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PubMed2026

Hyperlactate-Associated Lysine Lactylome Remodeling in Laryngeal Squamous Cell Carcinoma.

Laryngeal squamous cell carcinoma (LSCC) lacks reliable biomarkers, and the roles of lactate metabolism and lysine lactylation (Kla) remain largely unknown. We profiled the lysine lactylome of LSCC, paired it with adjacent normal tissues, and integrated the data with quantitative proteomic and transcriptomic analyses. LSCC exhibited a hyperlactate-associated phenotype characterized by dysregulated lactate-related genes (LRGs), altered protein abundance, increased tissue lactate, and globally increased Kla levels. Data-independent acquisition mass spectrometry (DIA-MS) identified 1616 Kla sites on 1468 peptides from 688 proteins, with most differential sites being upregulated in tumors. Differentially lactylated proteins were enriched in cell-matrix adhesion, cell migration, chromatin remodeling, and gene-regulatory processes and were clustered into cytoskeletal and nuclear regulatory modules. Multiple Kla sites were also detected on the core histones. Immunoblotting and tissue microarray analyses confirmed increased pan-Kla expression in the LSCC. Pan-Kla levels were independent of sex and age but positively correlated with the tumor stage and lymph-node metastasis. These findings provide a systematic resource for hyperlactate-associated lactylome remodeling in LSCCs and identify candidate Kla-related molecular features associated with clinicopathological progression for future functional and clinical evaluation.

Humans↗
PubMed2002

In vivo molecular imaging.

The relatively young field of molecular imaging is focused on the visualization of molecular phenotypes in whole organisms. This is achieved using imaging systems based on radionuclides, nuclear magnetic resonance, ultrasound, or the visible-IR region of the optical spectrum. Molecularly defined contrast in these modalities is generated by exogenous probes of the endogenous proteome, or through transgenes. Examples of exogenous probes include those that are transported and trapped (glucose, nucleoside analogs), those directed against extracellular receptors (somatostatin, opioid, melanotropin), and those activated by extracellular proteases. Transgenes that have been used in molecular imaging include the above receptors, non-mammalian enzymes that trap pro-drugs (HSV-tk, yeast CD), and optical reporter proteins (luciferase, fluorescent proteins). Cutting edge technologies in this field include in vivo assays for protein-protein interactions, and in vivo assays for mRNA expression patterns. The number of degrees of freedom in designing new agents is daunting, and advancements in this field will require a significant participation from molecular and cellular biochemists.

Animals↗
PubMed2002

[Pharmaco-proteomic analysis: application of proteomic analysis to the discovery and development of new drugs].

Pharmacoproteomics may be defined as proteomics applied to the discovery of new therapeutic targets and to the study of drug effects. Proteomics is a powerful technique for analyzing the protein expression profiles in a biological system and its modifications in response to a stimulus or according to the physiological or pathophysiological states. Thus it is a technique of choice for the discovery of new drug targets. It is also an interesting approach for the study of the mode of action of treatments and preclinical drug development. This pharmacoproteomic approach may be particularly useful for the research of new molecular alterations implicated in type 2 diabetes and/or obesity and for the further characterization of existing or new drugs.

Animals↗
PubMed2005

Carbonylation and glutathionylation of proteins in the blue mussel Mytilus edulis detected by proteomic analysis and Western blotting: Actin as a target for oxidative stress.

Protein expression profiles (PEPs) were generated by two-dimensional electrophoresis (2-D SDS-PAGE) for gill and digestive glands of Mytilus edulis sampled from a polluted and reference site in Cork Harbour, Ireland. Similar patterns and expression levels were found for both sites in silver stained gels. However, Western blotting for carbonylated proteins demonstrated higher levels of specific carbonylation of proteins in tissues from animals in the polluted site. Animals from the reference site were acclimated in holding tanks, exposed to 1 mM H2O2 for 24 h, dissected and analysed by 2-D SDS-PAGE. Again, generally similar PEPs were found in control and exposed animals for gill and digestive gland but carbonylation was more pronounced in polluted and exposed animals. Western blotting of extracts after one-dimensional electrophoresis with antibodies to glutathione and actin revealed that gill proteins are glutathionylated more strongly than digestive gland and that this process is more pronounced in polluted animals than in controls. We conclude that carbonylation and glutathionylation can occur in gill and digestive gland in response to oxidative stress in M. edulis. Actin is a major target for both glutathionylation and carbonylation under oxidative stress conditions.

Actins↗
PubMed2003

Gene and protein expression profiling of human cerebral endothelial cells activated with tumor necrosis factor-alpha.

An increase in permeability of the blood-brain barrier is a critical event in the pathophysiological process of multiple sclerosis and other neurodegenerative diseases. Tumor necrosis factor alpha (TNFalpha) is known to play a crucial role in this process and is a powerful activator of endothelial cell inflammatory responses. Although many reports describe effects of TNFalpha activation in endothelial cells, the molecular mechanisms specific for activation of cerebral endothelial cells remains unclear. The objective of this study was to identify potential pharmaceutical targets for the treatment of multiple sclerosis using molecular profiling techniques. Gene expression measurements (Affymetrix Hu6800 oligonucleotide arrays) and proteomics (two-dimensional gel electrophoresis and mass spectrometry) were applied to analyze early alterations in human cerebral endothelial cells (HCEC) activated by TNFalpha. Human umbilical vein endothelial cells (HUVEC) were used as the reference system. The results presented show that HCEC and HUVEC respond similarly with respect to cell adhesion molecules, chemotaxis, apoptosis and oxidative stress molecules. However, nuclear factors NFkB1 and NFkB2, plasminogen activator inhibitor 1 and cofilin 1 are examples of cerebral specific responses. Our results indicate involvements of the urokinase plasminogen activator system and cytoskeletal rearrangements unique to TNFalpha activation of cerebral endothelial cells.

Antineoplastic Agents↗
PubMed2004

Serum protein pattern in sarcoidosis analysed by a proteomics approach.

BACKGROUND: An altered protein expression in bronchoalveolar lavage fluid (BALF) of sarcoidosis patients has previously been reported. As this disease is systemic, involving not only the lungs, a change in the serum components is also to be expected. In the present study we therefore analysed the total serum protein profile of the patients earlier reported, with active sarcoidosis. METHODS: We used a proteomics approach to assess overall changes in the protein content of serum in patients with acute sarcoidosis (n = 6) compared to healthy controls (n = 4). RESULTS: Our results show a significantly higher number of protein-spots in serum of the patients compared to the healthy individuals in the pH range 4.5-6.7 (median 886 vs. 742, p < 0.05). The total protein concentrations of the patients' sera were also significantly higher compared to the controls (median 62 vs. 56 mg/mL, p < 0.05). Measurement of the optical densities of the protein-spots from two-dimensional electrophoresis gels, covering pH interval 4.5-6.7, showed varying levels of expression of 22 different serum proteins in the patients compared to the controls. These proteins are involved in immune responses and some are known markers of inflammation. We found three proteins, which were changed concomitantly in the BALF as described in a previous report, and sera of the same patients. CONCLUSIONS: Our results are of importance in order to identify biochemical markers in blood of sarcoidosis patients. Ideally, a combination of markers in BALF and serum may turn out to be disease specific.

Adult↗
PubMed2005

Identification of grass pollen allergens by two-dimensional gel electrophoresis and serological screening.

Approximately 50% of allergic patients are sensitized against grass pollen allergens. The characterization of specific immunoglobulin E (IgE) reactivity to allergen components in pollen-allergic patients is fundamental for clinical diagnosis and for immunotherapy. Complex allergen extracts are commonly used in diagnostic tests as well as in immunotherapy preparations, but their composition in single allergenic molecules is only partially known. Diagnostic tests which utilize recombinant or immuno-purified allergens have been made available in clinical practice. They allow to obtain specific profiles of IgE reactivity, but the panel of available molecules is far from complete. Here, we used a proteomic approach in order to detect grass allergens from a natural protein extract. A five-grass pollen extract used for diagnosis and immunotherapy was resolved by two dimensional gel electrophoresis (2-DE), and assayed with 9 sera from pollen-allergic patients whose sensitization profile was dissected by using IgE reactivity to recombinant allergens. 2-DE immunoreactivity patterns were matched with IgE reactivity to identify protein spots as candidate allergens. Identity was confirmed by mass spectrometry analysis. We identified 6 out of 8 expected clinically relevant allergens in the natural grass extract. Moreover, we identified different molecular isoforms of single allergens, thus obtaining a more detailed profile of IgE reactivity. Some discrepancies in protein isoform profile and sera immunoreactivity between recombinant and native allergen 5 from Phleum pratense were observed and a new putative allergen was described. The proteomic approach applied to the analysis of a natural allergen allows the comprehensive evaluation of the sensitization profile of allergic patients and the identification of new allergens.

Allergens↗
PubMed2006

Perspectives of proteomics in acute myeloid leukemia.

Acute myeloid leukemia (AML) is a frequent hematological malignancy. Despite enormous therapeutic efforts that range from various cytotoxic agents to allogeneic stem cell transplantation, overall survival of patients with AML remains unsatisfying. The poor survival rates are mainly due to therapy-related mortality, failure of induction chemotherapy and early relapses. Therefore, novel therapeutic agents that are more efficient and better tolerated are eagerly sought after. For existing therapeutic strategies, there is a lack of markers that are capable of reliably predicting prognosis or the therapeutic response prior to treatment. There is hope that elucidation of the AML-specific proteome will prompt the discovery of novel therapeutic targets and biomarkers in AML. Modern mass-spectrometry instrumentation has achieved excellent performance in terms of sensitivity, resolution and mass accuracy; however, so far, the contribution of proteomics to the care of patients with AML is virtually zero. This might be partly because mass spectrometry instrumentation and protein fractionation still lack true high-throughput capabilities with highest levels of reproducibility, thus hampering large-scale translational studies with clinical samples. Since mass-spectrometry instruments are very intricate devices, their successful operation will hinge on the willingness and ability of mass-spectrometry experts and clinical researchers to adopt new views, learn from each other and cooperate in order to ultimately benefit the patient suffering from AML. This review highlights some clinical problems circumventing the treatment of patients with AML. Furthermore, it provides a brief overview of the technical background of standard proteomics approaches and describes opportunities, challenges and pitfalls of proteomic studies with regards to AML.

Biomarkers, Tumor↗
PubMed2006

Metabolomic profiling of heat stress: hardening and recovery of homeostasis in Drosophila.

Frequent exposure of terrestrial insects to temperature variation has led to the evolution of protective biochemical and physiological mechanisms, such as the heat shock response, which markedly increases the tolerance to heat stress. Insight into such mechanisms has, so far, mainly relied on selective studies of specific compounds or characteristics or studies at the genomic or proteomic levels. In the present study, we have used untargeted NMR metabolomic profiling to examine the biological response to heat stress in Drosophila melanogaster. The metabolite profile was analyzed during recovery after exposure to different thermal stress treatments and compared with untreated controls. Both moderate and severe heat stress gave clear effects on the metabolite profiles. The profiles clearly demonstrated that hardening by moderate heat stress led to a faster reestablishment of metabolite homeostasis after subsequent heat stress. Several metabolites were identified as responsive to heat stress and could be related to known physiological and biochemical responses. The time course of the recovery of metabolite homeostasis mirrored general changes in gene expression, showing that recovery follows the same temporal pattern at these two biological levels. Finally, our data show that heat hardening permits a quicker return to homeostasis, rather than a reduction of the acute metabolic perturbation and that the reestablishment of homeostasis is important for obtaining maximal heat-hardening effect. The results display the power of NMR metabolomic profiling for characterization of the instantaneous physiological condition, enabling direct visualization of the perturbation of and return to homeostasis.

Adaptation, Physiological↗
PubMed2004

Proteomic response to amino acid starvation in Candida albicans and Saccharomyces cerevisiae.

Saccharomyces cerevisiae activates general amino acid control (GCN) in response to amino acid starvation. Some aspects of this response are known to be conserved in other fungi including Candida albicans, the major systemic fungal pathogen of humans. Here, we describe a proteomic comparison of the GCN responses in S. cerevisiae and C. albicans. We have used high-resolution two-dimensional (2-D) gel electrophoresis and peptide mass fingerprinting to develop a 2-D protein map of C. albicans. A total of 391 protein spots, representing 316 open reading frames, were identified. Fifty-five C. albicans and 65 S. cerevisiae proteins were identified that responded reproducibly to 3-aminotriazole (3AT) in a Gcn4p-dependent fashion. The changes in the S. cerevisiae proteome correlated with the response in the S. cerevisiae transcript profile to 3AT treatment (rank correlation coefficient = 0.59; Natarajan et al., Molec. Cell. Biol. 2001, 21, 4347-4368). Significant aspects of the GCN response were conserved in C. albicans and S. cerevisiae. In both fungi, amino acid biosynthetic enzymes on multiple metabolic pathways were induced by 3AT in a Gcn4p-dependent fashion. Carbon metabolism functions were also induced. However, subtle differences were observed between these fungi. For example, purine biosynthetic enzymes were induced in S. cerevisiae, but were not significantly induced in C. albicans. These differences presumably reflect the contrasting niches of these relatively benign and pathogenic yeasts, respectively.

Amino Acids↗
PubMed2004

Widespread distribution of antisense transcripts in the Plasmodium falciparum genome.

The availability of the complete genome sequence of Plasmodium falciparum has facilitated high-throughput profiling of its complex life cycle, following the application of micro-array, proteomic, and serial analysis of gene expression (SAGE) technologies in this system. These, in turn, have yielded unprecedented insight into global gene expression, including the foremost demonstration of antisense transcription in the parasite. For example, owing to its inherent ability to sample novel ORFs and to predict transcript orientation, SAGE analysis in asexual forms led to the initial discovery of highly abundant antisense RNAs. To determine the extent of this phenomenon in P. falciparum, we have surveyed the distribution of both sense and antisense transcripts across the asexual transcriptome for the first time. To this end, a relational database integrating SAGE expression data with genome annotation information was constructed. This allowed the comprehensive annotation of a total of 17245 SAGE tags, extending over a 350-fold expression range. Transcripts from approximately 30% of the estimated 3D7 gene loci were present at detectable levels in mixed asexual stages, where loci involved in invasion and immune evasion; and carbohydrate metabolism were highly represented in the sense transcriptome. Approximately 12% of SAGE tags, however, were derived from the non-coding strand of nuclear-encoded ORFs, indicating that endogenous antisense RNAs are widespread in this system. Notably, these antisense transcripts were absent from the mitochondrial genome. Interestingly, we note that sense and antisense tag counts from single loci across the transcriptome were inversely related. Taken together, this data may provide first hints as to the possible function of antisense transcription in this system.

Animals↗
PubMedDate not supplied

Proteomics: a paradigm shift.

Proteome--the protein complement of a genome--has become the protein renaissance and a key research tool in the post-genomic era. The basic technology involves the routine usage of gel electrophoresis and spectrometry procedures for deciphering the primary protein sequence/structure as well as knowing certain unique post-translational modifications that a particular protein has undergone to perform a specific function in the cell. However, the recent advancements in protein analysis have ushered this science to provide deeper, bigger and more valuable perspectives regarding performance of subtle protein-protein interactions. Applications of this branch of molecular biology are as vast as the subject is and include clinical diagnostics, pharmaceutical and biotechnological industries. The 21st century hails the use of products, procedures and advancements of this science as finer touches required for the grooming of fast-paced technology.

Animals↗
PubMed2006

Analysis of protein expression (secretome) by human and mouse preimplantation embryos.

OBJECTIVE: To analyze the protein production into the surrounding medium (secretome) of both human and mouse embryos and correlate these findings with ongoing blastocyst development. Along with improvements in culture systems, there is renewed focus on the development of noninvasive viability assays in human IVF. Because the majority of biologic functions are carried out by proteins, it is important to study the dynamics of the proteome during embryonic development and its response to both internal and external stimuli. DESIGN: Experimental study. SETTING: Research laboratory. PATIENT(S): Couples undergoing infertility treatment donated with consent spent culture media for research. INTERVENTION(S): Analysis by time-of-flight mass spectrometry. MAIN OUTCOME MEASURE(S): Protein profiles of spent culture media. RESULT(S): Distinctive and significantly different secretome profiles were observed at each embryonic developmental stage (P<0.05). Correlation of day 5 secretome data with ongoing blastocyst development revealed an 8.5-kDa protein biomarker that was significantly up-regulated (P<0.05). The best candidate for this protein biomarker was ubiquitin, which has been implicated in the implantation process of mammalian species. CONCLUSION(S): This approach to analyze the secretome should not only further our understanding of embryo physiology but provide the basis for the development of noninvasive assays of embryo viability in human IVF.

Animals↗
PubMed2006

Proteomic analysis of Saccharomyces cerevisiae under high gravity fermentation conditions.

Saccharomyces cerevisiae KAY446 was utilized for ethanol production, with glucose concentrations ranging from 120 g/L (normal) to 300 g/L (high). Although grown in a high glucose environment, S. cerevisiae still retained the ability to produce ethanol with a high degree of glucose utilization. iTRAQ-mediated shotgun proteomics was applied to identify relative expression change of proteins under the different glucose conditions. A total of 413 proteins were identified from three replicate, independent LC-MS/MS runs. Unsurprisingly, many proteins in the glycolysis/gluconeogenesis pathway showed significant changes in expression level. Twenty five proteins involved in amino acid metabolism decreased their expression, while the expressions of 12 heat-shock related proteins were also identified. Under high glucose conditions, ethanol was produced as a major product. However, the assimilation of glucose as well as a number of byproducts was also enhanced. Therefore, to optimize the ethanol production under very high gravity conditions, a number of pathways will need to be deactivated, while still maintaining the correct cellular redox or osmotic state. Proteomics is demonstrated here as a tool to aid in this forward metabolic engineering.

Ethanol↗
PubMed2006

Proteomic and computational methods in systems modeling of cellular signaling.

Cellular signaling lies at the core of cellular behavior, and is central for the understanding of many pathologic conditions. To comprehend how signal transduction is orchestrated at the molecular level remains the ultimate challenge for cell biology. In the last years there has been a revolution in the development of high-throughput methodologies in proteomics and genomics, which have provided extensive knowledge about expression profiles and molecular interaction-networks. However, these methods have typically provided qualitative and static information. This is about to turn, and several high-throughput methods are now available that provide quantitative and temporal information. These data are well suited for analysis by computational methods and bioinformatics, which are becoming increasingly valuable tools to grasp the complexity of cellular networks. At present, several cellular pathways have been modeled in silico and the analysis provides new understanding of the underlying properties that contribute to their dynamic features. Here, we review methodologies that are used for in silico modeling as well as methods to obtain large-scale quantitative data, and discuss how they can be integrated to generate powerful and predictive models of cellular processes. We argue that the generation of such models provide powerful tools to understand how systems properties emerges in healthy and pathologic states, and to generate efficient strategies for pharmacological intervention.

Computational Biology↗
PubMed2001

Global analysis of the general stress response of Bacillus subtilis.

Gene arrays containing all currently known open reading frames of Bacillus subtilis were used to examine the general stress response of Bacillus. By proteomics, transcriptional analysis, transposon mutagenesis, and consensus promoter-based screening, 75 genes had previously been described as sigma(B)-dependent general stress genes. The present gene array-based analysis confirmed 62 of these already known general stress genes and detected 63 additional genes subject to control by the stress sigma factor sigma(B). At least 24 of these 125 sigma(B)-dependent genes seemed to be subject to a second, sigma(B)-independent stress induction mechanism. Therefore, this transcriptional profiling revealed almost four times as many regulon members as the proteomic approach, but failure of confirmation of all known members of the sigma(B) regulon indicates that even this approach has not yet elucidated the entire regulon. Most of the sigma(B)-dependent general stress proteins are probably located in the cytoplasm, but 25 contain at least one membrane-spanning domain, and at least 6 proteins appear to be secreted. The functions of most of the newly described genes are still unknown. However, their classification as sigma(B)-dependent stress genes argues that their products most likely perform functions in stress management and help to provide the nongrowing cell with multiple stress resistance. A comprehensive screening program analyzing the multiple stress resistance of mutants with mutations in single stress genes is in progress. The first results of this program, showing the diminished salt resistance of yjbC and yjbD mutants compared to that of the wild type, are presented. Only a few new sigma(B)-dependent proteins with already known functions were found, among them SodA, encoding a superoxide dismutase. In addition to analysis of the sigma(B)-dependent general stress regulon, a comprehensive list of genes induced by heat, salt, or ethanol stress in a sigma(B)-independent manner is presented. Perhaps the most interesting of the sigma(B)-independent stress phenomena was the induction of the extracytoplasmic function sigma factor sigma(W) and its entire regulon by salt shock.

Bacillus subtilis↗
PubMed2006

2DDB - a bioinformatics solution for analysis of quantitative proteomics data.

BACKGROUND: We present 2DDB, a bioinformatics solution for storage, integration and analysis of quantitative proteomics data. As the data complexity and the rate with which it is produced increases in the proteomics field, the need for flexible analysis software increases. RESULTS: 2DDB is based on a core data model describing fundamentals such as experiment description and identified proteins. The extended data models are built on top of the core data model to capture more specific aspects of the data. A number of public databases and bioinformatical tools have been integrated giving the user access to large amounts of relevant data. A statistical and graphical package, R, is used for statistical and graphical analysis. The current implementation handles quantitative data from 2D gel electrophoresis and multidimensional liquid chromatography/mass spectrometry experiments. CONCLUSION: The software has successfully been employed in a number of projects ranging from quantitative liquid-chromatography-mass spectrometry based analysis of transforming growth factor-beta stimulated fi-broblasts to 2D gel electrophoresis/mass spectrometry analysis of biopsies from human cervix. The software is available for download at SourceForge.

Computational Biology↗
PubMed2005

SpecAlign--processing and alignment of mass spectra datasets.

SUMMARY: Pre-processing of chromatographic profile or mass spectral data is an important aspect of many types of proteomics and biomarker discovery experiments. Here we present a graphical computational tool, SpecAlign, that enables simultaneous visualization and manipulation of multiple datasets. SpecAlign not only provides all common processing functions, but also uniquely implements an algorithm that enables the complete alignment of each mass spectrum within a loaded dataset. We demonstrate its utility by aligning two datasets each containing six spectra; one set was acquired prior to instrument calibration and the other following calibration. AVAILABILITY: The software is free of charge and available for download from http://ptcl.chem.ox.ac.uk/~jwong/specalign. Supports Windows operating systems including Windows 9X/NT/2000/XP.

Algorithms↗