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PubMed2005

Analysis of candidate genes through a proteomics-based approach in primary cell lines from malignant melanomas and their metastases.

Proteomics provides a powerful approach for screening alterations in protein expression and post-translational modification associated with particular human diseases. In this study, the analysis of protein expression was focused on malignant melanoma in order to determine the candidate genes involved in tumour progression. The proteomes of cultured melanocytes and of cell lines from primary and metastatic lesions of one malignant melanoma patient were profiled using two-dimensional electrophoresis (2-DE) and mass spectrometry. Differentially expressed proteins were confirmed by 2-DE and mass spectrometry on an additional four malignant melanoma cell lines. Total RNA from the first subset of cell lines was used for quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) of the candidate genes identified after proteomics analysis. A very high similarity was observed in the 2-DE maps of two malignant melanoma cell lines derived from primary and secondary lesions of the same patient. Mass spectrometry identified 37 proteins which were found to be more abundant in tumour cells in comparison with control melanocytes (as confirmed on additional cell lines), with a relatively high prevalence of stress proteins. Eight candidate genes (PRDX2, HSP27, HSP60, HSPA8, HSP9B, STIP1, PDI and P4HB) were further characterized by evaluating their messenger RNA expression levels through real-time RT-PCR analysis. Overexpression of HSP27, HSP60 and HSPA8 and downregulation of PRDX2 were observed in cells from metastatic malignant melanoma in comparison with those from primary melanoma. Although further investigations with larger numbers of paired normal and tumour samples are needed, our findings strongly suggest that the dysregulation of stress pathways may be involved in melanoma progression.

Chaperonin 60↗

PubMed2004

Proteomic signature of human cancer cells.

We assessed proteomic profiles as biomarkers for monitoring cell phenotypes. Protein expression profiles were obtained by fluorescence two-dimensional difference gel electrophoresis (2-D-DIGE), in which quantitative ability is improved by labeling proteins with fluorescent dyes prior to electrophoresis. Integrated protein spot intensities were analyzed by a statistical approach. The proteomic data of two groups of cell lines: (1) adenocarcinoma (AC) cell lines derived from lung, pancreas and colon tissues and (2) lung cancer cell lines with different histological backgrounds, including AC, squamous cell carcinoma and small cell carcinoma, were assessed on the basis of prior biological information. Hierarchical clustering analysis and principal component analysis were used to divide the cell lines into subgroups on the basis of similarities between their protein expression profiles. The majority of cell lines were grouped according to their organ of origin or histological background. A machine-learning algorithm selected 32 protein spots that were responsible for the classification. The results indicate that proteomic data generated by 2-D-DIGE can provide a signature of essential cell phenotypes, suggesting that it might be possible to apply this technique to developing tumor markers that could identify the organ of origin of metastatic tumors and contribute to the differential diagnosis of lung cancer.

Cell Line, Tumor↗

PubMed2006

[Proteomics and breast cancer].

Breast cancer is the first cause of death between 35 and 55 years. Genetic alterations and modifications in gene expression are found during different steps of tumor progression. These changes are translated at the protein level where quantitative and qualitative modifications are found in tumor compared to normal samples. Similarly to studies aimed at deciphering transcriptional changes important in cancer, proteomic approaches allow the global and comparative study of proteins in normal and pathological samples. The objective of this article is to present common proteomic methods and to review the first published results concerning proteomics studies applied to breast cancer with an emphasis on reports obtained using the SELDI-TOF MS (Surface Enhanced Laser Desorption Ionization Time-Of-Flight Mass Spectrometry). In breast cancer, it is possible to explore the tumoral proteome and/or the blood derived proteome. The first studies are aimed at globally understanding the disease while the latter are aimed at discovering serum proteins or biomarkers useful for the early detection, diagnosis, prognosis and management of cancer. Promising results are obtained using these emerging methods and these novel biomarkers should be validated in the future and will have an important impact for the management of breast cancer patients.

Biomarkers, Tumor↗

PubMed2005

Identification of growth factor-regulated proteins using 2D electrophoresis and mass spectrometry.

Proteomic technology has recently emerged as a powerful tool for detecting both qualitative and quantitative changes of proteins that occur upon activation of complex signaling pathways. In the present study, comparison of the protein profile of platelet-derived growth factor (PDGF), epidermal growth factor (EGF) and nerve growth factor (NGF)-stimulated and unstimulated cells with two-dimensional electrophoresis followed by mass spectrometric analysis led to the identification of a number of proteins, several of which had not been previously shown to be regulated by receptor-tyrosine kinases. Using subcellular fractionation, our approach was able to identify not only changes due to altered gene transcription, but also due to intracellular protein translocation or modification. One of the proteins that was identified among other PDGF-regulated molecules was prohibitin, a potential tumour suppressor previously implicated in cell cycle regulation and protection of mitochondrial proteins from degradation. Further analysis confirmed that mitochondria-associated prohibitin translocates to an insoluble perinuclear compartment. This study demonstrates the utility of proteomic strategies in identifying potential growth factor-regulated effectors.

Amino Acid Sequence↗

PubMed2004

Proteomics to diagnose human tumors and provide prognostic information.

Proteomics is a rapidly emerging scientific discipline that holds great promise in identifying novel diagnostic and prognostic biomarkers for human cancer. Technologic improvements have made it possible to profile and compare the protein composition within defined populations of cells. Laser capture microdissection is a tool for procuring pure populations of cells from human tissue sections to be used for downstream proteomic analysis. Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) has been used traditionally to separate complex mixtures of proteins. Improvements in this technology have greatly enhanced resolution and sensitivity providing a more reproducible and comprehensive survey. Image analysis software and robotic instrumentation have been developed to facilitate comparisons of complex protein expression patterns and isolation of differentially expressed proteins spots. Differential in-gel electrophoresis (DIGE) facilitates protein expression by labeling different populations of proteins with fluorescent dyes. Isotope-coded affinity tagging (ICAT) uses mass spectroscopy for protein separation and different isotope tags for distinguishing populations of proteins. Although in the past proteomics has been primarily used for discovery, significant efforts are being made to develop proteomic technologies into clinical tools. Reverse-phase protein arrays offer a robust new method of quantitatively assessing expression levels and the activation status of a panel of proteins. Surface-enhanced laser-desorption/ionization time-of-flight (SELDI-TOF) mass spectroscopy rapidly assesses complex protein mixtures in tissue or serum. Combined with artificial intelligence-based pattern recognition algorithms, this emerging technology can generate highly accurate diagnostic information. It is likely that mass spectroscopy-based serum proteomics will evolve into useful clinical tools for the detection and treatment of human cancers.

Early Diagnosis↗

PubMed2005

The development of the DIGE system: 2D fluorescence difference gel analysis technology.

Two-dimensional (2D) gel electrophoresis is a powerful technique enabling simultaneous visualization of relatively large portions of the proteome. However, the well documented issues of variation and lack of sensitivity and quantitative capabilities of existing labeling reagents, has limited the use of this technique as a quantitative tool. Two-dimensional difference gel electrophoresis (2D DIGE) builds on this technique by adding a highly accurate quantitative dimension. 2D DIGE enables multiple protein extracts to be separated on the same 2D gel. This is made possible by labeling of each extract using spectrally resolvable, size and charge-matched fluorescent dyes known as CyDye DIGE fluors. 2D DIGE involves use of a reference sample, known as an internal standard, which comprises equal amounts of all biological samples in the experiment. Including the internal standard on each gel in the experiment with the individual biological samples means that the abundance of each protein spot on a gel can be measured relative (i.e. as a ratio) to its corresponding spot in the internal standard present on the same gel. Ettan DIGE is the system of technologies that has been optimized to fully benefit from the advantages provided by 2D DIGE.

Electrophoresis, Gel, Two-Dimensional↗

PubMed2006

Ionic (liquid) matrices for matrix-assisted laser desorption/ionization mass spectrometry-applications and perspectives.

A large number of matrix substances have been used for various applications in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). The majority of matrices applied in ultraviolet-MALDI MS are crystalline, low molecular weight compounds. A problem encountered with many of these matrices is the formation of hot spots, which lead to inhomogeneous samples, thus leading to increased measurement times and hampering the application of MALDI MS for quantitative purposes. Recently, ionic (liquid) matrices (ILM or IM) have been introduced as a potential alternative to the classical crystalline matrices. ILM are equimolar mixtures of conventional MALDI matrix compounds such as 2,5-dihydroxybenzoic acid (DHB), alpha-cyano-4-hydroxycinnamic acid (CCA) or sinapinic acid (SA) together with organic bases [e.g., pyridine (Py), tributylamine (TBA) or N,N-dimethylethylenediamine (DMED)]. The present article presents a first overview of this new class of matrices. Characteristic properties of ILM, their influence on mass spectrometric parameters such as sensitivity, resolution and adduct formation and their application in the fields of proteome analysis, the measurement of low molecular weight compounds, the use of MALDI MS for quantitative purposes and in MALDI imaging will be presented. Scopes and limitations for the application of ILM are discussed.

Ionic Liquids↗

PubMed2002

Complexities in ETS-domain transcription factor function and regulation: lessons from the TCF (ternary complex factor) subfamily. The Colworth Medal Lecture.

The ETS-domain transcription factor family can be divided into a series of subfamilies. Elk-1 represents the founding member of the ternary complex factor (TCF) subfamily. By focusing on the TCF subfamily, we can demonstrate the complexities that exist in the function and regulation of ETS-domain transcription factors. This article focuses on Elk-1 in detail and summarizes the functions of other TCFs. The key themes covered include the domain structure of the TCFs, the mechanisms of complex formation with serum response factor, regulation of TCFs by mitogen-activated protein kinase cascades, and transcriptional regulatory properties of the TCFs. Finally, the emerging role of the TCFs in vivo is discussed. A picture is developing indicating that, while these proteins exhibit significant sequence and functional conservation, key differences in their structure and regulation are being identified which may relate to unique functions of these proteins in vivo.

Amino Acid Sequence↗

PubMed2004

Candidate-based proteomics in the search for biomarkers of cardiovascular disease.

The key concept of proteomics (looking at many proteins at once) opens new avenues in the search for clinically useful biomarkers of disease, treatment response and ageing. As the number of proteins that can be detected in plasma or serum (the primary clinical diagnostic samples) increases towards 1000, a paradoxical decline has occurred in the number of new protein markers approved for diagnostic use in clinical laboratories. This review explores the limitations of current proteomics protein discovery platforms, and proposes an alternative approach, applicable to a range of biological/physiological problems, in which quantitative mass spectrometric methods developed for analytical chemistry are employed to measure limited sets of candidate markers in large sets of clinical samples. A set of 177 candidate biomarker proteins with reported associations to cardiovascular disease and stroke are presented as a starting point for such a 'directed proteomics' approach.

Animals↗

PubMed2026

Generation of Fibrin-Based Three-Dimensional Engineered Vascular Tissues from Human Aortic Smooth Muscle Cells for Proteomic Analysis.

Vascular smooth muscle cells (SMCs) reside within the medial layer of blood vessels, where they interact with an extracellular matrix (ECM) composed of collagen, elastin, and proteoglycans to maintain vascular structure and function. Aberrant ECM remodeling contributes to multiple vascular diseases; however, conventional two-dimensional culture systems do not adequately recapitulate the three-dimensional (3D) cellular and matrix environment required to study SMC-ECM interactions and matrix remodeling. This protocol describes the generation of engineered vascular tissues (EVTs) from primary human aortic SMCs cultured within fibrin-based 3D hydrogels. Following casting between flexible polydimethylsiloxane posts, EVTs undergo cellular alignment, contraction, and deposit de novo ECM, providing a physiologically relevant platform for studying vascular matrix biology. The protocol details tissue fabrication, culture, harvesting, and downstream analysis of newly deposited ECM by immunofluorescence staining. In addition, a workflow is presented for qualitative and quantitative characterization of EVT-derived proteins using Western blotting and mass spectrometry-based proteomics. Sequential protein extraction enables assessment of soluble and ECM-enriched protein fractions, facilitating in-depth evaluation of ECM composition. This platform provides a reproducible approach for investigating ECM production and remodeling by human SMCs in a 3D environment.

Humans↗

PubMed2003

Spot volume vs. amount of protein loaded onto a gel: a detailed, statistical comparison of two gel electrophoresis systems.

The long-term goal of this research program is to clarify the molecular mechanisms that participate in the formation of human pituitary macroadenomas. One approach to that goal is to characterize the differentially expressed proteins that are found by a comparison of the proteomes of control pituitary vs. macroadenoma tissues. In order to accurately perform a comparative proteomics study, based on the combination of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and PDQuest 2-D analysis software, a reproducible 2-DE separation system with a wide linear dynamic measure range is needed. A typical horizontal system is the Multiphor II system that analyzes one gel at a time, using a precast gradient gel (180 x 245 x 0.5 mm); a typical vertical system is the Dodeca system that analyzes up to 12 gels at a time on a single-concentration gel (190 x 205 x 1.0 mm). We have evaluated (Zhan and Desiderio, Electrophoresis 2003, 24, 1834-1846) the spatial and quantitative reproducibility of the two second-dimensional gel systems to separate a human pituitary proteome; that study showed a higher reproducibility for the Dodeca gel system. This present study investigated the relationship between the spot volume and the amount of protein loaded onto the gel for those two 2-D systems. The results demonstrated that the Dodeca gel system provides a wider linear dynamic range to measure the changes in the protein abundance in pituitary proteome.

Electronic Data Processing↗

PubMed2001

Proteomics -- the protein expression technology to study connective tissue biology.

During the formation of peribronchial fibrosis in asthma, remodeling of connective tissue is due to an increase in deposition of extracellular matrix components like that of specific types of collagens and proteoglycans. By taking bronchial biopsies, we were able to isolate cell cultures derived from asthmatic patients and healthy volunteers, which provides a good model system to study differences regarding cell morphology and key connective tissue proteins in the remodeling process. Proteomics, utilizing two-dimensional electrophoresis and modern image analysis systems have made it possible to study protein expression and regulation of proteins in biological systems. By using this powerful tool, it is possible to quantitatively study protein regulation and to obtain increased knowledge about the mechanism behind the inflammatory process and formation of peribronchial fibrosis. We have optimized a proteomic protocol enabling detailed investigation of the protein expression pattern in human lung cells. An increased expression pattern was obtained, whereby 20 protein spots could be detected by image analysis in the <45 kDa region. Out of these, specific regulations of four spots were found by quantitative image analysis and spots of interest were identified by MALDI TOF-MS. This protocol enables us to study 1000--2000 proteins simultaneously and the possibility to correlate protein expression to the physiological status of the cell culture investigated. We have found that two proteins, actin and tropomyosin, are increased in expression due to transforming growth factor-beta stimulation. These proteins are correlated to the transformation of normal fibroblasts to myofibroblasts which are involved in the remodeling processes observed in asthma.

Asthma↗

PubMed2003

Shotgun proteomics: integrating technologies to answer biological questions.

Proteomics is providing us with a variety of exciting new strategies to address biological questions. These strategies must integrate a series of seperative and analytical technologies to deal with the immense complexity involved. At some point in the process, the proteins are usually digested with a proteolytic enzyme to generate shorter peptides that are more easily analyzed by mass spectrometry. Shotgun proteomics relies on separation after this digestion step and takes advantage of tandem mass spectrometry to infer the amino acid sequence of individual peptides. Advances in quantitation, and the ability to find sites of post-translational modification are expanding the scope of questions that can be asked. The ultimate success of any proteomic experiment is dictated not only by an appropriate choice of seperative and analytical techniques, but also by making certain that the biological aspects of the experiment are focused and well designed.

Animals↗

PubMed2006

Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise.

A major goal of biology is to provide a quantitative description of cellular behaviour. This task, however, has been hampered by the difficulty in measuring protein abundances and their variation. Here we present a strategy that pairs high-throughput flow cytometry and a library of GFP-tagged yeast strains to monitor rapidly and precisely protein levels at single-cell resolution. Bulk protein abundance measurements of >2,500 proteins in rich and minimal media provide a detailed view of the cellular response to these conditions, and capture many changes not observed by DNA microarray analyses. Our single-cell data argue that noise in protein expression is dominated by the stochastic production/destruction of messenger RNAs. Beyond this global trend, there are dramatic protein-specific differences in noise that are strongly correlated with a protein's mode of transcription and its function. For example, proteins that respond to environmental changes are noisy whereas those involved in protein synthesis are quiet. Thus, these studies reveal a remarkable structure to biological noise and suggest that protein noise levels have been selected to reflect the costs and potential benefits of this variation.

Culture Media↗

PubMedDate not supplied

STEM: a software tool for large-scale proteomic data analyses.

We describe the software, STEM (STrategic Extractor for Mascot's results), which efficiently processes large-scale mass spectrometry-based proteomics data. V (View)-mode evaluates the Mascot peptide identification dataset, removes unreliable candidates and redundant assignments, and integrates the results with key information in the experiment. C (Comparison)-mode compares peptide coverage among multiple datasets and displays proteins commonly/specifically found therein, and processes data for quantitative studies that utilize conventional isotope tags or tags having a smaller mass difference. STEM significantly improves throughput of proteomics study.

Algorithms↗

PubMed2002

Genomes, proteomes, and dynamic networks in the cell nucleus.

Post-genome era experimental strategies seek to understand cellular pathways globally rather than through examination of individual components. Genomics and proteomics provide the experimental tools to establish the framework of gene and protein pathways present in a cell. These methods are complemented by emerging in vivo microscopy approaches, which permit placement of pathways within the architectural context of the cell. Analysis of dynamic live cell microscopy data combined with computational analyses finally allows the quantitative, mechanistic description of protein properties and pathways operating in living cells. Here we discuss how genomics and proteomics are changing the study of the cell nucleus and how in vivo microscopy methods have contributed to our changing conceptual and mechanistic understanding of nuclear architecture and function. Mapping of gene loci and genome regions are beginning to reveal organizational principles of the genome within the cell nucleus, proteomic analysis of subnuclear compartments and the gene expression machinery is providing insights into the molecular nature of nuclear events, and in vivo microscopy is illuminating the dynamic nature of nuclear organization. Initial findings from these efforts make clear that nuclear and cellular behavior can not be described by linear pathways. New tools such as computational modeling are providing evidence that emerging concepts such as network organizations and stochastic interactions are crucially important for cellular function and organization. These insights are changing our view of the nucleus and the cell as a whole.

Animals↗

PubMed2003

Application of proteomics to the study of molecular mechanisms in neurotoxicology.

The proteome is the protein compliment of the genome and is the result of genetic expression, ribosomal synthesis and proteolytic degradation. Proteins participate in most major cell processes and their function is highly regulated by post-translational modifications such as phosphorylation and glycosylation. As a result, neurotoxicant-induced changes in protein levels, function or regulation could have a negative impact on neuronal viability. At the molecular level, direct oxidative or covalent modifications of individual proteins by various chemicals or drugs is likely to lead to perturbation of tertiary structure and a loss of function. The proteome and the functional determinants of its individual protein components are, therefore, likely targets of neurotoxicant action and resulting characteristic disruptions could be critically involved in corresponding mechanisms of neurotoxicity. Clearly, investigating changes in the proteome can provide important clues for deciphering mechanisms of toxicant action and, therefore, proteomics, the study of the proteome, is currently, and will likely remain, a significant experimental approach for mechanistic research in neurotoxicology. The purpose of this review is to discuss proteomics as a tool for neurotoxicological investigations. A variety of classic proteomic techniques (e.g. liquid chromatography (LC)/tandem mass spectroscopy, two-dimensional gel image analysis) as well as more recently developed approaches (e.g. two-hybrid systems, antibody arrays, protein chips, isotope-coded affinity tags, ICAT) are available to determine protein levels, identify components of multiprotein complexes and to detect post-translational changes. Proteomics, therefore, offers a comprehensive overview of cell proteins, and in the case of neurotoxicant exposure, can provide quantitative data regarding changes in corresponding expression levels and/or post-translational modifications that might be associated with neuron injury.

Animals↗

PubMed2006

Dialysis-assisted two-dimensional gel electrophoresis.

2-DE is an important tool in proteomics research. However, intrinsic gel-to-gel variability of 2-DE often masks the biological differences between the samples and compromises quantitative comparison of protein expression levels. Here, we describe a modification of 2-DE that results in improved matching and quantification of proteins. This was accomplished by performing IEF of two samples in two IPG strips separated by a dialysis membrane. After IEF running, the strips were separated and the SDS-PAGE dimension was accomplished on two individual gels. After gel staining with CBB, ImageMaster 2D Platinum software (Amersham) was used for spot detection and quantification. Analysis of protein extracts from C2C12 myoblasts by this method resulted in 99% spot-matching efficiency and CV in stain intensity (% volume) was less than 0.5 for 98% of spots. We conclude that this technique, called dialysis-assisted gel electrophoresis, gives superior spot matching and quantitative reproducibility compared to IEF conducted on separate strips.

Dialysis↗