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PubMed2006

Proteomic analysis of Dictyostelium discoideum.

The social amoeba Dictyostelium discoideum is already known as a model organism for a variety of cellular and molecular studies. Now that the genome sequencing project has been completed and different tools with which to overexpress or knock out genes are available, this species has also moved into the spotlight of functional genomics studies. Consequently, this genomic sequence information can now be exploited to realize D. discoideum proteomics projects. Here, we present validated protocols adapted for analysis of the D. discoideum proteome. The workflow described in this chapter comprises two-dimensional polyacrylamide gel electrophoresis for protein separation and peptide mass fingerprint (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry) for protein identification.

Animals↗
PubMed2001

Fingerprinting Trichoderma reesei hydrolases in a commercial cellulase preparation.

Polysaccharide degrading enzymes from commercial T. reesei broth have been subjected to "fingerprint" analysis by high-resolution 2-D gel electrophoresis. Forty-five spots from 11 x 25 cm Pharmacia gels have been analyzed by LC-MS/MS and the resulting peptide sequences were compared to existing databases. Understanding the roles and relationships of component enzymes from the T. reesei cellulase system acting on complex substrates is key to the development of efficient artificial cellulase systems for the conversion of lignocellulosic biomass to sugars. These studies suggest follow-on work comparing induced and noninduced T. reesei cells at the proteome level, which may elucidate substrate-specific gene regulation and response.

Biotechnology↗
PubMed2006

Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study.

The HUPO Brain Proteome Project is an initiative coordinating proteomics studies to characterise human and mouse brain proteomes. Proteins identified in human brain samples during the project's pilot phase were put into biological context through integration with various annotation sources followed by a bioinformatics analysis. The data set was related to the genome sequence via the genes encoding identified proteins including an assessment of splice variant identification as well as an analysis of tissue specificity of the respective transcripts. Proteins were furthermore categorised according to subcellular localisation, molecular function and biological process, grouped into protein families and mapped to biological pathways they are known to act in. Involvement in pathological conditions was examined based on association with entries in the online version of Mendelian Inheritance in Man and an interaction network was derived from curated protein-proteininteraction data. Overall a non-redundant set of 1804 proteins was identified in human brain samples. In the majority of cases splice variants could be unambiguously identified by unique peptides, including matches to several hypothetical transcripts of known as well as predicted genes.

Alternative Splicing↗
PubMed2006

An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells.

Tandem affinity purification (TAP) is a generic two-step affinity purification protocol that enables the isolation of protein complexes under close-to-physiological conditions for subsequent analysis by mass spectrometry. Although TAP was instrumental in elucidating the yeast cellular machinery, in mammalian cells the method suffers from a low overall yield. We designed several dual-affinity tags optimized for use in mammalian cells and compared the efficiency of each tag to the conventional TAP tag. A tag based on protein G and the streptavidin-binding peptide (GS-TAP) resulted in a tenfold increase in protein-complex yield and improved the specificity of the procedure. This allows purification of protein complexes that were hitherto not amenable to TAP and use of less starting material, leading to higher success rates and enabling systematic interaction proteomics projects. Using the well-characterized Ku70-Ku80 protein complex as an example, we identified both core elements as well as new candidate effectors.

Affinity Labels↗
PubMed2000

A fast and convenient MALDI-MS based proteomic approach: identification of components scaffolded by the actin cytoskeleton of activated human thrombocytes.

A recently developed concentration and purification method (Gevaert, K., Demol, H., Puype, M., Broekaert, D., De Boeck, S., Houthaeve, T., Vandekerckhove, J., 1997. Electrophoresis 18, 2950-2960) for the analysis of diluted peptide samples by matrix-assisted laser desorption ionization-time-of-flight-mass spectrometry (MALDI-TOF-MS) is compared with conventional MALDI sample preparation methods. In the procedure developed, reverse-phase chromatographic beads are added to diluted peptide solutions and act as a peptide-trapping device. Peptides concentrated on the added beads are subsequently harvested, transferred to the MALDI-target disc and efficiently on target desorbed from the beads in a very small volume of an organic-aqueous mixture containing the aromatic MALDI-matrix components. Using this procedure, we show that it is possible to use the totality of in gel protein digests without negative interference of buffers and chaotropes that may be present in the digestion mixture. This method links MALDI-MS peptide analysis more efficiently to 2-D gel electrophoresis in the concept of proteome analysis. The procedure is illustrated by the identification of a class of proteins, which translocate to the actin cytoskeleton of human platelets upon thrombin stimulation.

Actins↗
PubMed2004

Proteomic study for the cellular responses to Cd2+ in Schizosaccharomyces pombe through amino acid-coded mass tagging and liquid chromatography tandem mass spectrometry.

Cadmium (Cd(2+)) is one of well-known toxic heavy metal ions. To gain a global understanding how Cd(2+) affects cells at the molecular level, we systematically studied the cellular response of the fission yeast Schizosaccharomyces pombe to Cd(2+) using our integrated proteomic strategy of amino acid-coded mass tagging (AACT) and liquid chromatography-tandem mass spectrometry. Our proteome-wide investigation unequivocally identified 1133 S. pombe proteins. Of which, the AACT-based quantitative analysis revealed 106 up-regulated and 55 down-regulated proteins on the Cd(2+) exposure. The most prevalent functional class in the up-regulated proteins, approximately 28% of our profile, was the proteins involved in protein biosynthesis, showing a time-dependent biphasic expression pattern characteristic with rapid initial induction and later repression. Most significantly, 27 proteins functionally classified as cell rescue and defense were up-regulated for oxygen and radical detoxification, heat shock response, and other stress response. Furthermore, the large precursor sequence coverage of our AACT approach allowed us to unequivocally identify and quantitate different isozymes for glutathione S-transferase, which have close similarity in their amino acid sequence. Our quantitative dataset also showed that 80% of the up-regulated proteins found in the S. pombe response were different from those in the Saccharomyces cerevisiae response. The function of some of the key identifications was validated through biochemical assays. It is very interesting that the induction of cysteine synthase expression was not observed in our study, although it has been proven as a critical enzyme to supply free cysteines for the enhancing synthesis of Cd(2+)-sequestering molecules such as glutathione and phytochelatins in plants and some yeasts. Our quantitative proteomic result instead suggested that, as an alternative mechanism for the detoxification of Cd(2+), S. pombe produced significantly higher level of inorganic sulfide to immobilize cellular Cd(2+) as a form of CdS nanocrystallites capped with glutathione and/or phytochelatins.

Amino Acid Sequence↗
PubMed2005

Proteomic identification of oxidatively modified retinal proteins in a chronic pressure-induced rat model of glaucoma.

PURPOSE: Based on the evidence of an amplified production of reactive oxygen species (ROS) during glaucomatous neurodegeneration, proteomic analysis was performed to determine oxidative modification of retinal proteins after experimental elevation of intraocular pressure (IOP). METHODS: IOP elevation was induced in rats by hypertonic saline injections into episcleral veins. Protein expression was determined by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of retinal protein lysates obtained from eyes matched for the cumulative IOP exposure and axon loss. To determine protein oxidation levels, protein carbonyls were detected through 2D-oxyblot analysis of 2,4-dinitrophenylhydrazine (DNPH)-treated samples using an anti-DNP antibody. For identification of oxidized proteins, peptide masses were analyzed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/MS) and liquid chromatography-tandem mass spectrometry (LC/MS/MS). In addition to use of different engines in a bioinformatic database search and performance of peptide sequencing and 2D-Western blot analysis for confirmation of the identified proteins, immunohistochemistry was used for further validation of the proteomic findings. RESULTS: Comparison of 2D-oxyblots with Coomassie Blue-stained 2D-gels revealed that approximately 60 protein spots obtained with retinal protein lysates from ocular hypertensive eyes (of >400 spots) exhibited protein carbonyl immunoreactivity, which reflects oxidatively modified proteins. There was a significant increase in anti-carbonyl reactivity in individual protein spots obtained with retinal protein lysates from ocular hypertensive eyes compared with the control (P < 0.01). The identified proteins through peptide mass fingerprinting and peptide sequencing included glyceraldehyde-3-phosphate dehydrogenase, a glycolytic enzyme; HSP72, a stress protein; and glutamine synthetase, an excitotoxicity-related protein. Immunolabeling of retina sections with specific antibodies demonstrated cellular localization of these proteins as well as retinal distribution of the increased protein carbonyl immunoreactivity in ocular hypertensive eyes. CONCLUSIONS: The findings of this in vivo study provide novel evidence for oxidative modification of many retinal proteins in ocular hypertensive eyes and identify three specific targets of retinal protein oxidation in these eyes, thereby supporting the association of oxidative damage with neurodegeneration in glaucoma. By using a proteomic approach, this study also exemplifies that proteomics provide a very promising way to elucidate pathogenic mechanisms in glaucoma at the protein level.

Animals↗
PubMed2006

[Application of proteomics in the research of discrepancy proteins in gastric cancer].

OBJECTIVE: To explore the discrepancy proteins in gastric cancer by proteome analysis. METHODS: Total proteins of gastric cancer tissues and matched normal gastric epithelial tissues were separated respectively by two-dimensional polyacrylamide gel electrophoresis (2-DE). Mass spectrometry was used to test the differentially expressed proteins. RESULTS: One thousand one hundred and forty-seven protein spots from gastric cancer tissue and 1079 spots from the normal tissue were gained. Out of 164 different protein spots, 41 were only expressed in gastric cancer tissue, 27 were unique in normal tissue, 39 were up-regulated and 57 were down-regulated in gastric cancer. Seven proteins, which were highly expressed in gastric cancer tissue, were identified. CONCLUSION: Different protein spots between gastric cancer tissues and normal gastric epithelial tissue were gained by proteomics. The 7 discrepancy proteins were further identified. It establishes the foundation of finding specific gastric cancer proteins, which act as biomarkers for the diagnosis and prognosis of gastric cancer.

Case-Control Studies↗
PubMed2000

Proteomic analysis of the atrophying rat soleus muscle following denervation.

A proteomic analysis was performed comparing normal rat soleus muscle to denervated soleus muscle at 0.5, 1, 2, 4, 6, 8 and 10 days post denervation. Muscle mass measurements demonstrated that the times of major mass changes occurred between 2 and 4 days post denervation. Proteomic analysis of the denervated soleus muscle during the atrophy process demonstrated statistically significant (at the p < 0.01 level) changes in 73 soleus proteins, including coordinated changes in select groups of proteins. Sequence analysis of ten differentially regulated proteins identified metabolic proteins, chaperone and contractile apparatus proteins. Together these data indicate that coordinated temporally regulated changes in the proteome occur during denervation-induced soleus muscle atrophy, including changes in muscle metabolism and contractile apparatus proteins.

Animals↗
PubMed2004

Proteomics of Medicago sativa cell walls.

A method for the sequential extraction and profiling by two-dimensional gel electrophoresis (2-DE) of Medicago sativa (alfalfa) stem cell wall proteins is described. Protein extraction included freezing, grinding in a sodium acetate buffer, separation by filtration of cell walls from cytosolic contents, and extensive washing. Cell wall proteins were then extracted sequentially with a solution containing 200 mM CaCl2 and 50 mM sodium acetate, followed by extraction with 3.0 M LiCl and 50 mM sodium acetate. Cell wall proteins from both the CaCl2 and LiCl fractions were profiled by 2-DE. Approximately 150 protein spots were extracted from these two gels, digested with trypsin, and analyzed using nanoscale HPLC coupled to a hybrid quadrupole time-of-flight (Q-tof) tandem mass spectrometer (LC/MS/MS). More than 100 proteins were identified and used in conjunction with the 2-DE profiles to generate proteomic reference maps for cell walls of this important legume. Identified proteins include classical cell wall proteins as well as proteins traditionally considered as non-secreted. Two unique extracellular proteins were also identified.

Cell Wall↗
PubMed2003

Analyzing antibody specificity with whole proteome microarrays.

Although approximately 10,000 antibodies are available from commercial sources, antibody reagents are still unavailable for most proteins. Furthermore, new applications such as antibody arrays and monoclonal antibody therapeutics have increased the demand for more specific antibodies to reduce cross-reactivity and side effects. An array containing every protein for the relevant organism represents the ideal format for an assay to test antibody specificity, because it allows the simultaneous screening of thousands of proteins for possible cross-reactivity. As an initial test of this approach, we screened 11 polyclonal and monoclonal antibodies to approximately 5,000 different yeast proteins deposited on a glass slide and found that, in addition to recognizing their cognate proteins, the antibodies cross-reacted with other yeast proteins to varying degrees. Some of the interactions of the antibodies with noncognate proteins could be deduced by alignment of the primary amino acid sequences of the antigens and cross-reactive proteins; however, these interactions could not be predicted a priori. Our findings show that proteome array technology has potential to improve antibody design and selection for applications in both medicine and research.

Antibodies↗
PubMed2005

A dataset of human cornea proteins identified by Peptide mass fingerprinting and tandem mass spectrometry.

Diseases of the cornea are extremely common and cause severe visual impairment worldwide. To explore the basic molecular mechanisms involved in corneal health and disease, the present study characterizes the proteome of the normal human cornea. All proteins were extracted from the central 7-mm region of 12 normal human donor corneas containing all layers: epithelium, Bowman's layer, stroma, Descemet's membrane, and endothelium. Proteins were fractionated and identified using two different procedures: (i) two-dimensional gel electrophoresis and protein identification by MALDI-MS and (ii) strong cation exchange or one-dimensional SDS gel electrophoresis followed by LC-MS/MS. All together, 141 distinct proteins were identified of which 99 had not previously been identified in any mammalian corneas by direct protein identification methods. The characterized proteins are involved in many processes including antiangiogenesis, antimicrobial defense, protection from and transport of heme and iron, tissue protection against UV radiation and oxidative stress, cell metabolism, and maintenance of intracellular and extracellular structures and stability. This proteome study of the healthy human cornea provides a basis for further analysis of corneal diseases and the design of bioengineered corneas.

Chemical Fractionation↗
PubMed2005

[Differential proteomic analysis of human colorectal carcinoma cell lines SW620 and SW480 with different metastatic potentials].

OBJECTIVE: To investigate differential protein expression profiles of human colorectal carcinoma cell lines with different metastatic potentials and screen metastasis-associated proteins for analyzing the relationship between metastasis-associated proteins and the tumorigenesis, progression and metastasis of colorectal carcinomas. METHODS: With two-dimensional electrophoresis (2-DE) and matrix assisted laser desorption/ionization-time of flight-mass spectrometry, we analyzed the differentially expressed proteins in two human colorectal carcinoma cell lines SW620 and SW480 with high and low metastatic potentials, and screened for proteins associated with colorectal carcinoma metastasis. RESULTS: Image analysis software Malenie III demonstrated good match and reproducibility of the 2-DE maps obtained from 3 independent experiments, with 1316+/-62 spots detected for SW620 cells and 1332+/-74 spots for SW480 cells with the average matching rate of 82% and 80%, respectively. The spots distributed in the greatest density at the isoelectric points of 4-7 and relative molecular mass weight of 20,000-70,000. Twenty-five distinctly different protein spots (14 spots for SW620 and 11 for SW480) in-gel digested by TPCK trypsin and 23 peptide mass fingerprint maps were obtained by mass spectrometry. Three highly matched proteins and 14 preliminarily matched proteins or fragments were obtained by analysis with Mascot software in the NCBInr database. Some of these differentially expressed proteins were related to gene transcription, cell cycle, signal transduction, cell apoptosis, etc, with possible involvement of cell differentiation, proliferation, invasion, adhesion, and metastasis of colorectal carcinoma. CONCLUSION: The 2-DE protein expression profile of SW620 cells with high metastatic potential displays obvious difference from that of SW480 cells with low metastatic potential, and a variety of proteins can be involved in the metastasis of colorectal carcinoma.

Cell Line, Tumor↗
PubMed2005

[Expression of IgVH and B7-1 in proteome of the human colorectal carcinoma cell lines].

OBJECTIVE: To conduct a proteomic analysis of human colorectal carcinoma cell lines LS174T and SW480 by two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS). METHODS: The total proteins of human colorectal carcinoma cell lines LS174T and SW480 were separated with 2-DE using immobilized pH gradient strips and analyzed by MALDI-TOF-MS to obtain peptide mass fingerprints (PMFs). Proteins were identified by using Mascot software to search protein databases. RESULTS: Good resolution 2-DE maps were obtained. Some proteins including immunoglobulin heavy chain variable region (IgVH) and co-stimulatory molecule B7-1 were identified. IgVH and B7-1 were confirmed by electrospray ionization tandem spectrometry (ESI-MS/MS) and immunocytochemistry. CONCLUSION: There are IgVH and B7-1 expressions in human colorectal carcinoma cell lines LS174T and SW480. Results obtained will help to elucidate the mechanisms of tumor immune escape.

B7-1 Antigen↗
PubMed2004

Proteomic evaluation of core biopsy specimens from breast lesions.

Analysis of tumour samples by a proteomic technology, which combines two-dimensional gel electrophoresis and mass spectrometry analysis, is a promising approach for molecular characterization of cancer. Proteomic analysis of neoplasms is usually performed on surgical material. The possibility to perform proteomic analysis on pre-operative samples might be useful for diagnostic purposes or for determination of tumour sensitivity to therapy. In this study, we report how tissues from core biopsy of breast lesions can be routinely used to obtain accurate protein expression profiles by proteomic analysis. Protein profiles from fibroadenomas were compared to those from ductal infiltrating carcinomas. By using mass spectrometry, identification of proteins overexpressed in carcinomas with respect to fibroadenomas was obtained. Thus, our study provides a methodology to perform proteomic analysis on pre-operative samples of breast lesions.

Biomarkers, Tumor↗
PubMed2006

Proteomic analysis of membrane microdomains derived from both failing and non-failing human hearts.

Eukaryotic cells plasma membranes are organized into microdomains of specialized function such as lipid rafts and caveolae, with a specific lipid composition highly enriched in cholesterol and glycosphingolipids. In addition to their role in regulating signal transduction, multiple functions have been proposed, such as anchorage of receptors, trafficking of cholesterol, and regulation of permeability. However, an extensive understanding of their protein composition in human heart, both in failing and non-failing conditions, is not yet available. Membrane microdomains were isolated from left ventricular tissue of both failing (n = 15) and non-failing (n = 15) human hearts. Protein composition and differential protein expression was explored by comparing series of 2-D maps and subsequent identification by LC-MS/MS analysis. Data indicated that heart membrane microdomains are enriched in chaperones, cytoskeletal-associated proteins, enzymes and protein involved in signal transduction pathway. In addition, differential protein expression profile revealed that 30 proteins were specifically up- or down-regulated in human heart failure membrane microdomains. This study resulted in the identification of human heart membrane microdomain protein composition, which was not previously available. Moreover, it allowed the identification of multiple proteins whose expression is altered in heart failure, thus opening new perspectives to determine which role they may play in this disease.

Adult↗
PubMed2004

Proteomic surveillance of autoimmunity in osteoarthritis: identification of triosephosphate isomerase as an autoantigen in patients with osteoarthritis.

OBJECTIVE: Autoimmunity to proteins, such as type II collagen and cartilage intermediate layer protein, that are produced by chondrocytes has been reported in patients with osteoarthritis (OA) as well as in patients with rheumatoid arthritis (RA). However, it remains to be determined whether the overall specificities of the autoimmunity differ between OA and RA patients. This study sought to clarify the differences by applying proteomic surveillance for the detection of autoantigens comprehensively. METHODS: Serum samples were obtained from 20 patients with OA, 20 patients with RA, and 20 healthy volunteers. Human chondrocyte proteins were separated from the sera by 2-dimensional electrophoresis, and antigenic protein spots were detected by Western blotting. The antigenic proteins were then identified by mass fingerprinting. The antigenicity of the identified proteins was confirmed and the prevalence of the autoantibodies in the OA, RA, and other disease groups was determined with the use of recombinant proteins. In addition, autoepitopes were mapped on the antigens. RESULTS: Nineteen protein spots were recognized only by the OA sera, but not by the RA sera. One of these proteins was identified as triosephosphate isomerase (TPI). IgG-type anti-TPI autoantibodies were detected in 24.7% of the serum samples and 24.1% of the synovial fluid samples from the patients with OA, whereas <6% of the RA and systemic lupus erythematosus samples were positive for anti-TPI. In addition, multiple autoepitopes were identified on TPI. CONCLUSION: The overall profile of autoimmunity in OA differs from that in RA, which may reflect the OA-specific pathologic role of autoimmunity. The autoantibody to TPI, detected predominantly in the OA samples and produced by the antigen-driven mechanism, has the potential to be used as a diagnostic marker for OA.

Adult↗