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Results for “Protein Array Analysis”

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PubMed2004

Evaluation of an integrated strategy for proteomic profiling of skeletal muscle.

Proteomic analysis of skeletal muscle presents particular challenges when trying to identify valid biomarkers of phenotypic change in small biopsies from genetically diverse human subjects. Currently, two-dimensional (2-D) gel electrophoresis and mass spectrometry are the chosen analytical strategies but 2-D gels are not appropriate for analyzing proteins less than 11 kDa, they can suffer from problems of reproducibility and in routine use are not a viable high-throughput technique. We have evaluated an integrated proteomic strategy employing Ciphergen ProteinChip arrays, one-dimensional polyacrylamide gel electrophoresis and mass spectrometry. Protein fingerprints characteristic of fast and slow contracting muscles from normal and kyphoscoliosis (ky) mutant mice were obtained from Ciphergen protein arrays. Eight statistically validated protein biomarkers have so far been identified capable of discriminating fast from slow muscle. Five of these showed further differential expression in ky versus normal BDL soleus muscles. Several biomarkers have been formally identified, and were myosin light chain isoforms shown previously to be expressed differentially by fast versus slow skeletal muscles. This integrated experimental approach using a model mouse muscle system shows the potential of Ciphergen protein array technology for proteomic analysis of small proteins in small muscle samples and its applicability for phenotypic characterization of skeletal muscle in general.

Animals↗

PubMed2004

Proteomic analysis as related to transcriptome data in the lung of chromium(VI)-treated rats.

Assessing the parallelism between transcriptome data and proteome data represents one of the major challenges of post-genomic research. We evaluated the levels of 380 proteins in lung S12 fractions from Sprague-Dawley rats by antibody microarrays. Approximately half of these proteins were detectable under physiological conditions. There was a poor parallelism between mRNA and protein levels for a subset of 84 coinciding or related activities, whose gene expression had previously been investigated by cDNA array. The proportion of detectable proteins was almost twice as high as the proportion of transcriptionally active genes, which reflects the longer half-life of proteins compared to mRNA. Following the local stimulus provided by a short-term and high-dose exposure to sodium dichromate by the intra-tracheal route, 64 additional proteins were detectable in lung S12 fractions, and the correlation between gene expression and protein levels became significant. Sixteen proteins were increased more than twice following chromium(VI) administration. They included ten activities involved in the positive regulation of the cell cycle, three proteins involved in stress response and protein repair, two pro-apoptotic activities, and one protein involved in lipoprotein catabolism. An increase of P53 protein was detected by Western blot in lung nuclear fractions. Post-genomic analyses, highlighting the stimulation of defence mechanisms triggered by DNA damage, contribute to explain the previously reported discrepancy between the ability of chromium(VI) to induce oxidative stress and genotoxic damage in the lung and its failure to induce lung tumors under comparable experimental conditions. The proteome analysis showed a prominent role of apoptosis, counter-balanced by a positive regulation of the cell cycle aimed at replacing lost cells. In conclusion, our results suggest that, under basal conditions, mRNA undergoes a selective inactivation and post-transcriptional regulation resulting in de-coupling of transcriptome data and proteome data. However, this parallelism is re-established when the cell undergoes genotoxic damage.

Animals↗

PubMed2006

Direct production and purification of T7 phage display cloned proteins selected and analyzed on microarrays.

Phage display technology has emerged into a powerful tool for identifying proteins with specific binding properties. This technology adds amino acid sequences to the carboxy terminus of a phage capsid protein, thus generating a fusion protein displayed on the surface of the phage. Here, we have developed a high-throughput strategy to synthesize purified protein that solves many of the problems associated with crude phage lysates. Phage DNA was used as a template for a nested PCR that added the T7 promoter, ribosome binding site, and a His6-tag. The PCR product was then used as a template for in vitro transcription/translation. The resulting His6-tagged recombinant protein was then purified by nickel affinity chromatography. The functionality of the purified protein was verified using protein microarray analysis.

Bacteriophage T7↗

PubMed2003

A MutS-based protein chip for detection of DNA mutations.

This paper describes a new protein chip method for detection of single-base mismatches and unpaired bases of DNA, using a genetic fusion molecular system Trx-His6-Linker peptide-Strep-tagII-Linker peptide-MutS (THLSLM). The THLSLM coding sequence was constructed by attaching Strep-tag II and mutS gene to pET32a (+) sequentially with insertion of a linker peptide coding sequence before and behind Strep-tagII gene, respectively. THLSLM was expressed in E. coli AD494 (DE3) and purified using Ni(2+)-chelation affinity resin. THLSLM retained both mismatch recognition activity and streptavidin binding affinity. THLSLM was then immobilized on the chip matrix coated with streptavidin through the Strep-tag II-streptavidin binding reaction. The resulting protein chip was used to detect the mismatched and unpaired mutations in the synthesized oligonucleotides, as well as a single-base mutation in rpoB gene from Mycobacterium tuberculosis, with high specificity. The method could potentially serve as a platform to develop the high-throughput technology for screening and analysis of genetic mutations.

Adenosine Triphosphatases↗

PubMed2005

DNA and protein microarray printing on silicon nitride waveguide surfaces.

Sputtered silicon nitride optical waveguide surfaces were silanized and modified with a hetero-bifunctional crosslinker to facilitate thiol-reactive immobilization of contact-printed DNA probe oligonucleotides, streptavidin and murine anti-human interleukin-1 beta capture agents in microarray formats. X-ray photoelectron spectroscopy (XPS) was used to characterize each reaction sequence on the native silicon oxynitride surface. Thiol-terminated DNA probe oligonucleotides exhibited substantially higher surface printing immobilization and target hybridization efficiencies than non-thiolated DNA probe oligonucleotides: strong fluorescence signals from target DNA hybridization supported successful DNA oligonucleotide probe microarray fabrication and specific capture bioactivity. Analogously printed arrays of thiolated streptavidin and non-thiolated streptavidin did not exhibit noticeable differences in either surface immobilization or analyte capture assay signals. Non-thiolated anti-human interleukin-1 beta printed on modified silicon nitride surfaces reactive to thiol chemistry exhibited comparable performance for capturing human interleukin-1 beta analyte to commercial amine-reactive microarraying polymer surfaces in sandwich immunoassays, indicating substantial non-specific antibody-surface capture responsible for analyte capture signal.

Biosensing Techniques↗

PubMedDate not supplied

Selective capture of prostatic basal cells and secretory epithelial cells for proteomic and genomic analysis.

Basal cells play an undefined role in signaling the growth and differentiation of normal secretory epithelial cells in the human prostate. Because basal cells disappear during malignant transformation, we hypothesize that loss of basal cell function may have a permissive role in progression of prostate intraepithelial neoplasia into invasive carcinoma. We describe an immuno-laser capture microdissection approach to selectively capture basal cells. Using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry, we identified several protein candidates selectively expressed in microdissected basal cells. We also demonstrate that the RNA derived form this technique is an excellent source for gene-array studies. Thus, we provide evidence that proteomic and microgenomic techniques can be successfully applied to investigate the expression profiles of basal and secretory cells after immuno-capture.

Cell Transformation, Neoplastic↗

PubMed2005

Microarrays based on affinity-tagged single-chain Fv antibodies: sensitive detection of analyte in complex proteomes.

Protein-based microarrays are among the novel class of rapidly emerging proteomic technologies that will allow us to efficiently perform global proteome analysis. However, the process of designing adequate protein microarrays is a major inherent problem. In this study, we have evaluated a protein microarray platform based on nonpurified affinity-tagged single-chain (sc) Fv antibody fragments to generate proof-of-principle and to demonstrate the specificity and sensitivity of the array design. To this end, we used our human recombinant scFv antibody library genetically constructed around one framework, the n-CoDeR library containing 2 x 10(10) clones, as a source for our probes. The probes were immobilized via engineered C-terminal affinity tags, his- or myc-tags, to either Ni(2+)-coated slides or anti-tag antibody coated substrates. The results showed that highly functional microarrays were generated and that nonpurified scFvs readily could be applied as probes. Specific and sensitive microarrays were obtained, providing a limit of detection in the pM to fM range, using fluorescence as the mode of detection. Further, the results showed that spotting the analyte on top of the arrayed probes, instead of incubating the array with large sample volumes (333 pL vs. 40 microL), could reduce the amount of analyte required 4000 times, from 1200 attomole to 300 zeptomole. Finally, we showed that a highly complex proteome, such as human sera containing several thousand different proteins, could be directly fluorescently labeled and successfully analyzed without compromising the specificity and sensitivity of the antibody microarrays. This is a prerequisite for the design of high-density antibody arrays applied in high-throughput proteomics.

Humans↗

PubMed2006

Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques.

MOTIVATION: We present a study of antigen expression signals from a newly developed high-throughput protein microarray technique. These signals are a measure of antibody-antigen binding activity and provide a basis for understanding humoral immune responses to various infectious agents and supporting vaccine and diagnostic development. RESULTS: We investigate the characteristics of these expression profiles and show that noise models, normalization, variance estimation and differential expression analysis techniques developed in the context of DNA microarray analysis can be adapted and applied to these protein arrays. Using a high-dimensional dataset containing measurements of expression profiles of antibody reactivity against each protein (295 antigens and 9 controls) in 42 malaria (Plasmodium falciparum) protein arrays derived from 22 donors with various clinical presentations of malaria, we present a methodology for the analysis and identification of significantly expressed antigens targeted by immune responses for individual sera, groups of sera and across stages of infection. We also conduct a short study highlighting the top immunoreactive antigens where we identify three novel high priority antigens for future evaluation. AVAILABILITY: All software programs (in R) used for the analysis described in this paper are freely available for academic purposes at www.igb.uci.edu/servers/servers.html.

Algorithms↗

PubMed2002

[New aspects of molecular biology diagnosis. Array technology and expression profile for characterization of rheumatic diseases].

Increasing availability of high throughput technologies, exponentially growing information about the human genome and gene expression, and the growing global network of databases on systematic biomedical information will change our view on inflammatory rheumatic diseases in a revolutionary way. Several research laboratories have already generated initial extensive datasets on gene expression analysis. Application of this technique has demonstrated that in addition to a precise analysis, verification and validation of the results also on the level of cell populations, a meticulous characterization of the patients according to current conventional clinical, laboratory, imaging and histological standards is essential. For functional interpretation, in vitro tests, animal models and therapeutic studies will provide further information. Bioinformatic structuring and development is needed for the large amounts of data. After an initial genome-wide screening, the objective is to identify those genes, which will allow characterization of the disease, classification according to molecular pathophysiology, evaluation of the prognosis and prediction of the correct and most potent therapeutic regimen. Derived from the improved knowledge about the molecular mechanisms, new and--as to expect--the crucial approaches for an effective therapy against chronic inflammation, organ destruction and pathological immune response in rheumatic diseases will emerge.

Autoantibodies↗

PubMed2003

Validation of tissue array technology in head and neck squamous cell carcinoma.

BACKGROUND: The recent development of tissue array technology has potentiated large-scale retrospective cohort studies using archival formalin-fixed, paraffin-embedded tissues. This study evaluates the potential for using archival head and neck cancer tissue in such arrays. METHOD: Tissue array blocks were made from 184 head and neck cancer specimens. Three core tissue biopsies (0.6 mm x 3-4 mm) were taken from individual "donor" paraffin-embedded tumor blocks and arrayed into a new "recipient" paraffin block. Immunohistochemical (IHC) analyses were performed using antibodies recognizing cyclin-D1, Rb, and EGFR. IHC was scored on a 6-point scale for extent and a 3-point scale for intensity. We compared the staining of tissue array disks with staining of full tissue sections. RESULTS: Seventy-four percent (475 of 640) of samples placed into tissue arrays were confirmed to represent tumor tissue. The remaining samples were lost during processing or contained too few tumor cells. Only 6% of cases were completely lost, whereas 55%, 28%, and 11% of cases were judged on 3, 2, or 1 disk, respectively. Cohen's kappa coefficient was 0.66 for cyclin-D1, 0.40 for EGFR, and 0.41 for Rb. CONCLUSIONS: Tissue array technology is a rapid and efficient method for retrospective analysis of protein expression and is a promising tool for validation of prognostic markers in large series of head and neck squamous cell carcinomas. The agreement in scoring of the full section and the tissue arrays is reasonable. Discordance is probably due to intraobserver variation and lack of robustness of the scoring inherent of the proteins studied.

Aged↗

PubMedDate not supplied

Immunohistochemical biomarkers in patients with early-onset breast carcinoma by tissue microarray.

UNLABELLED: Young women with breast cancer have a poor prognosis, and the role of biologic markers in young women is not well defined. We investigated the association of estrogen receptor, progesterone receptor, Bcl-2, HER-2/neu, p53, and Ki-67 with clinicopathologic features and outcome in young women with breast cancer. METHODS: A cohort of 103 patients with early-onset breast cancer treated with conservative surgery and radiotherapy were entered in this study. Age range was 25-45 years, and median follow-up was 8.7 years. Each of the paraffin-embedded specimens was immunologically stained for six biomarkers expression by a recently developed tissue microarray method. RESULTS: The 10-year overall breast relapse-free and distant relapse-free survival rates were 82.7%, 84.6.4%, and 66.7%, respectively, with 14 local relapses and 26 distant metastases among the 103 patients evaluated. Positive expression of estrogen receptor, progesterone receptor, bcl-2, HER-2/neu, p53, and Ki-67 were 42.7%, 48.5%, 35.6%, 28.0%, 36.9%, and 39.7%, respectively. Tumor stage and nodal status were significantly associated with overall survival and distant metastasis-free rate in univariate and multivariate analysis. Progesterone receptor negativity and Ki-67 positivity were associated with distant metastasis. There was no statistically significant correlation between the six biomarkers and local relapse. CONCLUSIONS: Progesterone receptor, Ki-67, tumor stage, and nodal status were prognostic factors for distant failure in early-stage breast cancer in young patients. Further studies are needed to find other biologic markers associated with local failure in this group of patients.

Adenocarcinoma, Mucinous↗

PubMed2003

ProteoChip: a highly sensitive protein microarray prepared by a novel method of protein immobilization for application of protein-protein interaction studies.

We have developed a highly sensitive microarray protein chip, ProteoChip, coated with ProLinker, novel calixcrown derivatives with a bifunctional coupling property that permits efficient immobilization of capture proteins on solid matrixes and makes high-throughput analysis of protein-protein interactions possible. The analysis of quartz crystal microbalance showed that both monoclonal antibody (mAb) and antigen (Ag) bound to the gold film of the sensor surface coated with ProLinker B and that it is useful for studies of Ab-Ag interactions. ProteoChip, aminated glass slide coated with ProLinker A, was also demonstrated to be useful for preparation of high-density array spots by using a microarrayer and for analysis of analyte Ags either by direct or sandwich methods of fluorescence immunoassay. The detection sensitivity of ProteoChip was as low as 1-10 femtogram/mL of analyte protein, useful for detection of tumor markers. ProteoChip was also useful for studies of direct protein-protein interactions as demonstrated by analysis of integrin-extracellular matrix protein interaction. These experimental results suggest that ProteoChip is a powerful tool for development of chip-based lead screening microarrays to monitor protein-protein interactions (i.e. drug target) as well as for biomarker assays which require high detection sensitivity.

Antibodies, Monoclonal↗

PubMedDate not supplied

Tissue microarray technology: principles, pitfalls and perspectives--lessons learned from hematological malignancies.

Detection, validation and incorporation into clinical use of new diagnostic, prognostic and therapeutic molecular targets in modern medical science should be time- and cost-efficient. Here, we discuss the principles, advantages, disadvantages and possible pitfalls of tissue microarray (TMA) technology, a powerful tool for high throughput large-scale morphological in situ analysis of molecular targets. Based on recent observations from molecular profiling of hematological malignancies, we review potential TMA applications assessing molecular targets in large collectives of tissue specimens.

Animals↗

PubMed2003

Mobility-shift analysis with microfluidics chips.

Electrophoretic mobility shift analysis (EMSA) is a well-characterized and widely used technique for the analysis of proten-DNA interaction and the analysis of transcription factor combinatorics. Currently implemented EMSA generally involves the time-consuming use of radiolabeled DNA and polyacrylamide gel electrophoresis. We are studying the bionanoscience of self-assembling supramolecular protein-nucleic nanostructures. We have undertaken these studies because they promise to enhance our understanding of assemblies formed during prebiotic evolution, provide tools for analysis of biological processes like DNA recombination, and may lead to the development of nanoscale biosensors designed for site-specific molecular targeting. During the course of that work, we noted that EMSA of these complex structures could be effectively implemented with microfluidics chips designed for the separation of DNA fragments. In this report we compare the two techniques and demonstrate that the microfluidics system is also capable of resolving complex mixtures produced by decorating DNA recombination intermediates with mixtures of DNA binding proteins. Moreover, the microfluidics chip system improves EMSA by permitting analysis with smaller samples, avoiding the use of radiolabeling, and reducing the time involved to a matter of minutes.

Computer Simulation↗

PubMed2003

Development of a common biosensor format for an enzyme based biosensor array to monitor fruit quality.

Individual enzyme-based biosensors involving three-electrode systems were developed for the detection of analytes comprising markers of the stage of maturity and quality in selected fruits of economic importance to tropical countries. Importantly, a common fabrication format has been developed to simplify manufacture and allow future integration of the individual sensors into a single multi-sensor array. Specifically, sensors for beta-D-glucose, total D-glucose, sucrose and ascorbic acid have been developed. Pectin, a natural polysaccharide present in plant cells, was used as a novel matrix to enhance enzyme entrapment and stabilisation in the sensors. Except for ascorbic acid, all the sensors function via the detection of enzymatically generated H2O2 at rhodinised carbon electrodes. Since ascorbic acid is electrochemically active at the working potential chosen (+350 mV vs. Ag/AgCl), it was measured directly. Enzyme sensors demonstrated expected response with respect to their substrates, typically 0-0.8 microA/20 mm2 electrode area response over analyte ranges of 0-7 mM. Interferences related to electrochemically active compounds present in fruits under study were significantly reduced by inclusion of a suitable cellulose acetate (CA) membrane or by enzymatic inactivation with ascorbate oxidase. Initial development was carried out into production of biosensor arrays. CA membranes were used to improve the linear range of the sensors, producing up to a fivefold improvement in the detection range compared to sensors without an additional diffusion barrier.

Ascorbic Acid↗

PubMed2004

A novel piezoelectric quartz micro-array immunosensor based on self-assembled monolayer for determination of human chorionic gonadotropin.

A novel multi-channel 2 x 5 model of piezoelectric quartz micro-array immunosensor has been developed for quantitative detection of human chorionic gonadotropin (hCG) in serum or urine samples. Every crystal unit of the fabricated piezoelectric hCG micro-array immunosensor can oscillate independently without interfering each other. A 2 x 5 model of micro-array immunosensor as compared with a one-channel immunosensor can provide eight times higher detection speeds for hCG assay. The anti-hCG antibody is deposited on the gold electrode's surface of 10 MHz quartz AT-cut crystal by self-assembled technique using sulfosuccinimidyl 6-[3'-(2-pyridyldithio) propionamido] hexanoate (Sulfo-LC-SPDP), and serves as an antibody recognizing layer. The highly ordered self-assembled monolayers (SAM) ensure well-controlled surface structure and offer many advantages to the performance of the sensor. Compared with conventional antibody immobilization methods, the amount and the reaction activity of antibody monolayer coated by the SAM binding are bigger than those by the SPA method, and less non-specific binding caused by other analytes in sample is found. Under the optimized experimental conditions, the results showed that micro-array immunosensor quantitatively detected serum or urine hCG in the range of 2.5-500 mIU/ml with high precision (CV<5%); other hormones in human serum and urine did not interfere with the determination markedly. Serum and urine samples of 60 patients were detected by the micro-array immunosensor, and the results agreed well with those given by the commercial radioimmunoassay test kit, with correlation coefficient of 0.92. After regeneration with urea solution the coated immunosensor can be reused five times without appreciable loss of activity.

Biosensing Techniques↗

PubMedDate not supplied

Proteomics: a paradigm shift.

Proteome--the protein complement of a genome--has become the protein renaissance and a key research tool in the post-genomic era. The basic technology involves the routine usage of gel electrophoresis and spectrometry procedures for deciphering the primary protein sequence/structure as well as knowing certain unique post-translational modifications that a particular protein has undergone to perform a specific function in the cell. However, the recent advancements in protein analysis have ushered this science to provide deeper, bigger and more valuable perspectives regarding performance of subtle protein-protein interactions. Applications of this branch of molecular biology are as vast as the subject is and include clinical diagnostics, pharmaceutical and biotechnological industries. The 21st century hails the use of products, procedures and advancements of this science as finer touches required for the grooming of fast-paced technology.

Animals↗

PubMed2002

Protein microarrays: from serodiagnosis to whole proteome scale analysis of the immune response against pathogenic microorganisms.

Microbial diseases remain the most common cause of global mortality and morbidity. Scientific and technical achievements have dramatically improved the possibilities of investigating the humoral immune response against the whole proteome of microbial organisms. A number of genomes of microbial organisms responsible for diseases of worldwide medical importance such as Plasmodium, Toxoplasma, Mycobacterium, Streptococcus, Neisseria, Salmonella, Borrelia, and Rickettsia species have already been sequenced or will be available in the very near future. High-throughput assays such as protein microarrays have been clinically validated in serum for detecting the presence of antibodies directed against microbial antigens. Computational technologies for processing large sets of data are rapidly being developed. Such a powerful combination of genomic information and assays now offers the opportunity to identify the microbial antigens that, either alone or in combination, function as targets of natural acquired immunity against infectious diseases. This information will prove invaluable for developing vaccines against a series of microorganisms of medical relevance that are urgently needed, e.g., malaria. Additional applications of these technologies include the development of a microbial antigen array for the early serodiagnosis of both common and rare infectious diseases. This review will focus on technical and scientific issues concerning the use of antigen microarrays for vaccine development and the serodiagnosis of infectious diseases.

Antigens↗