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PubMed2006

Application of two-dimensional gel electrophoresis to interrogate alterations in the proteome of gentically modified crops. 3. Assessing unintended effects.

The current procedures to assess the safety of food and feed derived from modern biotechnology include the investigation of possible unintended effects. To improve the probability of detecting unintended effects, profiling techniques such as proteomics are currently tested as complementary analytical tools to the existing safety assessment. An optimized two-dimensional gel electrophoresis (2DE) method was used as a proteomics approach to investigate insertional and pleiotropic effects on the proteome due to genetic engineering. Twelve transgenic Arabidopsis thaliana lines were analyzed by 2DE, and their seed proteomes were compared to that of their parental line as well as to 12 Arabidopsis ecotype lines. The genetic modification of the Arabidopsis lines, using three different genes and three different promoters, did not cause unintended changes to the analyzed seed proteome. Differences in spot quantity between transgenic and nontransgenic lines fell in the range of values found in the 12 Arabidopsis ecotype lines or were related to the introduced gene.

Arabidopsis↗
PubMed2000

Proteome analysis of mouse brain: two-dimensional electrophoresis profiles of tissue proteins during the course of aging.

Mouse brain proteins were isolated from five regions (cerebellum, cerebral cortex, hippocampus, striatum, and cervical spinal cord) at five ages from the 10th week to the 24th month, and separated by two-dimensional gel electrophoresis (2-DE). 2-DE was carried out with an immobilized pH gradient bar in the first dimension, and by sodium dodecyl sulfate-polyacrylamide gel electrophoresis in the second dimension. Over one thousand protein spots were visualized by silver staining and quantified by image processing. In the analyses, 58 protein spots were distinguishable among the above five brain regions, and 17 proteins were shown to be varied in quantity in the course of aging. Partial amino-terminal sequences and/or internal sequences for a total of 301 protein spots were analyzed. One hundred and eighty proteins appeared to have blocked N-termini and 122 proteins were identified. Twenty-seven new proteins were identified by sequence homology search. A mouse brain proteome database was constructed, which consists of the 2-DE map images and the respective spot data files with 15 related references.

Acrylic Resins↗
PubMed2005

A novel four-dimensional strategy combining protein and peptide separation methods enables detection of low-abundance proteins in human plasma and serum proteomes.

A novel strategy, termed protein array pixelation, is described for comprehensive profiling of human plasma and serum proteomes. This strategy consists of three sequential high-resolution protein prefractionation methods (major protein depletion, solution isoelectrofocusing, and 1-DE) followed by nanocapillary RP tryptic peptide separation prior to MS/MS analysis. The analysis generates a 2-D protein array where each pixel in the array contains a group of proteins with known pI and molecular weight range. Analysis of the HUPO samples using this strategy resulted in 575 and 2890 protein identifications from plasma and serum, respectively, based on HUPO-approved criteria for high-confidence protein assignments. Most importantly, a substantial number of low-abundance proteins (low ng/mL - pg/mL range) were identified. Although larger volumes were used in initial prefractionation steps, the protein identifications were derived from fractions equivalent to approximately 0.6 microL (45 microg) of plasma and 2.4 microL (204 microg) of serum. The time required for analyzing the entire protein array for each sample is comparable to some published shotgun analyses of plasma and serum proteomes. Therefore, protein array pixelation is a highly sensitive method capable of detecting proteins differing in abundance by up to nine orders of magnitude. With further refinement, this method has the potential for even higher capacity and higher throughput.

Biomarkers↗
PubMed2004

Large scale gene expression profiling of metabolic shift of mammalian cells in culture.

The metabolic state of hybridoma cells in continuous culture varies with the cultivation condition from which the culture is initiated. At a metabolically shifted state, cells have markedly reduced glucose and other nutrient consumption and lactate production as compared to cells in batch culture or in continuous culture without a metabolic shift. Taking a combined genomics and proteomics approach, we investigated the molecular mechanism of metabolic shift. Cells from continuous cultures at two different steady states with a glucose consumption to lactate production molar ratio (DeltaL/DeltaG) of 0.08 and 1.4 were studied. Affymetrix GeneChips as well as cDNA microarrays were employed to identify differentially expressed mRNA transcripts, and the differentially expressed proteins were identified using the 2D gel electrophoresis-mass spectrometry approach. The decrease in glucose metabolism upon metabolic shift is accompanied by a decrease in gene expression of a number of genes involved in its metabolism. However, the number of genes differentially expressed and the extent of differential expression upon metabolic shift are relatively moderate. The change in the expression of metabolic genes at the transcriptional level was confirmed by real time PCR. The results suggest that metabolic shift is a combined effect of both biochemical events at reaction level and gene expression at transcription and translation level. This approach of integrating transcriptional profiling, proteomic techniques and biochemical analysis provides a more global view of the metabolism of mammalian cells in culture.

Animals↗
PubMed2005

Identification of biomarkers for breast cancer in nipple aspiration and ductal lavage fluid.

PURPOSE: To establish a comprehensive proteomic approach for biomarker discovery and validation in breast fluid. EXPERIMENTAL DESIGN: A total of 95 specimens from three institutions were used including 10 nipple aspiration fluid (5 stage I/II cancerous breasts and 5 age-matched healthy controls), 42 ductal lavage fluid from 14 patients with unilateral stage I/II cancer (25 from 9 cancerous breasts and 17 from 7 contralateral breasts), and 42 ductal lavage fluid from 14 high-risk women (multiple ducts repeated lavage). Differentially expressed protein/peptides were discovered by proteomic analysis of training sample, using ProteinChip arrays and surface-enhanced laser desorption ionization (SELDI) time-of-flight mass spectrometry, and validated on independently collected testing samples. After protein identification, ELISA was done to confirm the SELDI findings. RESULTS: We were able to obtain reproducible protein profiles using minimal amount of protein (1 mug) by applying an optimized chip protocol and SELDI. We were able to select cancer-associated biomarkers despite large individual variability by applying both unsupervised and supervised cluster analysis. Furthermore, we were able to train and test candidate biomarkers on independently collected samples and identified one component of a multimarker panel as human neutrophil peptides 1 to 3. CONCLUSIONS: Breast fluid is a rich source of breast cancer biomarkers. In combination with high-throughput novel proteomic profiling technology and multicenter study design, markers that are highly specific to breast cancer can be discovered and validated. Our observations also suggest that persistent elevation of human neutrophil peptide in high-risk women may imply early onset of cancer not yet detectable by current detection method. Proof of this hypothesis requires follow-up on a larger study population.

Adenocarcinoma↗
PubMed2006

Quorum sensing affects virulence-associated proteins F1, LcrV, KatY and pH6 etc. of Yersinia pestis as revealed by protein microarray-based antibody profiling.

Protein microarray that consists of virulence-associated proteins of Yersinia pestis is used to compare antibody profiles elicited by the wild-type and quorum sensing (QS) mutant strain of this bacterium to define the immunogens that are impacted by QS. The results will lead the way for future functional proteomics studies. The antibody profile that was induced by the QS mutant differed from that of the parent strain. Detailed comparison of the antibody profiles, according to the proteins' functional annotations, showed that QS affects the expression of many virulence-associated proteins of Y. pestis. The antibodies to many virulence-associated proteins were not detected or lower titers of antibodies to many proteins were detected in the sera of rabbits immunized with the QS mutant, relative to those of the wild type, which indicated that these proteins were not expressed or expressed at relatively lower levels in the QS mutant. The results demonstrated that antibody profiling by protein microarrays is a promising high-throughput method for revealing the interactions between pathogens and the host immune system.

Animals↗
PubMed2004

Proteomics.

The growing discipline of proteomics is highly relevant in our quest to understand cause/effect relationships between environmental, Physiological, and pathological influences on bodily organ function. We present an overview of the principles and methods in profiling, functional, and structural proteomics and their applications to oncology and others related areas.

Drug Industry↗
PubMed2002

Proteomic analysis and identification of new biomarkers and therapeutic targets for invasive ovarian cancer.

Epithelial ovarian cancer kills almost 16 000 women each year in part due to late stage of presentation and lack of reliable biomarkers for disease detection. CA-125, the currently accepted serum marker, alone lacks the sensitivity for early stage diagnosis, as only 50% of early stage cases are detected with this marker. Although more early stage cases may be detected by lysophosphatidic acid, this marker is also elevated in other cancers. One major objective of the NCI-FDA Tissue Proteomics Initiative has been to combine the technique of laser capture microdissection (LCM) of epithelial tumor cells in human tissue specimens with two-dimensional gel electrophoresis (2-D PAGE) to identify proteins that may serve as invasive ovarian cancer-specific biomarkers for early detection and/or new therapeutic targets. We performed 2-D PAGE on lysates from five microdissected ovarian tumors (three invasive ovarian cancers and two noninvasive, low malignant potential (LMP) ovarian tumors). We then compared silver stained 2-D gels created from microdissected lysates with SYPRO-Ruby stained 2-D PAGE profiles of the patient-matched undissected bulk tumor lysates from all five patients. Twenty-three proteins were consistently differentially expressed between both the LMP and three invasive ovarian tumors in the limited study set. Thirteen were uniquely present in all three of the invasive ovarian cancer cases and absent or underexpressed in the two LMP cases. Ten were uniquely present in the LMP cases but absent or underexpressed in all invasive ovarian cancer cases. Credentialing and preliminary target validation of the mass spectrometry identified proteins cut from the Ruby-red stained gels was performed by LCM coupled Western blot and reverse-phase array technology in a study set of six cases (the aforementioned five cases used in the 2-D PAGE profiling component of the study plus one additional LMP case). The analysis revealed that the 52 kDa FK506 binding protein, Rho G-protein dissociation inhibitor (RhoGDI), and glyoxalase I are found to be uniquely overexpressed in invasive human ovarian cancer when compared to the LMP form of this cancer. The direct comparison of LCM generated proteomic profiles of invasive vs. LMP ovarian cancer may more directly generate important markers for early detection and/or therapeutic targets unique to the invasive phenotype.

Biomarkers, Tumor↗
PubMed2026

An Integrative Proteomic Approach to Reveal Altered Signaling Modules During Alzheimer's Disease Progression in PS19 Tauopathy Mice.

Alzheimer's disease (AD) is a slowly progressive neurodegenerative disease that is characterized by cognitive, functional, and behavioral impairments. These changes occur owing to the progressive accumulation of extracellular amyloid-beta plaques and intracellular neurofibrillary tangles of hyperphosphorylated tau protein. AD is associated with the dysfunction of several essential neurotransmitter systems, such as dopamine, and impaired neurotransmission. Despite the association of neurotransmitter changes within the brain and AD pathology, in-depth profiling studies on neurotransmitters and their related proteomic changes are limited. This study was conducted to profile and integrate the proteomes and neurotransmitters in seven brain regions of PS19 (Tau P301S) mice according to AD progression between 4 and 7 months. Proteomic analysis revealed significantly altered canonical pathways in various brain regions, including metabolic abnormalities. In the neurotransmitter profile, we found significant alterations in the levels of six neurotransmitters-dopamine, serotonin, homovanillic acid, norepinephrine, 3-methoxytyramine, and 3,4-dihydroxyphenylacetic acid-during AD progression. Using an integrative approach between proteome and neurotransmitter profiles, we found that AD progression-dependent dopamine- and serotonin-related signaling modules are closely related to neurotransmitter changes, especially in the hippocampus and cerebellum. This integrative approach could provide new signaling modules to help understand AD progression and thereby enable improved treatment and clinical outcomes.

Animals↗
PubMed2025

Analytical Considerations for the Development of Plate-Based Proteomics Platforms Using Isobaric Labeling.

Mass spectrometer-based proteomics platforms have great potential to rapidly advance our systematic understanding of complex biological problems, enable drug discovery, decipher drug mechanisms of action, and discover novel biomarkers. As the demand for processing large sets of samples in an automatic manner is constantly increasing, the integration of automation platforms (nanoliter dispensers, liquid handlers, etc.) has become a routinary configuration paired with liquid chromatography-mass spectrometers. The functional integration of all of those instruments into a single unit is what we call a plate-based high-throughput proteomics platform (HT proteomics). The readout of the platform is the quantitative proteome data at the protein or peptide level. In this work, we developed a plate-based HT proteomics standard that we called the HT-sKO. The HT-sKO allows the evaluation of accuracy and the estimation of the relative limit of quantification when the target proteins vary up to 60-fold in abundance. The HT-sKO utilizes nonhuman recombinant proteins that can be spiked into the samples, allowing for sample acquisition and HT proteomics platform evaluation at the same time. We also showed the foundational role of a robust acquisition strategy for developing a stable HT proteomics platform and the value of using a tube-based method as an informant assay on data quality expectations for the platform. Using this new standard, we demonstrated that the intra- and inter-plate variance is around 4-6% for the protein level or around 10% for the peptide-level readout. We also showed that the HT-sKO standard is compatible with whole-proteome, phospho-proteome, and reactive cysteine profiling platforms.

Proteomics↗
PubMed2006

Simple urinary sample preparation for proteomic analysis.

Since the completion of the human genome sequence, attention has now focused on establishing reference maps of body fluids such as plasma and urine for detecting diagnostic markers of disease. Although some progress has been made, challenges still remain in the development of an optimal sample preparation method for proteomic analysis of urine. We have developed a simple and efficient urine preparation method for two-dimensional (2-D) gel electrophoresis which involves precipitation of proteins with simultaneous desalting. Acetonitrile precipitation produced 2-D gel separations with the highest resolution and the greatest number of protein spots compared to precipitation by other organic solvents. The method was applied to observe changes in the urinary proteome over a 6 week period and to establish a reference map of a healthy subject. A total of 339 proteins from 159 genes was identified from healthy male urine by peptide mass fingerprinting. The profiles of the urinary proteome at three times in 1 day and on four different days were compared and were found to vary in number and spatial location of the proteins on the map. The method was also shown to be applicable to the higher concentrations of protein found in the urine of an ovarian cancer subject. We have developed a facile and robust method for preparing urine for 2-D gels that will encourage further use of urine.

Adult↗
PubMed2026

An overview of the use of proteomics and peptidomics to characterize alternative protein foods.

The global protein transition is accelerating the development of alternative protein foods, mainly derived from plants, insects, algae, fungi, and cellular agriculture. Ensuring the authenticity, safety, and nutritional adequacy of these emerging protein matrices requires molecular-level characterization beyond traditional compositional analyses. Proteomics and peptidomics have emerged as transformative analytical platforms capable of decoding the molecular signatures that define protein origin, structural integrity, digestibility, functionality, and health potential. The review comprehensively examines the application of proteomics, and peptidomics for profiling alternative protein foods. Further, the source authentication strategies based on species-specific protein and peptide biomarkers, detection of adulteration in complex matrices, and allergenicity assessment is discussed. Special attention is also given to nutritional proteomics with protein digestibility, gastrointestinal peptide release, and identification of bioactive sequences. SIGNIFICANCE: The importance of this review is that proteomics and peptidomics are becoming central in the management of the fast-growing environment of alternative protein foods, such as plant-based, insect, algal, fungal, and cultured meat products. It provides an explanation of the application of mass spectrometry-based processes to decode molecular signatures defining the origin of proteins, their structural integrity, digestibility, allergenicity, and bioactive properties, and thus directly contribute to safety, nutritional analysis, and authenticity of the product. Presentation of the article includes the integration of the knowledge of traditional muscle foods with alternative systems of proteins, where validated protein and peptide biomarkers are used in authentication, fraud detection, and allergy risk assessment in a wide variety of matrices. It also indicates the role of nutritional proteomics and peptidomics in informing the formulation strategy to promote digestibility and release of health-promoting peptides. In general, this review will guide scientists, the food industry, and regulatory bodies to use modern proteomic technologies in quality assurance, and decision-making, for the advancementof sustainable protein-based foods.

Proteomics↗
PubMed2004

Protein profiling of the medicinal leech salivary gland secretion by proteomic analytical methods.

Protein diversity of the high molecular weight fraction (molecular mass > 500 daltons) of salivary grand secretion of the medicinal leech Hirudo medicinalis has been demonstrated using methods of proteomic analysis. One-dimensional (1D) electrophoresis revealed the presence of more than 60 bands corresponding to molecular masses ranging from 11 to 483 kD. 2D-electrophoresis revealed more than 100 specific protein spots differing in molecular masses and pI values. SELDI-mass spectrometry analysis using the ProteinChip. System based on chromatography surfaces of strong anion or weak cation exchanger detected 45 individual compounds of molecular masses ranged from 1.964 to 66.5 kD. Comparison of SELDI-MS data with protein databases revealed eight known proteins from the medicinal leech. Other masses detected by proteomic analytical methods may be related to both modifications of known proteins and unknown biologically active components of leech saliva secretion.

Animals↗
PubMed2006

Molecular analysis of maturation processes by protein and phosphoprotein profiling during in vitro maturation of bovine oocytes: a proteomic approach.

Cellular maturation and differentiation processes are accompanied by the expression of specific proteins. Especially in oocytes, there is no reliable strict linear correlation between mRNA levels and the abundance of proteins. Furthermore, the activity of proteins is modulated by specific kinases and phosphatases which control cellular processes like cellular growth, differentiation, cell cycle and meiosis. During the meiotic maturation of oocytes, the activation of protein kinases, namely of the MPF and MAPK play a predominant role. Therefore, the present study was performed to analyze meiotic maturation at a molecular level, concerning alterations of the proteom and phosphoproteom during IVM. Using a proteomic approach by combining two-dimensional gel electrophoresis followed by selective protein and phosphoprotein staining and mass spectrometry, we identified proteins which were differentially expressed and/or phosphorylated during IVM. Furthermore, we used the MPF inhibitor butyrolactone I, to reveal new molecular effects which are potentially essential for successful maturation. The results show that approximately 550 protein spots could be visualized by the fluorescent dye Sypro ruby at any maturation stage (GV, M I, M II) investigated. From GV stage to M II, ProQ diamond staining indicate in GV 30%, in M I 50%, and in M II 45% of the spots were phosphorylated. The Identity of 40 spots could be established. These proteins belong to different families, for example, cytoskeleton, molecular chaperons, redox, energy and metabolism related proteins, nucleic acid binding proteins, cell cycle regulators, and protein kinases. Four of them were differentially expressed (alteration higher than factor 2) during IVM, namely tubulin beta-chain, cyclin E(2), protein disulfide isomerase and one of two different forms of peroxiredoxin 2. Seven proteins were differentially stained by ProQ diamond, indicating a differential phosphorylation. These are tubulin beta-chain, beta-actin, cyclin E(2), aldose reductase and UMP-synthase, protein disulfide isomerase 2, and peroxiredoxin 2. Furthermore, the results indicate that the phosphorylation of at least peroxiredoxin 2 respond to BL I treatment. This indicates that its phosphorylation is under the control of MPF or MAPK. In summary these results indicates that the reduction of cyclin Eexpression and the (partially) inactivation of peroxiredoxin 2 by phosphorylation, hence alterations in the peroxide levels which can mediate signal transduction are essential components for successful maturation.

4-Butyrolactone↗
PubMed2006

Impact of the accessory gene regulatory system (Agr) on extracellular proteins, codY expression and amino acid metabolism in Staphylococcus epidermidis.

The quorum-sensing system Agr is part of a complex regulatory network of gene expression in staphylococci. This study presents the effect of an agr mutation on a biofilm-forming Staphylococcus epidermidis isolate by employing proteome and transcriptome analysis. The agr mutant exhibited a significantly lowered amount of extracellular proteins: amongst others SspA, AtlE, GehD and the phenol soluble modulins PSM1/2. Cytoplasmic proteome analysis and expression profiling indicated that the agr inactivation led to a strongly altered regulation of metabolism and virulence. Most strikingly, expression of CodY, a global regulator of virulence and stationary phase gene expression, was decreased in the agr mutant. In this respect, homologous genes known to be controlled by CodY in Bacillus subtilis and Lactococcus lactis were found to be up-regulated in the S. epidermidis agr mutant. The combined data show that wild-type and agr mutant differ with respect to amino acid biosynthesis and oligopeptide transport, carbohydrate utilization, as well as GMP and IMP interconversion. Due to the varying physiological properties S. epidermidis agr mutants, which often occur spontaneously, might be capable of colonizing alternative ecological niches in the human host and could, therefore, have an advantage in adapting to changing environmental conditions.

Amino Acids↗
PubMed2005

Laser capture microdissection and colorectal cancer proteomics.

The ability to define protein profiles of normal and diseased cells is important in understanding cell function. Laser capture microdissection permits the isolation of specific cell types for subsequent molecular analysis. In this study we have established conditions for obtaining proteomic information from laser capture microdissected colorectal cancer cells. Laser capture microdissection was performed on toluidine blue-stained frozen sections of colorectal cancer. Proteins were solubilized from microdissected cells and the solubilized proteins were separated by two-dimensional gel electrophoresis: protein spots were characterized by peptide mass mapping using matrix assisted laser desorption ionization-time of flight mass spectrometry. Proteins isolated from laser capture microdissected tissue retained their expected electrophoretic mobility and peptide mass mapping was also unaffected. The ability to study the protein expression profile of specific cell types will allow for the identification of novel disease markers and therapeutic targets and also provide for the enhanced understanding of pathogenetic mechanisms.

Animals↗
PubMed2004

Proteome analysis of red deer antlers.

Deer antlers are the only mammalian organs capable of repeated regeneration. Although antlers are known to develop from pedicles, which arise from antlerogenic cells of cranial periosteum, their developmental process is not fully elucidated. For example, while endocrine and environmental factors influence the antler development, it is still unclear which signaling pathways are involved in the transduction of such stimuli. To study the developmental process of antlers and identify proteins functioning in their growth, we have established proteome maps of red deer (Cervus elaphus) antlers. With two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization mass spectrometry, we analyzed more than 800 protein spots and identified approximately 130 individual proteins derived from the growing tip of antlers. The overall profile of the antler proteome was dissimilar to those of other types of tissue. Also comparison of proteomes derived from proximal bony tissue and the growing tip of antlers revealed substantial differences. Moreover several cell growth or signaling-related proteins are expressed exclusively in the growing tip, suggesting that these proteins function in the growth and differentiation of antlers. Currently, using the antler proteome maps, we are actively searching for the regulatory factor(s) that may control the antler development.

Animals↗
PubMed2006

Higher dimensional (Hi-D) separation strategies dramatically improve the potential for cancer biomarker detection in serum and plasma.

The plasma proteome has a wide dynamic range of protein concentrations and is dominated by a few highly abundant proteins. Discovery of novel cancer biomarkers using proteomics is particularly challenging because specific biomarkers are expected to be low abundance proteins with normal blood concentrations of low nanograms per milliliter or less. Conventional, one- and two-dimensional proteomic methods including 2D PAGE, 2D DIGE, LC-MS/MS, and LC/LC-MS/MS do not have the capacity to consistently detect many proteins in this range. In contrast, new higher dimensional (Hi-D) separation strategies, utilizing more than two dimensions of fractionation, can profile the low abundance proteome.

Animals↗