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PubMed2005

Multiplexed protein analysis using antibody microarrays and label-based detection.

This chapter describes methods for the production and use of antibody microarrays. The experimental methods are divided into three sections. The first gives information relating to the preparation and handling of antibodies and the production of microarrays. The second relates to the preparation of the samples, from either blood, tissue, or cell lysates. The third section describes methods for using the samples on antibody microarrays. Two related detection methods are described in which the proteins of a sample to be analyzed are labeled with a tag to allow detection after capture on antibody microarrays.

Antibodies↗

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↗

PubMed2006

Expression and prognostic significance of prothymosin-alpha and ERp57 in human gastric cancer.

PURPOSE: Prothymosin-alpha and ERp57 were previously identified as markers for gastric metaplasia in a mouse model of Helicobacter-induced gastric metaplasia and neoplasia. In this paper we assess whether the expression of these putative biomarkers in humans is correlated with gastric metaplasia and adenocarcinoma and clinical outcomes. METHODS: Eight tissue microarrays, containing 749 paraffin-embedded tissue cores from 164 gastric cancer patients, were stained for prothymosin-alpha and ERp57 by horseradish peroxidase immunohistochemical techniques. The proportion of stained cells per core was quantitated using the Ariol SL-50 automated image analysis system. RESULTS: Prothymosin-alpha stained a significantly higher percentage of nuclei in cancer and metastases compared with normal gastric mucosa. ERp57 staining was significantly decreased in cancer and metastases compared with both normal gastric mucosa and metaplasias. ERp57 expression also correlated with greater depth of tumor invasion and advanced stage of disease. Kaplan-Meier survival analysis determined that tumors with the highest quartile of ERp57 expression were statistically associated with longer postoperative survival. A Cox proportional hazard analysis showed that maintenance of ERp57 expression was associated with longer postoperative survival. CONCLUSIONS: These results suggest that although prothymosin-alpha is overexpressed in gastric adenocarcinoma, it is not associated with alterations in survival. In contrast, loss of ERp57 expression correlated with more aggressive disease and could provide useful prognostic information for gastric cancer patients.

Adenocarcinoma↗

PubMed2003

Prognostic significance of CD44 expression in diffuse large B cell lymphoma of activated and germinal centre B cell-like types: a tissue microarray analysis of 90 cases.

BACKGROUND: Gene expression profiling of diffuse large B cell lymphoma (DLBCL) revealed three disease types: germinal centre B cell-like (GC), activated B cell-like (ABC), and a "third" type. Expression of CD44 variant isoforms (CD44v) is associated with an unfavourable clinical outcome in DLBCL, but previous studies did not consider the clinicopathological heterogeneity of this disease. AIMS: To analyse the expression and prognostic significance of CD44 in DLBCL types. METHODS: A tissue microarray (TMA) comprising 90 DLBCLs was constructed. CD10, CD20, bcl-2, bcl-6, CD44 standard isoform (CD44s), and CD44v4, CD44v6, and CD44v9 were analysed immunohistochemically and correlated with clinical follow up. RESULTS: TMA expression of CD10, CD20, bcl-2, and bcl-6 showed 100% concordance with results from conventional sections in 60 cases. Samples were segregated into 22 GC (bcl-6+/CD10+/bcl-2-), 25 ABC (bcl-6-/CD10-/bcl-2+), and 35 unclassifiable DLBCLs. Overall survival (OS) at 30 months was 89%, 44%, and 58% in GC, ABC, and unclassified types, respectively. CD44v6 was coexpressed with bcl-2, appeared predominantly on bcl-6 negative cases, and correlated with disease stage. Cases negative for CD44s could be separated into CD44v6 negative (OS, 82% at 70 months) and CD44v6 positive (OS, 58%). CONCLUSIONS: TMA technology is useful for immunophenotyping and clinicopathological analysis of large lymphoma populations. The GC phenotype of DLBCL is of independent prognostic significance for OS. Expression of CD44v6 correlates with disease stage, and might contribute to lymphoma dissemination. CD44v6 is expressed predominantly in ABC DLBCL, and in CD44 negative cases is associated with worse OS.

Biomarkers, Tumor↗

PubMed2005

Arteriogenic erectile dysfunction alters protein expression within the cavernosal tissue in an animal model.

INTRODUCTION: Erectile dysfunction (ED) is a highly prevalent and often untreated condition. It may be a marker of underlying chronic illness and negatively impacts quality of life. Penile arterial insufficiency, frequently found in association with hypertension, dyslipidemia, diabetes mellitus, pelvic irradiation, trauma, and smoking, is the most common cause of ED. AIM: This study was designed to measure the effect of penile hypoperfusion-induced alteration and injury on erectile tissue at the cellular and protein level. METHODS: Eighteen 4-month-old male Sprague Dawley rats were placed into three groups (n = 6): sham surgery, unilateral internal iliac artery ligation (UIIAL), and bilateral internal iliac artery ligation (BIIAL). MAIN OUTCOME MEASURE: Erectile function was assessed 4 weeks following arterial ligation surgery as measured by a rise in intracavernosal pressure induced by cavernosal nerve stimulation. Penile tissue alterations were characterized by immunohistochemistry, protein content measured by western blot, and "global" protein expression profile carried out by using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) ProteinChip technology. RESULTS: Significantly lower intracavernous pressures were demonstrated in animals subjected to UIIAL surgery, which correlated to the extent of artery ligation. The intensity and quantity of immunohistochemical staining for neuronal nitric oxide synthase, endothelial cell integrity, smooth muscle cell alpha-actin, and vascular endothelial growth factor (VEGF) receptor flk1 were decreased in the BIIAL group compared to sham controls. SELDI-TOF-MS analysis revealed changes in molecular expression of a approximately 6,560 Da protein relative to a 7,720 Da protein (peak ratio = 1.34 +/- 0.3, BIIAL; 0.36 +/- 0.1 controls, P < 0.05). CONCLUSIONS: In this report, an animal model of vascular penile insufficiency demonstrates altered protein expression associated with cavernosal tissue injury and reduced erectile function. Although the clinical significance of these observations is currently undefined, this model may allow greater insight into the complex biologic changes associated with arteriogenic ED in man.

Actins↗

PubMed2005

Using surface plasmon resonance to directly determine binding affinities of combinatorially selected cyclopeptides and their linear analogs to a streptavidin chip.

In our recent report, several HPQ-containing streptavidin ligands were identified from a structurally constrained combinatorial library, and the relative affinities in IC(50) of these tight-binding ligands were revealed by a captured enzyme-linked immunosorbent assay. In the present work, surface plasmon resonance was employed to directly evaluate the binding affinities between immobilized streptavidin and combinatorially selected ligands. The equilibrium dissociation constants and kinetic on/off rates of a previously identified N-to-side chain and newly synthesized N-to-C cyclopeptides were readily deduced using Scatchard analysis and computational simulation. It was found that both cyclopeptides bound streptavidin far more tightly than its linear counterpart ( approximately 1000-fold), while the reversed (QPH) linear and cyclic peptidyl ligands were hardly recognized by streptavidin. Consequently, not only was the binding specificity of synthetic ligands distinguished qualitatively but also the entropic advantage of conformationally constrained cyclopeptides over their linear forms was demonstrated quantitatively by surface plasmon resonance.

Amino Acid Sequence↗

PubMed2005

Molecularly engineered p(HEMA)-based hydrogels for implant biochip biocompatibility.

The strategy of phospholipid-based biomimicry has been used to molecularly engineer poly(2-hydroxyethyl methacrylate) [p(HEMA)]-based hydrogels for improved in vitro and potential in vivo biocompatibility. Two methacrylate-based monomers, poly(ethylene glycol) (200) monomethacrylate (PEGMA) and 2-methacryloyloxyethyl phosphorylcholine (MPC), were incorporated at varying mole fractions of 0.0-0.5 mol% PEGMA and 0-10 mol% MPC respectively, into 3 mol% tetraethyleneglycol diacrylate (TEGDA) cross-linked p(HEMA) networks. Upon hydration of these engineered hydrogels, a reduction in receding contact angle from 22+/-1.2 degrees for p(HEMA) to 8+/-2.7 degrees for p(HEMA) containing 0.5:10 mol% PEGMA:MPC was observed, reflecting the significant increase in surface hydrophilicity with increasing PEGMA and MPC content upon prolonged hydration. Hydrogels containing MPC showed a temporal increase in hydrophilicity following continuous immersion in DI water over 5 days. Hydrogels containing 0.5 mol% PEGMA and MPC in the range of 5-10 mol% displayed reduced protein adsorption when incubated with the common extracellular matrix proteins; fibronectin, collagen or laminin, producing up to 64% less protein adsorption compared to p(HEMA). Compositional optima for cell viability and proliferation established from two-factor Central Composite design analysis of human muscle fibroblasts cultured on these hydrogels suggest that those containing PEGMA between 0.3 and 0.5 mol% and MPC levels around 5-10 mol% exhibit desirable characteristics for implant material coatings-high viability (>80%) with low proliferation (<40%), confirming a lack of cytotoxicity.

Adsorption↗

PubMed2004

Telangiectatic focal nodular hyperplasia: a variant of hepatocellular adenoma.

BACKGROUND & AIMS: "Telangiectatic focal nodular hyperplasia" designate atypical lesions considered as variants of focal nodular hyperplasia (FNH). However, because "telangiectatic FNH" share several morphologic patterns with hepatocellular adenomas, classification of such lesions deserve further clarification. Therefore, the aim of the present study was to reconsider the classification of telangiectatic FNH with the help of a molecular approach. METHODS: Ten telangiectatic FNH, 6 typical FNH, and 6 hepatocellular adenomas were studied. DNA, RNA, and protein from each lesion were extracted. Clonality was assessed by the study of the X chromosome inactivation pattern (HUMARA assay). Angiopoietin (ANGPT-1 and ANGPT-2) mRNA, genes the expression of which is typically modified in FNH, were quantified by a real-time RT-PCR procedure. Protein profiles were analyzed by SELDI-TOF PROTEINCHIP (Cyphergen Biosystem, Inc., Fremont, CA) technology. RESULTS: Although all informative cases of FNH (5 of 6) and hepatocellular adenomas (6 of 6) were polyclonal and monoclonal, respectively, clonal analysis showed a nonrandom pattern of X chromosome inactivation consistent with a monoclonal lesion in 6 of 8 cases of telangiectatic FNH. The mean value of the ANGPT-1/ANGPT-2 mRNA ratio was 21.4 in FNH, 2.6 in adenomas, and 2.1 in telangiectatic FNH (P <or = 0.001 in telangiectatic FNH vs. FNH). SELDI-TOF PROTEINCHIP profiling and hierarchical clustering analysis showed that all except 1 telangiectatic FNH clustered within the group of hepatocellular adenomas. CONCLUSIONS: These results show that telangiectatic FNH display a molecular pattern closer to that of hepatocellular adenomas than to FNH and suggest that these lesions should instead be referred to as "telangiectatic hepatocellular adenomas."

Adenoma, Liver Cell↗

PubMed2006

Regulation of production of mucosal antibody to pneumococcal protein antigens by T-cell-derived gamma interferon and interleukin-10 in children.

Nasopharyngeal tonsils (adenoids) are part of human nasopharynx-associated lymphoid tissue, which may play an important role in local defense against pneumococci. Recent studies with animals have suggested that several pneumococcal proteins, including CbpA and pneumolysin (Ply), may be vaccine candidates. Our recent data obtained with children suggest that antibodies to these proteins may protect against carriage. This study was performed to investigate the regulation of the T-cell-dependent antibody responses to CbpA and pneumolysin by cytokines in adenoidal immune cells from children. Adenoidal mononuclear cells (MNC) were cultured with pneumococcal concentrated culture supernatants (CCS) or recombinant proteins. Cytokine expression profiles in adenoidal MNC after antigen stimulation were analyzed by reverse transcription-PCR, protein array analysis, and an immunoassay, along with an antibody production analysis. The roles, interactions, and cellular sources of the main cytokines identified were evaluated further. Pneumococcal CCS induced production of CbpA- and Ply-specific antibodies in association with several chemokines and cytokines, including gamma interferon (IFN-gamma) and interleukin-10 (IL-10) in MNC. The antibody production correlated well with the concentrations of these two cytokines. Addition of recombinant IFN-gamma or IL-10 enhanced antibody production, and monoclonal antibodies to these two cytokines and T-cell depletion significantly reduced antibody production. Intracellular cytokine staining showed that T cells are a major source of IFN-gamma and IL-10. Recombinant Ply and, to a lesser extent, recombinant CbpA induced significant production of IFN-gamma and IL-10 in MNC. T-cell-derived IFN-gamma and IL-10 may be key regulators of production of mucosal antibody to pneumococcal protein antigens in the nasopharynx and may play an important role in local protection against pneumococcal infection in children.

Adenoids↗

PubMed2006

Protein microarrays on hybrid polymeric thin films prepared by self-assembly of polyelectrolytes for multiple-protein immunoassays.

We report here the development and characterization of protein microarrays fabricated on nanoengineered 3-D polyelectrolyte thin films (PET) deposited on glass slide by consecutive adsorption of polyelectrolytes via self-assembly technique. Antibodies or antigens were immobilized in the PET-coated glass slides by electrostatic adsorption and entrapment of porous structure of the 3-D polymer film and thus establishing a platform for parallel analysis. Both antigen and antibody microarrays were fabricated on the PET-coated slides, and direct and indirect immunoassays on protein microarrays for multiple-analyte detection were demonstrated. Microarrays produced on these PET-coated slides have consistent spot morphology and provide performance features needed for proteomic analysis. The protein microarrays on the PET films provide LOD as low as 6 pg/mL and dynamic ranges up to three orders of magnitude, which are wider than the protein microarrays fabricated on aldehyde and poly-L-lysine functionalized slides. The PET films constructed by self-assembly technique in aqueous solution is green chemistry based, cost-effective method to generate 3-D thin film coatings on glass surface, and the coated slide is well suited for immobilizing many types of biological molecules so that a wide variety of microarray formats can be developed on this type of slide.

Adsorption↗

PubMed2006

Application of lectin microarray to crude samples: differential glycan profiling of lec mutants.

We recently developed a novel system for lectin microarray based on the evanescent-field fluorescence-detection principle, by which even weak lectin-oligosaccharide interactions are detectable without a washing procedure. For its practical application, cell glycan analysis was performed for Chinese hamster ovary (CHO) cells and their glycan profile was compared with those of their glycosylation-defective Lec mutants. Each of the cell surface extracts gave a significantly different profile from that of the parental CHO cells in a manner reflecting denoted biosynthetic features. Hence, the developed lectin microarray system is considered to be fully applicable for differential glycan profiling of crude samples.

Animals↗

PubMed2004

Multiplexed protein analysis using spotted antibody microarrays.

This chapter describes methods for the production and use of antibody microarrays. The methods are divided into (a) antibody handling and microarray production, (b) sample preparation, and (c) microarray use. Two types of detection methods are described: direct labeling and a fluorescence-linked immunosorbent assay (FLISA). In the direct labeling method, all proteins in a complex mixture are labeled with either a fluorophore or a hapten that allows subsequent detection. In FLISA detection, a capture antibody on the microarray captures the unlabeled protein target, which is detected by a detection antibody and a fluorophore-labeled secondary antibody. Each method has particular optimal uses, which are discussed in the text.

Antibodies↗

PubMed2003

Molecular evaluation using in silico protein interaction profiles.

MOTIVATION: To find a correlation between the activities and structures of molecules is one of the most important subjects for molecular evaluation study. Traditional quantitative structure-activity relationship (QSAR) methodologies represent those attempts using physicochemical descriptors. Creating a new molecular description factor based on the results of a computational docking study will add new dimensions to molecular evaluation. RESULTS: We propose a new molecular description factor analysis system called the Comparative Molecular Interaction Profile Analysis (CoMIPA) system in which the AutoDock program is used for docking evaluation of small molecule compound-protein complexes. Interaction energies are calculated, and the data sets obtained are called interaction profiles (IPFs). Using the IPF as a scoring indicator, the system could be a powerful tool to cluster the interacting properties between small molecules and bio macromolecules such as ligand-receptor bindings. Further development of the system will enable us to predict the adverse effects of a drug candidate.

Algorithms↗

PubMed2006

Solid-phase and bead-based cytokine immunoassay: a comparison.

Cytokines and chemoattractive cytokines (chemokines) are present in a wide variety of body fluids such as plasma, cerebrospinal fluid, bronchoaveolar fluid, amniotic fluid, synovial fluid, middle ear effusion fluid, and urine. Cytokines can be detected using classical solid-phase sandwich immunoassays such as enzyme-linked immunosorbent assay (ELISA) or with a bead based multiplex immunoassay (MIA). The physical chemical properties of the different body fluids (such as pH and total protein content) differ, which may have an impact on the outcome of the cytokine assay. Both ELISA as well as MIA cytokine detection systems are constructed by sandwiching the protein of interest between a capture and reporter antibody. When the biological sample contains heterophilic antibodies (such as in patients with auto-immune diseases), these non-specific antibodies can cause false positive results. During pathological conditions, cytokines may be found over a wide concentration range; likewise have to cover this dynamic range in a similar fashion. The correct (statistical) analysis of standard curves and (multiplexed) data are critical for proper interpretation. Classical ELISA based cytokine assays are robust, easy to use and very well suited for measurement of single cytokines. Due to an increased interest in the integral approach to understand biological processes (the omics era), multiplex immunoassays for detection of cytokines and the interpretation of these assays are gaining popularity.

Animals↗

PubMed2003

Development of protein microarray technology to monitor biomarkers of rheumatoid arthritis disease.

Most biological processes are mediated by complex networks of molecular interactions involving proteins. The analysis of protein expression in biological samples is especially important in the identification and monitoring of biomarkers for disease progression and therapeutic endpoints. In this paper, the development of a protein microarray format for multiplexed quantitative analysis of several potential markers for rheumatoid arthritis (RA) is described. Development of a high-performance protein microarray system depends on several key parameters such as surface chemistry, capture agents, immobilization technology, and methods used for signal detection and quantification. Several technical possibilities were investigated and compared: poly-L-lysine versus self-assembled monolayer of octadecyl phosphoric acid ester for surface chemistries; noncontact piezoelectric versus contact printing technology for antibody deposition; CCD camera capture versus fluorescent scanning for image detection; and the concentration of coating antibody. On the basis of reproducibility, signal-to-noise ratio, and sensitivity we have selected self-assembled monolayer, noncontact piezoelectric printer, and high-read-out fluorescence scanning for our microarray format. This format was used to perform multiplexed quantitative analysis of several potential markers of disease progression of rheumatoid arthritis: IL-1beta, IL-6, IL-8, MCP-1, and SAA. Some assays, such as MCP-1, provided a working range that covered physiologically relevant concentrations. Other assays, such as IL-6 and SAA, lacked sensitivity or were too sensitive for measuring biological concentrations, respectively. The results described demonstrate the applicability of protein microarrays to monitor RA markers; however, sandwich assay methodologies need to be further optimized to measure the appropriate biological ranges of these markers on one chip.

Arthritis, Rheumatoid↗

PubMed2002

Normal, benign, preneoplastic, and malignant prostate cells have distinct protein expression profiles resolved by surface enhanced laser desorption/ionization mass spectrometry.

PURPOSE: The objective of this study was to discover protein biomarkers that differentiate malignant from nonmalignant cell populations, especially early protein alterations that signal the initiation of a developing cancer. We hypothesized that Surface Enhanced Laser Desorption/Ionization-time of flight-mass spectrometry-assisted protein profiling could detect these protein alterations. EXPERIMENTAL DESIGN: Epithelial cell populations [benign prostatic hyperplasia (BPH), prostate intraepithelial neoplasia (PIN), and prostate cancer (PCA)] were procured from nine prostatectomy specimens using laser capture microdissection. Surface Enhanced Laser Desorption/Ionization-time of flight-mass spectrometry analysis was performed on cell lysates, and the relative intensity levels of each protein or peptide in the mass spectra was calculated and compared for each cell type. RESULTS: Several small molecular mass peptides or proteins (3000-5000 Da) were found in greater abundance in PIN and PCA cell lysates. Another peak, with an average mass of 5666 Da, was observed to be up-regulated in 86% of the BPH cell lysates. Higher levels of this same peak were found in only 22% of the PIN lysates and none of the PCA lysates. Expression differences were also found for intracellular levels of prostate-specific antigen, which were reduced in PIN and PCA cells when compared with matched normals. Although no single protein alteration was observed in all PIN/PCA samples, combining two or more of the markers was effective in distinguishing the benign cell types (normal/BPH) from diseased cell types (PIN/PCA). Logistic regression analysis using seven differentially expressed proteins resulted in a predictive equation that correctly distinguished the diseased lysates with a sensitivity and specificity of 93.3 and 93.8%, respectively. CONCLUSIONS: We have shown that the protein profiles from prostate cells with different disease states have discriminating differences. These differentially regulated proteins are potential markers for early detection and/or risk factors for development of prostate cancer. Studies are under way to identify these protein/peptides, with the goal of developing a diagnostic test for the early detection of prostate cancer.

Adult↗

PubMed2005

A compendium of signals and responses triggered by prodeath and prosurvival cytokines.

Cell-signaling networks consist of proteins with a variety of functions (receptors, adaptor proteins, GTPases, kinases, proteases, and transcription factors) working together to control cell fate. Although much is known about the identities and biochemical activities of these signaling proteins, the ways in which they are combined into networks to process and transduce signals are poorly understood. Network-level understanding of signaling requires data on a wide variety of biochemical processes such as posttranslational modification, assembly of macromolecular complexes, enzymatic activity, and localization. No single method can gather such heterogeneous data in high throughput, and most studies of signal transduction therefore rely on series of small, discrete experiments. Inspired by the power of systematic datasets in genomics, we set out to build a systematic signaling dataset that would enable the construction of predictive models of cell-signaling networks. Here we describe the compilation and fusion of approximately 10,000 signal and response measurements acquired from HT-29 cells treated with tumor necrosis factor-alpha, a proapoptotic cytokine, in combination with epidermal growth factor or insulin, two prosurvival growth factors. Nineteen protein signals were measured over a 24-h period using kinase activity assays, quantitative immunoblotting, and antibody microarrays. Four different measurements of apoptotic response were also collected by flow cytometry for each time course. Partial least squares regression models that relate signaling data to apoptotic response data reveal which aspects of compendium construction and analysis were important for the reproducibility, internal consistency, and accuracy of the fused set of signaling measurements. We conclude that it is possible to build self-consistent compendia of cell-signaling data that can be mined computationally to yield important insights into the control of mammalian cell responses.

Amino Acid Sequence↗

PubMed2004

Systematic delineation of a calmodulin peptide interaction.

We present a comprehensive profile of amino acid side-chain constraints in a calmodulin (CaM) peptide complex. These data were obtained from the analysis of calmodulin binding to an array of all single substitution analogues as well as N- and C-terminal truncations of the skMLCK derived M13 peptide ligand. The experimentally derived binding data were evaluated with respect to the known 3D-structure of the CaM/M13 complex. Besides an almost perfect agreement between the measured affinities and the structural data, the unexpected high-affine Asn5Ala variant of the M13(*) peptide described by Montigiani et al. could be verified. In contrast to other reports our data clearly support the postulate of the minor and major hydrophobic anchors of this calcium dependent interaction.

Amino Acid Sequence↗