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Proteomic analysis of mdx skeletal muscle: Great reduction of adenylate kinase 1 expression and enzymatic activity.

To investigate the pathophysiological events of Duchenne muscular dystrophy, we analyzed alterations of protein expression in hindlimb muscles of three month old mdx mice using two-dimensional gel electrophoresis and mass spectrometry. About 40 differentially expressed proteins from the cytosolic fraction and 20 from the microsomal fraction of mdx hindlimb muscles were identified. Among these altered proteins, adenylate kinase 1 (AK 1) was particular interesting because its decrease in abundance was so dramatic (> four-fold). Enzymatic assays demonstrated that AK 1 activity was also decreased in mdx mice. Furthermore, the expression and enzymatic activity of AK 1 were consistently reduced in mdx mice at one and six months of age, suggesting a direct relationship between the lack of dystrophin and alteration of AK 1. Along with AK 1, creatine kinase (CK) provides a major pathway for regulation of nucleotide ratios and energy metabolism in muscles. To gain a better understanding of mechanisms of energy metabolism, we also investigated CK activities in these mdx mice at different ages. Our results suggested that decreased AK 1 expression and activity might result in redistribution of energy flow through the alternative CK system, thus a compensatory potential might limit cellular energy failure in mdx skeletal muscle.

Adenylyl Cyclases↗

Differential domain evolution and complex RNA processing in a family of paralogous EPB41 (protein 4.1) genes facilitate expression of diverse tissue-specific isoforms.

The EPB41 (protein 4.1) genes epitomize the resourcefulness of the mammalian genome to encode a complex proteome from a small number of genes. By utilizing alternative transcriptional promoters and tissue-specific alternative pre-mRNA splicing, EPB41, EPB41L2, EPB41L3, and EPB41L1 encode a diverse array of structural adapter proteins. Comparative genomic and transcript analysis of these 140- to 240-kb genes indicates several unusual features: differential evolution of highly conserved exons encoding known functional domains interspersed with unique exons whose size and sequence variations contribute substantially to intergenic diversity; alternative first exons, most of which map far upstream of the coding regions; and complex tissue-specific alternative pre-mRNA splicing that facilitates synthesis of functionally different complements of 4.1 proteins in various cells. Understanding the splicing regulatory networks that control protein 4.1 expression will be critical to a full appreciation of the many roles of 4.1 proteins in normal cell biology and their proposed roles in human cancer.

Alternative Splicing↗

DNA microarray analysis of differential gene expression in Borrelia burgdorferi, the Lyme disease spirochete.

DNA microarrays were used to survey the adaptive genetic responses of Borrelia burgdorferi (Bb) B31, the Lyme disease spirochete, when grown under conditions analogous to those found in unfed ticks (UTs), fed ticks (FTs), or during mammalian host adaptation (Bb in dialysis membrane chambers implanted in rats). Microarrays contained 95.4% of the predicted B31 genes, 150 (8.6%) of which were differentially regulated (changes of > or = 1.8-fold) among the three growth conditions. A substantial proportion (46%) of the differentially regulated genes encoded proteins with predicted export signals (29% from predicted lipoproteins), emphasizing the importance to Bb of modulating its extracellular proteome. For B31 cultivated at the more restrictive UT condition, microarray data provided evidence of a bacterial stringent response and factors that restrict cell division. A large proportion of genes were responsive to the FT growth condition, wherein increased temperature and reduced pH were prominent environmental parameters. A surprising theme, supported by cluster analysis, was that many of the gene expression changes induced during the FT growth condition were transient and largely tempered as B31 adapted to the mammalian host, suggesting that once Bb gains entry and adapts to mammalian tissues, fewer differentially regulated genes are exploited. It therefore would seem that although widely dissimilar, the UT and dialysis membrane chamber growth conditions promote more static patterns of gene expression in Bb. The microarray data thus provide a basis for formulating new testable hypotheses regarding the life cycle of Bb and attaining a more complete understanding of many aspects of Bb's complex parasitic strategies.

Animals↗

Proteome analysis in hippocampus of mice overexpressing human Cu/Zn-superoxide dismutase 1.

Cu/Zn-superoxide dismutase 1 (SOD1), encoded on chromosome 21, is a key enzyme in metabolism of oxygen free radicals and oxidative stress. Transgenic mice overexpressing human SOD1 (Tg-hSOD1) are useful model for Down syndrome (trisomy 21) and familial amyotrophic lateral sclerosis (ALS). It was shown recently that Tg-hSOD1 mice develop a characteristic set of neurodegenerative changes in hippocampus and we therefore decided to study differential protein expression patterns, constructing a mouse hippocampal proteome map using two-dimensional electrophoresis (2-DE) with in-gel digestion of spots followed by matrix-assisted laser desorption/ionisation-time of flight (MALDI-TOF) identification and quantitatively compared protein profiles between non-transgenic mice, hemizygous and homozygous Tg-hSOD1 mice. In total 1056 spots were analysed, resulting in the identification of 445 polypeptides that were the products of 157 different genes. Among these a series of proteins involved in scaffolding, metabolism, signaling and other functions were deranged. Our findings suggest that overexpressed SOD1 directly or by generating reactive oxygen species may lead to aberrant protein expressional patterns that in turn may lead to or reflect neurodegeneration observed in this animal model.

Animals↗

Saliva and salivary pellicle composition and proteomic profile in smokers vs. non-smokers and its effect on dental erosion.

OBJECTIVE: To analyse the salivary composition and proteomic profile of saliva and the salivary pellicle in smokers compared to non-smokers, and to examine potential differences in the erosion-protective capacity of the salivary pellicle. METHODS: Twenty-five smokers and 25 non-smokers were included. Unstimulated and stimulated saliva samples were analysed regarding flow rate, pH, buffer capacity, calcium, phosphate, fluoride, and protein content. Saliva and salivary pellicle samples were analysed by data-independent acquisition mass spectrometry (DIA-MS) for proteome profiling. In an in situ experiment, intraoral splints were loaded with bovine enamel and dentine specimens for 120 min. Pellicle-covered specimens were extraorally eroded (HCl, pH 2.3, 60 s). Calcium release was determined photometrically and compared to pellicle-free controls. RESULTS: Except for phosphate in stimulated saliva (padj.=0.003), salivary parameters were not significantly different between smokers and non-smokers. Proteome profiling detected 1759±154 proteins (cumulative 1963) in saliva, and 4262±362 proteins (cumulative 4625) in the salivary pellicle. The relative abundances of 282 (unstimulated saliva), 338 (stimulated saliva), and 4 (salivary pellicle) protein groups differed significantly between smokers and non-smokers. Functional enrichment analysis of differentially abundant human proteins revealed biological processes such as coagulation, immune response, and carcinogenic reactive oxygen species processes to be impacted by smoking. The salivary pellicle had a significant erosion-protective effect in enamel compared to the control (41.4 ± 6.3 nmol/mm2), but no differences between smokers (33.2 ± 10.6 nmol/mm2, padj.=0.001) and non-smokers (32.7 ± 8.6 nmol/mm2, padj.=0.001) were found. CONCLUSION: The proteomic profiles of both unstimulated and stimulated saliva and the salivary pellicle differ between smokers and non-smokers. CLINICAL SIGNIFICANCE: Despite the different proteomic profiles indicating a significant impact of smoking on the oral cavity, the erosion-protective capacity of the salivary pellicle of smokers and non-smokers does not differ.

Dental Pellicle↗

Functional discrimination of gene expression patterns in terms of the gene ontology.

The ever-growing amount of experimental data in molecular biology and genetics requires its automated analysis, by employing sophisticated knowledge discovery tools. We use an Inductive Logic Programming (ILP) learner to induce functional discrimination rules between genes studied using microarrays and found to be differentially expressed in three recently discovered subtypes of adenocarcinoma of the lung. The discrimination rules involve functional annotations from the Proteome HumanPSD database in terms of the Gene Ontology, whose hierarchical structure is essential for this task. While most of the lower levels of gene expression data (pre)processing have been automated, our work can be seen as a step toward automating the higher level functional analysis of the data. We view our application not just as a prototypical example of applying more sophisticated machine learning techniques to the functional analysis of genes, but also as an incentive for developing increasingly more sophisticated functional annotations and ontologies, that can be automatically processed by such learning algorithms.

Adenocarcinoma↗

Mitochondrial dysfunction in schizophrenia: evidence for compromised brain metabolism and oxidative stress.

The etiology and pathophysiology of schizophrenia remain unknown. A parallel transcriptomics, proteomics and metabolomics approach was employed on human brain tissue to explore the molecular disease signatures. Almost half the altered proteins identified by proteomics were associated with mitochondrial function and oxidative stress responses. This was mirrored by transcriptional and metabolite perturbations. Cluster analysis of transcriptional alterations showed that genes related to energy metabolism and oxidative stress differentiated almost 90% of schizophrenia patients from controls, while confounding drug effects could be ruled out. We propose that oxidative stress and the ensuing cellular adaptations are linked to the schizophrenia disease process and hope that this new disease concept may advance the approach to treatment, diagnosis and disease prevention of schizophrenia and related syndromes.

Brain↗

A proteome analysis of livers from obese (ob/ob) mice treated with the peroxisome proliferator WY14,643.

The PPAR (peroxisome proliferator activated receptor) transcription factors are ligand-activated receptors which regulate genes involved in lipid metabolism and homeostasis. PPARalpha is preferentially expressed in the liver and PPARgamma preferentially in adipose tissue. Activation of PPARalpha leads to peroxisome proliferation in rodents and increased beta-oxidation of fatty acids. PPARgamma-activation leads to adipocyte differentiation and improved insulin signaling of mature adipocytes. Both of these PPAR receptors are potential targets for treatment of dyslipidemia in man. Studies by others using a proteomics approach have characterized the effects of PPARalpha agonists in livers from lean healthy mice. However, we wanted to map the effects of a therapeutic dose of a PPARalpha agonist in a disease model of insulin resistance and diabetes, the obese diabetic ob/ob mouse, by proteomics. Therefore, ob/ob mice, which have highly elevated levels of plasma triglycerides, glucose and insulin, were treated for one week with WY14,643 (180 micromol/kg/day), a well-characterized selective PPARalpha agonist. Plasma triglycerides, glucose and insulin levels were determined and we found significant therapeutic effects on triglycerides and glucose levels. The liver protein compositions were investigated by high-resolution two-dimensional gel electrophoresis which showed that WY14,643 produced up-regulation of at least 16 spots. These were identified by mass spectrometry and 14 spots were found to be components of the peroxisomal fatty acid metabolism. Thus, WY14,643 at a therapeutic dose, caused induction of peroxisomal fatty acid beta-oxidation in obese diabetic mice.

Animals↗

[Analysis of the different proteomes between the acute leukemia cells and normal white blood cells].

This study was aimed to analyze the different proteomes between human acute leukemia (AL) cells and normal white blood cells by proteomic technology in order to lay the basis for diagnosing AL and understanding the mechanism of leukemogenesis. The proteins from AL cells of 40 AL patients identified by FAB classification and proteins from normal lymphocytes and granulocytes of 20 normal volunteers were separated by two-dimensional electrophoresis (2-DE), and the differentially expressed proteins between the two groups were identified by both matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) and electronspray ionization (ESI)-MS/MS. The results showed that among the differentially expressed proteins between AL cells and normal lymphocytes and granulocytes, some proteins involved in the process of malignant transformation (such as Op18, NM23-H1), cell proliferation (such as PCNA) and apoptosis inhibition (such as tumor necrosis factor inhibitor protein) were found to be up regulated in AL cells. However, some proteins involved in differentiation and physiological functions of normal cells were down regulated in AL cells. It is concluded that there are many events involved in the process of leukemogenesis, expression of some proteins relating to the malignant transformation, cell proliferation and apoptosis inhibition are up-regulated in AL cells. The proteome analysis may provide a new approach to explaining the molecular mechanism underlying the pathogenesis of AL.

Adolescent↗

Integrated multi-omics profiling identifies aging-related molecular signatures and convergent interferon signaling in systemic lupus erythematosus.

BACKGROUND: Systemic lupus erythematosus (SLE) is characterized by chronic immune activation and molecular alterations that overlap with aging-related biological processes. However, how these alterations are organized across molecular layers and whether they converge on shared regulatory networks remain incompletely understood. METHODS: We performed an integrative multi-omics analysis combining in-house proteomic and phosphoproteomic data from 130 patients with SLE and 90 healthy controls (HCs) and publicly available transcriptomic datasets comprising 1,461 SLE patients. Proteins and phosphorylation sites were annotated using established aging-related gene resources. Differential protein abundance and phosphorylation changes were analyzed across disease-status and disease-activity comparisons. Nominal P-value thresholds were used for exploratory feature selection, whereas FDR-adjusted P values were used to assess robustness after multiple-testing correction. Kinase-substrate enrichment, transcription factor annotation, and cell-type-resolved transcriptomic comparison were used to explore potential regulatory programs. RESULTS: We identified 128 nominally altered proteins annotated to aging-related biological processes, including genomic instability, mitochondrial dysfunction, and epigenetic alterations. Phosphoproteomic analysis revealed 36 nominally altered phosphorylation sites, including previously unreported sites in IFI16 (S153, S780) and PKCδ (S507, S664). Clustering analysis demonstrated heterogeneous protein co-regulation patterns across disease states. Kinase activity inference suggested altered activity of TBK1 and IKKβ. TF analysis further highlighted STAT1, RELA, and PML as potential central nodes within the inferred regulatory network. Notably, these multi-omic alterations were not randomly distributed but showed convergence toward shared signaling pathways, particularly those related to interferon responses. CONCLUSIONS: This integrative multi-omics study identifies inflammatory and interferon-dominated molecular alterations in SLE PBMCs that overlap with aging-related biological processes and converge on shared regulatory networks. These findings provide a hypothesis-generating framework for investigating the intersection between chronic immune activation and aging-related molecular remodeling in SLE.

Humans↗

Application of mass spectrometry in proteomics.

Mass spectrometry has arguably become the core technology in proteomics. The application of mass spectrometry based techniques for the qualitative and quantitative analysis of global proteome samples derived from complex mixtures has had a big impact in the understanding of cellular function. Here, we give a brief introduction to principles of mass spectrometry and instrumentation currently used in proteomics experiments. In addition, recent developments in the application of mass spectrometry in proteomics are summarised. Strategies allowing high-throughput identification of proteins from highly complex mixtures include accurate mass measurement of peptides derived from total proteome digests and multidimensional peptide separations coupled with mass spectrometry. Mass spectrometric analysis of intact proteins permits the characterisation of protein isoforms. Recent developments in stable isotope labelling techniques and chemical tagging allow the mass spectrometry based differential display and quantitation of proteins, and newly established affinity procedures enable the targeted characterisation of post-translationally modified proteins. Finally, advances in mass spectrometric imaging allow the gathering of specific information on the local molecular composition, relative abundance and spatial distribution of peptides and proteins in thin tissue sections.

Affinity Labels↗

Update and challenges on proteomics in rice.

Rice is not only an important agricultural resource but also a model plant for biological research. Our previous review highlighted different aspects of the construction of rice proteome database, cataloguing rice proteins of different tissues and organelle, differential proteomics using 2-DE and functional characterization of some of the proteins identified (Komatsu, S., Tanaka, N., Proteomics 2005, 5, 938-949). In this review, the powerfulness and weaknesses of proteomic technologies as a whole and limitations of the currently used techniques in rice proteomics are discussed. The information obtained from these techniques regarding proteins modification, protein-protein interaction and the development of new methods for differential proteomics will aid in deciphering more precisely the functions of known and/or unknown proteins in rice.

Cluster Analysis↗

Chromatin-related proteins in pluripotent mouse embryonic stem cells are downregulated after removal of leukemia inhibitory factor.

Embryonic stem (ES) cells have generated enormous interest due to their capacity to self-renew and the potential for growing many different cell types in vitro. Leukemia inhibitory factor (LIF), bone morphogenetic proteins, octamer-binding protein 3 or 4, and Nanog are important factors in the maintenance of pluripotency in mouse ES cells. However, the mechanisms by which these factors regulate the pluripotency remain poorly understood. To identify other proteins involved in this process, we did a proteomic analysis of mouse ES cells that were cultured in the presence or absence of LIF. More than 100 proteins were found to be involved specifically in either the differentiation process or the maintenance of undifferentiated state. Among these, chromatin-related proteins were identified as the major proteins in nuclear extracts of undifferentiated cells. Analysis with real-time RT-PCR revealed that enrichment of these proteins in pluripotent ES cells was regulated at the transcriptional levels. These results suggest that specific chromatin-related proteins may be involved in maintaining the unique properties of pluripotent ES cells.

Animals↗

Do retroviruses preferentially integrate within highly plastic regions of the human genome?

Whether retroviral integration is a phenomenon specific to properties of the surrounding genomic region is a widely debated question. In this paper we attempt to enlight the involvement of genomic regions prone to DNA double strand breaks in such process, as well as the more general concept of genome plasticity concerning repair, recombination, transposition events. While performing a differential display analysis of the promonocytic cell line U937 and clone U42 HIV infected counterpart, we found, out of about 15 highly dysregulated genes, expected according to our previous proteomic analysis, two dysregulated cellular transcripts that are shown in the present study to colocalize on band 22q11. The LB14 transcript maps within the DiGeorge critical region. Whereas the AG46 transcript encodes the immunoglobulin-lambda like polypeptide 1 (IGLL1) 4.7Mb apart from LB14. The 22q11 band is remarkable for its high plasticity involving DNA double strand breaks, that may lead to translocations, large deletions, and immunoglobulin rearrangements, frequently observed in this region. We suggest that provirus integration preferentially occurs in such genomic regions and that the subsequent insertional mutagenesis leads to the present observations. Finally, we stress out the possibility that the small size of chromosome 22 is associated with this physical property of the genome.

Chromosomes, Human, Pair 22↗

Tumor specimen cold ischemia time impacts molecular cancer drug target discovery.

Tumor tissue collections are used to uncover pathways associated with disease outcomes that can also serve as targets for cancer treatment, ideally by comparing the molecular properties of cancer tissues to matching normal tissues. The quality of such collections determines the value of the data and information generated from their analyses including expression and modifications of nucleic acids and proteins. These biomolecules are dysregulated upon ischemia and decompose once the living cells start to decay into inanimate matter. Therefore, ischemia time before final tissue preservation is the most important determinant of the quality of a tissue collection. Here we show the impact of ischemia time on tumor and matching adjacent normal tissue samples for mRNAs in 1664, proteins in 1818, and phosphosites in 1800 cases (tumor and matching normal samples) of four solid tumor types (CRC, HCC, LUAD, and LUSC NSCLC subtypes). In CRC, ischemia times exceeding 15 min impacted 12.5% (mRNA), 25% (protein), and 50% (phosphosites) of differentially expressed molecules in tumor versus normal tissues. This hypoxia- and decay-induced dysregulation increased with longer ischemia times and was observed across tumor types. Interestingly, the proteomics analysis revealed that specimen ischemia time above 15 min is mostly associated with a dysregulation of proteins in the immune-response pathway and less so with metabolic processes. We conclude that ischemia time is a crucial quality parameter for tissue collections used for target discovery and validation in cancer research.

Humans↗

Activity-based probes for protein tyrosine phosphatases.

Protein tyrosine phosphatases (PTPs) are involved in the regulation of many aspects of cellular activity including proliferation, differentiation, metabolism, migration, and survival. Given the large number and complexity of PTPs in cell signaling, new strategies are needed for the integrated analysis of PTPs in the whole proteome. Unfortunately, the activities of many PTPs are tightly regulated by posttranslational mechanisms, limiting the utility of standard genomics and proteomics methods for functional characterization of these enzymes. To facilitate the global analysis of PTPs, we designed and synthesized two activity-based probes that consist of alpha-bromobenzylphosphonate as a PTP-specific trapping device and a linker that connects the trapping device with a biotin tag for visualization and purification. We showed that these probes are active site-directed irreversible inactivators of PTPs and form a covalent adduct with PTPs involving the active site Cys residue. Additionally, we demonstrated that the probes are extremely specific toward PTPs while remaining inert to other proteins, including the whole proteome from Escherichia coli. Consequently, these activity-based PTP probes can be used to profile PTP activity in complex proteomes. The ability to interrogate the entire PTP family on the basis of changes in their activity should greatly accelerate both the assignment of PTP function and the identification of potential therapeutic targets.

Binding Sites↗

A cross-species multi-omics analyze uncovers conserved molecular mechanisms underlying age-related erectile dysfunction.

BACKGROUND: The urgent need for new treatments is driven by the challenging clinical situation of age-related erectile dysfunction (ARED). AIM: To clarify the conserved molecular mechanisms of ARED across species using multi-omics. METHODS: Rat and mouse models with ARED were developed to facilitate the extraction of mRNA and proteins from the corpus cavernosum for high-throughput sequencing. Bioinformatics techniques were employed to analyze differentially expressed genes and to conduct analyses using the Kyoto Encyclopedia of Genes and Genomes, Gene Ontology, and protein-protein interaction networks. Verification of the results was carried out using immunofluorescence, hematoxylin-eosin staining, and Masson staining. OUTCOMES: The multi-omics profiles of ARED rats and mice were analyzed and validated across species. RESULTS: In both species, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses of transcriptomic and proteomic data revealed that differentially expressed genes were predominantly enriched in pathways associated with alterations in extracellular matrix composition, downregulation of mitochondrial activity, and disruption of protein homeostasis. Immunofluorescence analysis demonstrated an upregulation of reactive oxygen species expression, coupled with a downregulation of Aldh18a1, collagen, and collagen I expression in the corpus cavernosum of mice and rats with ARED. CLINICAL IMPLICATIONS: To offer a novel approach for enhancing the erectile function in patients with ARED. STRENGTHS AND LIMITATIONS: The primary strength of this study lies in its utilization of cross-species multi-omics sequencing, which has elucidated the conserved molecular mechanisms underlying ARED. However, a significant limitation is the absence of subsequent validation in patients with ARED. CONCLUSIONS: Cross-species multi-omics comparisons present a potentially innovative approach for elucidating the underlying mechanisms and identifying preventive and therapeutic targets for ARED.

aging↗

Ontogenetic variations in the venom proteome of the Amazonian snake Bothrops atrox.

BACKGROUND: Bothrops atrox is responsible for the majority of snakebite accidents in the Brazilian Amazon region. Previous studies have demonstrated that the biological and pharmacological activities of B. atrox venom alter with the age of the animal. Here, we present a comparative proteome analysis of B. atrox venom collected from specimens of three different stages of maturation: juveniles, sub-adults and adults. RESULTS: Optimized conditions for two-dimensional gel electrophoresis (2-DE) of pooled venom samples were achieved using immobilized pH gradient (IPG) gels of non-linear 3-10 pH range during the isoelectric focusing step and 10-20% gradient polyacrylamide gels in the second dimension. Software-assisted analysis of the 2-DE gels images demonstrated differences in the number and intensity of spots in juvenile, sub-adult and adult venoms. Although peptide mass fingerprinting (PMF) failed to identify even a minor fraction of spots, it allowed us to group spots that displayed similar peptide maps. The spots were subjected to a combination of tandem mass spectrometry and Mascot and MS BLAST database searches that identified several classes of proteins, including metalloproteinases, serine proteinases, lectins, phospholipases A2, L-amino oxidases, nerve growth factors, vascular endothelial growth factors and cysteine-rich secretory proteins. CONCLUSION: The analysis of B. atrox samples from specimens of different ages by 2-DE and mass spectrometry suggested that venom proteome alters upon ontogenetic development. We identified stage specific and differentially expressed polypeptides that may be responsible for the activities of the venom in each developmental stage. The results provide insight into the molecular basis of the relation between symptomatology of snakebite accidents in humans and the venom composition. Our findings underscore the importance of the use of venoms from individual specimen at various stages of maturation for the production of antivenoms.

Journal Article↗