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PubMed2026

The influence of neuroprotector isatin on haloperidolinduced catalepsy and proteomic profile of mice brain.

Isatin (indol-2,3-dione) is an endogenous regulator found in humans and animals. It interacts with numerous target proteins and exhibits a wide range of biological activities, including neuroprotective action in animal models of Parkinson's disease (PD) induced by administration of neurotoxins MPTP (1-methyl-4-phenyl-1,2,3,6- tetrahydropyridine) or rotenone. An antipsychotic drug haloperidol, which impairs neurotransmitter balance in the nigrostriatal pathway, models dopamine deficiency and promotes the development of motor disorders characteristic of PD. In this work, the effect of two doses of isatin (10 mg/kg and 80 mg/kg) on the haloperidol catalepsy and on the proteomic profile of mice brain was investigated. The pretreatment of animals with isatin (1 h before haloperidol administration) reduced the occurrence of haloperidol catalepsy. The administration of haloperidol and also isatin with haloperidol influenced the relative content of a number of proteins associated with PD and other neurodegenerative diseases.

Animals↗

PubMed2026

Plasma proteomic profiling of septic shock and acute pancreatitis identifies shared signatures and disease-specific pathways.

Septic shock represents the most severe form of infection-driven systemic inflammation, whereas acute pancreatitis induces a sterile inflammatory response. Although clinically similar, their molecular profiles may reveal distinct mechanisms underlying infectious and non-infectious inflammation. We performed plasma proteomic profiling using LC-MS/MS in patients with septic shock (n = 13), acute pancreatitis (n = 8), and healthy controls (n = 8). Among 663 quantified proteins, 231 were differentially expressed in septic shock versus controls, 83 in pancreatitis versus controls, and 29 in septic shock versus pancreatitis. Septic shock was characterized by higher plasma concentrations of MARCKS, HSP90AA1, PSAP, CD163, and GANAB, whereas pancreatitis showed higher levels of CPA1, APOC4, APOC3, BPGM, and APOC2. Cluster analysis demonstrated separation between groups, with overlapping proteomic patterns in sepsis and pancreatitis. Gene Ontology and KEGG analyses revealed shared inflammatory signatures, including upregulation of acute-phase responses and downregulation of coagulation pathways. However, septic shock exhibited more extensive proteomic alterations, with distinct activation of PI3K-Akt signaling and suppression of lipid metabolism. In conclusion, septic shock and pancreatitis share common inflammatory pathways, while proteomic differences highlight divergent regulation of coagulation, lipid metabolism, and anti-inflammatory signaling, offering potential biomarkers to distinguish infectious from sterile systemic inflammation.

Shock, Septic↗

PubMedDate not supplied

Primary cell cultures arising from normal kidney and renal cell carcinoma retain the proteomic profile of corresponding tissues.

Renal cell carcinoma (RCC) tissue is composed of a mixture of neoplastic and normal cells, which complicate proteome analysis. The aim of our study was to investigate whether it is feasible to establish primary cell cultures of RCC and of renal cortex maintaining the tissue phenotype along with a more homogeneous and enriched cytological material. Fourteen (82.3%) primary cultures from 17 surgical cases were established and characterized by morphology, growth rate, immunocytochemistry, and molecular analysis performed by Real-time PCR, Western blotting, two-dimensional electrophoresis (2-DE), and mass spectrometry. Cultures showed >90% cytokeratine-positive epithelial cells. In primary tumor cultures, the molecular phenotype of manganese superoxide dismutase and heat shock protein 27 was the same as that found in tumor tissues with overexpression and increased number of isoforms. Moreover, 27 out 28 specific proteins and their isoforms, present in spots excised from 2-DE gel of cortex or RCC cultures, corresponded to those identified on the 2-DE tissue cortex reference map, suggesting that these primary cultures retain the proteomic profile of the corresponding tissues.

Adult↗

PubMed2004

Genomic and proteomic profiling for biomarkers and signature profiles of toxicity.

Toxicity profiling measures and compares all gene expression changes among biological samples after toxicant exposure. Toxicity profiling with DNA microarrays to measure all mRNA transcripts (transcriptomics), or by global separation and identification of proteins (proteomics), has led to the discovery of better descriptors of toxicity, toxicant classification and exposure monitoring than current indicators. A shared goal in transcript and proteomic profiling is the development of biomarkers and signatures of chemical toxicity. In this review, biomarkers and signature profiles are described for specific chemical toxicants that affect target organs such as liver, kidney, neural tissues, gastrointestinal tract and skeletal muscle, for specific disease models such as cancer and inflammation, and for unique chemical-protein adducts underlying cell injury. The recent introduction of toxicogenomics databases support researchers in sharing, analyzing, visualizing and mining expression data, assist the integration of transcriptomics, proteomics and toxicology datasets, and eventually will permit in silico biomarker and signature pattern discovery.

Animals↗

PubMed2003

Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays.

Because most potential molecular markers and targets are proteins, proteomic profiling is expected to yield more direct answers to functional and pharmacological questions than does transcriptional profiling. To aid in such studies, we have developed a protocol for making reverse-phase protein lysate microarrays with larger numbers of spots than previously feasible. Our first application of these arrays was to profiling of the 60 human cancer cell lines (NCI-60) used by the National Cancer Institute to screen compounds for anticancer activity. Each glass slide microarray included 648 lysate spots representing the NCI-60 cell lines plus controls, each at 10 two-fold serial dilutions to provide a wide dynamic range. Mouse monoclonal antibodies and the catalyzed signal amplification system were used for immunoquantitation. The signal levels from the >30,000 data points for our first 52 antibodies were analyzed by using p-scan and a quantitative dose interpolation method. Clustered image maps revealed biologically interpretable patterns of protein expression. Among the principal early findings from these arrays were two promising pathological markers for distinguishing colon from ovarian adenocarcinomas. When we compared the patterns of protein expression with those we had obtained for the same genes at the mRNA level by using both cDNA and oligonucleotide arrays, a striking regularity appeared: cell-structure-related proteins almost invariably showed a high correlation between mRNA and protein levels across the NCI-60 cell lines, whereas non-cell-structure-related proteins showed poor correlation.

Blotting, Western↗

PubMed2005

Proteomic profiling of human stem cells derived from umbilical cord blood.

CD34+ preparations from five different umbilical cord samples were compared with respect to their proteome profile using 2-D gel electrophoresis. Fifty-two protein spots were found to match in all preparations referring to the high heterogeneity of such samples indicating a not fully developed (or instable) proteome of stem cells. All matching spots were subjected to in-gel digestion and nano-LC-MS/MS sequence analysis, from which 22 proteins were unambiguously identified.

Cells, Cultured↗

PubMed2006

Systematical evaluation of the effects of sample collection procedures on low-molecular-weight serum/plasma proteome profiling.

Blood is an ideal source for biomarker discovery. However, little has been done to address the effects of sampling, handling and storage procedures on serum/plasma proteomes. We used magnetic bead-based MALDI-TOF MS to systematically evaluate the influence of each procedure on low-molecular-weight serum/plasma proteome profiling on the basis of the whole spectra. We found that sampling procedures, including the selection of blood collection tubes and anticoagulants, variations in clotting time or time lag before centrifugation, and hemolysis, displayed significant effects on the proteomes. Moreover, serum and plasma were mutually incompatible for proteome comparison. By contrast, overnight fasting, handling procedures, including centrifugation speeds (1500 x g vs. 3000 x g) or time (15 min vs. 30 min), and storage conditions, such as at 4 degrees C or 25 degrees C for up to 24 h or at -80 degrees C for up to 3 months, and repeated freeze/thaw of up to ten cycles, had relatively minor effects on the proteomes based upon our analysis of about 100 peaks. We concluded that low-molecular-weight serum/plasma proteomes were diversely affected by sampling, handling and storage with most change from variations of sampling procedures. We therefore suggest the necessity of standardizing sampling procedure for proteome comparison and biomarker discovery.

Adult↗

PubMed2005

Proteomic profiling of cerebrospinal fluid identifies biomarkers for amyotrophic lateral sclerosis.

Amyotrophic lateral sclerosis (ALS) is characterized by degeneration of motor neurons. We tested the hypothesis that proteomic analysis will identify protein biomarkers that provide insight into disease pathogenesis and are diagnostically useful. To identify ALS specific biomarkers, we compared the proteomic profile of cerebrospinal fluid (CSF) from ALS and control subjects using surface-enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF-MS). We identified 30 mass ion peaks with statistically significant (p < 0.01) differences between control and ALS subjects. Initial analysis with a rule-learning algorithm yielded biomarker panels with diagnostic predictive value as subsequently assessed using an independent set of coded test subjects. Three biomarkers were identified that are either decreased (transthyretin, cystatin C) or increased (carboxy-terminal fragment of neuroendocrine protein 7B2) in ALS CSF. We validated the SELDI-TOF-MS results for transthyretin and cystatin C by immunoblot and immunohistochemistry using commercially available antibodies. These findings identify a panel of CSF protein biomarkers for ALS.

Adult↗

PubMed2006

Comparison of the proteome profiles of Entamoeba histolytica and its close but non-pathogenic relative Entamoeba dispar.

The microaerophilic protist Entamoeba histolytica is a source of considerable morbidity and mortality in many countries of the world by acting as a causative agent of amoebic dysentery and liver abscess. Its close relative, Entamoeba dispar, also colonises the human colon but is non-pathogenic. In the present study, we wanted to assess if the close relatedness of these two organisms could be used to identify virulence factors in E. histolytica through a comparison of the protein expression profiles of the pathogenic and the non-pathogenic species. We applied two-dimensional polyacrylamide gel electrophoresis in order to identify proteins which are specifically expressed in E. histolytica and which therefore could constitute candidate proteins potentially involved in E. histolytica pathogenicity. The evaluation of overall protein expression profiles derived from whole cell extracts, however, revealed that, in spite of the close relatedness at the genetic level, the disparity of the proteomic profiles of these two Entamoeba species is far too great in order to pinpoint proteins whose expression might render E. histolytica pathogenic. Taken together, our study performed at the proteomic level clearly supports the notion of E. histolytica and E. dispar as two distinct species.

Animals↗

PubMed2003

Proteomic profiling of urinary proteins in renal cancer by surface enhanced laser desorption ionization and neural-network analysis: identification of key issues affecting potential clinical utility.

Recent advances in proteomic profiling technologies, such as surface enhanced laser desorption ionization mass spectrometry, have allowed preliminary profiling and identification of tumor markers in biological fluids in several cancer types and establishment of clinically useful diagnostic computational models. There are currently no routinely used circulating tumor markers for renal cancer, which is often detected incidentally and is frequently advanced at the time of presentation with over half of patients having local or distant tumor spread. We have investigated the clinical utility of surface enhanced laser desorption ionization profiling of urine samples in conjunction with neural-network analysis to either detect renal cancer or to identify proteins of potential use as markers, using samples from a total of 218 individuals, and examined critical technical factors affecting the potential utility of this approach. Samples from patients before undergoing nephrectomy for clear cell renal cell carcinoma (RCC; n = 48), normal volunteers (n = 38), and outpatients attending with benign diseases of the urogenital tract (n = 20) were used to successfully train neural-network models based on either presence/absence of peaks or peak intensity values, resulting in sensitivity and specificity values of 98.3-100%. Using an initial "blind" group of samples from 12 patients with RCC, 11 healthy controls, and 9 patients with benign diseases to test the models, sensitivities and specificities of 81.8-83.3% were achieved. The robustness of the approach was subsequently evaluated with a group of 80 samples analyzed "blind" 10 months later, (36 patients with RCC, 31 healthy volunteers, and 13 patients with benign urological conditions). However, sensitivities and specificities declined markedly, ranging from 41.0% to 76.6%. Possible contributing factors including sample stability, changing laser performance, and chip variability were examined, which may be important for the long-term robustness of such approaches, and this study highlights the need for rigorous evaluation of such factors in future studies.

Adult↗

PubMed2026

Proteomic profile of the dentine pellicle modified with plant polyphenols and fluoride.

OBJECTIVES: Despite its protective role, the dentine pellicle has rarely been studied, therefore we aimed to map out the proteomic profile of in vitro dentine pellicles before and after modification. MATERIALS AND METHODS: A total of 135 human dentine specimens were prepared. After initial pellicle formation with 150 µl pooled human saliva (37 °C, 30 min), the dentine specimens were immersed in one of 9 pellicle modification solutions (2 ml/specimen): deionized water (non-modified pellicle), SnCl2/NaF/AmF (commercial solution containing 800 ppm Sn2+ and 500 ppm F-), NaF solution (500 ppm F- ), and six polyphenol solutions (2 mg / ml) with or without 500 ppm F-: blueberry extract (BBE and BBE + F-), green tea extract (GTE and GTE + F-) and grape seed extract (GSE and GSE + F-). After another aliquot of saliva (150 µl, 37 °C, 60 min), the pellicles were harvested with sodium dodecyl sulphate by rubbing with cotton balls, and taken to proteomic analyses by Liquid Chromatography-Tandem Mass Spectrometry after tryptic digestion. RESULTS: A total of 382 proteins were identified in all the proteomic analyses for all groups. Pellicle modification with fluoride, either NaF or SnCl2/NaF/AmF, led to the presence of 12 or 14 exclusive proteins, respectively, whereas modification with the solutions containing polyphenols presented less exclusive proteins (4-6 proteins). The number of exclusive proteins was even lower for when polyphenols and fluoride (GTE + F- and GSE + F-) were used, with lower abundance of proteases. CONCLUSIONS: We conclude that NaF and SnCl2/NaF/AmF significantly modify the proteome of the dentine pellicle. The combination of fluoride with polyphenols further lowers the abundance of proteins and proteases, which explains the positive effect of these solutions on the dentine pellicles. CLINICAL RELEVANCE: Plant extract solutions with fluoride can significantly modify the proteomic structure of the dentine pellicle, which clarifies the mechanism of action of polyphenols on the protection of dentine demineralization.

Humans↗

PubMed2026

Proteomic Profile Differences in Immune-Related Diseases in Pediatric Patients Under Five Years Old: Asthma and IgE-Dependent Allergies-A Pilot Study.

Asthma is a heterogeneous disease that often begins in childhood and frequently occurs alongside allergic conditions. In asthma research, it is important to focus on proteins that are the primary regulators of cellular physiology. The differences in the proteome between children with asthma and those with an atopic background remain poorly understood. The present study included 130 serum samples from four groups of pediatric patients under the age of five: (1) with asthma and IgE-dependent allergies; (2) with non-atopic asthma; (3) non-asthmatics with IgE-dependent allergy; and (4) a control group without asthma and IgE-dependent allergies. The serum samples were used for protein-peptide profiling and proteomic identification using nanoLC-MALDI-TOF/TOF MS/MS. The obtained data were analyzed using univariate statistics and the STRING tool v12.0 to identify protein-protein potential interactions. A total of seven proteins were identified as discriminative between the study groups: A2M, AACT, IgG3, C3, ITIH2, IgG3 and IGK. All of them were upregulated in patients with IgE-dependent allergy compared to other study groups. STRING analysis identified functional associations among four proteins (AACT, A2M, C3, and ITIH2) with discriminatory potential for distinguishing between non-atopic asthma and non-asthmatic patients with IgE-dependent allergy. The results suggest that the identified putative protein markers overlap in cellular pathways, including those associated with the pathophysiology of asthma and allergic disorders. These findings provide further insight into the overall proteomic profile of pediatric patients with asthma and IgE-dependent allergy, highlighting its heterogeneity across the analyzed groups.

Humans↗

PubMed2006

Pilot study using SELDI-TOF-MS based proteomic profile for the identification of diagnostic biomarkers of thyroid proliferative diseases.

Biomarkers for thyroid cancer (TCa) lack specificity. To develop TCa specific biomarkers, SELDI-TOF-MS was used to examine the proteomic profile of biopsies obtained from papillary TCa along with adjacent normal tissue. Sixty-three potential biomarkers were categorized by univariate analysis into single biomarker candidates and segregated by multivariate analysis into normal and cancerous groups. Our studies demonstrate the sensitivity and reproducibility of this approach to detect biomarkers for TCa.

Biomarkers, Tumor↗

PubMed2006

Serial changes in urinary proteome profile of membranous nephropathy: implications for pathophysiology and biomarker discovery.

Membranous nephropathy is one of the most common causes of primary glomerular diseases worldwide. The present study adopted a gel-based proteomics approach to better understand the pathophysiology and define biomarker candidates of human membranous nephropathy using an animal model of passive Heymann nephritis (PHN). Clinical characteristics of Sprague-Dawley rats injected with rabbit anti-Fx1A antiserum mimicked those of human membranous nephropathy. Serial urine samples were collected at Days 0, 10, 20, 30, 40, and 50 after the injection with anti-Fx1A (number of rats = 6; total number of gels = 36). Urinary proteome profiles were examined using 2D-PAGE and SYPRO Ruby staining. Quantitative intensity analysis and ANOVA with Tukey post-hoc multiple comparisons revealed 37 differentially expressed proteins among 6 different time-points. These altered proteins were successfully identified by MALDI-TOF MS and classified into 6 categories: (i) proteins with decreased urinary excretion during PHN; (ii) proteins with increased urinary excretion during PHN; (iii) proteins with increased urinary excretion during PHN, but which finally returned to basal levels; (iv) proteins with increased urinary excretion during PHN, but which finally declined below basal levels; (v) proteins with undetectable levels in the urine during PHN; and (vi) proteins that were detectable in the urine only during PHN. Most of these altered proteins have functional significance in signaling pathways, glomerular trafficking, and controlling the glomerular permeability. The ones in categories (v) and (vi) may serve as biomarkers for detecting or monitoring membranous nephropathy. After normalization of the data with 24-h urine creatinine excretion, changes in 34 of initially 37 differentially expressed proteins remained statistically significant. These data underscore the significant impact of urinary proteomics in unraveling disease pathophysiology and biomarker discovery.

Biomarkers↗

PubMed2005

Novel application of layered expression scanning for proteomic profiling of plucked hair follicles.

BACKGROUND: There is a need for a technology that can quantitatively assay multiple proteins from a single hair follicle while preserving the morphology of the follicle. For proteomic profiling, the technology should be less labor intensive, with a higher throughput, more quantitative and more reproducible than immunohistochemistry. OBJECTIVE: To test the ability of a novel method, layered expression scanning of hair (LES-hair) to detect the levels and localization of proteins in plucked hair follicles. METHODS: LES-hair was used to assay proteins in the plucked hair follicle. RESULTS: LES-hair detected differential expression of proteins within discrete regions of the plucked hair follicle. These proteins included cleaved caspase 3, Ki-67 and the phosphorylated forms of c-Kit, epidermal growth factor receptor and vascular endothelial growth factor receptor. CONCLUSION: LES-hair provides a research tool for studying the basic biology of plucked hair follicles and has potential clinical applications such as monitoring treatment of alopecia or using plucked hair follicles as a surrogate tissue to monitor pharmacodynamic effects of targeted cancer therapies.

Adult↗

PubMed2003

Potential for proteomic profiling of Helicobacter pylori and other Helicobacter spp. using a ProteinChip array.

The Helicobacter genus is associated with a wide spectrum of pathologies in the gastrointestinal tract. However, in contrast to Helicobacter pylori, few data are available regarding proteomic characteristics of enterohepatic helicobacters. Proteomic analysis of this genus has predominantly utilised two-dimensional gel electrophoresis methodology. In the present study we applied an innovative technique using ProteinChip arrays coupled with surface-enhanced laser desorption/ionisation time of flight mass spectroscopy to accurately assess the M(r) of proteins for comparative proteomic profiling. We analysed binding of outer membrane fractions to a weak cation exchange array for strains of H. pylori from culture collections and compared these profiles to fresh clinical isolates. In addition, we analysed profiles from Helicobacter pullorum, Helicobacter bilis and 'Helicobacter sp. flexispira'. The system proved rapid, accurate and reproducible. Distinct specific profiles for all the strains studied were identified. However, strains from culture collections that have undergone numerous subcultures had almost identical profiles. In contrast, profiles from fresh clinical isolates were markedly different. Moreover, certain features of the profiles from the enterohepatic species were conserved.

Animals↗

PubMed2007

Activity-based probes for proteomic profiling of histone deacetylase complexes.

Histone deacetylases (HDACs) are key regulators of gene expression that require assembly into larger protein complexes for activity. Efforts to understand how associated proteins modulate the function of HDACs would benefit from new technologies that evaluate HDAC activity in native biological systems. Here, we describe an active site-directed chemical probe for profiling HDACs in native proteomes and live cells. This probe, designated SAHA-BPyne, contains structural elements of the general HDAC inhibitor suberoylanilide hydroxamic acid (SAHA), as well as benzophenone and alkyne moieties to effect covalent modification and enrichment of HDACs, respectively. Both class I and II HDACs were identified as specific targets of SAHA-BPyne in proteomes. Interestingly, multiple HDAC-associated proteins were also enriched by SAHA-BPyne, even after denaturation of probe-labeled proteomes. These data indicate that certain HDAC-associated proteins are directly modified by SAHA-BPyne, placing them in close proximity to HDAC active sites where they would be primed to regulate substrate recognition and activity. We further show that SAHA-BPyne can be used to measure differences in HDAC content and complex assembly in human disease models. This chemical proteomics probe should thus prove valuable for profiling both the activity state of HDACs and the binding proteins that regulate their function.

Cell Line↗

PubMed2006

Strategies for plasma proteomic profiling of cancers.

Despite a voluminous literature on potential protein biomarkers and a compelling need for diagnostic tests based on biomarkers to detect cancers at much earlier, more treatable stages, progress has been limited. New methods and new instruments for analysis of differences in gene expression, gene methylation, and proteomics are being employed to try to accelerate the discovery phase. Given the heterogeneity of tumor mechanisms and the limitations of analytical methods, it is likely that a variety of strategies will be needed and will be complementary. That is the basis of this review of proteomic approaches. This article adopts a systems biology view, starting with mRNA transcripts in tumors and cultured tumor cells to detect mRNA overexpression, some of which will be correlated with protein overexpression. Some of those proteins may be secreted or released into proximal biofluids and plasma. Detection of low-abundance tumor proteins in the complex and dynamic mixture that is plasma requires combinations of increasingly powerful technologies. The biological amplification of protein signals through the immune system offers autoantibodies as potential biomarkers. Higher abundance proteins, including acute-phase reactants, may have practical value, especially if the proteins are modified as part of the cancer processes. Low molecular weight proteins, fragments, and peptides may offer complementary biomarkers. Promising biomarker candidates must be confirmed in independent studies. Then they must be submitted to higher-throughput methods practical for large-scale validation studies and, hopefully, for clinical and epidemiological applications. Standardized operating procedures for specimen handling, design and use of various reference standards, care to avoid bias and confounding, and guidelines for reporting findings and contributing datasets should enhance the prospects for predictive proteomic profiling of people at risk for cancers.

Biomarkers, Tumor↗