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Biomarkers and multiple drug resistance in breast cancer.

Breast cancer, the most common form of cancer among women in North America and almost all of Europe, is a significant health problem in terms of both morbidity and mortality. It is estimated that each year this disease is diagnosed in over one million people worldwide and is the cause of more than 400,000 deaths. Although chemotherapy forms part of a successful treatment regime in many cases, as few as 50% patients may benefit from this, as a result of intrinsic or acquired multiple drug resistance (MDR). Through the use of in vitro cell culture models, a number of mechanisms of MDR have been identified; many, if not all, of which may contribute to breast cancer resistance in the clinical setting. This phenomenon is complicated by the likely multi-factorial nature of clinical resistance combined with the fact that, although apparently studied extensively in breast cancer, reported analyses have been performed using a range of analytical techniques; many on small sub-groups of patients, with different clinicopathological characteristics and receiving a range of therapeutic approaches. Larger defined studies, using standardised genomic and proteomics profiling approaches followed by functional genomics studies, are necessary in order to definitively establish the degree of complexity contributing to drug resistance and to identify novel therapeutic approaches - possibly involving chemotherapy, drug resistance modulators, and novel targeted therapies - to combat this disease.

Antineoplastic Agents↗

The KEGG database.

KEGG (http://www.genome.ad.jp/kegg/) is a suite of databases and associated software for understanding and simulating higher-order functional behaviours of the cell or the organism from its genome information. First, KEGG computerizes data and knowledge on protein interaction networks (PATHWAY database) and chemical reactions (LIGAND database) that are responsible for various cellular processes. Second, KEGG attempts to reconstruct protein interaction networks for all organisms whose genomes are completely sequenced (GENES and SSDB databases). Third, KEGG can be utilized as reference knowledge for functional genomics (EXPRESSION database) and proteomics (BRITE database) experiments. I will review the current status of KEGG and report on new developments in graph representation and graph computations.

Amino Acid Sequence↗

[Toxicogenomics--a new paradigm of toxicology and birth of reverse toxicology].

Toxicogenomics is, similar to other genome science fields, based on DNA microarray and/or DNA chip technologies, which has enabled a large number of gene expressions, thus, have been applied to such functional genomics as pharmacogenomics, oncogenomics, proteomics, metabonomics, etc. Toxicogenomics has advantages such as deducing the number of test animals and the test period, and adopts simpler techniques using new biomarkers. What toxicogenomics can offer to conventional toxicology is given herein.

Computational Biology↗

Hybrid and customized approach in telemedicine systems: an unavoidable destination.

Several important problems in the majority of industrialized countries have challenged the centralized and overburdened current model of healthcare. Telehealthcare systems are presented as a new paradigm, offering high expectations to provide effective solutions to this picture. With this paper we present a new methodological approach for telehealthcare systems that pursues the generation of clinical and physiological knowledge of the patient in a real time and personalized manner. This approach is based on a computational component, identified as patient physiological image (PPI), which is responsible for generating an image of the state of the patient and therapy devices. Three key issues of the proposed methodological approach are evaluated. With the objective to validate the capability of the PPI to determine the internal state of a patient, a digital simulation experiment over the mathematical model of a PPI is done. Numerical results are compared to those obtained by a validated mathematical model. Secondly, a laboratory prototype of a novel human physical activity monitor that follows the designed methodological approach will be tested, in order to evaluate the trade-off between processing capacity, portability, and cost-efficiency and power consumption, which are necessary to assure its compliance with the methodology. As a third key issue, the capability of our methodology to integrate physiological information belonging to different scales is analyzed. This is done by means of a case study related to the integration of the regulation of water function of AQP2 channels (genomic, proteomic and cellular levels) into a kidney collecting duct epithelium mathematical model of a PPI. The analysis and preliminary evaluation of the proposed telehealthcare methodological approach, featured by an advanced personalization of health assistance, have been satisfactory.

Delivery of Health Care↗

[Analysis of differential proteins in laryngeal carcinoma cell line Hep-2 with transfection of LCRG1].

BACKGROUND & OBJECTIVE: Laryngeal carcinoma-related gene 1 (LCRG1), a novel laryngeal carcinoma-related tumor suppressor gene, was cloned with mRNA differential display method. Previous researches showed LCRG1 might inhibit cell growth, proliferation, colony formation in soft agar, and tumorigenesis of laryngeal carcinoma cell line Hep-2. This study was to screen the proteins associated with the tumor suppressive function of LCRG1 by comparative proteomics method. METHODS: The whole cellular proteins of Hep-2/LCRG1 and Hep-2/pcDNA3.1(+) cells were extracted and separated by two-dimensional gel electrophoresis (2-DE) technology. After electrophoresis, the gels were stained by Coomassie Brilliant Blue G-250, and analyzed using PDQuest software. The differentially expressed proteins were cut from the gels, analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), or electrospray ionization-quadrupole time-of-flight MS/MS (ESI-Q-TOF MS/MS), and identified through searching database with Mascot software. RESULTS: The well-resolved, reproducible 2-DE patterns of Hep-2/LCRG1 and Hep-2/pcDNA3.1(+) cells were established. The total protein spots were 1,075+/-43 in Hep-2/LCRG1 cells and 1,027+/-23 in Hep-2/pcDNA3.1(+) cells, with an average matching rate of 91%. Using mass spectrometry technology, 20 differential protein spots between the 2 cell lines were identified. Among them, 16 were identified by MALDI-TOF-MS, and 4 were identified by ESI-Q-TOF MS/MS. Some of the identified proteins were characterized as members of cellular transcription and metabolism enzymes. CONCLUSIONS: In this study, 2-DE gels of Hep-2/LCRG1 cell line with high expression of LCRG1 mRNA and vector control Hep-2/pcDNA3.1(+) cell line were established; some differential proteins related to LCRG1 were identified by mass spectrometry. These data will help to illustrate the molecular mechanism of LCRG1.

Adaptor Proteins, Signal Transducing↗

[From structural to functional genomics: theoretical and applied aspects].

The paper considers the results of studies of human genome and several eukariotic genomes, which have led to the establishment of the new genetic subject Structural Genomics and some other scientific areas. Particular attention is given to Proteomics considered to be the most developed section of Functional Genomics. The systems approach is ascertained to underlie proteomic strategy to study the protein products of gene expression with an ultimate goal of drawing up complete protein indices for definite organisms, such as proteomes, human proteomes in particular. The studies carried out at the Research Center of Medical Genetics, Russian Academy of Medical Sciences, have been used as an example to show that advances in Functional Genomics and the data of proteomic studies may be employed both for solution of theoretical problems and for different applied purposes (for development of diagnostic methods, for control of products derived from genetically modified plants, as well as during cellular therapy).

Genome, Human↗

Enzyme activity profiles of the secreted and membrane proteome that depict cancer cell invasiveness.

By primarily measuring changes in transcript and protein abundance, conventional genomics and proteomics methods may fail to detect significant posttranslational events that regulate protein activity and, ultimately, cell behavior. To address these limitations, activity-based proteomic technologies that measure dynamics in protein function on a global scale would be of particular value. Here, we describe the application of a chemical proteomics strategy to quantitatively compare enzyme activities across a panel of human breast and melanoma cancer cell lines. A global analysis of the activity, subcellular distribution, and glycosylation state for the serine hydrolase superfamily resulted in the identification of a cluster of proteases, lipases, and esterases that distinguished cancer lines based on tissue of origin. Strikingly, nearly all of these enzyme activities were down-regulated in the most invasive cancer lines examined, which instead up-regulated a distinct set of secreted and membrane-associated enzyme activities. These invasiveness-associated enzymes included urokinase, a secreted serine protease with a recognized role in tumor progression, and a membrane-associated hydrolase KIAA1363, for which no previous link to cancer had been made. Collectively, these results suggest that invasive cancer cells share discrete proteomic signatures that are more reflective of their biological phenotype than cellular heritage, highlighting that a common set of enzymes may support the progression of tumors from a variety of origins and thus represent attractive targets for the diagnosis and treatment of cancer.

Biomarkers, Tumor↗

Mitochondrial dysfunction and oxidative damage in parkin-deficient mice.

Loss-of-function mutations in parkin are the predominant cause of familial Parkinson's disease. We previously reported that parkin-/- mice exhibit nigrostriatal deficits in the absence of nigral degeneration. Parkin has been shown to function as an E3 ubiquitin ligase. Loss of parkin function, therefore, has been hypothesized to cause nigral degeneration via an aberrant accumulation of its substrates. Here we employed a proteomic approach to determine whether loss of parkin function results in alterations in abundance and/or modification of proteins in the ventral midbrain of parkin-/- mice. Two-dimensional gel electrophoresis followed by mass spectrometry revealed decreased abundance of a number of proteins involved in mitochondrial function or oxidative stress. Consistent with reductions in several subunits of complexes I and IV, functional assays showed reductions in respiratory capacity of striatal mitochondria isolated from parkin-/- mice. Electron microscopic analysis revealed no gross morphological abnormalities in striatal mitochondria of parkin-/- mice. In addition, parkin-/- mice showed a delayed rate of weight gain, suggesting broader metabolic abnormalities. Accompanying these deficits in mitochondrial function, parkin-/- mice also exhibited decreased levels of proteins involved in protection from oxidative stress. Consistent with these findings, parkin-/- mice showed decreased serum antioxidant capacity and increased protein and lipid peroxidation. The combination of proteomic, genetic, and physiological analyses reveal an essential role for parkin in the regulation of mitochondrial function and provide the first direct evidence of mitochondrial dysfunction and oxidative damage in the absence of nigral degeneration in a genetic mouse model of Parkinson's disease.

Animals↗

Protein functions and biological contexts.

The availability of a rough draft of the predicted human proteome allows an evaluation of the extent to which the predicted and biochemical functions of proteins are in alignment, and the roles of different technologies and approaches to understanding human diseases and instantiating therapeutics. Microarray technologies at the transcriptomic and proteomic levels can be high throughput and excellent for diagnostic purposes, but their informational outputs are inferior in quality to those emerging from the co- and post-translational levels and from antibody-based molecular anatomy. It is now abundantly clear that data transfer between the transcriptome and proteome is not straightforward, and that increasing emphasis needs to be placed on pure proteomic approaches at the structural, quantitative, cell biological and phenomic levels, with special focus on embryogenic and foetal processes. Finally, the precision genetic engineering that is required to evaluate the functional significance of context-dependent protein interactions underpinned by post-translational modifications and proteolytic cleavage events, is still too time consuming and rudimentary to be implemented on a large scale in the mouse, and basic principles and first order networks will need to be sorted out in even simpler model systems such as Drosophila.

Databases, Protein↗

Accelerated discovery of novel protein function in cultured human cells.

Experimental approaches that enable direct investigation of human protein function are necessary for comprehensive annotation of the human proteome. We introduce a cell-based platform for rapid and unbiased functional annotation of undercharacterized human proteins. Utilizing a library of antibody biomarkers, the full-length proteins are investigated by tracking phenotypic changes caused by overexpression in human cell lines. We combine reverse transfection and immunodetection by fluorescence microscopy to facilitate this procedure at high resolution. Demonstrating the advantage of this approach, new annotations are provided for two novel proteins: 1) a membrane-bound O-acyltransferase protein (C3F) that, when overexpressed, disrupts Golgi and endosome integrity due likely to an endoplasmic reticulum-Golgi transport block and 2) a tumor marker (BC-2) that prompts a redistribution of a transcriptional silencing protein (BMI1) and a mitogen-activated protein kinase mediator (Rac1) to distinct nuclear regions that undergo chromatin compaction. Our strategy is an immediate application for directly addressing those proteins whose molecular function remains unknown.

Biomarkers↗

The application of mass spectrometry to membrane proteomics.

Membrane proteins perform some of the most important functions in the cell, including the regulation of cell signaling through surface receptors, cell-cell interactions, and the intracellular compartmentalization of organelles. Recent developments in proteomic strategies have focused on the inclusion of membrane proteins in high-throughput analyses. While slow and steady progress continues to be made in gel-based technologies, significant advances have been reported in non-gel shotgun methods using liquid chromatography coupled to mass spectrometry (LC/MS). These latter strategies facilitate the identification of large numbers of membrane proteins and modifications, and have the potential to provide insights into protein topology and orientation in membranes.

Amino Acid Sequence↗

Glycomics: an integrated systems approach to structure-function relationships of glycans.

In comparison with genomics and proteomics, the advancement of glycomics has faced unique challenges in the pursuit of developing analytical and biochemical tools and biological readouts to investigate glycan structure-function relationships. Glycans are more diverse in terms of chemical structure and information density than are DNA and proteins. This diversity arises from glycans' complex nontemplate-based biosynthesis, which involves several enzymes and isoforms of these enzymes. Consequently, glycans are expressed as an 'ensemble' of structures that mediate function. Moreover, unlike protein-protein interactions, which can be generally viewed as 'digital' in regulating function, glycan-protein interactions impinge on biological functions in a more 'analog' fashion that can in turn 'fine-tune' a biological response. This fine-tuning by glycans is achieved through the graded affinity, avidity and multivalency of their interactions. Given the importance of glycomics, this review focuses on areas of technologies and the importance of developing a bioinformatics platform to integrate the diverse datasets generated using the different technologies to allow a systems approach to glycan structure-function relationships.

Animals↗

Dynamic lysine acetylation and succinylation of platelet proteins regulates platelet storage lesion: mechanistic insights from multi-omics.

OBJECTIVES: Platelet storage lesion (PSL) severely impairs platelet function during storage, presenting a major hurdle in transfusion medicine; however, the dynamic interplay between global proteomic changes and post-translational modifications (PTMs) underlying these functional deteriorations remains insufficiently characterized. Here, we report the first comprehensive multi-omics analysis integrating global proteomics, acetylomics, and succinylomics to dissect the molecular dynamics during platelet storage. METHODS: We performed quantification of global proteomics, acetylome and succinylome based on TMT-labeled LC-MS/MS analysis, combined with antibody-affinity enrichment and purification. Dynamic molecular changes and functional transformation of platelet were also characterized under proper conditions stored for 1, 3, 5, 7 days, respectively. RESULTS: We systematically characterized 3,609 proteins, 1,308 acetylation sites, and 1,947 succinylation sites across multiple storage time points (D1, D3, D5, D7). We distinct temporal patterns of post-translational modifications, with succinylation showing more extensive coverage than acetylation in platelets. Pathway enrichment analysis revealed extensive metabolic reprogramming involving complement activation, energy metabolism, and cellular detoxification processes. The identification of specific motif patterns provided mechanistic insights into the functional specificity of these modifications. Random forest machine learning identified 20 core regulatory proteins representing critical nodes in PSL development. Furthermore, we employed real - time quantitative polymerase chain reaction (RT - QPCR) to measure the expression levels of key genes related to platelet function and PTM - associated pathways. CONCLUSION: By mapping the interplay between proteomic abundance shifts and PTM dynamics, this study provides a multidimensional understanding of PSL, establishing a foundational framework for optimizing storage protocols and enhancing transfusion safety.

Blood Platelets↗

MTH187 from Methanobacterium thermoautotrophicum has three HEAT-like repeats.

With the completion of genome sequencing projects, there are a large number of proteins for which we have little or no functional information. Since protein function is closely related to three-dimensional conformation, structural proteomics is one avenue where the role of proteins with unknown function can be investigated. In the present structural project, the structure of MTH187 has been determined by solution-state NMR spectroscopy. This protein of 12.4 kDa is one of the 424 non-membrane proteins that were cloned and purified for the structural proteomic project of Methanobacterium thermoautotrophicum [Christendat, D., Yee, A., Dharamsi, A., Kluger, Y., Gerstein, M., Arrowsmith, C.H. and Edwards, A.M. (2000) Prog. Biophys. Mol. Biol., 73, 339-345]. Methanobacterium thermoautotrophicum is a thermophilic archaeon that grows optimally at 65 degrees C. A particular characteristic of this microorganism is its ability to generate methane from carbon dioxide and hydrogen [Smith, D.R., Doucette-Stamm, L.A., Deloughery, C., Lee, H., Dubois, J., Aldredge, T., Bashirzadeh, R., Blakely, D., Cook, R., Gilbert, K., Harrison, D., Hoang, L., Keagle, P., Lumm, W., Pothier, B., Qiu, D., Spadafora, R., Vicaire, R., Wang, Y., Wierzbowski, J., Gibson, R., Jiwani, N., Caruso, A., Bush, D., Reeve, J. N. et al. (1997) J. Bacteriol., 179, 7135-7155].

Archaeal Proteins↗

Identification of a novel archaebacterial thioredoxin: determination of function through structure.

As part of a high-throughput, structural proteomic project we have used NMR spectroscopy to determine the solution structure and ascertain the function of a previously unknown, conserved protein (MtH895) from the thermophilic archeon Methanobacterium thermoautotrophicum. Our findings indicate that MtH895 contains a central four-stranded beta-sheet core surrounded by two helices on one side and a third on the other. It has an overall fold superficially similar to that of a glutaredoxin. However, detailed analysis of its three-dimensional structure along with molecular docking simulations of its interaction with T7 DNA polymerase (a thioredoxin-specific substrate) and comparisons with other known members of the thioredoxin/glutaredoxin family of proteins strongly suggest that MtH895 is more akin to a thioredoxin. Furthermore, measurement of the pK(a) values of its active site thiols along with direct measurements of the thioredoxin/glutaredoxin activity has confirmed that MtH895 is, indeed, a thioredoxin and exhibits no glutaredoxin activity. We have also identified a group of previously unknown proteins from several other archaebacteria that have significant (34-44%) sequence identity with MtH895. These proteins have unusual active site -CXXC- motifs not found in any known thioredoxin or glutaredoxin. On the basis of the results presented here, we predict that these small proteins are all members of a new class of truncated thioredoxins.

Amino Acid Sequence↗

P1D6 inhibits FnBP-induced extracellular proteome remodeling: proteomic evidence for a novel intervention strategy in atopic dermatitis.

Atopic dermatitis (AD) is an inflammatory skin disorder characterized by skin barrier impairment, chronic inflammation, and intense pruritus. Staphylococcus aureus (S. aureus) critically contributes to its pathogenesis; however, the mechanistic role of its virulence factor fibronectin-binding protein (FnBP) in keratinocytes remains poorly understood. This study used bibliometric analysis and quantitative proteomics to examine the relationship. We first performed a bibliometric analysis, revealing a sustained increase in publications on S. aureus and AD, peaking at 99 articles in 2023, with hotspots focused on skin barrier function, immune inflammation, and pediatrics. Quantitative proteomics was employed to investigate how FnBP reshapes the extracellular proteome and whether the anti-α5 integrin antibody P1D6 exerts interventional effects. HaCaT cells were stimulated with recombinant FnBP alone or in combination with P1D6, followed by data-independent acquisition (DIA)-based proteomic analysis of secretome changes. Proteomic analysis identified FnBP-induced differentially expressed proteins enriched in immune- and barrier-related pathways, including cell adhesion, cell junctions, and VEGFA-VEGFR2 signaling. P1D6 intervention significantly inhibited the secretome profile and identified 241 core responsive proteins, of which approximately 52% returned to baseline levels after intervention (P > 0.05). These proteins were primarily enriched in pathways governing protein homeostasis, folding, proteasomal degradation, and interleukin-7 signaling. Notably, P1D6 modulated the downregulation of ATP5F1B and P4HB, key effectors within the interleukin-7 pathway. This study demonstrates that FnBP remodels the keratinocyte secretome by disrupting protein homeostasis, consequently inducing barrier injury and chronic inflammation related to AD, which can be effectively blocked by P1D6. Combined with bibliometric trends and proteomic evidence, this study focuses on FnBP, an underexplored virulence factor, and provides novel insights into AD pathogenesis and therapeutic interventions.

Humans↗

Analyzing the cardiac muscle proteome by liquid chromatography-mass spectrometry-based expression proteomics.

Cardiomyopathies are diseases of the heart resulting in impaired cardiac muscle function, which can lead to heart dilation or overt heart failure. These diseases represent a major cause of global morbidity and death. Innovative preventive and therapeutic measures are urgently needed for early detection, categorization, and treatment of patients at risk of cardiomyopathy. These developments will require a more complete understanding of the molecular effects of impaired cardiac function, even prior to overt disease. The use of gel-free expression proteomics in the detailed analysis of cardiac tissues should yield significant insight into the pathophysiology of these diseases.

Animals↗

Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli.

Structural proteomics projects are generating three-dimensional structures of novel, uncharacterized proteins at an increasing rate. However, structure alone is often insufficient to deduce the specific biochemical function of a protein. Here we determined the function for a protein using a strategy that integrates structural and bioinformatics data with parallel experimental screening for enzymatic activity. BioH is involved in biotin biosynthesis in Escherichia coli and had no previously known biochemical function. The crystal structure of BioH was determined at 1.7 A resolution. An automated procedure was used to compare the structure of BioH with structural templates from a variety of different enzyme active sites. This screen identified a catalytic triad (Ser82, His235, and Asp207) with a configuration similar to that of the catalytic triad of hydrolases. Analysis of BioH with a panel of hydrolase assays revealed a carboxylesterase activity with a preference for short acyl chain substrates. The combined use of structural bioinformatics with experimental screens for detecting enzyme activity could greatly enhance the rate at which function is determined from structure.

Biotin↗