. NCC-UPS2-C1 cells were maintained as a monolayer culture for over 80 passages during 30 mo and exhibited spindle-like morphology, continuous growth, and ability for spheroid formation and invasion. Proteomic profiling using mass spectrometry and functional treemap analysis revealed that the original tumor and the derived NCC-UPS2-C1 cells had similar but distinct protein expression patterns. Our results indicate that a novel UPS cell line was successfully established and could be used to study UPS development and effects of anti-cancer drugs. However, the revealed difference between proteomes of the original tumor and NCC-UPS2-C1 cells should be further investigated to determine the appropriate applications of this cell line in UPS research.     

1st NCI Annual Meeting on Clinical Proteomic Technologies for Cancer

The National Cancer Institute of the US National Institutes of Health established a Clinical Proteomic Technologies Initiative for Cancer (CPTI) in 2006. The first annual meeting organized by the CPTI program provided up-to-date information on the research activities and achievements at its first anniversary of this program. Presentations were made by leaders from the five centers nationwide of the Clinical Proteomic Technology Assessment for Cancer (CPTAC), and other principal investigators funded by the CPTI.     

Proteomic patterns for cancer diagnosis--promise and challenges

Proteomic patterns have been discovered for a variety of cancers and cancer related diseases. The platforms used have been both mass spectrometry and microarrays and the incorporation of computer informatics has resulted in innovative possibilities for novel diagnostics.