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Results for “proteomic profiling”

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At least 1,333 records · Page 74Linked to original sources
PubMed2003

Mesenchymal chondrosarcoma: molecular characterization by a proteomic approach, with morphogenic and therapeutic implications.

This study characterizes 3 cases of mesenchymal chondrosarcoma (MC) utilizing a proteomic approach that allows for the detection, visual quantification, cellular compartmentalization, and assessment of the functional state of certain proteins that may promote tumor growth and/or oppose apoptosis. Immunohistochemical procedures were performed to detect the following protein antigens: CD99, interleukin (IL)-1alpha, IL-6, transforming growth factor (TGF)-alpha, conventional (c) protein kinase C (cPKC)-alpha, cPKC-betaII, phosphorylated (p)-PKC-alpha/betaII, c-kit (CD117), platelet-derived growth factor receptor (PDGFR)-alpha, PDGFR-beta, epidermal growth factor receptor (EGFR), human epidermal growth factor receptor (HER)-2/neu, cathepsin D, angiotensin-converting enzyme (ACE), angiotensin II type 1 (AT1) receptor, p21ras, the alpha subunit of farnesyl and geranylgeranyl transferase (FTalpha/GGTalpha), phospho (p)-c-Jun N-terminal kinase (p-JNK), p-p38 mitogen-activated protein kinase (MAPK), cyclin D1, c-Jun, Ki-67, bcl-2, TGF-beta1 latency-associated peptide (LAP), TGF-betaRII, and cyclooxygenase (COX)-2. Immunoreactivities were scored from 0 to 3+ positivity using bright-field microscopy. The results showed that malignant mesenchymal chondroblasts exhibit stronger expressions of CD99, IL-1alpha, cPKC-alpha, p-PKC-alpha/betaII, PDGFR-alpha, p-JNK, Ki-67, and bcl-2 antigens than their more mature-appearing chondrocytic counterparts in MC. In conclusion, molecular profiling of mesenchymal chondrosarcoma using a proteomic approach characterized the mesenchymal chondroblasts as possessing pathways that incorporate PKC-alpha and PDGFR-alpha signaling and anti-apoptotic bcl-2 expression. Specific therapies to target the mesenchymal chondroblasts in mesenchymal chondrosarcoma might include interferon-alpha, rapamycin, ciprofloxacin, and STI571.

Adult↗
PubMedDate not supplied

Novel characterization of proteomics maps by sequential neighborhoods of protein spots.

We consider a characterization of proteomics maps based on an alternative kind of neighborhood graphs for the protein spots on 2-D gel. The novel approach considers for every protein spot only the nearest neighborhood consisting of protein spots of higher abundance. The approach has the simplicity and advantages of the recently introduced characterization of proteome maps based on considering the nearest neighborhoods of protein spots, but it also has important additional desirable computational features. The characterization of the nearest neighborhood graphs of 2-D gel proteomics maps is sensitive to the number of spots considered and may lead to changes in the degree of similarity of different maps when the number of points has been changed, thus imposing restrictions on the protocol used for comparison of maps. The novel approach presented in this work is less sensitive to the number of points used in the analysis because graphs are constructed in a stepwise process in which the role of more distant neighbors has been diminished by linking a new spot to the nearest spot that has been already part of the neighborhood graph. In this way a graph with N + 1 spots is obtained from the graph on N spots by adding a single new link, while in the case of the nearest neighborhood graphs adding a new spot introduces novel neighborhoods and generally results in a graph that may differ significantly from the neighborhood graph on N points.

Animals↗
PubMed2006

Challenges for molecular profiling of chronic fatigue syndrome.

Chronic fatigue syndrome (CFS) is prevalent, disabling and costly. Despite extensive literature describing the epidemiology and clinical aspects of CFS, it has been recalcitrant to diagnostic biomarker discovery and therapeutic intervention. This is due to the fact that CFS is a complex illness defined by self-reported symptoms and diagnosed by the exclusion of medical and psychiatric diseases that may explain the symptoms. Studies attempting to dissect the pathophysiology are challenging to design as CFS affects multiple body systems, making the choice of which system to study dependent on an investigators area of expertise. However, the peripheral blood appears to be facilitating the molecular profiling of several diseases, such as CFS, that involve bodywide perturbations that are mediated by the CNS. Successful molecular profiling of CFS will require the integration of genetic, genomic and proteomic data with environmental and behavioral data to define the heterogeneity in order to optimize intervention.

Animals↗
PubMed2004

Proteomics of the injured rat sciatic nerve reveals protein expression dynamics during regeneration.

Using proteomics, we investigated the temporal expression profiles of proteins in rat sciatic nerve after experimental crush. Extracts of sciatic nerves collected at 5, 10, and 35 days after injury were analyzed by two-dimensional gel electrophoresis and quantitative image analysis. Of the approximately 1,500 protein spots resolved on each gel, 121 showed significant regulation during at least one time point. Using cluster analysis, these proteins were grouped into two expression profiles of down-regulation and four of up-regulation. These profiles mainly reflected differences in cellular origins in addition to different functional roles. Mass spectrometric analysis identified 82 proteins pertaining to several functional classes, i.e. acute-phase proteins, antioxidant proteins, and proteins involved in protein synthesis/maturation/degradation, cytoskeletal (re)organization, and in lipid metabolism. Several proteins not previously implicated in nerve regeneration were identified, e.g. translationally controlled tumor protein, annexin A9/31, vitamin D-binding protein, alpha-crystallin B, alpha-synuclein, dimethylargininases, and reticulocalbin. Real-time PCR analysis of selected genes showed which were expressed in the nerve versus the dorsal root ganglion neurons. In conclusion, this study highlights the complexity and temporal aspect of the molecular process underlying nerve regeneration and points to the importance of glial and inflammatory determinants.

Animals↗
PubMed2006

Proteome analysis of human follicular fluid.

We used proteomic approach to analyze the protein profile of human follicular fluid (HFF) obtained from 25 normo-ovulatory women undergoing assisted reproduction techniques due to a male infertility factor. In all HFF samples analyzed we found 695 common spots distributed in the 3 to 10 pH range and in the 10-200 kDa range. Only 625 of these spots were also present in the plasma. We used MALDI-TOF-MS analysis to unequivocally assign 183 HFF/plasma matched spots and 27 HFF/plasma unmatched spots. A large number of acute-phase proteins, including transferrin, ceruloplasmin, afamin, hemopexin, haptoglobin and plasma amyloid protein, were identified in HFF in relatively high concentration supporting the hypothesis that mammalian ovulation can be compared to an inflammatory event. We also identified several important antioxidant enzymes; i.e., catalase, superoxide dismutase, glutathione transferase, paraoxonase, heat shock protein 27 and protein disulfide isomerase. This indicates that during maturation the human follicle is well protected against toxic injury due to oxidative stress.

Electrophoresis, Gel, Two-Dimensional↗
PubMed2005

Isolation and proteomic analysis [corrected] of cell wall-deficient Haematococcus pluvialis mutants.

The green alga Haematococcus pluvialis has a plant-like cell wall consisting of glycoproteins and cellulose that is modified during the cell cycle and under various conditions. These features allow Haematococcus to be used as a model organism for studying cell wall biology. Development of the Haematococcus model is hampered by the absence of mutants that could provide insight into the biosynthesis and assembly of wall components. Haematococcus mutants (WM#537 and WM#2978) (WM--wall mutant) with defective cell walls were obtained by chemical mutagenesis. WM#537 features a secondary wall of considerably reduced thickness, whereas WM#2978 possesses a somewhat reduced secondary wall with little intervening space between the wall and plasmalemma. 2-DE revealed that a majority of the cell wall proteins were present in the wild-type and mutant cell walls throughout the cell cycle. PMF identified 55 wall protein orthologs from these strains, including a subset of induced proteins known to be involved in wall construction, remodeling, and defense. Down-regulation of certain wall proteins in the two mutants was associated with the wall defects, whereas overexpression of other proteins may have compensated for the defective walls in the two mutants.

Algal Proteins↗
PubMedDate not supplied

Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags.

The effectiveness of proteome-wide protein identification and quantitative expression profiling is dependent on the ability of the analytical methodologies employed to routinely obtain information on low-abundance proteins, as these are frequently of great biological importance. Two-dimensional gel electrophoresis, the traditional method for proteome analysis, has proven to be biased toward highly expressed proteins. Recently, two-dimensional chromatography of the complex peptide mixtures generated by the digestion of unseparated protein samples has been introduced for the identification of their components, and isotope-coded affinity tags (ICAT) have been introduced to allow for accurate quantification of the components of protein mixtures by mass spectrometry. Here, we demonstrate that the combination of isotope coded affinity protein tags and multidimensional chromatography/mass spectrometry of tryptic peptide mixtures is capable of detecting and quantifying proteins of low abundance in complex samples.

Animals↗
PubMed2006

Proteomic analysis of rat aorta during atherosclerosis induced by high cholesterol diet and injection of vitamin D3.

1. Atherosclerosis (AS) in rats displays important clinical similarities to human AS. 2. After the experimental model of AS in rat was established and using a proteomic approach, we compared the protein profiling of aorta tissues from healthy and AS rats. 3. Using two-dimensional electrophoresis (2-DE), over 1878 protein species were separated; among them, 1239 protein spots were matched between different gels with average matching rate of approximately 66%. Gel analysis and protein characterization have identified 58 protein spots whose abundance is significantly altered in AS rats. 4. By using matrix-associated laser desorption ionization time-of-flight mass spectrometer (MALDI-TOF-MS) and NCBInr database, 46 proteins were successfully identified. Among them, 18 proteins were of increased abundance in diseased tissues including a group of oxidization-related enzymes such as peroxiredoxin2 and NADH dehydrogenase Fe-S protein 6, components of inflammatory pathways such as lamin A, while 28 proteins were of decreased abundance in the diseased state, including CaM-KII inhibitory protein, transferring, fructose-bisphosphate aldolase. 5. We believe that these results would give insights into the cellular and molecular mechanisms involved in AS development and might lead to the discovery of novel diagnostic markers and new therapeutic opportunities.

Animals↗
PubMed2026

Integrated histone and proteome analyses reveal convergent and distinct hepatotoxic mechanisms of tenuazonic acid and deoxynivalenol.

Mycotoxins are widespread dietary contaminants whose health impacts are expected to intensify under climate change. Although their mechanisms of toxicity remain incompletely understood, epigenetic dysregulation has been increasingly implicated. Here, mass spectrometry-based multi-omics was used to profile histone post-translational modifications and proteome dynamics in HepG2 cells exposed to seven mycotoxin conditions. Time-resolved analyses identified tenuazonic acid as the dominant cellular disruptor, inducing alterations in H3K27 and H1 variants, and revealing a previously unrecognized oxidative modification of the H1.0 N-terminal methionine (H1.0N-term0AcM0Ox) that retains the protein's N-terminal acetylation. An Alternaria toxin mixture induced similar H1 responses, largely driven by tenuazonic acid, while deoxynivalenol produced convergent chromatin and proteomic alterations. Proteomic remodeling was characterized by increased protein translation, reduced mitochondrial complex IV expression, and impaired cholesterol biosynthesis, whereas sterigmatocystin activated DNA replication and repair pathways. Together, these findings demonstrate that mycotoxins disrupt chromatin organization, protein synthesis, and lipid metabolism, providing toxicological insight into hepatocellular dysfunction. These findings warrant further validation and mechanistic investigation in future hypothesis-driven studies of mycotoxin exposure.

Trichothecenes↗
PubMed2026

Height variation independent of known genetic variants and health in later life: a cohort study.

BACKGROUND: Adult-attained height is associated with later-life health, but it reflects both genetic and nongenetic influences. The health implications of height variation not explained by known common height-associated genetic variants remain unclear. OBJECTIVES: This study aimed to examine associations of residual height (height variation independent of known genetic variants) with multiple disease incidence and all-cause mortality in later life. METHODS: In this cohort study of 407,366 adults of European ancestry (aged 40-70 y) in the United Kingdom Biobank (2006-2010), sex- and age-specific genetically predicted height was estimated from 9863 height-associated variants, adjusted for 30 principal components of ancestry. Residual height was calculated as the difference between observed and genetically predicted height. Plasma proteomics (2054 proteins; Olink Explore) were profiled. Deaths and 49 incident diseases were ascertained through national registries. Multivariable Cox models estimated associations of residual height and related proteins with disease incidence and mortality. RESULTS: Higher residual height [mean (standard deviation, SD), 0.0 (4.8)] was associated with more favorable self-reported preadulthood exposures (e.g., later birth years, no maternal smoking around birth, being breastfed as an infant, no adoption experience, and lower childhood adversity scores) and lower hazard ratios (HRs) of 32 out of 49 diseases (median follow-up = &#x223c;12.5 y). Using participants with residual height within &#xb1;0.5 SDs from the mean as reference, those with residual height < -2 SDs had higher adjusted HRs of mortality [1.61; 95% confidence interval (CI): 1.50, 1.72], multimorbidity (1.28; 95% CI: 1.12, 1.46), cardiovascular disease (1.45; 95% CI: 1.32, 1.60), psychiatric/neurological disease (1.38; 95% CI: 1.28, 1.48), and other disease categories (e.g., diabetes, digestive, and musculoskeletal diseases). In contrast, higher genetically predicted height was associated with a higher incidence of 19 diseases, including subtypes of cancer, non-atherosclerotic cardiovascular diseases, and musculoskeletal diseases, as well as higher all-cause mortality. We identified 806 plasma proteins related to inflammation, immune response, and autophagy via tumor necrosis factor, Nuclear factor-kappa B, phosphoinositide-3 kinase/protein kinase B, and Janus kinase/signal transducer and activator of transcription signaling pathways, which were associated with residual height and multiple diseases and mortality. CONCLUSIONS: Higher residual height is associated with lower disease incidence and mortality, with associations that are distinct from those for genetically predicted height.

Humans↗
PubMed2004

Non-self-discrimination as a driving concept in the identification of an immunodominant HMW-MAA epitopic peptide sequence by autoantibodies from melanoma cancer patients.

We analyzed the sera of patients with melanoma to define the human humoral autoantibody profile towards HMW-MAA. Computational proteome scanning using the non-self-discrimination principle as a guide led to the individuation of the low-similarity HMW-MAA781-789RATVWMLRL peptide fragment as an immunodominant B-cell epitope. Linear B-cell determinant individuation was experimentally validated by dot blot immunoassay and NMR spectroscopy analysis. Regulation of physiologic self-reactivity by the non-self-discrimination principle is discussed.

Antigens, Neoplasm↗
PubMed2002

N-Terminal peptide labeling strategy for incorporation of isotopic tags: a method for the determination of site-specific absolute phosphorylation stoichiometry.

Determining the phosphorylation stoichiometry at specific sites in a phosphoprotein is a very challenging task. We describe here a novel mass spectrometry based method that is capable of measuring the absolute phosphorylation stoichiometry at specific sites without the need for specific internal standards, phospho-site antibodies or radioactivity. The method is based on a gentle chemical labeling strategy which specifically and differentially labels the N-terminus of all peptides in a sample with either a D(5)- or D(0)-propionyl group and measures the ratio of the abundance of the D(5)/D(0) peptide pairs simultaneously using mass spectrometry. Using matrix-assisted laser desorption/ionization (MALDI), the method can measure absolute stoichiometry to within at least 10% and can be applied to both in vitro and in vivo phosphorylated peptides and proteins. Furthermore, this method can potentially be applied to the quantitative study of other types of protein post-translational modifications, and the profiling of protein expression on the proteome level.

Amino Acid Sequence↗
PubMed2005

Structural genomics of eukaryotic targets at a laboratory scale.

Structural genomics programs are distributed worldwide and funded by large institutions such as the NIH in United-States, the RIKEN in Japan or the European Commission through the SPINE network in Europe. Such initiatives, essentially managed by large consortia, led to technology and method developments at the different steps required to produce biological samples compatible with structural studies. Besides specific applications, method developments resulted mainly upon miniaturization and parallelization. The challenge that academic laboratories faces to pursue structural genomics programs is to produce, at a higher rate, protein samples. The Structural Biology and Genomics Department (IGBMC - Illkirch - France) is implicated in a structural genomics program of high eukaryotes whose goal is solving crystal structures of proteins and their complexes (including large complexes) related to human health and biotechnology. To achieve such a challenging goal, the Department has established a medium-throughput pipeline for producing protein samples suitable for structural biology studies. Here, we describe the setting up of our initiative from cloning to crystallization and we demonstrate that structural genomics may be manageable by academic laboratories by strategic investments in robotic and by adapting classical bench protocols and new developments, in particular in the field of protein expression, to parallelization.

Crystallization↗
PubMed2006

Cytogenetics and molecular cytogenetics in multiple myeloma.

Multiple myeloma (MM) is characterized by frequent and complex genomic abnormalities that not only essentially contribute to the pathogenesis of this disease but also reflect its prognostic heterogeneity. There is evidence for two more or less mutually exclusive oncogenic pathways in the early development of clonal plasma cell disorders. Approximately half the tumours are non-hyperdiploid and carry translocations of the immunoglobulin heavy-chain (IgH) locus and various oncogenes, for example Cyclin D1, Cyclin D3, and FGFR3. The remaining hyperdiploid tumours exhibit recurrent trisomies - typically of chromosomes 5, 7, 9, 11, 15, 19, and 21 - but infrequently exhibit IgH translocations. While some chromosomal aberrations, such as deletion of chromosome arm 13q, deliver independent prognostic information that is already utilized for risk stratification within clinical trials, the prognostic significance of most other genetic aberrations in MM is undetermined.

Chromosome Aberrations↗
PubMed2004

Eicosanomics: targeted lipidomics of eicosanoids in biological systems.

Recent advancements in mass spectrometry, especially the development of electrospray tandem mass spectrometry (ESI/LC/MS2) and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI/TOF), have greatly facilitated analysis of complex biomolecules. It has now become possible to profile, in relatively short periods of time, large multicomponent groups of compounds biosynthesized by biological systems. The efficiency and accuracy of analysis have led to the development of new concepts of mass spectrometric profiling, mapping, and imaging. Profiling of proteins in biological material (proteomics) has become a widely accepted strategy for identification of mechanisms involved in the biochemistry of disease processes, and has become a novel tool for unraveling new drug targets. Evolution of proteomics has relied on ESI/LC/MS2 and MALDI/TOF, techniques that are also useful in the novel area of quantitative proteomics.

Animals↗
PubMed2001

The use of toxicodynamics in risk assessment.

Risk assessment of xenobiotics is a qualitative and quantitative assessment of toxic properties conventionally based on data resulting from tests in animals exposed to the substance. The assessment of dose-effect relationship includes evaluation of exposure at the site of action. More recently, emphasis is put on understanding the relationship between exposure at the site of action and the resulting effect, i.e. toxicodynamic. In this respect, results from genotoxicity studies may be a measure for exposure and at the same time of an effect. Results of toxicodynamic endpoints such as binding to receptors or release of hormones have been used when replacing default values for interspecies extrapolation. It may also be envisaged to use toxicodynamic endpoints in order to get an estimate of intraspecies variability. It was demonstrated that this approach may be helpful only if the relationship between the toxicodynamic endpoint and the definite endpoint is known by using the example of bisphenol A. Whereas there are clear effects of bisphenol A in in vitro and ex vivo studies, the classical two generation study has not been able to detect an effect on reproduction and/or fertility. Looking in the future development of toxicodynamic endpoints, gene profiling and the analysis of proteins ('proteomics') may be helpful tools employed in screening and being related to the mode of action are explored for their suitability in terms of toxicodynamic endpoints.

Animals↗
PubMedDate not supplied

Are there biofilm-specific physiological pathways beyond a reasonable doubt?

The development of surface-attached communities called biofilms is often thought to be a regulated developmental process involving profound biofilm-specific modifications. Despite intense scrutiny and a growing body of evidence correlating changes in gene expression with the switch from planktonic-to-biofilm lifestyle, an integrated view of biofilm formation is still missing.

Biofilms↗
PubMed2001

Protein biochips for differential profiling.

Progress has been made in utilizing ProteinChip technology to profile and compare protein expression in normal and diseased states, particularly in the areas of cancer, infectious disease and toxicology. The past year has also seen the development of several novel chip types designed to analyze proteins in a fashion analogous to the array-based format of DNA microarrays. Some of these platforms may be used for differential profiling.

Bacterial Proteins↗