An integrated approach to proteome analysis: identification of proteins associated with cardiac hypertrophy

A crayfish molar tooth protein with putative mineralized exoskeletal chitinous matrix properties

Some crustaceans possess exoskeletons that are reinforced with calcium carbonate. In the crayfish Cherax quadricarinatus, the molar tooth, which is part of the mandibular exoskeleton, contains an unusual crystalline enamel-like apatite layer. As this layer resembles vertebrate enamel in composition and function, it offers an interesting example of convergent evolution. Unlike other parts of the crayfish exoskeleton, which is periodically shed and regenerated during the molt cycle, molar mineral deposition takes place during the pre-molt stage. The molar mineral composition transforms continuously from fluorapatite through amorphous calcium phosphate to amorphous calcium carbonate and is mounted on chitin. The process of crayfish molar formation is entirely extracellular and presumably controlled by proteins, lipids, polysaccharides, low-molecular weight molecules and calcium salts. We have identified a novel molar protein termed Cq-M15 from C. quadricarinatus and cloned its transcript from the molar-forming epithelium. Its transcript and differential expression were confirmed by a next-generation sequencing library. The predicted acidic pI of Cq-M15 suggests its possible involvement in mineral arrangement. Cq-M15 is expressed in several exoskeletal tissues at pre-molt and its silencing is lethal. Like other arthropod cuticular proteins, Cq-M15 possesses a chitin-binding Rebers-Riddiford domain, with a recombinant version of the protein found to bind chitin. Cq-M15 was also found to interact with calcium ions in a concentration-dependent manner. This latter property might make Cq-M15 useful for bone and dental regenerative efforts. We suggest that, in the molar tooth, this protein might be involved in calcium phosphate and/or carbonate precipitation.

A crayfish insulin-like-binding protein: another piece in the androgenic gland insulin-like hormone puzzle is revealed

Across the animal kingdom, the involvement of insulin-like peptide (ILP) signaling in sex-related differentiation processes is attracting increasing attention. Recently, a gender-specific ILP was identified as the androgenic sex hormone in Crustacea. However, moieties modulating the actions of this androgenic insulin-like growth factor were yet to be revealed. Through molecular screening of an androgenic gland (AG) cDNA library prepared from the crayfish Cherax quadricarinatus, we have identified a novel insulin-like growth factor-binding protein (IGFBP) termed Cq-IGFBP. Based on bioinformatics analyses, the deduced Cq-IGFBP was shown to share high sequence homology with IGFBP family members from both invertebrates and vertebrates. The protein also includes a sequence determinant proven crucial for ligand binding, which according to three-dimensional modeling is assigned to the exposed outer surface of the protein. Recombinant Cq-IGFBP (rCq-IGFBP) protein was produced and, using a "pulldown" methodology, was shown to specifically interact with the insulin-like AG hormone of the crayfish (Cq-IAG). Particularly, using both mass spectral analysis and an immunological tool, rCq-IGFBP was shown to bind the Cq-IAG prohormone. Furthermore, a peptide corresponding to residues 23-38 of the Cq-IAG A-chain was found sufficient for in vitro recognition by rCq-IGFBP. Cq-IGFBP is the first IGFBP family member shown to specifically interact with a gender-specific ILP. Unlike their ILP ligands, IGFBPs are highly conserved across evolution, from ancient arthropods, like crustaceans, to humans. Such conservation places ILP signaling at the center of sex-related phenomena in early animal development.

Exception discovery: a novel method for the identification of differentially expressed proteins

The identification of differentially expressed proteins (DEPs) observed under specific conditions is one of the key issues in proteomics research. There are currently several ways to detect the changes of a specific protein's expression level in two-dimensional electrophoresis (2-DE) gel images such as statistical analysis and graphical visualization. However, it is quite difficult to handle the information of an individual protein manually by these methods due to the large distortions of patterns in 2-DE images. This paper proposes a method of analyzing DEPs for a specific disease. In order to automatically extract meaningful DEPs in a set of 2-DE gel images, we have designed an exception function that is suitable to measure the anomalous change of the expression level of an individual protein. We present the comparison results of the proposed method versus a Wilcoxon paired t -test that is one of the widely used statistical analysis methods. Several experiments are performed to address not only the effectiveness of the exception function but also the fact that these two methods can compensate each other practically.

A protein involved in the assembly of an extracellular calcium storage matrix

Gastroliths, the calcium storage organs of crustaceans, consist of chitin-protein-mineral complexes in which the mineral component is stabilized amorphous calcium carbonate. To date, only three proteins, GAP 65, gastrolith matrix protein (GAMP), and orchestin, have been identified in gastroliths. Here, we report a novel protein, GAP 10, isolated from the gastrolith of the crayfish Cherax quadricarinatus and specifically expressed in its gastrolith disc. The encoding gene was cloned by partial sequencing of the protein extracted from the gastrolith matrix. Based on an assembled microarray cDNA chip, GAP 10 transcripts were found to be highly (12-fold) up-regulated in premolt gastrolith disc and significantly down-regulated in the hypodermis at the same molt stage. The deduced protein sequence of GAP 10 lacks chitin-binding domains and does not show homology to known proteins in the GenBank data base. It does, however, have an amino acid composition that has similarity to proteins extracted from invertebrate and ascidian-calcified extracellular matrices. The GAP 10 sequence contains a predicted signal peptide and predicted phosphorylation sites. In addition, the protein is phosphorylated and exhibits calcium-binding ability. Repeated daily injections of GAP 10 double strand RNA to premolt C. quadricarinatus resulted in a prolonged premolt stage and in the development of gastroliths with irregularly rough surfaces. These findings suggest that GAP 10 may be involved in the assembly of the gastrolith chitin-protein-mineral complex, particularly in the deposition of amorphous calcium carbonate.

Proteomic profiling reveals comprehensive insights into adrenergic receptor-mediated hypertrophy in neonatal rat cardiomyocytes

Myocardial adrenergic receptors (ARs) play important roles in cardiac hypertrophy. However, the detailed molecular mechanism of AR-mediated cardiac hypertrophy remains elusive to date. To gain full insight into how ARs are involved in the regulation of cardiac hypertrophy, protein expression profiling was performed with comparative proteomics approach on neonatal rat cardiomyocytes. Forty-six proteins were identified as differentially expressed in hypertrophic cardiomyocytes induced by AR stimulation. To better understand the biological significance of the obtained proteomic data, we utilized the ingenuity pathway analysis tool to construct biological networks and analyze function and pathways that might associate with AR-mediated cardiac hypertrophy. Pathway analysis strongly suggested that ROS may be involved in the development of AR-mediated cardiac hypertrophy, which was then confirmed by further experimentation. The results showed that a marked increase in ROS production was detected in AR-mediated cardiac hypertrophy and blocking of ROS production significantly inhibited AR-mediated cardiac hypertrophy. We further proved that the ROS production was through NADPH oxidase or the mitochondrial electron transport chain and this ROS accumulation resulted in activation of extracellular signal-regulated kinase 1/2 leading to AR-mediated cardiac hypertrophy. These experimental results support the hypothesis, from the ingenuity pathway analysis, that AR-mediated cardiac hypertrophy is associated with the dysregulation of a complicated oxidative stress-regulatory network. In conclusion, our results provide a basis for understanding the detailed molecular mechanisms of AR-mediated cardiac hypertrophy.

Differential protein expression profiling of myocardial tissue in a mouse model of hypertrophic cardiomyopathy

Hypertrophic cardiomyopathy (HCM) is a genetic disorder caused by mutations in genes encoding sarcomere proteins. The mechanisms involved in the development of cardiac hypertrophy and heart failure remain poorly understood. Global proteomic profiling was used to study the cardiac proteome of mice predisposed to developing HCM. Hearts from three groups of mice (n=3 hearts per group) were studied: non-transgenic (NTG) and cardiac-specific transgenic models over-expressing either the normal (TnI(WT)) or a mutant cardiac troponin I gene (Gly203Ser; TnI(G203S)). Two-dimensional gel electrophoresis (2-DE) coupled with tandem mass spectrometry was used to identify proteins. Image analysis was performed using Progenesis SameSpots. A total of 34 proteins with at least a twofold change in the TnI(G203S) mouse model were identified. Alterations were detected in components involved in energy production, Ca(2+) handling, and cardiomyocyte structure. Expression level changes in cytoskeletal and contractile proteins were well represented in the study, including the intermediate filament protein desmin, which was further investigated in two additional physiological and pathological settings, i.e., exercise treatment, and severe heart failure in a novel double-mutant TnI-203/MHC-403 model of HCM. This study highlights the potential role of tissue proteomic profiling for mapping proteins, which may be critical in cardiac dysfunction and progression to heart failure in HCM.

Guanine deaminase functions as dihydropterin deaminase in the biosynthesis of aurodrosopterin, a minor red eye pigment of Drosophila

Dihydropterin deaminase, which catalyzes the conversion of 7,8-dihydropterin to 7,8-dihydrolumazine, was purified 5850-fold to apparent homogeneity from Drosophila melanogaster. Its molecular mass was estimated to be 48 kDa by gel filtration and SDS-PAGE, indicating that it is a monomer under native conditions. The pI value, temperature, and optimal pH of the enzyme were 5.5, 40 degrees C, and 7.5, respectively. Interestingly the enzyme had much higher activity for guanine than for 7,8-dihydropterin. The specificity constant (k(cat)/K(m)) for guanine (8.6 x 10(6) m(-1).s(-1)) was 860-fold higher than that for 7,8-dihydropterin (1.0 x 10(4) m(-1).s(-1)). The structural gene of the enzyme was identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis as CG18143, located at region 82A1 on chromosome 3R. The cloned and expressed CG18143 exhibited both 7,8-dihydropterin and guanine deaminase activities. Flies with mutations in CG18143, SUPor-P/Df(3R)A321R1 transheterozygotes, had severely decreased activities in both deaminases compared with the wild type. Among several red eye pigments, the level of aurodrosopterin was specifically decreased in the mutant, and the amount of xanthine and uric acid also decreased considerably to 76 and 59% of the amounts in the wild type, respectively. In conclusion, dihydropterin deaminase encoded by CG18143 plays a role in the biosynthesis of aurodrosopterin by providing one of its precursors, 7,8-dihydrolumazine, from 7,8-dihydropterin. Dihydropterin deaminase also functions as guanine deaminase, an important enzyme for purine metabolism.

In-gel digestion of proteins for MALDI-MS fingerprint mapping

Mass spectrometry (MS) has emerged as a sensitive, versatile, and rapid method for protein identification, following the advent of electrospray ionization mass spectrometry (ESI-MS) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The advantages of MALDI-MS over ESI-MS include its relatively high tolerance to contamination from biological matrices, its high sensitivity, the relative ease of interpreting spectra from mixtures, and the formation of singly protonated molecular ions for tandem analysis. Peptide fingerprint mass mapping and partial peptide sequencing using post-source decay and ladder sequencing by MALDI-MS in combination with algorithms for sequence database interrogation have the potential for identification and structural investigation of proteins. This unit describes in-gel digestion for peptide mass mapping of picomole to subpicomole quantities of protein derived from Coomassie- or silver-stained polyacrylamide gels. After digestion, the peptides are extracted from the gel and mass analyzed.

Redox signalling in cardiovascular disease

Oxidative stress has almost universally and unequivocally been implicated in the pathogenesis of all major diseases, including those of the cardiovascular system. Oxidative stress in cells and cardiovascular biology was once considered only in terms of injury, disease and dysfunction. However, it is now appreciated that oxidants are also produced in healthy tissues, and they function as signalling molecules transmitting information throughout the cell. Conversely, when cells move to a more reduced state, as can occur when oxygen is limiting, this can also result in alterations in the function of biomolecules and subsequently cells. At the centre of this 'redox signalling' are oxidoreductive chemical reactions involving oxidants or reductants post translationally modifying proteins. These structural alterations allow changes in cellular redox state to be coupled to alterations in cell function. In this review, we consider aspects of redox signalling in the cardiovascular system, focusing on the molecular basis of redox sensing by proteins and the array of post-translational oxidative modifications that can occur. In addition, we discuss studies utilising proteomic methods to identify redox-sensitive cardiac proteins, as well as those using this technology more broadly to assess redox signalling in cardiovascular disease.

Proteomics of the heart: unraveling disease

Heart diseases resulting in heart failure are among the leading causes of morbidity and mortality in developed countries. Underlying molecular causes of cardiac dysfunction in most heart diseases are still largely unknown but are expected to result from causal alterations in gene and protein expression. Proteomic technology now allows us to examine global alterations in protein expression in the diseased heart and can provide new insights into cellular mechanisms involved in cardiac dysfunction. The majority of proteomic investigations still use 2D gel electrophoresis (2-DE) with immobilized pH gradients to separate the proteins in a sample and combine this with mass spectrometry (MS) technologies to identify proteins. In spite of the development of novel gel-free technologies, 2-DE remains the only technique that can be routinely applied to parallel quantitative expression profiling of large sets of complex protein mixtures such as whole cell lysates. It can resolve >5000 proteins simultaneously (approximately 2000 proteins routinely) and can detect <1 ng of protein per spot. Furthermore, 2-DE delivers a map of intact proteins, which reflects changes in protein expression level, isoforms, or post-translational modifications. The use of proteomics to investigate heart disease should result in the generation of new diagnostic and therapeutic markers. In this article, we review the current status of proteomic technologies, describing the 2-DE proteomics workflow, with an overview of protein identification by MS and how these technologies are being applied to studies of human heart disease.

The chaotrope-soluble glycoprotein GP2 is a precursor of the insoluble glycoprotein framework of the Chlamydomonas cell wall

The cell wall of the unicellular green alga Chlamydomonas reinhardtii consists of an insoluble, hydroxyproline-rich glycoprotein framework and several chaotrope-soluble, hydroxyproline-containing glycoproteins. Up to now, there have been no data concerning the amino acid sequences of the hydroxyproline-containing polypeptides of the insoluble wall fraction. Matrix-assisted laser desorption ionization time-of-flight analyses of peptides released from the insoluble cell wall fraction by trypsin treatment revealed the presence of 14 peptide fragments that could be attributed to non-glycosylated domains of the chaotrope-soluble cell wall glycoprotein GP2. However, these peptides cover only 15% of the GP2 polypeptide backbone. Considerably more information concerning the presence of GP2 in the insoluble cell wall fraction was obtained by an immunochemical approach. For this purpose, 407 overlapping pentadecapeptides covering the whole known amino acid sequence of GP2 were chemically synthesized and probed with a polyclonal antibody raised against the deglycosylated, insoluble cell wall fraction. This particular antibody reacted with 297 of the 407 GP2-derived peptides. The peptides that were recognized by this antibody are distributed over the whole known GP2 sequence. The epitopes recognized by polyclonal antibodies raised against the 64- and 45-kDa constituents purified from the deglycosylation products of the insoluble cell wall fraction are also distributed over the whole GP2 backbone, although the corresponding antigens are considerably smaller than GP2. The significance of the latter results for the structure of the insoluble cell wall fraction is discussed.

Proteome analysis of antibody-producing CHO cell lines with different metabolic profiles

Two-dimensional gel electrophoresis and tandem mass spectrometry were used to identify proteins associated with a metabolic shift during fed-batch cultures of two recombinant antibody-producing CHO cell lines. The first cell line underwent a marked change in lactate metabolism during culture, initially producing lactate and then consuming it, while the second cell line produced lactate for a similar duration but did not later consume it. The first cell line displayed a declining specific antibody productivity during culture, correlating to the 2-D gel results and the intracellular antibody concentration determined by HPLC. Several statistical analysis methods were compared during this work, including a fixed fold-change criterion and t-tests using standard deviations determined in several ways from the raw data and mathematically transformed data. Application of a variance-stabilizing transformation enabled the use of a global empirical standard deviation in the t-tests. Most of the protein spots changing in each cell line did not change significantly in the other cell line. A substantial fraction of the changing proteins were glycolytic enzymes; others included proteins related to antibody production, protein processing, and cell structure. Enolase, pyruvate kinase, BiP/GRP78, and protein disulfide isomerase were found in spots that changed over time in both cell lines, and some protein changes differed from previous reports. These data provide a foundation for future investigation of metabolism in industrially relevant mammalian cell culture processes, and suggest that along with differences between cell types, the proteins expressed in cultures with low lactate concentrations may depend on how those conditions were generated.

Proteomics in human cancer research

Proteomics is now widely employed in the study of cancer. Many laboratories are applying the rapidly emerging technologies to elucidate the underlying mechanisms associated with cancer development, progression, and severity in addition to developing drugs and identifying patients who will benefit most from molecular targeted compounds. Various proteomic approaches are now available for protein separation and identification, and for characterization of the function and structure of candidate proteins. In spite of significant challenges that still exist, proteomics has rapidly expanded to include the discovery of novel biomarkers for early detection, diagnosis and prognostication (clinical application), and for the identification of novel drug targets (pharmaceutical application). To achieve these goals, several innovative technologies including 2-D-difference gel electrophoresis, SELDI, multidimensional protein identification technology, isotope-coded affinity tag, solid-state and suspension protein array technologies, X-ray crystallography, NMR spectroscopy, and computational methods such as comparative and de novo structure prediction and molecular dynamics simulation have evolved, and are being used in different combinations. This review provides an overview of the field of proteomics and discusses the key proteomic technologies available to researchers. It also describes some of the important challenges and highlights the current pharmaceutical and clinical applications of proteomics in human cancer research.

siRNA binding proteins of microglial cells: PKR is an unanticipated ligand

Small interfering RNA (siRNA), double-stranded RNA (dsRNA) 21-23 nucleotides (nt) long with two nt 3' overhangs, has been shown to mediate powerful sequence-specific gene silence in mammalian cells through RNA interference (RNAi). Due to its high efficiency and high specificity siRNA has been used as a powerful post genomic tool and a potent therapeutic candidate. However, there is still a lot to learn about the mobility of siRNA inside cells and the cellular factors that might interfere with the specificity and activity of siRNA. Microglia are the brain's effector cells of the innate immune system and suitable targets in the development of novel therapeutic strategies. Here, we show the cellular uptake and intracellular distribution of siRNA in murine microglial N9 cells. siRNA was internalized by microglial N9 cells without transfection reagent and mainly localized to the endosomes However, no significant gene silencing effects were observed. Its cellular uptake and cellular distribution pattern were similar with that of a same length single stranded DNA (ssDNA). Further, cellular binding proteins of siRNA were purified and identified by mass spectrometry. Negative control siRNA and siRNA targeted to beta-actin were used in this part of experiment. Most of the siRNA binding proteins for negative control siRNA and siRNA targeted to beta-actin were dsRNA-binding proteins, such as dsRNA-dependent protein kinase R (PKR). Furthermore, both control siRNA and siRNA targeted to beta-actin activated PKR in N9 cells, which suggest that siRNA might cause off-target effects through activation of PKR.

Changes in the rat heart proteome induced by exercise training: Increased abundance of heat shock protein hsp20

Chronic exercise training elicits adaptations in the heart that improve pump function and confer cardioprotection. To identify molecular mechanisms by which exercise training stimulates this favorable phenotype, a proteomic approach was employed to detect rat cardiac proteins that were differentially expressed or modified after exercise training. Exercise-trained rats underwent six weeks of progressive treadmill training five days/week, 0% grade, using an interval training protocol. Sedentary control rats were age- and weight-matched to the exercise-trained rats. Hearts were harvested at various times (0-72 h) after the last bout of exercise and were used to generate 2-D electrophoretic proteome maps and immunoblots. Compared with hearts of sedentary rats, 26 protein spot intensities were significantly altered in hypertrophied hearts of exercise-trained rats (p <0.05), and 12 spots appeared exclusively on gels from hearts of exercise-trained rats. Immunoblotting confirmed that chronic exercise training, but not a single bout of exercise, elicited a 2.5-fold increase in the abundance of one of the candidate proteins in the heart, a 20 kDa heat shock protein (hsp20) that persisted for at least 72 h of detraining. Thus, exercise training alters the cardiac proteome of the rat heart; the changes include a marked increase in the expression of hsp20.

Differential expression proteomics of human colon cancer

The focus of this study was to use differential protein expression to investigate operative pathways in early stages of human colon cancer. Colorectal cancer represents an ideal model system to study the development and progression of human tumors, and the proteomic approach avoids overlooking posttranslational modifications not detected by microarray analyses and the limited correlation between transcript and protein levels. Colon cancer samples, confined to the intestinal wall, were analyzed by expression proteomics and compared with matched samples from normal colon tissue. Samples were processed by two-dimensional gel electrophoresis, and spots differentially expressed and consistent across all patients were identified by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry analyses and by Western blot analyses. After differentially expressed proteins and their metabolic pathways were analyzed, the following main conclusions were achieved for tumor tissue: 1) a shift from beta-oxidation, as the main source of energy, to anaerobic glycolysis was observed owed to the alteration of nuclear- versus mitochondrial-encoded proteins and other proteins related to fatty acid and carbohydrate metabolism; 2) lower capacity for Na(+) and K(+) cycling; and 3) operativity of the apoptosis pathway, especially the mitochondrial one. This study of the human colon cancer proteome represents a step toward a better understanding of the metabolomics of colon cancer at early stages confined to the intestinal wall.

Application of proteomics in cardiovascular medicine

Proteomics is an emerging field that has the potential to uncover new therapeutic targets for the treatment and prevention of cardiovascular disease, as well as new diagnostic biomarkers for early disease detection. The basic strategy when carrying out proteomic analysis of cardiovascular disease is to compare the protein complements of diseased hearts or sera with controls. Any proteins that have altered expression between the two groups can be studied further for their involvement in disease pathogenesis. A number of steps need to be taken to identify changes in protein expression, including sample preparation, protein separation, imaging, and protein identification. Such studies are already underway in some cardiovascular conditions including dilated cardiomyopathy and atrial fibrillation. This review provides a summary of the techniques used in proteomic analysis and their application to cardiovascular research.

Modeling biological variability in 2-D gel proteomic carcinogenesis experiments

We propose a statistical method to model the underlying distribution of protein spot volumes in 2-D gels using a generalized model (GM). We apply this approach to discover mechanisms of chemical carcinogenesis in a rodent model. We generated 247 protein spots that were common to all gels (n = 18). Traditional statistical methods found 6.5% (13 out of 247) significant protein spots, our GM approach yielded a total of 53 (22.5%) differentially expressed protein spots.

Proteome analysis of the silkworm (Bombyx mori. L) colleterial gland during different development stages

The silkworm, Bombyx mori, colleterial gland developed very slowly until 2 days before emergence, then markedly enlarged due to the accumulation of a glue-like substances (mainly including 85% water and 11% proteins). However, the No glue (Ng) mutant female moth secreted only very little glue-like substance and laid loose eggs naturally. High-resolution two-dimensional polyacrylamide gel electrophoresis, followed by computer-assisted analysis, was used to screen the secretory region of colleterial gland protein patterns during different development stages to find quantitative and qualitative difference in protein expression during the pupae and moth stages. More than 700 protein spots were resolved in different developmental stages from the secretory region of the glands and most of the proteins were distributed in the mass range from 30 to 70 kD with pH 4-8. Through comparison and analysis, it was found that 3 proteins were only expressed in the later pupae stage (one or two days before emergence) and moth stage. Furthermore, these proteins were not expressed in the Ng mutant especially actin. There was a great variation of some protein expression volume during the development. Protein spots that changed more than 1.5-fold in expression level (relative to day 9), including 6 spots that were down-regulated and 2 spots that were up-regulated in expression were excised for identification by matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Results indicated that actins that participated or regulated the exocytosis of colleterial gland and other differentially expressed proteins might be related to colleterial gland development or the secretion of a glue-like substance.

Pigpen is a cellular binding protein of therapeutic oligonucleotides

BACKGROUND

Understanding the mechanism of oligonucleotide (ON) uptake and cellular distribution is important for rational design of ON-based therapeutic strategies. The aim of this study was to investigate the possible relationship between cellular distribution of ON and the protein pigpen.

METHODS

In vitro interaction of ON with the protein pigpen was detected using mass spectrometry. Cellular distribution of pigpen and co-localization of pigpen with ON was studied by fluorescence microscopy in endothelial YPEN and microglial N9 cells.

RESULTS

Pigpen had similar distribution patterns in endothelial YPEN and microglial N9 cells. Pigpen was localized to the cytoplasm of both cell types. In addition, pigpen distributed to nuclei, excluding the nucleoli, and concentrated along the nuclear membrane and plasma membrane. Intensely stained foci were only observed in the nucleus and cytoplasm of YPEN cells. Although co-localization of pigpen with phosphorothioate (PS) ON was not observed for the first hour after ON uptake, co-localization was observed 8 h later.

DISCUSSION

These data suggest that pigpen binds therapeutic ON and thus might contribute to ON cellular distribution.

Uptake, cellular distribution and novel cellular binding proteins of immunostimulatory CpG oligodeoxynucleotides in glioblastoma cells

Glioblastomas are the most malignant and most frequent brain tumors and exciting targets of gene and immunotherapy. Despite rapid development of experimental therapy little is known about the cellular behaviour of therapeutic oligodeoxynucleotides (ODNs). Here we designed uptake, cellular distribution and cellular binding proteins of immunostimulatory CpG-ODNs in glioblastoma cells by flow cytometry, fluorescence microscopy and mass spectrometry. Our data show that the phosphorothioate (PS) CpG-ODNs uptake in T98G and C6 cells is dose-, time-, temperature-dependent and independent of the CpG dinucleotides. Uptake can be inhibited by sodium azide, polyanions but not by chloroquine. After internalisation FITC labelled CpG-ODNs showed a spotted distribution in cytoplasm. Dozens of cellular binding proteins were identified using mass spectrometry. The binding of ODNs to proteins is dependent on modification and sequence but independent on CpG motif. ODNs bind to cellular proteins that are important for RNA processing and transport. Furthermore, three novel membrane proteins were identified, which might contribute to uptake of ODNs. ODNs binding to these proteins might interfere with the physiological function and thus might cause unwanted effects. Such binding also might influence the uptake efficiency or cellular distribution of therapeutic ODNs.

Analysis of polymorphic sites in the promoter of the nitric oxide synthase 2 gene

A point mutation (G --> C) in the gene promoter for the human nitric oxide synthase (NOS) 2 at position -954 is associated with protection against severe Plasmodium falciparum malaria in Gabon. Carriers of this mutation show higher basal levels of nitric oxide production than wild type individuals. To obtain information about the possible binding transcription factors, nucleic proteins from the lung carcinoma cell line were enriched by affinity chromatography using DEAE-Sepharose and immobilized oligonucleotides derived from the promoter sequence. A mutational analysis was performed on 30 samples to detect polymorphisms in the NOS2 promoter region that contains important NF-kappaB sites. Three point mutations were identified in this region. In vitro studies with promoter constructs showed an altered expression of the marker gene depending on the promoter variant used.

MALDI mass spectrometry analysis of high molecular weight proteins from whole bacterial cells: pretreatment of samples with surfactants

The use of surfactants as additives in conjunction with on-probe whole cell bacterial protein analysis employing MALDI-TOF-MS is described. Nonionic and zwitterionic surfactants were used to enhance the detection of high molecular weight proteins. Three nonionic, N-octyl-B-D-glactopyranoside, N-decyl-B-D-maltopyranoside, and N-dodecyl-B-D-maltoside, and two zwitterionic surfactants, N,N-dimethyldodecylamine-N-oxide and zwittergent 3-12 were evaluated with five different MALDI matrix systems. New peaks in the mass range of 2 to 80 kDa were produced with all of the various combinations of matrix and surfactant from both whole cell gram-positive and gram-negative bacteria. Ferulic acid used in conjunction with a 1.0 mM solution of N-octyl-B-D-glactopyranoside produced the highest quality spectra with high signal to noise ratios and peaks up to 140 kDa.

Data analysis methods for detection of differential protein expression in two-dimensional gel electrophoresis

The recent development of microarray technology has led statisticians and bioinformaticians to develop new statistical methodologies for comparing different biological samples. The objective is to identify a small number of differentially expressed genes from among thousands. In quantitative proteomics, analysis of protein expression using two-dimensional gel electrophoresis shows some similarities with transcriptomic studies. Thus, the goal of this study was to evaluate different data analysis methodologies widely used in array analysis using different proteomic data sets of hundreds of proteins. Even with few replications, the significance analysis of microarrays method appeared to be more powerful than the Student's t test in truly declaring differentially expressed proteins. This procedure will avoid wasting time due to false positives and losing information with false negatives.

Proteomic Analysis Reveals Different Protein Changes during Endothelin-1- or Leukemic Inhibitory Factor-induced Hypertrophy of Cardiomyocytes in Vitro

Proteomic analyses are being increasingly used to identify protein changes accompanying changes in cellular function. An advantage of this approach is that it is largely unbiased by prior assumptions on the importance of each protein in the process under investigation. Here we have evaluated the protein changes that accompany the enlargement, or hypertrophy, of cardiomyocytes in culture. We have taken the additional step of comparing the changes that accompany a concentric hypertrophic phenotype stimulated by endothelin-1 exposure and an eccentric hypertrophic phenotype stimulated by leukemic inhibitory factor exposure. Following separation of the protein extracts by two-dimensional gel electrophoresis and staining with colloidal Coomassie Brilliant Blue, we identified 15 protein spots representing 12 proteins that changed in response to endothelin-1. In comparison, 17 protein spots representing 17 proteins changed in response to leukemic inhibitory factor, and 35 protein spots representing 28 proteins did not change under these conditions. Importantly the well established marker of cardiac pathology, atrial natriuretic factor, was identified as a protein up-regulated by both endothelin-1 and leukemic inhibitory factor (2.4+/-0.8- and 2.2+/-0.3-fold, respectively). However, nine of the observed protein changes occurred for only endothelin-1, whereas 11 of the changes occurred only with leukemic inhibitory factor exposure. These two different stimuli are therefore able to elicit unique changes in the protein expression profile of cardiac myocytes. This is consistent with the differences in morphologies noted as well as the different signaling pathways utilized by these different stimuli.

Staphylococcus aureus deficient in lipidation of prelipoproteins is attenuated in growth and immune activation

A lipoprotein diacylglyceryl transferase (lgt) deletion mutant of Staphylococcus aureus SA113 was constructed. The lipoprotein and prelipoprotein expression, the growth behavior, and the ability of the mutant to elicit an immune response in various host cells were studied. In the wild type, the majority of [14C]palmitate-labeled lipoproteins were located in the membrane fraction, although some lipoproteins were also present on the cell surface and in the culture supernatant. The lgt mutant completely lacked palmitate-labeled lipoproteins and released high amounts of some unmodified prelipoproteins, e.g., the oligopeptide-binding protein OppA, the peptidyl-prolyl cis-trans isomerase PrsA, and the staphylococcal iron transporter SitC, into the culture supernatant. The growth of the lgt mutant was hardly affected in rich medium but was retarded under nutrient limitation. The lgt mutant and its crude lysate induced much fewer proinflammatory cytokines and chemokines in human monocytic (MonoMac6), epithelial (pulmonary A549), and endothelial (human umbilical vein endothelial) cells than the wild type. However, in whole blood samples, the culture supernatant of the lgt mutant was equal or even superior to the wild-type supernatant in tumor necrosis factor alpha induction. Lipoprotein fractionation experiments provided evidence that a small proportion of the mature lipoproteins are released by the S. aureus wild type despite the lipid anchor and are trapped in part by the cell wall, thereby exposing the immune-activating lipid structure on the cell surface. Bacterial lipoproteins appear to be essential for a complete immune stimulation by gram-positive bacteria.

Applying proteomics to drug discovery

Proteomics is a technology that has come to prominence over the last few years largely as a result of the advances that have been made in the equipment and software associated with the performance and analysis of two dimensional (2D) gel electrophoresis. With this technique it is now possible to resolve and identify proteins on 2D gels with a high degree of reproducibility and sensitivity. This facilitates the detection and quantification of thousands of proteins from complex biological samples in a single analysis and, more significantly, the comparison of these data accurately and reproducibly between samples. Thus, qualitative and quantitative assessments of changes are possible between the healthy and diseased state, in the presence and absence of drug, or between responders and non-responders. The added ability of carrying out such analysis at a high throughput opens up the possibilities for using proteomics to great effect throughout the drug discovery process. This review outlines the proteomic process and indicates areas where its potential has begun to be realised.

Uptake, intracellular distribution, and novel binding proteins of immunostimulatory CpG oligodeoxynucleotides in microglial cells

Microglial cells are central components of the innate immune system of the brain and contribute to inflammatory and degenerative processes. DNA with unmethylated CpG dinucleotides is a potent stimulant of microglial cells. We have analyzed uptake, intracellular distribution, and cellular binding proteins of CpG oligdeoxynucleotides (ODNs) by the microglial cell line N9. The uptake of CpG-ODN is concentration-, time-, and temperature-dependent, but, interestingly, independent of the CpG dinucleotides. After internalisation, CpG-ODN localized to the cytoplasm and showed a typical speckled distribution pattern. We further purified the cellular binding proteins of CpG-ODN and identified several binding proteins by tryptic digestion and mass spectrometry. Most of the CpG-ODN binding proteins are RNA processing enzymes, which are important for RNA splicing, export, and stability. Further, we identified a protein, pigpen, which has not been observed in microglial cells, so far. These proteins apparently bind CpG-ODN with low selectivity, as binding is independent of CpG dinucleotides. Interference of immunostimulatory and therapeutic oligonucleotides with proteins and enzymes of RNA transport and processing has not been described so far and might affect the physiological functions of these proteins and also might influence cellular localization of therapeutic ODN. These findings are helpful in understanding the cellular fate of ODN and the nonsequence-specific effects of ODN and for rational design and evaluation of ODN-based therapeutic strategies.

Bioinformatic methods to exploit mass spectrometric data for proteomic applications

The new technologies in mass spectrometric analysis of peptides and proteins necessary to accommodate proteomics-scale analyses require, in turn, concomitant development of informatics technologies suitable for very large-scale data handling and analysis. This chapter focuses on the data analysis tools available to the community for analysis of mass spectrometric proteomics data. Different database searching strategies are discussed for peptide and protein identification, and approaches and tools available for comparative quantitative analysis of samples are outlined.

Glycan side chains on naturally presented MHC class II ligands

The molecular characterization of unknown naturally presented major histocompatibility complex (MHC) class II glycopeptides carrying complex glycans has so far not been achieved, reflecting the different fragmentation characteristics of sugars and peptides in mass spectrometric analysis. Human leukocyte antigen (HLA)-DR-bound peptides were isolated by affinity purification, separated via high performance liquid chromatography and analyzed by matrix-assisted laser desorption/ionization and electrospray ionization mass spectrometry. We were able to identify two naturally processed MHC class II ligands, CD53(122-136) and CD53(121-136), carrying complex N-linked glycan side chains by a combination of in-source and collision-induced fragmentation on a quadrupole time-of-flight tandem mass spectrometer.

Proteomics

Proteomics is the measurement of one or more protein populations or proteomes, preferably in a quantitative manner. A protein population may be the set of proteins found in an organism, in a tissue or biofluid, in a cell, or in a subcellular compartment. A population also may be the set of proteins with a common characteristic, for example, those that interact with each other in molecular complexes, those involved in the same process such as signal transduction or cell cycle control, or those that share a common posttranslational modification such as phosphorylation or glycosylation. Proteomics experiments that involve mass spectrometry are divided into five categories: (1) protein identification, (2) protein quantitation or differential analysis, (3) protein-protein interactions, (4) post-translational modifications, and (5) structural proteomics. Each of these proteomics categories is reviewed. Examples are given for quantitative experiments involving two-dimensional gel electrophoresis, and for gel-free analysis using isotope-coded affinity tags. The impact of proteomics on biological research and on drug development is discussed. Challenges for further development in proteomics are presented, including sample preparation, sensitivity, dynamic range, and automation.

Genomic and Proteomic Profiles of Heart Disease

Genomics and proteomics are becoming powerful tools for profiling diseased states. The human genome is estimated to encode 30,000 to 40,000 genes, generating more than 100,000 functionally distinct proteins. Microarray data are available for multiple models of heart disease as well as for diseased and failing human hearts. Similarly, two-dimensional gel data banks of normal and diseased myocardium from multiple species are published and are available on the Internet. The combined technologies are beginning to provide new insights into the causes and pathways of cardiac dysfunction. This article reviews the novel findings that have been acquired from genomic and proteomic screens of diseased hearts in animal models and humans.

Studies on middle silkgland proteins of cocoon colour sex-limited silkworm (Bombyx mori L.) using two-dimensional polyacrylamide gel electrophoresis

Qualitative and quantitative differences in proteins expressed in the middle silkglands of male and female silkworm larvae that differ in silk colour were investigated by high resolution two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), followed by computer assisted image analysis. About 1000 protein spots were resolved in both the sexes and most proteins were shown to be distributed in the area from 15 kDa to 70 kDa and pH 4-8. It was found that some proteins displayed higher expression in yellow cocoon, while two proteins were only expressed in female silkworm silkgland tissue through the comparison and analysis by two-D software. These proteins especially existed in female silkworm middle silkgland tissue of yellow cocoon. Furthermore, these proteins might be involved in the expression of cocoon colour phenotype

A 14-3-3 protein of Chlamydomonas reinhardtii associated with the endoplasmic reticulum: nucleotide sequence of the cDNA and the corresponding gene and derived amino acid sequence

Two major 14-3-3 proteins of the unicellular green alga Chlamydomonas reinhardtii were purified and partially sequenced. The obtained data show that the 30-kDa isoform predominant in the cytosol is encoded by a previously cloned and sequenced 14-3-3 cDNA whereas the 27-kDa isoform represents a new 14-3-3 protein which is largely associated with the endoplasmic reticulum (ER). Therefore, the corresponding cDNA was cloned and sequenced. The nucleotide sequence of this new cDNA species and the derived amino acid sequence differ considerably from the previously cloned Chlamydomonas 14-3-3 cDNA. The conclusion that the divergent evolution of the corresponding genes must have started rather early as compared to the 14-3-3 genes of other organisms was corroborated by their different genomic organization. The amino acid sequences of both 14-3-3 isoforms were comparatively analysed to find differences which might be responsible for their differential binding to the ER.

Proteomics in myocardial diseases

Recently, proteome analysis has been introduced to analyze differential protein expression and cellular protein composition in cardiovascular medicine. Proteins expressed by diseased hearts (myocardial proteomics) were first investigated over a decade ago using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). However, while 2D-PAGE is very successful for the abundant and moderately expressed proteins, it struggles to identify proteins expressed at low levels. However, the sensitivity of mass spectrometry has increased considerably during recent years, and technical progress widens the detection limits of mass-spectrometric analysis. Proteomics now allows us to examine global alterations in protein expression in the diseased hearts, and will provide new insights into the cellular mechanisms involved in cardiac dysfunction. This review will summarize the present knowledge about the use of proteome analysis in myocardial diseases.

Protein identification: the origins of peptide mass fingerprinting

Peptide mass fingerprinting (PMF) grew from a need for a faster, more efficient method to identify frequently observed proteins in electrophoresis gels. We describe the genesis of the idea in 1989, and show the first demonstration with fast atom bombardment mass spectrometry. Despite its promise, the method was seldom used until 1992, with the coming of significantly more sensitive commercial instrumentation based on MALDI-TOF-MS. We recount the evolution of the method and its dependence on a number of technical breakthroughs, both in mass spectrometry and in other areas. We show how it laid the foundation for high-throughput, high-sensitivity methods of protein analysis, now known as proteomics. We conclude with recommendations for further improvements, and speculation of the role of PMF in the future.

The allograft inflammatory factor-1 in Creutzfeldt-Jakob disease brains

The allograft inflammatory factor-1 (AIF-1) is a 17-kDa IFN-gamma inducible Ca(2+)-binding EF-hand protein that is encoded within the HLA class III genomic region and is involved in immune dysfunction and smooth muscle cell activation. We used immunohistochemistry double labelling experiments to analyse the spatial distribution and cell-type-specific localization of AIF-1 in the brains of patients who died as a result of sporadic Creutzfeldt-Jakob disease (CJD) and neuropathologically unaltered controls. Significantly more AIF-1 immunoreactive macrophages/microglial cells and, interestingly, neurones were observed in CJD patients compared to controls. Western blotting confirmed more prominent AIF-1 immunoreactive bands of approximately 50 kDa in four CJD patients compared to three controls. Chaotropic SDS-PAGE of the recombinant AIF-1 resulted in almost complete reduction of the 50 kDa band and mass spectrometry revealed only AIF-1-specific tryptic protein fragments suggesting that trimerized AIF-1 is the predominant form in vivo. Finally, we analysed mechanisms of neuronal AIF-1 induction. Following H2O2 challenge, a model of general cell stress, we observed the gradual induction of AIF-1 and, more interestingly, release to the supernatant of SKNSH neurones. Parallel reverse transcriptase polymerase chain reaction and sequencing was used to confirm AIF-1 mRNA expression.

Suppression of coatomer mutants by a new protein family with COPI and COPII binding motifs in Saccharomyces cerevisiae

Protein trafficking is achieved by a bidirectional vesicle flow between the various compartments of the eukaryotic cell. COPII coated vesicles mediate anterograde protein transport from the endoplasmic reticulum to the Golgi apparatus, whereas retrograde Golgi-to-endoplasmic reticulum vesicles use the COPI coat. Inactivation of COPI vesicle formation in conditional sec21 (gamma-COP) mutants rapidly blocks transport of certain proteins along the early secretory pathway. We have identified the integral membrane protein Mst27p as a strong suppressor of sec21-3 and ret1-1 mutants. A C-terminal KKXX motif of Mst27p that allows direct binding to the COPI complex is crucial for its suppression ability. Mst27p and its homolog Yar033w (Mst28p) are part of the same complex. Both proteins contain cytoplasmic exposed C termini that have the ability to interact directly with COPI and COPII coat complexes. Site-specific mutations of the COPI binding domain abolished suppression of the sec21 mutants. Our results indicate that overexpression of MST27 provides an increased number of coat binding sites on membranes of the early secretory pathway and thereby promotes vesicle formation. As a consequence, the amount of cargo that can bind COPI might be important for the regulation of the vesicle flow in the early secretory pathway.

Fast-response proteomics by accelerated in-gel digestion of proteins

Kinetics of in-gel digestion of proteins by modified and native trypsins was studied by MALDI TOF mass spectrometry using 18O-labeled peptides as internal standards. The effect of the temperature, enzyme concentration, digestion time, and surface area of gel pieces on the yield of digestion products was characterized. Based on the kinetic data, we developed a protocol that enabled the identification of gel-separated proteins with 30-min digestion time without compromising the peptide yield and the sensitivity compared to conventional protocols that typically rely upon overnight enzymatic cleavage. The accelerated digestion protocol was tested in identification of more than 120 proteins from budding and fission yeasts at the subpicomole level.

Analysis of the cytosolic proteome in a cell culture model of familial amyotrophic lateral sclerosis reveals alterations to the proteasome, antioxidant defenses, and nitric oxide synthetic pathways

Injury to motor neurons associated with mutant Cu,Zn-superoxide dismutase (SOD1)-related familial amyotrophic lateral sclerosis (FALS) results from a toxic gain-of-function of the enzyme. The mechanisms by which alterations to SOD1 elicit neuronal death remain uncertain despite intensive research effort. Analysis of the cellular proteins that are differentially expressed in the presence of mutant SOD1 represents a novel approach to investigate further this toxic gain-of-function. By using the motor neuron-like cell line NSC34 stably transfected with wild-type, G93A, or G37R mutant human SOD1, we investigated the effects of mutant human SOD1 on protein expression using proteomic approaches. Seven up-regulated proteins were identified as argininosuccinate synthase, argininosuccinate lyase, neuronal nitric-oxide synthase, RNA-binding motif protein 3, peroxiredoxin I, proteasome subunit beta 5 (X), and glutathione S-transferase (GST) Alpha 2. Seven down-regulated proteins were identified as GST Mu 1, GST Mu 2, GST Mu 5, a hypothetical GST Mu, GST Pi B, leukotriene B(4) 12-hydroxydehydrogenase, and proteasome subunit beta5i (LMP7). GST assays demonstrated a significant reduction in the total GST activity of cells expressing mutant human SOD1. Proteasome assays demonstrated significant reductions in chymotrypsin-like, trypsin-like, and post-glutamylhydrolase proteasome activities. Laser capture microdissection of spinal cord motor neurons from human FALS cases, in conjunction with reverse transcriptase-PCR, demonstrated decreased levels of mRNA encoding GST Mu 1, leukotriene B(4) 12-hydroxydehydrogenase, and LMP7. These combined approaches provide further evidence for involvement of alterations in antioxidant defenses, proteasome function, and nitric oxide metabolism in the pathophysiology of FALS.

The Application of Clinical Proteomics to Cancer and other Diseases

The term "clinical proteomics" refers to the application of available proteomics technologies to current areas of clinical investigation. The ability to simultaneously and comprehensively examine changes in large numbers of proteins in the context of disease or other changes in physiological conditions holds great promise as a tool to unlock the solutions to difficult clinical research questions. Proteomics is a rapidly growing field that combines high throughput analytical methodologies such as two-dimensional gel electrophoresis and SELDI mass spectrometry methods with complex bioinformatics to study systems biology--the system of interest is defined by the investigator. Even with all its potential, however, studies must be carefully designed in order to differentiate true clinical differences in protein expression from differences originating from variation in sample collection, variation in experimental condition, and normal biological variability. Proteomic analyses are already widely in use for clinical studies ranging from cancer to other diseases such as cardiovascular disease, organ transplant, and pharmacodynamic studies.

Structural Diversity of Cancer-related and Non-Cancer-related Prostate-specific Antigen

Background: Heterogeneity among the various molecular forms of prostate-specific antigen (PSA) has not been well characterized, despite the critical importance of PSA in the detection of prostate cancer. The purpose of this study was to examine PSA heterogeneity in cancerous and noncancerous materials by extensive and systematic protein analysis.

Methods: A catalog of molecular forms of PSA was established with the PSA purified from seminal fluid. This catalog was used to analyze PSA heterogeneity in cancerous and noncancerous materials by immunoblotting with polyclonal antibodies.

Results: PSA from noncancerous materials showed a wider range of molecular mass, from 6000 to 28 000 Da. PSA from cancerous materials did not contain lower molecular mass forms.

Conclusions: The PSA protein catalog may be useful for the analysis of differences among PSA forms in men with and without prostate cancer and for analysis of antibodies used to detect PSA.

In situ alkylation with acrylamide for identification of cysteinyl residues in proteins during one- and two-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis

Cysteinyl residues in proteins were alkylated with acrylamide during sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) to yield a thioether derivative, cys-S-beta-propionamide (PAM cys). The process was termed in situ alkylation with acrylamide. Using this method, the recovery of PAM-cys peptides from bovine serum albumin (BSA) was 88.6% at 10 picomol in one-dimensional (1-D) SDS-PAGE and 97.1% at 50 picomol in two-dimensional (2-D) SDS-PAGE. The coverage of tryptic peptide of BSA in 1-D and 2-D SDS-PAGE was 83.7% and 81.1%, respectively. The advantages of in situ alkylation with acrylamide were the following: (i) cysteinyl peptides were effectively derived in a single PAM cys and then proteins were precisely identified using databases; (ii) marked reduction of salts compared with post alkylation, e.g., using carboxymethylamide (CAM), resulting in higher signal intensity and wider coverage of cysteinyl peptides from PAM cys, compared with those of CAM derivatives, in mass spectrometry peptide mapping; and (iii) shorter duration by excluding the processes of post alkylation and desalting before peptide mapping.

Release of regulators of angiogenesis following Hypocrellin-A and -B photodynamic therapy of human brain tumor cells

Photodynamic therapy (PDT) is an innovative strategy for the treatment of solid neoplasms of the brain. Aside from inducing cell death in tumor cells, PDT induces endothelial cell death and promotes formation of blood clots; however, exact mechanisms that trigger these phenomena remain largely unknown. We now used Western blotting to analyze secretion of regulators of angiogenesis to the supernatants of one glioma, one macrophage, and one endothelial cell line following Hypocrellin-A and -B photodynamic therapy. We observed induction of proangiogenic VEGF (vascular endothelial growth factor) and of antiangiogenic sFlt-1, angiostatin, p43, allograft inflammatory factor-1, and connective tissue growth factor. Release of thrombospondin-1 was diminished in a glioma cell line supernatant. Endostatin release was induced in glioma cells and reduced in macrophages and endothelial cells. These data show that a wide range of antiangiogenic factors are secreted by brain tumor cells following Hypocrellin photochemotherapy. However, VEGF release is also induced thus suggesting both favorable and deleterious effects on tumor outgrowth.