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PubMed2004

PARIS: a proteomic analysis and resources indexation system.

UNLABELLED: We developed a system for managing data from two-dimensional electrophoresis-based proteomic experiments. Named PARIS, the system stores gel image and information about experiments and analysis procedures, allows the user to search and navigate in genomic and proteomic data, supports visual verification and validation of the analysis results, and provides tools for cross multi-experiment and multi-experimenter data validation and exploration. AVAILABILITY: The software is freely available from http://www.inra.fr/bia/J/imaste/Projets/PARIS/index.html

Abstracting and Indexing↗
PubMed2003

Incorporating basic nutrition science into health interventions for cancer prevention.

Increasing evidence points to numerous dietary components that modify cancer incidence as well as the biological behavior of tumors. These inhibitory or stimulatory effects depend not only on the dietary component examined, but on a number of factors including the cellular DNA profile (nutrigenetic and nutrigenomic effects), protein formation and regulation (proteomic effect), and the effective delivery of the active intermediate at specific target sites (metabolomic effect). Unfortunately, the diet and cancer research domain is strewn with studies that were inadequately designed to monitor biological endpoints, used invalid biomarkers, or monitored irrelevant intakes or exposures. The scientific frontiers in health risk prediction and disease prevention strategies will greatly expand with the building of reliable nutrition and cancer biomarker databases that use modeling techniques to integrate information about intakes, effect biomarkers, and susceptibility biomarkers. Fundamental to this database will be the elucidation of the specific molecular sites of action (targets) for the specific dietary component. Clustering techniques that build on either genes or ratios of genetic expressions or their products will be needed to assess the merit of a particular dietary intervention. Models are already surfacing about how dietary-induced fluctuations in genes and their expression products can modify pathways associated with carcinogen activation and detoxification, alter rates of cellular proliferation, influence apoptosis, and modify angiogenesis. Embracing new genomic technologies offers exciting opportunities for advancing nutrition, especially those related to cancer prevention. We must effectively communicate, within a responsible bioethical framework, the potential value of knowledge about genes and gene products.

DNA Methylation↗
PubMed2005

Protein and small molecule microarrays: powerful tools for high-throughput proteomics.

Advances in genomics and proteomics have opened up new possibilities for the rapid functional assignment and global characterization of proteins. Large-scale studies have accelerated this effort by using tools and strategies that enable highly parallel analysis of huge repertoires of biomolecules. Organized assortments of molecules on arrays have furnished a robust platform for rapid screening, lead discovery and molecular characterization. The essential advantage of microarray technology is attributed to the massive throughput attainable, coupled with a highly miniaturized platform--potentially driving discovery both as an analytical and diagnostic tool. The scope of microarrays has in recent years expanded impressively. Virtually every biological component--from diverse small molecules and macromolecules (such as DNA and proteins) to entire living cells--has been harnessed on microarrays in attempts to dissect the bewildering complexity of life. Herein we highlight strategies that address challenges in proteomics using microarrays of immobilized proteins and small molecules. Of specific interest are the techniques involved in stably immobilizing proteins and chemical libraries on slide surfaces as well as novel strategies developed to profile activities of proteins on arrays. As a rapidly maturing technology, microarrays pave the way forward in high-throughput proteomic exploration.

Gene Expression Profiling↗
PubMed2004

Protein profiling of microdissected prostate tissue links growth differentiation factor 15 to prostate carcinogenesis.

Identification of proteomic alterations associated with early stages in the development of prostate cancer may facilitate understanding of progression of this highly variable disease. Matched normal, high-grade prostatic intraepithelial neoplasia (hPIN) and prostate cancer cells of predominantly Gleason grade 3 were procured by laser capture microdissection from serial sections obtained from snap-frozen samples dissected from 22 radical prostatectomy specimens. From these cells, protein profiles were generated by surface-enhanced laser desorption/ionization-time of flight mass spectrometry. A 24-kDa peak was observed at low or high intensity in profiles of prostate cancer cells in 19 of 27 lesions and at low intensity in 3 of 8 hPIN lesions but was not detectable in matched normal cells. SDS-PAGE analysis of prostate cancer and matched normal epithelium confirmed expression of a prostate cancer-specific 24-kDa protein. Mass spectrometry and protein data-based analysis identified the protein as the dimeric form of mature growth differentiation factor 15 (GDF15). The increased expression of mature GDF15 protein in prostate cancer cells cannot be explained on the basis of up-regulation of GDF15 mRNA because reverse transcription-PCR analysis showed similar amounts of transcript in normal, hPIN, and prostate cancer cells that were obtained by laser capture microdissection in the same set of serial sections from which the protein profiles were obtained. Our findings suggest that early prostate carcinogenesis is associated with expression of mature GDF15 protein.

Adenocarcinoma↗
PubMed2005

Metabolome analysis: the potential of in vivo labeling with stable isotopes for metabolite profiling.

Metabolome analysis technologies are still in early development because, unlike genome, transcriptome and proteome analyses, metabolome analysis has to deal with a highly diverse range of biomolecules. Combinations of different analytical platforms are therefore required for comprehensive metabolomic studies. Each of these platforms covers only part of the metabolome. To establish multiparallel technologies, thorough standardization of each measured metabolite is required. Standardization is best achieved by addition of a specific stable isotope-labeled compound, a mass isotopomer, for each metabolite. This suggestion, at first glance, seems unrealistic because of cost and time constraints. A possible solution to this problem is discussed in this article. Saturation in vivo labeling with stable isotopes enables the biosynthesis of differentially mass-labeled metabolite mixtures, which can be exploited for highly standardized metabolite profiling by mass isotopomer ratios.

Biochemistry↗
PubMed2006

Identification of substrates of the extracellular protease ADAMTS1 by DIGE proteomic analysis.

Proteolytic modification of components of the extracellular milieu by metalloproteinases plays important roles in the regulation of multiple cellular and physiological processes and pathological conditions. ADAMTS1 is a secreted enzyme of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) family of proteases, which is related to angiogenesis and inflammation processes. Here, we describe a proteomic screening for putative ADAMTS1 substrates by analyzing the protein profiles obtained from cultures of transfected cells overexpressing the protease as compared to parental cells. Conditioned medium proteins of cultures of the two cell lines have been quantitatively compared by DIGE. Proteins showing differential levels have been identified by MS techniques leading to the finding of five potential new substrates of ADAMTS1: the basement membrane proteins nidogen-1 and -2, the desmosomal protein desmocollin-3, and the extracellular glycoproteins dystroglycan 1 and Mac-2-binding protein. Nidogen-1 and -2 have been further validated as substrates by immunochemical analysis. Our results demonstrate the utility of the DIGE proteomic technique for the discovery of specific substrates of matrix proteases.

ADAM Proteins↗
PubMed2026

NR3C1 Modulates Wnt Signalling to Influence the Invasiveness and Immune Features of Nonfunctioning Invasive Pituitary Adenomas.

Pituitary adenomas (PAs) are common intracranial tumours, and invasiveness in nonfunctioning invasive pituitary adenomas (NIPAs) predicts poor prognosis. The molecular mechanisms driving this phenotype remain unclear. This study explored the role of nuclear receptor subfamily 3 group C member 1 (NR3C1) in NIPA invasiveness and its regulation of Wnt signalling. mRNA expression profiles of 32 PA samples were generated by RNA-seq, and proteomic data from 19 samples were obtained by mass spectrometry. Immune-related differentially expressed genes (DEGs) were retrieved from GeneCards. Weighted gene coexpression network analysis identified modules and hub genes linked to invasiveness, while machine learning methods (support vector machine, LASSO, random forest) prioritised key genes. Gene set enrichment analysis (GSEA) assessed pathways associated with candidate gene expression. NR3C1 expression and function were validated by immunohistochemistry, Western blotting and invasion assays. Integration of transcriptomic, proteomic and immune-related datasets yielded 11 overlapping genes, with NR3C1 emerging as the top candidate. NR3C1 was significantly upregulated in NIPAs and demonstrated good discriminatory power by ROC analysis. GSEA associated high NR3C1 expression with Wnt pathway activation. Functional experiments confirmed that NR3C1 overexpression enhances the invasive capacity of PA cells. NR3C1 promotes the invasive phenotype of NIPAs by activating Wnt signalling. These findings suggest NR3C1 as a potential biomarker and therapeutic target for invasive pituitary adenomas.

Humans↗
PubMed2006

Identification of proteomic signatures of exposure to marine pollutants in mussels (Mytilus edulis).

Bivalves and especially mussels are very good indicators of marine and estuarine pollution, and so they have been widely used in biomonitoring programs all around the world. However, traditional single parameter biomarkers face the problem of high sensitivity to biotic and abiotic factors. In our study, digestive gland peroxisome-enriched fractions of Mytilus edulis (L., 1758) were analyzed by DIGE and MS. We identified several proteomic signatures associated with the exposure to several marine pollutants (diallyl phthalate, PBDE-47, and bisphenol-A). Animals collected from North Atlantic Sea were exposed to the contaminants independently under controlled laboratory conditions. One hundred and eleven spots showed a significant increase or decrease in protein abundance in the two-dimensional electrophoresis maps from the groups exposed to pollutants. We obtained a unique protein expression signature of exposure to each of those chemical compounds. Moreover a set of proteins composed a proteomic signature in common to the three independent exposures. It is remarkable that the principal component analysis of these spots showed a discernible separation between groups, and so did the hierarchical clustering into four classes. The 14 proteins identified by MS participate in alpha- and beta-oxidation pathways, xenobiotic and amino acid metabolism, cell signaling, oxyradical metabolism, peroxisomal assembly, respiration, and the cytoskeleton. Our results suggest that proteomic signatures could become a valuable tool to monitor the presence of pollutants in field experiments where a mixture of pollutants is often present. Further studies on the identified proteins could provide crucial information to understand possible mechanisms of toxicity of single xenobiotics or mixtures of them in marine ecosystems.

Animals↗
PubMedDate not supplied

Evaluation of biomarker discovery approaches to detect protein biomarkers of acute renal allograft rejection.

Management of host responses to allografts by immunosuppressive therapy is the cornerstone of transplantation medicine, but it is still deficient in one important element: biomarkers that are readily accessible and predict the fate of the transplant early, specifically, and reliably. Using a Brown Norway (BN)-to-Lewis rat renal allograft model of kidney transplantation, this study aims at evaluating two proteomic approaches to discover biomarkers for acute rejection: SELDI-MS technology and 2D gel electrophoresis combined with mass spectrometry. Several novel potential serum biomarkers have been identified for follow up. Overall, the conclusion is that apparently at the serum protein level, dramatic changes only occur at a stage where kidney function is already severely affected. Multivariate analysis of serum profiles suggests that there is an ensemble of subtle changes, comprising a proteomic signature of acute rejection at an early stage, a more detailed evaluation of which might provide novel opportunities for the diagnosis of acute rejection. Profiling of the excreted proteins indicates that urine might even present the earliest signs of the rejection process.

Animals↗
PubMed2006

'Oming in on schistosomes: prospects and limitations for post-genomics.

The recent release of version 3 of the Schistosoma mansoni genome assembly has made a wealth of information available to researchers. Here, progress made in schistosome genomics and post-genomics is considered. The current status of knowledge about the genome, transcriptome, proteome, glycome and immunome is summarized and recent publications briefly reviewed. The prospects for advances in understanding schistosome biology are highlighted. Most importantly, the limitations (which are mostly technical) that need to be addressed before the full potential of the genome database(s) can be realized are emphasized.

Animals↗
PubMed2000

Operomics: molecular analysis of tissues from DNA to RNA to protein.

The identification of coding sequences in a number of species, including human in the near future, has ushered in the post-genome era. In this era, technologies are becoming available that allow the profiling of tissues and cell populations at the genomic, transcriptomic and proteomic levels. The molecular analysis of tissues at all three levels has been referred to as operomics. This review covers some basic technologies for operomics and their application to some lymphoid disorders. It is proposed that no one type of analysis is fully informative and that information that can be derived from the different compartments encompassed in operomics is complementary. Prospects for introducing such profiling technologies into the clinical laboratory will depend on their robustness, their user friendliness and the clinical relevance of the added information they provide, which cannot be captured through other technologies in use in the clinical laboratory.

Genomics↗
PubMedDate not supplied

Enabling proteomics discovery through visual analysis. The peptide permutation and protein prediction tool.

Proteins play a key role in cellular processes, making proteomics central to understanding systems biology. MS techniques provide a means to observe entire proteomes at a global level. Yet, high-throughput MS proteomics techniques generate data faster than it can currently be analyzed. The success of proteomics depends on high-throughput experimental techniques coupled with sophisticated visual analysis and data-mining methods. Visual analysis has been applied successfully in a number of fields plagued with huge, complex data sets and will likely be an important tool in proteomics discovery. PQuad, a novel visualization of MS proteomics data, provides powerful analysis capabilities that support a number of proteomic data applications. In particular, PQuad supports differential proteomics by simplifying the comparison of peptide sets from different experimental conditions as well as different protein identification or confidence scoring techniques. Finally, PQuad supports data validation and quality control by providing a variety of resolutions for huge amounts of data to reveal errors undetected by other methods.

Algorithms↗
PubMed2006

An efficient protein preparation for proteomic analysis of developing cotton fibers by 2-DE.

Preparation of high-quality proteins from cotton fiber tissues is difficult due to high endogenous levels of polysaccharides, polyphenols, and other interfering compounds. To establish a routine procedure for the application of proteomic analysis to cotton fiber tissues, a new protocol for protein extraction was developed by optimizing a phenol extraction method combined with methanol/ammonium acetate precipitation. The protein extraction for 2-DE was remarkably improved by the combination of chemically and physically modified processes including polyvinylpolypyrrolidone (PVPP) addition, acetone cleaning, and SDS replacement. The protocol gave a higher protein yield and vastly greater resolution and spot intensity. The efficiency of this protocol and its feasibility in fiber proteomic study were demonstrated by comparison of the cotton fiber proteomes at two growth stages. Furthermore, ten protein spots changed significantly were identified by MS/tandem MS and their potential relationships to fiber development were discussed. To the best of our knowledge, this is the first time that a protocol for protein extraction from cotton fiber tissues appears to give satisfactory and reproductive 2-D protein profiles. The protocol is expected to accelerate the process of the proteomic study of cotton fibers and also to be applicable to other recalcitrant plant tissues.

Databases, Protein↗
PubMed2026

Next-Generation Disease Profiling by Integrating Histopathology with Spatial Multi-Omics Data.

The field of pathology has experienced several transformative changes in recent years with the advent of digital pathology and spatial multi-omics. These technologies have enhanced every aspect of pathology practice, from streamlining daily workflows to generating high-fidelity multi-omics data that provide pathologists with novel tools to refine disease profiling and clinical diagnosis. Each layer of multimodal data (genomic, metabolomic, proteomic, or transcriptomic) has uncovered a distinct facet of disease pathologies, and combined with machine learning/artificial intelligence-based data analysis and pattern recognition models, has provided holistic understanding of regulatory mechanisms underpinning them. However, high-dimensional data have far exceeded the volume, scale, and complexity of immunostaining methods implemented by pathologists and, thus, have generated significant challenges related to deconvolution, interpretation, and clinical translation. Furthermore, these multimodal studies have predominantly relied on computational methods to process data and extract disease-relevant insights, thus raising questions around relevance or role of a pathologist in this new era of multi-omics. This review will provide a perspective on the evolving fields of molecular histopathology and spatial -omics, leveraging them to approach disease profiling, and redefining the role of a pathologist during this process.

Humans↗
PubMedDate not supplied

Proteomics in malaria.

The recent completion of human, Anopheles gambiae, and Plasmodium falciparum genomes relevant to the study of human malaria allows the application of modern proteomic technologies to complement previously implemented conventional approaches. Proteomic analysis has been employed to elucidate global protein expression profiles, subcellular localization of gene products, and host-pathogen interactions that are central to disease pathogenesis and treatment. The high-throughput nature of these techniques is in accord with the pace of drug and vaccine development that have the potential to directly reduce the morbidity and mortality of disease.

Animals↗
PubMed2002

Multiplexed protein profiling on microarrays by rolling-circle amplification.

Fluorescent-sandwich immunoassays on microarrays hold appeal for proteomics studies, because equipment and antibodies are readily available, and assays are simple, scalable, and reproducible. The achievement of adequate sensitivity and specificity, however, requires a general method of immunoassay amplification. We describe coupling of isothermal rolling-circle amplification (RCA) to universal antibodies for this purpose. A total of 75 cytokines were measured simultaneously on glass arrays with signal amplification by RCA with high specificity, femtomolar sensitivity, 3 log quantitative range, and economy of sample consumption. A 51-feature RCA cytokine glass array was used to measure secretion from human dendritic cells (DCs) induced by lipopolysaccharide (LPS) or tumor necrosis factor-alpha (TNF-alpha). As expected, LPS induced rapid secretion of inflammatory cytokines such as macrophage inflammatory protein (MIP)-1beta, interleukin (IL)-8, and interferon-inducible protein (IP)-10. We found that eotaxin-2 and I-309 were induced by LPS; in addition, macrophage-derived chemokine (MDC), thymus and activation-regulated chemokine (TARC), soluble interleukin 6 receptor (sIL-6R), and soluble tumor necrosis factor receptor I (sTNF-RI) were induced by TNF-alpha treatment. Because microarrays can accommodate approximately 1,000 sandwich immunoassays of this type, a relatively small number of RCA microarrays seem to offer a tractable approach for proteomic surveys.

Antibodies↗
PubMed2001

One-step subcellular fractionation of rat liver tissue using a Nycodenz density gradient prepared by freezing-thawing and two-dimensional sodium dodecyl sulfate electrophoresis profiles of the main fraction of organelles.

In the present study, we describe a new procedure using freezing-thawing to density gradient solution of Nycodenz for one-step separation of organelles from the rat liver and subsequent proteome analysis of subcellular fractions. To prepare two-dimensional electrophoresis (2-D PAGE) profiles of tissue organelles, we performed one-step subcellular fractionation of rat liver homogenate using a density gradient of Nycodenz solution, which resulted in the separation of the cytosolic fraction from the postnuclear supernatant. The density gradient of Nycodenz was prepared from a 20% solution in a centrifuge tube by freezing-thawing overnight at -20 degrees C and at room temperature for a few hours without the initial centrifugation procedure. The shape of the gradient density curve was dependent on Nycodenz concentration and tube size. After fractionation, the protein profiles were examined using one-dimensional sodium dodecyl sulfate (SDS)-PAGE. The organelles were confirmed using Western blotting. Our results indicate that our procedure provides a simple method for the separation of organelle fractions from the rat liver tissue.

Animals↗