Proteomics in hematologic malignancies

Basic science research in hematology has been determining the functions of gene products using classical approaches that typically involve studying one or a few genes at a time. Proteomics, defined as the study of protein properties on a large scale, provides tools to globally analyze malignant hematologic cells. A major challenge in cancer therapy is the identification of drugs that kill tumor cells while preserving normal cells. Differential display via proteomics enables analysis of direct as well as side-effects of drugs at a molecular level. Proteomics also allows a better understanding of cell signaling pathways involved during apoptosis in hematologic cells. Storing the information in a 2D electrophoresis database enhances the efficiency of proteome research on malignant cells. Finally, the work needed to be carried out on proteomic analysis prior to routine clinical adoption is discussed, and the necessity for multi-institutional collaborations is emphasized.     

蛋白质组学在结核分枝杆菌研究中的应用

蛋白质组学是在基因组学基础上发展起来的新兴学科, 其基本技术包括样品制备、蛋白质分离和蛋白质鉴定分析, 其中的核心技术是双向凝胶电泳技术(2-Dimensional Electrophoresis, 2-DE)和质谱技术(Mass Spectrometry, MS)。近年来, 蛋白质组学技术已应用于结核分枝杆菌的研究领域。应用蛋白质组学技术分离、鉴定、检测结核分枝杆菌致病株的全菌蛋白及分泌蛋白, 分析其蛋白组成, 可深入解析结核分枝杆菌的致病机理和耐药机制。通过对结核分枝杆菌致病株抗原的分析, 为研制预防结核病的新型疫苗拓展了空间。通过对结核分枝杆菌临床分离株的蛋白组成分析还发现了一些有意义的结核病早期诊断标志物。蛋白质组学技术还应用于寻找新的药物靶标, 在研制和筛选新的抗结核药物等方面展示了一些有价值的研究成果, 为更好地开展结核病的预防、早期诊断及治疗打下了基础。     

Development and application of proteomics technologies in Saccharomyces cerevisiae

Proteomics research focuses on the identification and quantification of "all" proteins present in cells, organisms or tissue. Proteomics is technically complicated because it encompasses the characterization and functional analysis of all proteins that are expressed by a genome. Moreover, because the expression levels of proteins strongly depend on complex regulatory systems, the proteome is highly dynamic. This review focuses on the two major proteomics methodologies, one based on 2D gel electrophoresis and the other based on liquid chromatography coupled to mass spectrometry. The recent developments of these methodologies and their application to quantitative proteomics are described. The model system Saccharomyces cerevisiae is considered to be the optimal vehicle for proteomics and we review studies investigating yeast adaptation to changes in (nutritional) environment.     

药物蛋白质组学与药物发现

21世纪,科学家面临着从基因组到蛋白质组的转变,蛋白质组学是基因组和药物发现的效率。药物蛋白质组学研究不仅有助于发现治疗的可能靶点,也将明显提高药物发现的效率。药物蛋白质组学的研究内容,在临床前包括发现新的治疗靶点和发现针对所有靶点的全部化合物,在临床研究方面应包括药物作用的特异蛋白作为诊断和治疗的标志,或以蛋白质谱的差异来分类者。本文主要综述了蛋白质组学在药物靶点的发现和确认,以有药物发现过程中最有关的技术物研究进展。     

The International Proteomics Tutorial Programme (IPTP): a teaching tool box for the proteomics community

The most critical functions of the various proteomics organisations are the training of young scientists and the dissemination of information to the general scientific community. The education committees of the Human Proteome Organisation (HUPO) and the European Proteomics Association (EuPA) together with their national counterparts are therefore launching the International Proteomics Tutorial Programme to meet these needs. The programme is being led by Peter James (Sweden), Thierry Rabilloud (France) and Kazuyuki Nakamura (Japan). It involves collaboration between the leading proteomics journals: Journal of Proteome Research, Journal of Proteomics, Molecular and Cellular Proteomics, and Proteomics. The overall level is aimed at Masters/PhD level students who are starting out their research and who would benefit from a solid grounding in the techniques used in modern protein-based research. The tutorial program will cover core techniques and basics as an introduction to scientists new to the field. At a later stage the programme may be expanded with a series of more advanced topics focussing on the application of proteomics techniques to biological problem solving. The entire series of articles and slides will be made freely available for teaching use at the Journals and Organisations homepages and at a special website, www.proteomicstutorials.org.     

Translocation of nucleoside analogs across the plasma membrane in hematologic malignancies

Nucleoside analogs are currently used in the treatment of various hematologic malignancies due to their ability to induce apoptosis of lymphoid cells. For nucleoside-derived drugs to exert their action, they must enter cells via nucleoside transporters from two gene families, SLC28 and SLC29 (CNT and ENT, respectively). Once inside the cell, these drugs must be phosphorylated to their active forms. In contrast, some members of the ATP-binding cassette (ABC) protein family have been identified as responsible for the efflux of the phosphorylated forms of these nucleoside-derived drugs. Here, we review the main nucleoside analogs used in hematologic malignancies and focus especially on those that are currently used in chronic lymphocytic leukemia (CLL). Moreover, we discuss the pharmacological profile of the nucleoside transporters, which determines the bioavailability of and cell sensitivity to these nucleoside-derived drugs. We also discuss the expression of nucleoside transporters and their activities in CLL as well as the possibility of modulating these transporter activities as a means of modulating intracellular drug availability and, consequently, responsiveness to therapy.     

Cytogenetic markers in hematoproliferative disorders

In the last decade the improvement of methods of chromosome analysis has allowed new insights into the correlation of specific chromosome changes and certain types of malignant hematologic disorders. Even if a clear-cut correlation between a certain chromosomal marker and a certain malignancy is the exception, it is well established that specific chromosome aberrations occur nonrandomly in specific tumors. Moreover, it has been shown that so-called cellular oncogenes are located on those chromosome regions which are involved in translocations and other structural chromosome abnormalities in particular malignant tumors. The significance of chromosome alterations in leukemias and lymphomas is illustrated by examples concerning well-established data, on the one hand, and findings which have still to be confirmed, on the other. This may demonstrate that human tumor cytogenetics are a dynamically and vigorously developing branch of cancer research.     

蛋白质组学研究技术及其进展

蛋白质组学是在后基因组时代出现的一个新的研究领域,它是对机体、组织或细胞的全部蛋白质的表达和功能模式进行研究。对蛋白质组的研究可以使我们更容易接近对生命过程的认识。本文对蛋白质组学研究所使用的主要技术例如二维凝胶电泳、质谱、酵母双杂交、蛋白质芯片、表面等离子共振和生物信息学等作一简要综述。     

At a glance: Proteomics in China

Proteomics is a new science that focuses on the comprehensive analysis of proteins in intact organisms or in molecule machineries,organelles,cells,tissues,or or...     

Elimination of clonogenic tumor cells from bone marrow using methylprednisolone (MP) and etoposide VP16: an in vitro pharmacologic study

The ability to eliminate malignant cells from bone marrow (BM) while retaining sufficient numbers of normal progenitors to ensure engraftment, may well establish the future of autologous BM transplantation (ABMT) for hematologic malignancies. In this study, we describe the effects of methylprednisolone (MP) and etoposide (VP16) alone or in combination on 5 tumor cell lines (HL-60, a promyelocytic cell line; Molt-4, a T cell leukemia; Daudi, a Burkitt's lymphoma and R10/8226 and R40/8226, doxorubicin-resistant myeloma cell lines). The tumor cell kill efficiency of the drugs was assayed using the limiting dilution assay. We determined the toxic effect on progenitor cells by assaying granulocyte-macrophage colony-forming units (CFU). With a combination of MP at 10(-3) M and VP16 at 75 microM, we observed the following log reduction in tumor cell clones: HL-60, 4.695 +/- 0.001; Molt-4, 3.626 +/- 0.036; Daudi, 5.633 +/- 0.001; R10/8226, 3.052 +/- 0.544; R40/8226, 3.126 +/- 0.080. CFU recovery was 24% +/- 5%. Mixing tumor cell lines with a 20-fold excess of normal irradiated BM cells did not eliminate the inhibitory effect of the drug combination. We propose that MP and VP16 used in concert produce effective purging of malignant hematopoietic cells from BM while sparing normal progenitors needed for engraftment.     

Proteomic analysis of human plasma and blood cells in nutritional studies: development of biomarkers to aid disease prevention

Proteomics is emerging as a valuable tool in nutritional research. Proteome analysis from plasma and blood cells can identify thousands of proteins that can potentially provide valuable new biomarkers for health, reveal early indications for disease disposition, assist in dietary responders from nonresponders, and enable the discovery of mechanisms of beneficial food component effects. This review discusses the latest developments in plasma, platelet and peripheral blood mononuclear cell proteomics, specifically in the field of nutritional proteomics, including issues relating to study design, sample preparation and data interpretation.     

Recent progress in polyamine research

Polyamines are recognized as cell growth factors in relation to cell proliferation, differentiation, regeneration and malignant transformation. Polyamines play an important role in the growth of normal cells like vascular endothelial cells and also exert various effects on the proliferation and metastasis of malignant cells. The recent studies on the biosynthesis have clearly elucidated its mechanism at the gane levels, which reflects to the development of the inhibitors of the polyamine biosynthesis. One of the main purposes of the studies on the various polyamine synthesis inhibitors is for the development of new anti-cancer agents, based on the characteristics of the polyamine functions. The clinical effects of several inhibitors, however, have not been shown to be satisfactory and the reason is now the most important research subject in this field. The measurement of the polyamine contents in biological fluids including urine and blood has been shown to be useful as the tumor marker. The recent studies have indicated that the mechanism of increased secretion of urinary polyamines is due to the release from the degraded cancer cells. The results now stimulated the research which aims to elucidate the usefulness of the measurement of urinary polyamines as the parameters of the sensitivity to the anticancer drugs in patients with cancer.     

The antimalarial amodiaquine causes autophagic-lysosomal and proliferative blockade sensitizing human melanoma cells to starvation- and chemotherapy-induced cell death

Pharmacological inhibition of autophagic-lysosomal function has recently emerged as a promising strategy for chemotherapeutic intervention targeting cancer cells. Repurposing approved and abandoned non-oncological drugs is an alternative approach to the identification and development of anticancer therapeutics, and antimalarials that target autophagic-lysosomal functions have recently attracted considerable attention as candidates for oncological repurposing. Since cumulative research suggests that dependence on autophagy represents a specific vulnerability of malignant melanoma cells, we screened a focused compound library of antimalarials for antimelanoma activity. Here we report for the first time that amodiaquine (AQ), a clinical 4-aminoquinoline antimalarial with unexplored cancer-directed chemotherapeutic potential, causes autophagic-lysosomal and proliferative blockade in melanoma cells that surpasses that of its parent compound chloroquine. Monitoring an established set of protein markers (LAMP1, LC3-II, SQSTM1) and cell ultrastructural changes detected by electron microscopy, we observed that AQ treatment caused autophagic-lysosomal blockade in malignant A375 melanoma cells, a finding substantiated by detection of rapid inactivation of lysosomal cathepsins (CTSB, CTSL, CTSD). AQ-treatment was associated with early induction of energy crisis (ATP depletion) and sensitized melanoma cells to either starvation- or chemotherapeutic agent-induced cell death. AQ displayed potent antiproliferative effects, and gene expression array analysis revealed changes at the mRNA (CDKN1A, E2F1) and protein level (TP53, CDKN1A, CCND1, phospho-RB1 [Ser 780]/[Ser 807/811], E2F1) consistent with the observed proliferative blockade in S-phase. Taken together, our data suggest that the clinical antimalarial AQ is a promising candidate for repurposing efforts that aim at targeting autophagic-lysosomal function and proliferative control in malignant melanoma cells.     

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.     

蛋白质组学技术在网络药理学中的应用

蛋白质组学发展至今已日趋成熟,在生物医药相关领域研究中的应用显著增加,与之相关的样品制备技术、蛋白定量方法及先进的质谱仪器也得到了快速发展。网络药理学是近年来提出的新药发现新策略,是药理学的新兴分支学科,它从整体的角度探索药物与疾病的关联性,发现药物靶标,指导新药研发。将蛋白质组学技术应用于网络药理学研究,能使研究人员系统地预测和解释药物的作用,加速药物靶点的确认,从而设计多靶点药物或药物组合。综述了蛋白质组学技术的新近研究进展,并简单概述了其在网络药理学中的应用。     

Update in research and methods in proteomics and bioinformatics

The 3rd International Conference on Proteomics & Bioinformatics (Proteomics 2013)

Philadelphia, PA, USA, 15–17 July 2013

The Third International Conference on Proteomics & Bioinformatics (Proteomics 2013) was sponsored by the OMICS group and was organized in order to strengthen the future of proteomics science by bringing together professionals, researchers and scholars from leading universities across the globe. The main topics of this conference included the integration of novel platforms in data analysis, the use of a systems biology approach, different novel mass spectrometry platforms and biomarker discovery methods. The conference was divided into proteomic methods and research interests. Among these two categories, interactions between methods in proteomics and bioinformatics, as well as other research methodologies, were discussed. Exceptional topics from the keynote forum, oral presentations and the poster session have been highlighted. The topics range from new techniques for analyzing proteomics data, to new models designed to help better understand genetic variations to the differences in the salivary proteomes of HIV-infected patients.