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PubMed2006

Attractin is elevated in the cerebrospinal fluid of patients with malignant astrocytoma and mediates glioma cell migration.

PURPOSE: There are a limited number of noninvasive methods available for the monitoring of neoplastic disease in the central nervous system. The goal of our study was to find reliable markers that could be used for disease monitoring as well as to identify new targets for the therapeutic intervention for malignant astrocytoma (WHO grades 3 and 4). EXPERIMENTAL DESIGN: We employed proteomic techniques to identify secreted proteins in the cerebrospinal fluid that were specific to patients with malignant astrocytoma. RESULTS: Among 60 cerebrospinal fluid samples of patients with various central nervous system diseases, attractin was consistently found to be elevated in the samples of patients with malignant astrocytoma. To independently validate these results, we examined attractin expression in a new set of 108 normal and tumoral brain tissue specimens and found elevated expression in 97% of malignant astrocytomas, with the highest levels in grade 4 tumors. Using immunohistochemistry, we further showed that attractin is produced and secreted by the tumor cells. Finally, we showed that cerebrospinal fluid from brain tumor patients induces glioma cell migration and that attractin is largely responsible for this promigratory activity. CONCLUSIONS: Our results find attractin to be a reliable secreted marker for high-grade gliomas. Additionally, our migration studies suggest that it may be an important mediator of tumor invasiveness, and thus, a potential target in future therapies.

Astrocytoma↗

PubMed2004

Progression of malignancy in clear cell renal cell carcinomas.

Much progress has recently been obtained in the classification and characterization of RCC by using cytogenetic, gene microarray and proteomic techniques. Pivotal for the understanding of the progression of malignancy of clear cell renal cell carcinomas are findings connecting its biology to inactivation of the von Hippel-Lindau tumour suppressor gene product (VHLp), found in most CC-RCCs. Disruption of VHLp function appears to be involved in altered cell cycle control, resistance to hypoxia, hyperangiogenesis and changes in the organization of cytoskeletal and extracellular matrix proteins in RCC. These changes are reflected in the overexpression of the vascular endothelial growth factor (VEGF) and the subunits of hypoxia-inducible factor (HIF), and other angiogenetic and metastasis-promoting factors. Other changes related to progression of malignancy in RCC are the upregulation of proinflammatory cytokines and changes in cell adhesion proteins.

Carcinoma, Renal Cell↗

PubMed2005

An update of the management of multiple myeloma: the changing landscape.

The management of multiple myeloma is rapidly changing. Cytogenetic, molecular and proteomic techniques have led to a better understanding of the pathophysiology of this heterogeneous malignancy. Novel agents designed to interrupt myeloma growth and survival pathways have entered into clinical usage with unprecedented speed, while new prognostic systems based on clinical and biologic features, such as cytogenetic abnormalities, have been developed. A plethora of clinical trials have been initiated utilizing novel agents, alone or in conjunction with established modalities such as conventional cytotoxic agents and stem cell transplantation. These newer treatments have increased the antitumor response rates in this disease and have provided options for patients whose disease has become resistant to conventional therapy. A major challenge is to define the optimal use of these new agents and combinations in order to significantly impact the natural history of myeloma.

Antineoplastic Agents↗

PubMed2006

A regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data.

BACKGROUND: As a variety of functional genomic and proteomic techniques become available, there is an increasing need for functional analysis methodologies that integrate heterogeneous data sources. METHODS: In this paper, we address this issue by proposing a general framework for gene function prediction based on the k-nearest-neighbor (KNN) algorithm. The choice of KNN is motivated by its simplicity, flexibility to incorporate different data types and adaptability to irregular feature spaces. A weakness of traditional KNN methods, especially when handling heterogeneous data, is that performance is subject to the often ad hoc choice of similarity metric. To address this weakness, we apply regression methods to infer a similarity metric as a weighted combination of a set of base similarity measures, which helps to locate the neighbors that are most likely to be in the same class as the target gene. We also suggest a novel voting scheme to generate confidence scores that estimate the accuracy of predictions. The method gracefully extends to multi-way classification problems. RESULTS: We apply this technique to gene function prediction according to three well-known Escherichia coli classification schemes suggested by biologists, using information derived from microarray and genome sequencing data. We demonstrate that our algorithm dramatically outperforms the naive KNN methods and is competitive with support vector machine (SVM) algorithms for integrating heterogenous data. We also show that by combining different data sources, prediction accuracy can improve significantly CONCLUSION: Our extension of KNN with automatic feature weighting, multi-class prediction, and probabilistic inference, enhance prediction accuracy significantly while remaining efficient, intuitive and flexible. This general framework can also be applied to similar classification problems involving heterogeneous datasets.

Algorithms↗

PubMed2003

Combinatorial peptidomics: a generic approach for protein expression profiling.

Traditional approaches to protein profiling were built around the concept of investigating one protein at a time and have long since reached their limits of throughput. Here we present a completely new approach for comprehensive compositional analysis of complex protein mixtures, capable of overcoming the deficiencies of current proteomics techniques. The Combinatorial methodology utilises the peptidomics approach, in which protein samples are proteolytically digested using one or a combination of proteases prior to any assay being carried out. The second fundamental principle is the combinatorial depletion of the crude protein digest (i.e. of the peptide pool) by chemical crosslinking through amino acid side chains. Our approach relies on the chemical reactivities of the amino acids and therefore the amino acid content of the peptides (i.e. their information content) rather than their physical properties. Combinatorial peptidomics does not use affinity reagents and relies on neither chromatography nor electrophoretic separation techniques. It is the first generic methodology applicable to protein expression profiling, that is independent of the physical properties of proteins and does not require any prior knowledge of the proteins. Alternatively, a specific combinatorial strategy may be designed to analyse a particular known protein on the basis of that protein sequence alone or, in the absence of reliable protein sequence, even the predicted amino acid translation of an EST sequence. Combinatorial peptidomics is especially suitable for use with high throughput micro- and nano-fluidic platforms capable of running multiple depletion reactions in a single disposable chip.

Journal Article↗

PubMed2006

Phosphoprotein analysis: from proteins to proteomes.

Characterization of protein modification by phosphorylation is one of the major tasks that have to be accomplished in the post-genomic era. Phosphorylation is a key reversible modification occurring mainly on serine, threonine and tyrosine residues that can regulate enzymatic activity, subcellular localization, complex formation and degradation of proteins. The understanding of the regulatory role played by phosphorylation begins with the discovery and identification of phosphoproteins and then by determining how, where and when these phosphorylation events take place. Because phosphorylation is a dynamic process difficult to quantify, we must at first acquire an inventory of phosphoproteins and characterize their phosphorylation sites. Several experimental strategies can be used to explore the phosphorylation status of proteins from individual moieties to phosphoproteomes. In this review, we will examine and catalogue how proteomics techniques can be used to answer specific questions related to protein phosphorylation. Hence, we will discuss the different methods for enrichment of phospho-proteins and -peptides, and then the various technologies for their identification, quantitation and validation.

Journal Article↗

PubMed2005

Identification, cloning, and expression of potential diagnostic markers for Q fever.

The clinical diagnosis of Q fever is difficult. Whole cell antigens are currently used in several serological methods, but antigens are limited due to the hazardous nature of Coxiella burnetii cultivation. In this report, we described the method of detecting immunodominant antigens of C. burnetii by using proteomic techniques with patient sera, and cloning and expressing the selected antigens using a novel vector known for its ease of expression, purification, and downstream application.

Antigens, Bacterial↗

PubMed2006

Disease biomarkers in cerebrospinal fluid of patients with first-onset psychosis.

BACKGROUND: Psychosis is a severe mental condition that is characterized by a loss of contact with reality and is typically associated with hallucinations and delusional beliefs. There are numerous psychiatric conditions that present with psychotic symptoms, most importantly schizophrenia, bipolar affective disorder, and some forms of severe depression referred to as psychotic depression. The pathological mechanisms resulting in psychotic symptoms are not understood, nor is it understood whether the various psychotic illnesses are the result of similar biochemical disturbances. The identification of biological markers (so-called biomarkers) of psychosis is a fundamental step towards a better understanding of the pathogenesis of psychosis and holds the potential for more objective testing methods. METHODS AND FINDINGS: Surface-enhanced laser desorption ionization mass spectrometry was employed to profile proteins and peptides in a total of 179 cerebrospinal fluid samples (58 schizophrenia patients, 16 patients with depression, five patients with obsessive-compulsive disorder, ten patients with Alzheimer disease, and 90 controls). Our results show a highly significant differential distribution of samples from healthy volunteers away from drug-naïve patients with first-onset paranoid schizophrenia. The key alterations were the up-regulation of a 40-amino acid VGF-derived peptide, the down-regulation of transthyretin at approximately 4 kDa, and a peptide cluster at approximately 6,800-7,300 Da (which is likely to be influenced by the doubly charged ions of the transthyretin protein cluster). These schizophrenia-specific protein/peptide changes were replicated in an independent sample set. Both experiments achieved a specificity of 95% and a sensitivity of 80% or 88% in the initial study and in a subsequent validation study, respectively. CONCLUSIONS: Our results suggest that the application of modern proteomics techniques, particularly mass spectrometric approaches, holds the potential to advance the understanding of the biochemical basis of psychiatric disorders and may in turn allow for the development of diagnostics and improved therapeutics. Further studies are required to validate the clinical effectiveness and disease specificity of the identified biomarkers.

Adult↗

PubMed2006

A new strategy for estimating recombination fractions between dominant markers from an F2 population.

Although most high-density linkage maps have been constructed from codominant markers such as single-nucleotide polymorphisms (SNPs) and microsatellites due to their high linkage information, dominant markers can be expected to be even more significant as proteomic technique becomes widely applicable to generate protein polymorphism data from large samples. However, for dominant markers, two possible linkage phases between a pair of markers complicate the estimation of recombination fractions between markers and consequently the construction of linkage maps. The low linkage information of the repulsion phase and high linkage information of coupling phase have led geneticists to construct two separate but related linkage maps. To circumvent this problem, we proposed a new method for estimating the recombination fraction between markers, which greatly improves the accuracy of estimation through distinction between the coupling phase and the repulsion phase of the linked loci. The results obtained from both real and simulated F2 dominant marker data indicate that the recombination fractions estimated by the new method contain a large amount of linkage information for constructing a complete linkage map. In addition, the new method is also applicable to data with mixed types of markers (dominant and codominant) with unknown linkage phase.

Algorithms↗

PubMed2005

CSF biomarkers for Alzheimer's disease: use in early diagnosis and evaluation of drug treatment.

Early diagnosis of Alzheimer's disease is important in initiating symptomatic treatment with acetylcholine esterase inhibitors, and will be of even greater significance if drugs with a potential to slow down the degenerative process, such as beta-secretase inhibitors and beta-amyloid vaccination, prove to have a clinical effect. During the last decade, research efforts have focused on developing cerebrospinal fluid (CSF) biomarkers for Alzheimer's disease. In this review, the background and principles for, and the diagnostic performance of, the CSF biomarkers total tau, phosphorylated tau and the 42-amino acid form of beta-amyloid, are reviewed. New candidate CSF biomarkers and new strategies, including multiparameter immunoassays and CSF proteomics techniques, in the search of additional CSF biomarkers are also reviewed. Finally, the rationale for the use of CSF biomarkers to identify and monitor the biochemical effect of new drug candidates is reviewed.

Alzheimer Disease↗

PubMed2006

Use of nanotechnology for the development of novel cancer biomarkers.

Novel nanotechnologies can complement and augment existing genomic and proteomic techniques employed to analyze variations across different tumor types, thus offering the potential to distinguish between normal and malignant cells. Sensitive biosensors constructed out of nanoscale components (e.g., nanocantilevers, nanowires and nanochannels) can recognize genetic and molecular events and have reporting capabilities, thereby offering the potential to detect rare molecular signals associated with malignancy. Such signals may then be collected for analysis by nanoscale harvesters that selectively isolate cancer-related molecules from tissues. Another area with near-term potential for the early detection of cancer is the identification of mutations and genomic instability.

Animals↗

PubMedDate not supplied

The proacrosin binding protein, sp32, is tyrosine phosphorylated during capacitation of pig sperm.

Mammalian sperm must undergo capacitation, a preparation period in the female reproductive tract or in vitro, in order to fertilize. We have previously described a Mr 32 000 tyrosine phosphorylated protein, "p32," that appears in pig sperm during capacitation. The identity of p32 remains unknown; if and how it is involved during capacitation is not understood. The objective of the present study was to identify p32 by proteomic techniques. Western blotting of proteins separated successively under nonreducing and then reducing conditions showed the appearance of the tyrosine phosphorylated p32 only when sperm were incubated in capacitating conditions. The spot was sequenced by mass spectrometry/mass spectrometry and identified as "sp32," a protein implicated in proacrosin maturation. The same membranes probed with anti-sp32 antibody demonstrated that sp32 is present in both noncapacitating and capacitating conditions and revealed exactly the same spot as p32. Immunoprecipitation with either anti-phosphotyrosine or anti-sp32 antibody corroborated these results. Indirect immunofluorescence with anti-phosphotyrosine antibody or anti-sp32 antibody show similar labeling of capacitated sperm, supporting the hypothesis that p32 is a tyrosine phosphorylated form of sp32. After ionophore treatment to induce the acrosome reaction, anti-sp32 and anti-phosphotyrosine labeling on the acrosome disappeared. These results demonstrate that sp32, a (pro)acrosin binding protein, is the p32, a tyrosine phosphorylated protein related to capacitation. We will now focus on the significance of tyrosine phosphorylation on sp32 function during fertilization-related events.

Acrosin↗

PubMed2002

Computational function assignment for potential drug targets: from single genes to cellular systems.

Biomedical science is currently undergoing an epoch-marking transition from its classical phase to the post-genome era. The outstanding success of world-wide genome sequencing efforts, evidenced by the recent publication of the draft of the human genome, together with the completion of several genomes of eukaryotic model organisms and the availability of microbial genome sequences, is opening up data sources of unprecedented scale for drug discovery. Furthermore, the elucidation of genome expression states through transcriptomic and proteomic techniques is playing a crucial role in the characterisation of disease at the molecular level. At the same time, our still very limited knowledge of the biological functions of genes and proteins at different levels of cellular organisation is preventing full exploitation of the available data. This review will discuss current computational techniques for function prediction based on the sequence-structure-function paradigm. Newly emerging approaches aimed at gaining an expanded understanding of function through integration of data from various sources and modelling of complex cellular systems will also be highlighted.

Amino Acid Sequence↗

PubMed2002

Immunologic targets for breast cancer.

Breast cancer is an immunogenic tumor. Over the last decade, investigations have shown that patients with breast cancer have pre-existent immune responses, both humoral and cellular, against a variety of proteins expressed in their tumors. Researchers using genomic and proteomic techniques have defined dozens of proteins that may serve as immunologic targets in breast cancer patients. In addition, other investigators focusing on a more directed approach of evaluating well-defined breast cancer proteins that are immunogenic have begun to translate some of the candidate antigens into human clinical trials of immune-based therapies in breast cancer. Immunogenic proteins associated with breast cancer are abundant. The major experimental question now facing breast cancer immunologists is how to prioritize these many candidate antigens for further evaluation for clinical use.

Journal Article↗

PubMed2007

Hepatitis B virus-induced oncogenesis.

Hepatocellular carcinoma (HCC) is one of the most common cancers in the world with an annual incidence of more than 500000 in the year 2000. Its incidence is rising in many countries. Recently, it has been estimated that about 53% of HCC cases in the world are related to hepatitis B virus (HBV). The epidemiological association of HBV with HCC is well established. In recent studies, it was revealed that HBsAg carriers have a 25-37 times increased risk of developing HCC as compared to non-infected people. At present, HBV-associated carcinogenesis can be seen as a multi-factorial process that includes both direct and indirect mechanisms that might act synergistically. The integration of HBV DNA into the host genome occurs at early steps of clonal tumor expansion. The integration has been shown in a number of cases to affect a variety of cancer-related genes and to exert insertional mutagenesis. The permanent liver inflammation, induced by the immune response, resulting in a degeneration and regeneration process confers to the accumulation of critical mutations in the host genome. In addition to this, the regulatory proteins HBx and the PreS2 activators that can be encoded by the integrate exert a tumor promoter-like function resulting in positive selection of cells producing a functional regulatory protein. Gene expression profiling and proteomic techniques may help to characterize the molecular mechanisms driving HBV-associated carcinogenesis, and thus potentially identify new strategies in diagnosis and therapy.

Carcinoma, Hepatocellular↗

PubMed2002

The IUPS Physiome Project. International Union of Physiological Sciences.

Modern medicine is currently benefiting from the development of new genomic and proteomic techniques, and also from the development of ever more sophisticated clinical imaging devices. This will mean that the clinical assessment of a patient's medical condition could, in the near future, include information from both diagnostic imaging and DNA profile or protein expression data. The Physiome Project of the International Union of Physiological Sciences (IUPS) is attempting to provide a comprehensive framework for modelling the human body using computational methods which can incorporate the biochemistry, biophysics and anatomy of cells, tissues and organs. A major goal of the project is to use computational modelling to analyse integrative biological function in terms of underlying structure and molecular mechanisms. To support that goal the project is establishing web-accessible physiological databases dealing with model-related data, including bibliographic information, at the cell, tissue, organ and organ system levels. This paper discusses the development of comprehensive integrative mathematical models of human physiology based on patient-specific quantitative descriptions of anatomical structures and models of biophysical processes which reach down to the genetic level.

Biophysics↗

PubMed2005

[Effect of chronic enhanced external counterpulsation on arterial endothelial cells of porcine with hypercholesteremia].

OBJECTIVE: To verify whether chronic enhanced external counterpulsation (EECP) may repair artery endothelial cells (ECs) damage resulted from hypercholesteremia in pigs. METHODS: EECP was performed for 36 hours in pigs with hypercholesteremia and the left descending artery (LDA) was isolated for scanning electron microscopy (SEM). The ECs were collected from the thoracic aorta and analyzed by proteomic technique. RESULTS: The ECs of hypercholesteremia pigs showed irregular arrangement with obvious desquamation of coronary ECs and formation of atherosclerotic plaque, and these lesions were milder in EECP-treated pigs. Six over-expressed proteins were detected in the endothelial cells in EECP-treated pigs in comparison with those of the hypercholesteremia pigs. CONCLUSION: Chronic EECP helps restore cell morphology and repair functional damage of ECs resulted from hypercholesteremia by regulating endothelial protein expressions, and consequently improves cell adhesion and intracellular metabolism and reduces EC apoptosis.

Animals↗

PubMed2005

[Prevalence of antiepithelial cell antibody in systemic vasculitis and identification of the target antigen thereof].

OBJECTIVE: To investigate the prevalence of antiepithelial cell antibody (AECA) in systemic vasculitis (SV) and the target antigen thereof. METHOD: Sera of 113 patients with SV of different kinds, 46 patients with Behcet's disease, 23 patients with Takayasu arteritis, 19 patients with Wegener's granulomatosis, 8 patients with polyarteritis nodosa, 7 patients with microscopic polyangiitis, and 10 patients with Churg-Strauss syndrome were collected to detect the protein expression of AECA by Western blotting, with the protein of the endothelial cells of the line EA. hy926 line as substrate. Two-dimensional electrophoresis combined with immunoblotting, liquid chromatography-electrospray ionization mass spectrography was used to detect the target antigens related to vasculitis. Sera of 57 patients with systemic lupus erythematosus (SLE), 25 patients with rheumatoid arthritis (RA), and 20 healthy persons were collected as controls. RESULTS: The AECA-positive rate of the SV patients was 69.0%, not significantly different from that of the SLE patients (66.7%), but significantly higher than those of the RA patients (6.7%, P < 0.01) and healthy persons (0, P < 0.01). The AECA from the SV patients reacted with the endothelial cell (EC) antigens with the molecular size of 26 to 125 kDa, and the AECA from the SLE patients reacted with the EC antigens with the molecular size of 15 to 97 kDa. The EC antigens with the molecular size of 47 kDa was commonly found in the sera of the AECA-positive SV patients and SLE patients, however, was not found in the RA, and polymyositis-dermatomyositis patients. The EC protein reacted by 47 kDa protein was identified by proteomic techniques as alpha-enolase. CONCLUSION: A group of heterogeneous antibodies, AECA can be found frequently in patients with SV and SLA. AECA reacts against a common EC antigen, alpha-enolase.

Adolescent↗