SEARCH · PubMed Health

Results for “multiplexed proteomics”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 199 records · Page 11Linked to original sources

PubMed2005

Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium.

In this chapter we describe the core Protein Production Platform of the Northeast Structural Genomics Consortium (NESG) and outline the strategies used for producing high-quality protein samples using Escherichia coli host vectors. The platform is centered on 6X-His affinity-tagged protein constructs, allowing for a similar purification procedure for most targets, and the implementation of high-throughput parallel methods. In most cases, these affinity-purified proteins are sufficiently homogeneous that a single subsequent gel filtration chromatography step is adequate to produce protein preparations that are greater than 98% pure. Using this platform, over 1000 different proteins have been cloned, expressed, and purified in tens of milligram quantities over the last 36-month period (see Summary Statistics for All Targets, ). Our experience using a hierarchical multiplex expression and purification strategy, also described in this chapter, has allowed us to achieve success in producing not only protein samples but also many three-dimensional structures. As of December 2004, the NESG Consortium has deposited over 145 new protein structures to the Protein Data Bank (PDB); about two-thirds of these protein samples were produced by the NESG Protein Production Facility described here. The methods described here have proven effective in producing quality samples of both eukaryotic and prokaryotic proteins. These improved robotic and?or parallel cloning, expression, protein production, and biophysical screening technologies will be of broad value to the structural biology, functional proteomics, and structural genomics communities.

Chromatography, Gel↗

PubMedDate not supplied

[Pasteurella: insights into the virulence determinants of a heterogenous bacterial type].

Pasteurella (P.) multocida is the causative agent of numerous economically relevant diseases worldwide. These are enzootic bronchopneumonia in cattle and sheep and hemorraghic septicemia in cattle and buffaloes, Rhinitis atrophicans in swine, snuffles in rabbit, and fowl cholera. All disease complexes are associated with certain capsular and somatic antigens. Even as human pathogen P. multocida is of increasing importance, causing wound infections, and even septicemia, meningitis, and endocarditis. Despite extensive research activities including the genome analysis of one fowl cholera isolate in the year 2001 there are a lot of open questions concerning the molecular pathogenic mechanisms. Problems encountered are the high antigenic variability and the wide host spectrum of P. multocida as well as different courses of infection. In consequence there are enormous difficulties in producing vaccines. Transcriptomics and proteomics hopefully will give new insight into the pathogenesis of P. multocida infections in different hosts. A frequent problem particular in classical diagnostic laboratories is the diagnosis of P. multocida and its differentiation from other P. species and Mannheimia (M.) haemolytica. The biochemical identification of P. multocida is not reliable due to variable phenotypical characteristics often caused by different culture conditions, and it is time consuming and cost-intensive. Extensive molecular biologic studies concerning the prevalence and distribution of virulence associated genes known so far in P. species, which will be described in detail in this paper, could contribute to the establishment of a diagnostic tool, such as a multiplex polymerase chain reaction, that would provide a cheap and time-saving identification and characterization of wildtype strains.

Animal Diseases↗

PubMed2003

Signal pathway profiling of prostate cancer using reverse phase protein arrays.

Reverse phase protein arrays represent a new proteomics microarray technology with which to study the fluctuating state of the proteome in minute quantities of cells. The activation status of cell signaling pathways controls cellular fate and deregulation of these pathways underpins carcinogenesis. Changes in pathway activation that occur between early stage prostatic epithelial lesions, prostatic stroma and the extracellular matrix can be analyzed by obtaining pure populations of cell types by laser capture microdissection (LCM) and analyzing the relative states of several key phosphorylation points within the cellular circuitry. We have applied reverse phase protein array technology to analyze the status of key points in cell signaling involved in pro-survival, mitogenic, apoptotic and growth regulation pathways in the progression from normal prostate epithelium to invasive prostate cancer. Using multiplexed reverse phase protein arrays coupled with LCM, the states of signaling changes during disease progression from prostate cancer study sets were analyzed. Focused analysis of phospho-specific endpoints revealed changes in cellular signaling events through disease progression and between patients. We have used a new protein array technology to study specific molecular pathways believed to be important in cell survival and progression from normal epithelium to invasive carcinoma directly from human tissue specimens. With the advent of molecular targeted therapeutics, the identification, characterization and monitoring of the signaling events within actual human biopsies will be critical for patient-tailored therapy.

Antigens, Neoplasm↗

PubMed2007

Protein arrays: a versatile toolbox for target identification and monitoring of patient immune responses.

Functional proteomics is a promising technique for the rational identification of novel therapeutic targets and biological markers. The studies of protein-protein interactions have been gained from the development of high-throughput technologies such as the yeast two-hybrid system, protein arrays, phage display, and systematic analysis of interaction maps for the prediction of protein functions. Because antibodies are used extensively as diagnostic and clinical tools, the characterization of their antigen specificity is of prime importance. Indeed, screening protein arrays with sera from patients with either cancer or autoimmune diseases would facilitate the identification of autoantibody signatures that can be used for diagnosis and/or prognosis of patients. The usefulness of multiplexed measurements lies not only in the ability to screen many individual marker candidates but also in evaluating the use of multiple markers in combination. Here, we review the advantage of protein and serum screening of peptides and cDNA repertoires displayed on phages as well as the fabrication of protein microarrays for probing immune responses in patients.

Autoantibodies↗

PubMed2004

Serum protein profiling by SELDI mass spectrometry: detection of multiple variants of serum amyloid alpha in renal cancer patients.

The molecular analysis of serum is an important field for the definition of potential diagnostic markers or disease-related protein alterations. Novel proteomic technologies such as the mass spectrometric-based surface-enhanced laser desorption/ionization (SELDI) ProteinChip technique facilitate a rapid and reproducible analysis of such protein mixtures and affords the researcher a new dimension in the search for biomarkers of disease. Here, we have applied this technology to the study of a cohort of serum samples from well-characterized renal cell carcinoma patients for the identification of such proteins by comparison to healthy controls. We detected and characterized haptoglobin 1 alpha and serum amyloid alpha-1 (SAA-1) as disease related, in addition to an as-yet-unidentified marker of 10.84 kDa. Of particular note is the detection of multiple variants of SAA-1 in multiplex that have not been described in the sera of cancer patients. SAA-1 is detected as full-length protein, des-Arginine and des-Arginine/des-Serine variants at the N terminus by SELDI. In addition, we could also detect a low-abundant variant minus the first five N-terminal amino acids. Such variants may impact the function of the protein. We conclude the technique to be a reproducible, fast and simple mode for the discovery and analysis of marker proteins of disease in serum.

Adult↗

PubMed2005

Expression genomics and drug development: towards predictive pharmacology.

Expression genomics can be defined as the study of the dynamic transciptome and its regulatory elements. Technologies are available that can assess transcripts on a genome-wide scale over time and across many samples. This comprehensive and dynamic database is being used to decipher signalling pathways and to identify new biomarkers and targets. Biomarkers emerging from these studies have prognostic potential and can be used to predict therapeutic outcome. The multiplex nature of this approach not only telescopes the time to discovery, but also allows for detection of complex interactions. Taken together, these capabilities, if carefully used, can speed drug development, enhance the identification of potent drug combinations and identify patient populations that will benefit from these new drugs.

Biomarkers↗

PubMed2006

On the discovery of the genetic association of Apolipoprotein E genotypes and common late-onset Alzheimer disease.

The association of Apolipoprotein E-4 with the age of onset of common late-onset Alzheimer's disease (AD) was originally reported in three 1993 papers from the Duke ADRC (Alzheimer's Disease Research Center) group. The Center was investigating two diverse experimental streams that led to this discovery. The first being a genetic linkage study performed in multiplex familial late-onset AD in which a linkage was discovered at chromosome 19q13. The 1991 multilocus analysis of linkage had been considered very controversial. The second stream came from a series of amyloid-beta binding studies in which a consistent protein "impurity" was present on gel separation analyses. After sequencing this "impurity" band, several tryptic peptide sequences were found to be identical for apoE which, at that time, had no known association with Alzheimer's disease. The flash of recognition was the knowledge that APOE was one of the first genes localized to chromosome 19 in the mid-1980's. Within a three week period in late 1992, a highly significant association was identified in clinical patients from multiplex families, in sporadic clinical patients, and in autopsy diagnosed series. Within the first two months of 1993, it was possible to clearly demonstrate that the APOE isoforms were associated with differing ages of onset, but the course of illness following diagnosis was related more to age than APOE genotype. The earliest submitted paper reported the familial association and amyloid-beta binding. The second reported the association with common sporadic late-onset, [not-known to be familial] AD patients. The third reported that APOE4 carriers had earlier rates of onset of clinical disease than APOE2 or APOE3 carriers. Subsequently, over more than a decade, the biological expression of apoE in human neurons was confirmed as distinct from rodent brain. Proteomic experiments and positron emission tomography data have led to a series of clinical trials with agents selected to increase glucose utilization. These agents also regulate inflammatory responses of neural cells. Rosiglitazone, a PPARgamma agonist which also leads to mitochondrial proliferation shown efficacy as a monotherapy in a Phase IIB clinical trial of 511 patients in an APOE allele-specific analysis.

Alzheimer Disease↗

PubMed2006

Automated quantification of quantum-dot-labelled epidermal growth factor receptor internalization via multiscale image segmentation.

The ability to monitor epidermal growth factor receptor (EGFr) internalization specifically, and cellular protein concentrations and activation states in general, has been recently improved by the use of appropriately functionalized quantum dots (QDs), as a result of the long-lasting fluorescence, brightness and multicolour of these nanoparticles. However, important quantitative information about locational proteomics is based on the analysis of the properties of many cells and cell cultures on a per-cell basis, rather than tracking individual events within one cell. Moreover, relative positional information is often gained from traditional staining protocols of distinct cellular compartments that are prone to noise, fading and low contrast. We apply a novel multiscale image segmentation based on region growing to classify automatically objects in fixed cell preparations and to define regional zones in all cells prior to QD concentration measures. This allows rapid quantitative description of EGFr internalization as it changes with incubation time. The capabilities realizable by simultaneous application of confocal imaging and functionalized QDs in conjunction with advanced image analysis are a prerequisite for automated and multiplexed cytomics assays.

Biotin↗

PubMed2006

New analytical tools for studying autoimmune diseases.

Protein microarrays with immobilised proteins on their surface are new analytical tools to overcome the current limits with respect to sample volume and throughput. They have a great potential as well with respect to multiplexing of complex samples, as a research tool and in diagnostics. Based on recent advances in this technology, new applications for protein microarrays in studying autoimmune diseases were described. Required tools for bioinformatical analysis of protein microarrays concerning normalisation, clustering and classification methods are discussed. The huge potential of this technology as well as future requirements such as protein microarray based diagnostics are presented.

Animals↗

PubMed2004

Computational lipidomics: a multiplexed analysis of dynamic changes in membrane lipid composition during signal transduction.

Recent successes in defining the roles of lipids in cell signaling have stimulated greater interest in these versatile biomolecules. Until recently, analysis of these molecules at the species level has required labor-intensive techniques. The development of electrospray ionization mass spectrometry (ESI-MS) has made possible the detection and identification of thermally labile biological molecules, such as phospholipids. The "soft" ionization does not cause extensive fragmentation, is highly sensitive, accurate, and reproducible. Thus, this method is well suited for analyzing a broad range of phospholipids without elaborate chromatographic separation. Evaluating the vast amounts of data resulting from these measurements is a rate-limiting step in the assessment of phospholipid composition, requiring the development and application of computational algorithms for mass spectrometry data. Here we describe computational lipidomics, a novel analytical technique, coupling mass spectrometry with statistical algorithms to facilitate the comprehensive analysis of hundreds of lipid species from cellular extracts. As a result, lipid arrays are generated to indicate qualitative changes that occur in lipid composition between experimental or disease states, similar to proteomic and genomic analyses. This review presents a methodological strategy for using ESI-MS combined with a high-power computational analysis to profile time-dependent changes in cellular phospholipids after the addition of an agonist or to evaluate changes promoted by pathophysiological processes. As an illustration, we describe the methods and approaches used to generate lipid arrays for The Alliance for Cellular Signaling (AfCS). These arrays are contributing to a more complete understanding of the participants of cellular signaling pathways after activation of cell surface receptors.

Animals↗

PubMed2004

Stm1p, a G4 quadruplex and purine motif triplex nucleic acid-binding protein, interacts with ribosomes and subtelomeric Y' DNA in Saccharomyces cerevisiae.

The Saccharomyces cerevisiae protein Stm1 was originally identified as a G4 quadruplex and purine motif triplex nucleic acid-binding protein. However, more recent studies have suggested a role for Stm1p in processes ranging from antiapoptosis to telomere maintenance. To better understand the biological role of Stm1p and its potential for G(*)G multiplex binding, we used epitope-tagged protein and immunological methods to identify the subcellular localization and protein and nucleic acid partners of Stm1p in vivo. Indirect immunofluorescence microscopy indicated that Stm1p is primarily a cytoplasmic protein, although a small percentage is also present in the nucleus. Conventional immunoprecipitation found that Stm1p is associated with ribosomal proteins and rRNA. This association was verified by rate zonal separation through sucrose gradients, which showed that Stm1p binds exclusively to mature 80 S ribosomes and polysomes. Chromatin immunoprecipitation experiments found that Stm1p preferentially binds telomere-proximal Y' element DNA sequences. Taken together, our data suggest that Stm1p is primarily a ribosome-associated protein, but one that can also interact with DNA, especially subtelomeric sequences. We discuss the implications of our findings in relation to prior genetic, genomic, and proteomic studies that have identified STM1 and/or Stm1p as well as the possible biological role of Stm1p.

Amino Acid Motifs↗

PubMedDate not supplied

Proteins, recognition networks and developing interfaces for macromolecular biosensing.

Genomics and proteomics discovery is leading to the identification of all proteins and to the opportunity, and challenge, to reveal the protein recognition networks that drive virtually all biological processes. Over the past decade, biosensors have emerged as a key technology for detection and analysis of biomolecular interactions. An important limitation in developing such biosensors is that the focus has been mainly on sensor platforms, the transducing hardware that converts interaction signals into recorded data, without adequately considering the role of molecular interfaces, the elements of sensors that interact with analytes to produce signals. We have investigated this alternative focus by identifying and, where necessary, designing molecular interfaces that will more effectively drive new biosensor development and utilization in biomedical and biotechnological investigations. Here we describe our recent studies of coiled coil and lipid bilayer interfaces and the potential to use these to expand sensing technologies for multiplexed target detection and analysis in increasingly biologically relevant membrane like environments.

Amino Acid Motifs↗

PubMed2003

Signal pathway profiling of ovarian cancer from human tissue specimens using reverse-phase protein microarrays.

Defects in cell signaling pathways play a central role in cancer cell growth, survival, invasion and metastasis. An important goal of proteomics is to characterize and develop "circuit maps" of these signaling pathways in normal and diseased cells. We have used reverse-phase protein array technology coupled with laser capture microdissection and phospho-specific antibodies to examine the activation status of several key molecular "gates" involved in cell survival and proliferation signaling in human ovarian tumor tissue. The levels of activated extracellular-regulated kinase (ERK1/2) varied considerably in tumors of the same histotype, but no significant differences between histotypes were observed. Advanced stage tumors had slightly higher levels of phosphorylated ERK1/2 compared to early stage tumors. The activation status of Akt and glycogen synthase kinase 3beta, key proteins and indicators of the state of the phosphatidylinositol 3-kinase/Akt pro-survival pathway also showed more variation within each histotype than between the histotypes studied. Our results demonstrate the utility of reverse phase protein microarrays for the multiplexed analysis of signal transduction from discreet cell populations of cells procured directly from human ovarian tumor specimens and suggest that patterns in signal pathway activation in ovarian tumors may be patient-specific rather than type or stage specific.

Biomarkers, Tumor↗

PubMed2004

Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents.

We describe here a multiplexed protein quantitation strategy that provides relative and absolute measurements of proteins in complex mixtures. At the core of this methodology is a multiplexed set of isobaric reagents that yield amine-derivatized peptides. The derivatized peptides are indistinguishable in MS, but exhibit intense low-mass MS/MS signature ions that support quantitation. In this study, we have examined the global protein expression of a wild-type yeast strain and the isogenic upf1Delta and xrn1Delta mutant strains that are defective in the nonsense-mediated mRNA decay and the general 5' to 3' decay pathways, respectively. We also demonstrate the use of 4-fold multiplexing to enable relative protein measurements simultaneously with determination of absolute levels of a target protein using synthetic isobaric peptide standards. We find that inactivation of Upf1p and Xrn1p causes common as well as unique effects on protein expression.

Cations↗

PubMedDate not supplied

Increased protein identification capabilities through novel tandem MS calibration strategies.

High mass measurement accuracy is critical for confident protein identification and characterization in proteomics research. Fourier transform ion cyclotron resonance (FTICR) mass spectrometry is a unique technique which can provide unparalleled mass accuracy and resolving power. However, the mass measurement accuracy of FTICR-MS can be affected by space charge effects. Here, we present a novel internal calibrant-free calibration method that corrects for space charge-induced frequency shifts in FTICR fragment spectra called Calibration Optimization on Fragment Ions (COFI). This new strategy utilizes the information from fixed mass differences between two neighboring peptide fragment ions (such as y(1) and y(2)) to correct the frequency shift after data collection. COFI has been successfully applied to LC-FTICR fragmentation data. Mascot MS/MS ion search data demonstrate that most of the fragments from BSA tryptic digested peptides can be identified using a much lower mass tolerance window after applying COFI to LC-FTICR-MS/MS of BSA tryptic digest. Furthermore, COFI has been used for multiplexed LC-CID-FTICR-MS which is an attractive technique because of its increased duty cycle and dynamic range. After the application of COFI to a multiplexed LC-CID-FTICR-MS of BSA tryptic digest, we achieved an average measured mass accuracy of 2.49 ppm for all the identified BSA fragments.

Algorithms↗

PubMed2007

Quantitative protein analysis from formalin-fixed tissues: implications for translational clinical research and nanoscale molecular diagnosis.

Owing to its cross-linking effects, it is currently believed that formalin fixation of routinely processed tissues in the clinic prevents protein extraction and profiling. The aim of our study was to develop a robust, fast, standardized, and easy to use technique for the solubilization of non-degraded, full length, and immunoreactive proteins from formalin-fixed tissues for western blot and protein microarray analysis. Sections of routinely processed formalin-fixed and paraffin-embedded tissues of various origin were analysed. After deparaffination, tissues were manually dissected from the slides and transferred into an optimized protein extraction buffer system. Proteins were solubilized and subsequently analysed by western blot and reverse phase protein microarrays. We succeeded in isolating non-degraded, soluble, and immunoreactive proteins from routinely processed formalin-fixed tissues. We were able to detect membrane, cytoplasmic and nuclear proteins at the expected molecular weight. No differences were found in the protein yield and protein abundances between fresh frozen and formalin-fixed tissues. Using western blots and reverse phase protein microarrays, the receptor tyrosine kinase HER2, an important protein target for antibody based cancer treatment, was reliably measured in formalin-fixed breast cancer biopsy samples when compared with measurement by immunohistochemistry and fluorescence in situ hybridization; remarkably, immunohistochemically equivocal cases (score 2+) can be categorized according to HER2 protein abundance. Our new clinically orientated multiplexed protein measurement system may be generally applicable to determine the relative abundances of known disease-related proteins in small amounts of routinely processed formalin-fixed tissue samples for research and diagnosis. This technique may also be used to identify, characterize, and validate known and new protein markers in a variety of human diseases.

Animals↗

PubMedDate not supplied

Pegylated, steptavidin-conjugated quantum dots are effective detection elements for reverse-phase protein microarrays.

Protein microarray technologies provide a means of investigating the proteomic content of clinical biopsy specimens in order to determine the relative activity of key nodes within cellular signaling pathways. A particular kind of protein microarray, the reverse-phase microarray, is being evaluated in clinical trials because of its potential to utilize limited amounts of cellular material obtained through biopsy. Using this approach, cellular lysates are arrayed in dilution curves on nitrocellulose substrates for subsequent probing with antibodies. To improve the sensitivity and utility of reverse-phase microarrays, we tested whether a new reporter technology as well as a new detection instrument could enhance microarray performance. We describe the use of an inorganic fluorescent nanoparticle conjugated to streptavidin, Qdot 655 Sav, in a reverse-phase protein microarray format for signal pathway profiling. Moreover, a pegylated form of this bioconjugate, Qdot 655 Sav, is found to have superior detection characteristics in assays performed on cellular protein extracts over the nonpegylated form of the bioconjugate. Hyperspectral imaging of the quantum dot microarray enabled unamplified detection of signaling proteins within defined cellular lysates, which indicates that this approach may be amenable to multiplexed, high-throughput reverse-phase protein microarrays in which numerous analytes are measured in parallel within a single spot.

Calibration↗

PubMed2003

High-throughput miniature cylindrical ion trap array mass spectrometer.

A fully multiplexed cylindrical ion trap (CIT) array mass spectrometer with four parallel ion source/mass analyzer/detector channels has been built to allow simultaneous high-throughput analysis of multiple samples. A multielement external chemical ionization/electron ionization source was coupled to a parallel array of CITs each of equal size (internal radius 2.5 mm), and the signal was recorded using an array of four miniature (2-mm inner diameter) electron multipliers. Using external electron ionization, the spectra of four separate samples were recorded simultaneously in real time using a four-channel preamplifier system and a data acquisition program written using LabVIEW software. These experiments mark the first demonstration of externally generated ions being successfully trapped in a miniature CIT mass analyzer. The instrument currently provides mass/charge range of approximately m/z 50-500. Average peak width is m/z 0.3, corresponding to a resolution of 1000 at m/z 300. The four-channel mass spectrometer is housed in a single vacuum manifold and operated with a single set of control electronics. The modular design of this instrument allows scale-up to many more channels of analysis for future applications in the areas of industrial process monitoring and combinatorial analysis and in the fields of proteomics and metabolomics.

Journal Article↗