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PubMed2003

Protein expression profiling arrays: tools for the multiplexed high-throughput analysis of proteins.

The completion of the human genome sequence has led to a rapid increase in genetic information. The invention of DNA microarrays, which allow for the parallel measurement of thousands of genes on the level of mRNA, has enabled scientists to take a more global view of biological systems. Protein microarrays have a big potential to increase the throughput of proteomic research. Microarrays of antibodies can simultaneously measure the concentration of a multitude of target proteins in a very short period of time. The ability of protein microarrays to increase the quantity of data points in small biological samples on the protein level will have a major impact on basic biological research as well as on the discovery of new drug targets and diagnostic markers. This review highlights the current status of protein expression profiling arrays, their development, applications and limitations.

Journal Article↗

PubMed2006

State-based discovery: a multidimensional screen for small-molecule modulators of EGF signaling.

As an alternative to conventional, target-oriented drug discovery, we report a strategy that identifies compounds on the basis of the state that they induce in a signaling network. Immortalized human cells are grown in microtiter plates and treated with compounds from a small-molecule library. The target network is then activated and lysates derived from each sample are arrayed onto glass-supported nitrocellulose pads. By probing these microarrays with antibodies that report on the abundance or phosphorylation state of selected proteins, a global picture of the target network is obtained. As proof of concept, we screened 84 kinase and phosphatase inhibitors for their ability to induce different states in the ErbB signaling network. We observed functional connections between proteins that match our understanding of ErbB signaling, indicating that state-based screens can be used to define the topology of signaling networks. Additionally, compounds sort according to the multidimensional phenotypes they induce, suggesting that state-based screens may inform efforts to identify the targets of biologically active small molecules.

Antibodies↗

PubMed2004

In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium.

The intermediary metabolism of Haemophilus influenzae strain Rd KW20 was studied by a combination of protein expression analysis using a recently developed direct proteomics approach, mutational analysis, and mathematical modeling. Special emphasis was placed on carbon utilization, sugar fermentation, TCA cycle, and electron transport of H. influenzae cells grown microaerobically and anaerobically in a rich medium. The data indicate that several H. influenzae metabolic proteins similar to Escherichia coli proteins, known to be regulated by low concentrations of oxygen, were well expressed in both growth conditions in H. influenzae. An in silico model of the H. influenzae metabolic network was used to study the effects of selective deletion of certain enzymatic steps. This allowed us to define proteins predicted to be essential or non-essential for cell growth and to address numerous unresolved questions about intermediary metabolism of H. influenzae. Comparison of data from in vivo protein expression with the protein list associated with a genome-scale metabolic model showed significant coverage of the known metabolic proteome. This study demonstrates the significance of an integrated approach to the characterization of H. influenzae metabolism.

Biochemistry↗

PubMed2005

Hyperosmolar saline is a proinflammatory stress on the mouse ocular surface.

PURPOSE: To investigate whether hyperosmolar stress stimulates production of inflammatory mediators and activates the mitogen-activated protein kinase (MAPK) signaling pathways, c-jun n-terminal kinases (JNKs), extracellular-regulated kinases (ERKs), and p38 on the mouse ocular surface. METHODS: 129SvEv/CD-1 mixed mice were treated with a balanced salt solution (BSS) (305 mOsM) or a hyperosmotic saline solution (HOSS) (500 mOsM). Untreated age-matched mice were used as controls. The concentrations of interleukin 1beta (IL-1beta) and tumor necrosis factor alpha (TNF-alpha) were measured by enzyme-linked immunosorbent assay. Gelatinase activity was determined by in situ zymography. Corneal and conjunctival epithelia were lysed for Western blot with MAPK antibodies or used for semiquantitative reverse transcription and polymerase chain reaction and gene array. RESULTS: Compared with age-matched controls and mice treated with BSS, the concentration of IL-1beta in tear fluid washings and the concentrations of IL-1beta and TNF-alpha and gelatinolytic activity in the corneal and conjunctival epithelia were significantly increased in mice treated with HOSS for 2 days. The expressions of IL-1beta, TNF-alpha, and matrix metalloproteinase 9 (MMP-9) messenger RNA by the corneal and conjunctival epithelia were also notably stimulated in mice treated with HOSS. The levels of phosphorylated JNK1/2, ERK1/2, and p38 MAPKs in the corneal and conjunctival epithelia were slightly increased in mice treated with BSS, but markedly increased in mice treated with HOSS. CONCLUSIONS: These results show that the hyperosmolarity stimulates expression and production of IL-1beta, TNF-alpha, and MMP-9 and activates JNK, ERK, and p38 MAPK signaling pathways on the mouse ocular surface. These findings suggest that hyperosmolar stress, as it may occur in dry eye, promotes ocular surface inflammation.

Animals↗

PubMed2006

Host cell responses induced by hepatitis C virus binding.

Initiation of hepatitis C virus (HCV) infection is mediated by docking of the viral envelope to the hepatocyte cell surface membrane followed by entry of the virus into the host cell. Aiming to elucidate the impact of this interaction on host cell biology, we performed a genomic analysis of the host cell response following binding of HCV to cell surface proteins. As ligands for HCV-host cell surface interaction, we used recombinant envelope glycoproteins and HCV-like particles (HCV-LPs) recently shown to bind or enter hepatocytes and human hepatoma cells. Gene expression profiling of HepG2 hepatoma cells following binding of E1/E2, HCV-LPs, and liver tissue samples from HCV-infected individuals was performed using a 7.5-kd human cDNA microarray. Cellular binding of HCV-LPs to hepatoma cells resulted in differential expression of 565 out of 7,419 host cell genes. Examination of transcriptional changes revealed a broad and complex transcriptional program induced by ligand binding to target cells. Expression of several genes important for innate immune responses and lipid metabolism was significantly modulated by ligand-cell surface interaction. To assess the functional relevance and biological significance of these findings for viral infection in vivo, transcriptional changes were compared with gene expression profiles in liver tissue samples from HCV-infected patients or controls. Side-by-side analysis revealed that the expression of 27 genes was similarly altered following HCV-LP binding in hepatoma cells and viral infection in vivo. In conclusion, HCV binding results in a cascade of intracellular signals modulating target gene expression and contributing to host cell responses in vivo. Reprogramming of cellular gene expression induced by HCV-cell surface interaction may be part of the viral strategy to condition viral entry and replication and escape from innate host cell responses.

Antigens, Viral↗

PubMed2004

Functional protein microarrays for parallel characterisation of p53 mutants.

Understanding the way in which single nucleotide polymorphisms and mutations in the human genome result in individual susceptibility to disease is a major goal in the postgenomic era. Such knowledge should accelerate the development of personalised medicine in which drug treatment can specifically match an individual's genotype. High-throughput DNA sequencing is generating the initial information required, but new technologies are required that can rapidly characterise the phenotypic effects of the identified polymorphisms. For example, many thousands of allelic variants of the p53 gene have been described and are responsible for more than 50% of cancers, however few of the protein products have been functionally characterised. Here we have quantified in parallel the effects of mutations and polymorphisms on the DNA-binding function of the p53 oncoprotein using a protein microarray, allowing their subclassification according to functional effect. Protein-protein interactions between p53 variants and (i) a regulatory oncoprotein, (ii) a regulatory kinase resulting in on-chip phosphorylation, are also described, suggesting the more general utility of this high-throughput assay format.

Alleles↗

PubMed2002

Multi-analyte analysis system using an antibody-based biochip.

A multi-analyte detection system using a unique antibody (Ab) biochip is described. The Ab-based biochip, also referred to as the protein biochip, uses a sensor array based on a complementary metal oxide silicon (CMOS) integrated circuit. The Ab-biochip has a sampling platform of four-by-four microarrays of antibodies deposited onto a Nylon membrane substrate. The micro-arrayed antibodies can be interrogated simultaneously or sequentially using the biochip sensing array detector with the use of a diffractive optical element illuminating each antibody spot individually. The usefulness of the Ab biochip is illustrated by the measurements of immunoglobulin G (IgG) used as the model analyte system. The detection limit for Cy5-labeled IgG molecules was 13 pg.

Animals↗

PubMed2005

Overexpression of CC3/TIP30 is associated with HER-2/neu status in breast cancer.

PURPOSE: The human CC3/TIP30 gene is a putative metastasis suppressor gene, based on the results of experimental studies using lung, colon and melanoma cell lines. However, there is very little evidence from studies on clinical material, in support of such a role for the gene. In this study, we evaluated the expression of CC3/TIP30 in human breast cancer tissue and investigated the possible associations with the clinicopathological parameters. METHODS: Total RNA and proteins were extracted from the frozen breast tumor and matched normal tissues. Evaluation of CC3/TIP30 expression was assessed by reverse transcription (RT)-PCR and reverse phase protein array. Immunohistochemistry of CC3/TIP30 on breast tissue microarrays was also analyzed. RESULTS: We have found that CC3/TIP30 expression is significantly associated with positive HER-2/neu status at both mRNA (P=0.023) and protein (P=0.016) levels. Immunohistochemical analysis on tissue microarrays also shows a positive correlation between CC3 expression and HER-2/neu status (P=0.0028). CONCLUSION: Our findings suggest a potential link between the expression of CC3/TIP30 gene and the HER-2/neu oncogene-mediated signal pathway.These findings could not have been predicted from previous experimental studies, and suggest that CC3/TIP30 may play a complex role in breast cancer.

Acetyltransferases↗

PubMed2004

Androgen-independent prostate cancer is a heterogeneous group of diseases: lessons from a rapid autopsy program.

Understanding the biology of prostate cancer metastasis has been limited by the lack of tissue for study. We studied the clinical data, distribution of prostate cancer involvement, morphology, immunophenotypes, and gene expression from 30 rapid autopsies of men who died of hormone-refractory prostate cancer. A tissue microarray was constructed and quantitatively evaluated for expression of prostate-specific antigen, androgen receptor, chromogranin, synaptophysin, MIB-1, and alpha-methylacylCoA-racemase markers. Hierarchical clustering of 16 rapid autopsy tumor samples was performed to evaluate the cDNA expression pattern associated with the morphology. Comparisons were made between patients as well as within the same patient. Metastatic hormone-refractory prostate cancer has a heterogeneous morphology, immunophenotype, and genotype, demonstrating that "metastatic disease" is a group of diseases even within the same patient. An appreciation of this heterogeneity is critical to evaluating diagnostic and prognostic biomarkers as well as to designing therapeutic targets for advanced disease.

Aged↗

PubMed2004

Loss of the tumor suppressor PML in human cancers of multiple histologic origins.

BACKGROUND: The PML gene is fused to the RARalpha gene in the vast majority of acute promyelocytic leukemias (APL) and has been implicated in the control of key tumor-suppressive pathways. However, its role in the pathogenesis of human cancers other than APL is still unclear. We therefore assessed the status and expression of the PML gene in solid tumors of multiple histologic origins. METHODS: We created tumor tissue microarrays (TTMs) with samples from patients with colon adenocarcinoma (n = 109), lung carcinoma (n = 19), prostate adenocarcinoma (n = 36), breast carcinoma (n = 38), central nervous system (CNS) tumors (n = 51), germ cell tumors (n = 60), thyroid carcinoma (n = 32), adrenal cortical carcinoma (n = 12), and non-Hodgkin's lymphoma (n = 251) and from normal tissue corresponding to each histotype and analyzed PML protein and mRNA expression by immunohistochemistry and in situ hybridization, respectively. Tumor cell lines (n = 64) of various histologic origins were analyzed for PML protein and mRNA expression by immunofluorescence and northern blotting, respectively. DNA from microdissected tumor samples and cell lines was analyzed for PML mutations and loss of heterozygosity (LOH). For some tumor types, the association between PML expression and tumor stage and grade was analyzed. Statistical tests were two-sided. RESULTS: All normal tissues expressed PML protein. PML protein expression was reduced or abolished in prostate adenocarcinomas (63% [95% confidence interval [CI] = 48% to 78%] and 28% [95% CI = 13% to 43%], respectively), colon adenocarcinomas (31% [95% CI = 22% to 40%] and 17% [95% CI = 10% to 24%]), breast carcinomas (21% [95% CI = 8% to 34%] and 31% [95% CI = 16% to 46%]), lung carcinomas (36% [95% CI = 15% to 57%] and 21% [95% = 3% to 39%]), lymphomas (14% [95% CI = 10% to 18%] and 69% [95% CI = 63% to 75%]), CNS tumors (24% [95% CI = 13% to 35%] and 49% [95% CI = 36% to 62%]), and germ cell tumors (36% [95% CI = 24% to 48%] and 48% [95% CI = 36% to 60%]) but not in thyroid or adrenal carcinomas. Loss of PML protein expression was associated with tumor progression in prostate cancer (the progression from prostatic intraepithelial neoplasia to invasive carcinoma was associated with complete PML loss; P<.001), breast cancer (complete PML loss was associated with lymph node metastasis; P =.01), and CNS tumors (complete PML loss was associated with high-grade tumors; P =.003). PML mRNA was expressed in all tumor and cell line samples. The PML gene was rarely mutated and was not subject to LOH. CONCLUSIONS: PML protein expression is frequently lost in human cancers of various histologic origins, and its loss associates with tumor grade and progression in some tumor histotypes.

Adenocarcinoma↗

PubMedDate not supplied

Novel transducers for nano-optical biosensor chips based on biological and synthetic polymers with analyte-dependent swelling/shrinking behavior.

Analyte-dependent swelling/shrinking properties of ultrathin polymer layers are an appropriate means for the detection of various analytes. Optical metal nanoclusters can be used to determine the change of the layer's thickness, which is shown by a change in the color of the chip. By using different cross-linking agents and different polymers (biological or artificial as well) it was possible to design various sensitive layers showing different swelling/shrinking behaviors. Sensitivity on various analytes could be observed, since the different types of polymers employed differed in structure, functional groups, or biorecognitive properties.

Biopolymers↗

PubMed2005

High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID).

BACKGROUND: We previously developed GoMiner, an application that organizes lists of 'interesting' genes (for example, under-and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. The original version of GoMiner was oriented toward visualization and interpretation of the results from a single microarray (or other high-throughput experimental platform), using a graphical user interface. Although that version can be used to examine the results from a number of microarrays one at a time, that is a rather tedious task, and original GoMiner includes no apparatus for obtaining a global picture of results from an experiment that consists of multiple microarrays. We wanted to provide a computational resource that automates the analysis of multiple microarrays and then integrates the results across all of them in useful exportable output files and visualizations. RESULTS: We now introduce a new tool, High-Throughput GoMiner, that has those capabilities and a number of others: It (i) efficiently performs the computationally-intensive task of automated batch processing of an arbitrary number of microarrays, (ii) produces a human-or computer-readable report that rank-orders the multiple microarray results according to the number of significant GO categories, (iii) integrates the multiple microarray results by providing organized, global clustered image map visualizations of the relationships of significant GO categories, (iv) provides a fast form of 'false discovery rate' multiple comparisons calculation, and (v) provides annotations and visualizations for relating transcription factor binding sites to genes and GO categories. CONCLUSION: High-Throughput GoMiner achieves the desired goal of providing a computational resource that automates the analysis of multiple microarrays and integrates results across all of the microarrays. For illustration, we show an application of this new tool to the interpretation of altered gene expression patterns in Common Variable Immune Deficiency (CVID). High-Throughput GoMiner will be useful in a wide range of applications, including the study of time-courses, evaluation of multiple drug treatments, comparison of multiple gene knock-outs or knock-downs, and screening of large numbers of chemical derivatives generated from a promising lead compound.

Binding Sites↗

PubMed2005

Elevated levels of human alpha -defensin in tears of patients with allergic conjunctival disease complicated by corneal lesions: detection by SELDI ProteinChip system and quantification.

PURPOSE: To analyze levels of alpha -defensin in the tears of allergic patients (with/without corneal lesions) comparing the results with those of normal control subjects. METHODS: Screening of the protein profiles of the tears of allergic patients with corneal epithelial lesions and normal controls was performed by surface enhanced laser desorption/ionization (SELDI) ProteinChip array initially. ELISA was then performed to quantify the levels of alpha -defensin in the tears of allergic patients (with/without corneal epithelial lesions) and normal control patients. RESULTS: Proteins expressing significant differences between patients and controls by SELDI analysis were examined. Several peptides with molecular weights similar to alpha -defensins were found to be expressed to a greater extent in allergic patients. ELISA was performed in tears of allergic patients and control subjects to ascertain the presence and increased expression of alpha -defensins in allergic patients. Concentrations of alpha -defensins in allergic patients with corneal epithelial lesions were significantly higher than those of allergic patients without epithelial lesions or normal controls. CONCLUSIONS: Alpha-defensins were found in greater concentrations in tears of allergic patients with corneal lesions. The antimicrobial effects of alpha -defensins may play a role in the prevention of secondary infection of corneal lesions in allergic patients. SELDI ProteinChip technology is a useful and effective tool in profiling the differential expression of proteins in tears.

Conjunctivitis, Allergic↗

PubMed2005

Antibody microarrays for native toxin detection.

We have developed antibody-based microarray techniques for the multiplexed detection of cholera toxin beta-subunit, diphtheria toxin, anthrax lethal factor and protective antigen, Staphylococcus aureus enterotoxin B, and tetanus toxin C fragment in spiked samples. Two detection schemes were investigated: (i) a direct assay in which fluorescently labeled toxins were captured directly by the antibody array and (ii) a competition assay that employed unlabeled toxins as reporters for the quantification of native toxin in solution. In the direct assay, fluorescence measured at each array element is correlated with labeled toxin concentration to yield baseline binding information (Langmuir isotherms and affinity constants). Extending from the direct assay, the competition assay yields information on the presence, identity, and concentration of toxins. A significant advantage of the competition assay over reported profiling assays is the minimal sample preparation required prior to analysis because the competition assay obviates the need to fluorescently label native proteins in the sample of interest. Sigmoidal calibration curves and detection limits were established for both assay formats. Although the sensitivity of the direct assay is superior to that of the competition assay, detection limits for unmodified toxins in the competition assay are comparable to values reported previously for sandwich-format immunoassays of antibodies arrayed on planar substrates. As a demonstration of the potential of the competition assay for unlabeled toxin detection, we conclude with a straightforward multiplexed assay for the differentiation and identification of both native S. aureus enterotoxin B and tetanus toxin C fragment in spiked dilute serum samples.

Antibodies, Monoclonal↗

PubMed2004

Discovery of laryngeal carcinoma by serum proteomic pattern analysis.

Laryngeal carcinoma is the most common malignancy among head and neck tumors. The purpose of this study is to find biomarkers for laryngeal carcinoma in patient blood serum using the Surface Enhanced Laser Desorption/Ionization (SELDI) technique. Serum samples from 33 laryngeal carcinoma (12 cases of glottis, 18 of supraglottis and 3 of subglottis) patients and 31 age- and sex-matched healthy people were analyzed by SELDI-TOF on a ProteinChip reader, PBSII-C. Protein profiles were generated using WCX2 protein chips. Protein peak clustering and classification analyses were performed utilizing the Biomarker Wizard and Biomarker Pattern software packages, respectively. The results showed that sixteen peaks had significant difference between laryngeal cancer patients and healthy group, eight of which were up-regulated in the patient samples, and the others were down-regulated. Two protein peaks 8153 Da and 2035 Da were automatically chosen for the system training and development of a classification tree. The analysis yielded a correct percentage of 96.9% for patients and 96.7% for control. The results suggest that serum is a useful resource for the detection of specific biomarkers for laryngeal carcinoma. Proteinchip Array System was a useful tool for a high throughput screening of large-sized serum samples to discover potential biomarkers for carcinoma.

Adult↗

PubMed2006

Severe acute respiratory syndrome diagnostics using a coronavirus protein microarray.

To monitor severe acute respiratory syndrome (SARS) infection, a coronavirus protein microarray that harbors proteins from SARS coronavirus (SARS-CoV) and five additional coronaviruses was constructed. These microarrays were used to screen approximately 400 Canadian sera from the SARS outbreak, including samples from confirmed SARS-CoV cases, respiratory illness patients, and healthcare professionals. A computer algorithm that uses multiple classifiers to predict samples from SARS patients was developed and used to predict 206 sera from Chinese fever patients. The test assigned patients into two distinct groups: those with antibodies to SARS-CoV and those without. The microarray also identified patients with sera reactive against other coronavirus proteins. Our results correlated well with an indirect immunofluorescence test and demonstrated that viral infection can be monitored for many months after infection. We show that protein microarrays can serve as a rapid, sensitive, and simple tool for large-scale identification of viral-specific antibodies in sera.

Algorithms↗

PubMed2005

Proteomic analysis of mantle-cell lymphoma by protein microarray.

Mantle-cell lymphoma (MCL) is a unique subtype of B-cell non-Hodgkin lymphoma (NHL) that behaves aggressively and remains incurable. In order to understand the pathogenesis of MCL and design new therapies, it is important to accurately analyze molecular changes in pathways dysregulated in MCL. We used antibody microarrays to compare patterns of protein expression between CD19(+) purified B lymphocytes from normal tonsil and 7 cases of histologically confirmed MCL. Protein overexpression was defined as a higher than 1.3-fold or 2-fold increase in at least 67% of tumor samples compared with normal B-cell control. Of the polypeptides, 77 were overexpressed using the higher than 1.3-fold cutoff, and 13 were overexpressed using the 2-fold cutoff. These included cell cycle regulators (regulator of chromosome condensation 1 [RCC1], murine double minute 2 [MDM2]), a kinase (citron Rho-interacting kinase [CRIK]), chaperone proteins (heat shock 90-kDa protein [Hsp90], Hsp10), and phosphatase regulators (A-kinase anchor protein 1 [AKAP149], protein phosphatase 5 [PP5], and inhibitor 2). The elevated expression of some of these polypeptides was confirmed by immunoblotting and immunohistochemistry, whereas elevated expression of others could not be confirmed, illustrating the importance of confirmatory studies. This study describes a novel technique that identifies proteins dysregulated in MCL.

Aged↗

PubMed2003

Comparison of the performance characteristics of poly(dimethylsiloxane) and Pyrex microchip electrophoresis devices for peptide separations.

A comparative study of electrophoretic separations of fluorescently labeled peptides and amino acids on poly(dimethylsiloxane) (PDMS) and Pyrex microchips is presented. The separation parameters for each microchip substrate were compared, including electroosmotic flow, plate numbers, resolution, and limits of detection. The effect of buffer composition on the separation was also investigated. Acceptable separations were obtained for most peptides with both substrates; however, PDMS chips exhibited much lower separation efficiencies and longer analysis times.

Amino Acids↗