Proteome Science[JOURNAL]
Sun
200 papers
Examination of the skeletal proteome of the brittle star Ophiocoma wendtii reveals overall conservation of proteins but variation in spicule matrix proteins.
Seaver RW, Livingston BT
Proteome Sci · 2015 · PMID 25705131 · Full text
BACKGROUND: While formation of mineralized tissue is characteristic of many animal taxa, the proteins that interact with mineral are diverse and appear in many cases to be of independent origin. Extracellular matrix prot...
BACKGROUND: While formation of mineralized tissue is characteristic of many animal taxa, the proteins that interact with mineral are diverse and appear in many cases to be of independent origin. Extracellular matrix proteins involved in mineralization do share some common features. They tend to be disordered, secreted proteins with repetitive, low complexity. The genes encoding these proteins are often duplicated and undergo concerted evolution, further diversifying the repetitive domains. This makes it difficult to identify mineralization genes and the proteins they encode using bioinformatics techniques. Here we describe the use of proteomics to identify mineralization genes in an ophiuroid echinoderm, Ophiocoma wendtii (O. wendtii). RESULTS: We have isolated the occluded proteins within the mineralized tissue of the brittle star Ophiocoma wendtii. The proteins were analyzed both unfractionated and separated on SDS-PAGE gels. Each slice was analyzed using mass spectroscopy and the amino acid sequence of the most prevalent peptides was obtained. This was compared to both an embryonic transcriptome from the gastrula stage when skeleton is being formed and a tube foot (an adult mineralized tissue) transcriptome. Thirty eight proteins were identified which matched known proteins or protein domains in the NCBI databases. These include C-type lectins, ECM proteins, Kazal-type protease inhibitors, matrix metalloproteases as well as more common cellular proteins. Many of these are similar to those found in the sea urchin Strongylocentrotus purpuratus (S. purpuratus) skeleton. We did not, however, identify clear homologs to the sea urchin spicule matrix proteins, and the number of C-type lectin containing genes was much reduced compared to sea urchins. Also notably absent was MSP-130. CONCLUSIONS: Our results show an overall conservation of the types of proteins found in the mineralized tissues of two divergent groups of echinoderms, as well as in mineralized tissues in general. However, the extensive gene duplication and concerted evolution seen in the spicule matrix proteins found in the sea urchin skeleton was not observed in the brittle star.
Proteomic characterization of adrenal gland embryonic development reveals early initiation of steroid metabolism and reduction of the retinoic acid pathway.
Dihazi GH, Mueller GA, Asif AR … +3 more , Eltoweissy M, Wessels JT, Dihazi H
Proteome Sci · 2015 · PMID 25694770 · Full text
BACKGROUND: Adrenal glands are essential endocrine organs composed of two embryological distinct tissues. Morphological changes during their development are well described, but less understood with regard to their molecu...
BACKGROUND: Adrenal glands are essential endocrine organs composed of two embryological distinct tissues. Morphological changes during their development are well described, but less understood with regard to their molecular mechanisms. To identify proteins and pathways, which drive the initial steps of the specification of the endocrine function of the adrenal gland, rat's adrenal glands were isolated at different embryonic days (E): E14, E16, E18, E19 and postnatal day 1 (P1). RESULTS: The alteration of the proteome during the stages E16, E19 and P1 was investigated by combining two dimensional gel electrophoresis and mass spectrometric analysis. Out of 594 excised protein spots, 464 spots were identified, resulting in 203 non-redundant proteins. The ontogenic classification of the identified proteins according to their molecular function resulted in 10 different categories, whereas the classification of their biological processes resulted in 19 different groups. This gives an insight into the complex mechanisms underlying adrenal gland development. Interestingly, the expression of retinoic acid pathway proteins was decreased during the development of the adrenal gland, suggesting that this pathway is only important at early stages. On the other hand, key proteins of the cholesterol synthesis increased their expression significantly at E19 revealing the initiation of the endocrine specialization of the adrenal glands. CONCLUSIONS: This study presents the first comprehensive wide proteome analysis of three different stages of embryonic adrenal gland development. The identified proteins, which were expressed in early stages of development, will shed light on the molecular mechanisms underlying embryonic development of the adrenal gland.
Selection of a protein solubilization method suitable for phytopathogenic bacteria: a proteomics approach.
Malafaia CB, Guerra ML, Silva TD … +4 more , Paiva PM, Souza EB, Correia MT, Silva MV
Proteome Sci · 2015 · PMID 25670925 · Full text
BACKGROUND: Finding the best extraction method of proteins from lysed cells is the key step for detection and identification in all proteomics applications. These are important to complement the knowledge about the mecha...
BACKGROUND: Finding the best extraction method of proteins from lysed cells is the key step for detection and identification in all proteomics applications. These are important to complement the knowledge about the mechanisms of interaction between plants and phytopathogens causing major economic losses. To develop an optimized extraction protocol, strains of Acidovorax citrulli, Pectobacterium carotovorum subsp. carotovorum and Ralstonia solanacearum were used as representative cells in the study of phytopathogenic bacteria. This study aims to compare four different protein extraction methods, including: Trizol, Phenol, Centrifugation and Lysis in order to determine which are more suitable for proteomic studies using as parameters the quantity and quality of extracted proteins observed in two-dimensional gels. RESULTS: The bacteria studied showed different results among the tested methods. The Lysis method was more efficient for P. carotovorum subsp. carotovorum and R. solanacearum phytobacteria, as well as simple and fast, while for A. citrulli, the Centrifugation method was the best. This evaluation is based on results obtained in polyacrylamide gels that presented a greater abundance of spots and clearer and more consistent strips as detected by two-dimensional gels. CONCLUSIONS: These results attest to the adequacy of these proteins extraction methods for proteomic studies.
Interaction of peroxiredoxin V with dihydrolipoamide branched chain transacylase E2 (DBT) in mouse kidney under hypoxia.
Ahn SH, Yang HY, Tran GB … +8 more , Kwon J, Son KY, Kim S, Dinh QT, Jung S, Lee HM, Cho KO, Lee TH
Proteome Sci · 2015 · PMID 25670924 · Full text
BACKGROUND: Peroxiredoxin V (Prdx V) plays a major role in preventing oxidative damage as an effective antioxidant protein within a variety of cells through peroxidase activity. However, the function of Prdx V is not lim...
BACKGROUND: Peroxiredoxin V (Prdx V) plays a major role in preventing oxidative damage as an effective antioxidant protein within a variety of cells through peroxidase activity. However, the function of Prdx V is not limited to peroxidase enzymatic activity per se. It appears to have unique function in regulating cellular response to external stimuli by directing interaction with signaling protein. In this study, we identified Prdx V interacting partners in mouse kidney under hypoxic stress using immunoprecipitation and shotgun proteomic analysis (LC-MS/MS). RESULTS: Immunoprecipitation coupled with nano-UPLC-MS(E) shotgun proteomics was employed to identify putative interacting partners of Prdx V in mouse kidney in the setting of hypoxia. A total of 17 proteins were identified as potential interacting partners of Prdx V by a comparative interactomics analysis in kidney under normoxia versus hypoxia. Dihydrolipoamide branched chain transacylase E2 (DBT) appeared to be a prominent candidate protein displaying enhanced interaction with Prdx V under hypoxic stress. Moreover, hypoxic kidney exhibited altered DBT enzymatic activity compared to normoxia. An enhanced colocalization of these two proteins under hypoxic stress was successfully observed in vitro. Furthermore, peroxidatic cysteine residue (Cys48) of Prdx V is likely to be responsible for interacting with DBT. CONCLUSIONS: We identified several proteins interacting with Prdx V under hypoxic condition known to induce renal oxidative stress. In hypoxic condition, we observed an enhanced interaction of Prdx V and DBT protein as well as increased DBT enzymatic activity. The results from this study will contribute to enhance our understanding of Prdx V's role in hypoxic stress and may suggest new directions for future research.
Proteome changes induced by Pyrenophora tritici-repentis ToxA in both insensitive and sensitive wheat indicate senescence-like signaling.
Day J, Gietz RD, Rampitsch C
Proteome Sci · 2015 · PMID 25663824 · Full text
BACKGROUND: Pyrenophora tritici-repentis is a phytopathogenic fungus which causes tan spot on wheat. Some races of P. tritici-repentis produce host-specific toxins which present symptoms of chlorosis or necrosis on susce...
BACKGROUND: Pyrenophora tritici-repentis is a phytopathogenic fungus which causes tan spot on wheat. Some races of P. tritici-repentis produce host-specific toxins which present symptoms of chlorosis or necrosis on susceptible wheat cultivars. One such toxin is Ptr ToxA, which enters mesophyll cells through a putative toxin-receptor and localizes with chloroplasts, ultimately causing damage and necrosis on leaves. These symptoms can occur even in the absence of the pathogen. Insensitive cultivars lack the receptor and Ptr ToxA cannot enter cells. The molecular mechanisms surrounding this plant-pathogen interaction are still largely unknown, although some details have begun to emerge. RESULTS: Using 2-D electrophoresis, fifteen protein changes were identified reproducibly in the leaf proteomes of a sensitive and an insensitive cultivar over three days after inoculation of purified Ptr ToxA. Functional analysis of the proteins indicated that senescence signals may be induced in the sensitive cultivar. In the insensitive cultivar proteins involved in some features of senescence inhibition were seen. Complementary responses at the biochemical level may be actively promoting a localized senescence-like response in sensitive wheat cultivars whilst actively inhibiting this response in insensitive cultivars. CONCLUSION: This is the first report of a biochemical response in an insensitive cultivar in this plant-pathogen interaction. Findings support the involvement of ethylene, and the activation of complementary pathways in sensitive versus insensitive wheat cultivars responding to Ptr ToxA. The nature of the system permits using purified toxin to mimic disease, which eliminates the pathogen proteome and ensures a synchronous response in inoculated leaves.
Proteomics analysis of urine reveals acute phase response proteins as candidate diagnostic biomarkers for prostate cancer.
Davalieva K, Kiprijanovska S, Komina S … +3 more , Petrusevska G, Zografska NC, Polenakovic M
Proteome Sci · 2015 · PMID 25653573 · Full text
Despite the overall success of prostate specific antigen (PSA) in screening and detection of prostate cancer (PCa), its use has been limited due to the lack of specificity. The principal driving goal currently within PCa...
Despite the overall success of prostate specific antigen (PSA) in screening and detection of prostate cancer (PCa), its use has been limited due to the lack of specificity. The principal driving goal currently within PCa research is to identify non-invasive biomarker(s) for early detection of aggressive tumors with greater sensitivity and specificity than PSA. In this study, we focused on identification of non-invasive biomarkers in urine with higher specificity than PSA. We tested urine samples from PCa and benign prostatic hyperplasia (BPH) patients by 2-D DIGE coupled with MS and bioinformatics analysis. Statistically significant (p < 0.05), 1.8 fold variation or more in abundance, showed 41 spots, corresponding to 23 proteins. The Ingenuity Pathway Analysis showed significant association with the Acute Phase Response Signaling pathway. Nine proteins with differential abundances were included in this pathway: AMBP, APOA1, FGA, FGG, HP, ITIH4, SERPINA1, TF and TTR. The expression pattern of 4 acute phase response proteins differed from the defined expression in the canonical pathway. The urine levels of TF, AMPB and HP were measured by immunoturbidimetry in an independent validation set. The concentration of AMPB in urine was significantly higher in PCa while levels of TF and HP were opposite (p < 0.05). The AUC for the individual proteins ranged from 0.723 to 0.754. The combination of HP and AMBP yielded the highest accuracy (AUC = 0.848), greater than PSA. The proposed biomarker set is quickly quantifiable and economical with potential to improve the sensitivity and specificity of PCa detection.
Comparative proteomics analysis of differential proteins in respond to doxorubicin resistance in myelogenous leukemia cell lines.
Qinghong S, Shen G, Lina S … +6 more , Yueming Z, Xiaoou L, Jianlin W, Chengyan H, Hongjun L, Haifeng Z
Proteome Sci · 2015 · PMID 25628518 · Full text
BACKGROUND: Chemoresistance remains a significant challenge in chronic myelogenous leukemia (CML) management, which is one of the most critical prognostic factors. Elucidation the molecular mechanisms underlying the resi...
BACKGROUND: Chemoresistance remains a significant challenge in chronic myelogenous leukemia (CML) management, which is one of the most critical prognostic factors. Elucidation the molecular mechanisms underlying the resistance to chemoresistance may lead to better clinical outcomes. RESULTS: In order to identify potential protein targets involved in the drug-resistant phenotype of leukemia, especially the chronic myelogenous leukemia (CML), we used a high-resolution "ultra-zoom" 2DE-based proteomics approach to characterize global protein expression patterns in doxorubicin-resistant myelogenous leukemia cells compared with parental control cells. Ultra-high resolution of 2DE was achieved by using a series of slightly overlapping narrow-range IPG strips during isoelectric focusing (IEF) separation. A total number of 44 proteins with altered abundances were detected and identified by MALDI-TOF or LC-MS/MS. Among these proteins, enolase, aldolase, HSP70 and sorcin were up-regulated in doxorubicin-resistant myelogenous leukemia cell line, whereas HSP27 was down-regulated. Some of the results have been validated by Western blotting. Both enolase and aldolase were first reported to be involved in chemoresistance, suggesting that process of glycolysis in doxorubicin-resistant myelogenous leukemia cells was accelerated to some extent to provide more energy to survive chemical stress. Possible roles of most of the identified proteins in development of chemoresistance in myelogenous leukemia cells were fully discussed. The results presented here could provide clues to further study for elucidating the mechanisms underlying drug resistance in leukemia. CONCLUSIONS: As a whole, under the chemical stress, the doxorubicin-resistant myelogenous leukemia cells may employ various protective strategies to survive. These include: (i) pumping the cytotoxic drug out of the cells by P-glycoprotein, (ii) increased storage of fermentable fuel, (iii) sophisticated cellular protection by molecular chaperones, (iv) improved handling of intracellular calcium, (v) increased glucose utilization via increased rates of glycolysis. In the present study, proteomic analysis of leukemia cells and their drug resistant variants revealed multiple alterations in protein expression. Our results indicate that the development of drug resistance in doxorubicin-resistant myelogenous leukemia cells is a complex phenomenon undergoing several mechanisms.
Effects of mycophenolate mofetil on kidney function and phosphorylation status of renal proteins in Alport COL4A3-deficient mice.
Petrova DT, Schultze FC, Brandhorst G … +7 more , Luchs KD, Lenz C, Urlaub H, Rubel D, Gross O, Walson PD, Oellerich M
Proteome Sci · 2014 · PMID 25525413 · Full text
BACKGROUND: We investigated the effects of mycophenolate mofetil (MMF) on kidney function and on protein phosphorylation in a mouse model for the human Alport syndrome. METHODS: COL4A3-deficient (COL4A3-/-) mice were ran...
BACKGROUND: We investigated the effects of mycophenolate mofetil (MMF) on kidney function and on protein phosphorylation in a mouse model for the human Alport syndrome. METHODS: COL4A3-deficient (COL4A3-/-) mice were randomly allocated to receive a placebo (PLC COL4A3-/-) or MMF treatment (MMF COL4A3-/-). Wild type mice (WT) were used as controls. Changes in serum creatinine, total protein and blood urea nitrogen (BUN), concentrations of mycophenolic acid (MPA) and its glucuronide metabolite (MPAG), serum protein electrophoresis, urine dipstick chemistry and sediment were measured. Changes in the phosphorylation status of renal proteins and histology were analyzed. RESULTS: MMF influenced kidney function and protein phosphorylation. Serum creatinine and BUN were lower in MMF treated compared to PLC treated COL4A3-/- mice. Serum albumin and alpha-1 globulins were significantly decreased while serum creatinine, alpha-2 globulins, urine dipstick protein, leukocyte esterase, hemoglobin and red blood cells were all increased in both COL4A3-/- groups compared to WT. Differential 2DE-gel analysis identified six phosphorylated kidney protein spots that were significantly altered by MMF. CONCLUSIONS: These data suggest that the MMF treatment in this murine model moderately improved kidney function and reversed the phosphorylation status of six renal phosphoprotein spots to that seen in WT mice.
Proteomic analysis of seed storage proteins in wild rice species of the Oryza genus.
Jiang C, Cheng Z, Zhang C … +4 more , Yu T, Zhong Q, Shen JQ, Huang X
Proteome Sci · 2014 · PMID 25505850 · Full text
BACKGROUND: The total protein contents of rice seeds are significantly higher in the three wild rice species (Oryza rufipogon Grill., Oryza officinalis Wall. and Oryza meyeriana Baill.) than in the cultivated rice (Oryza...
BACKGROUND: The total protein contents of rice seeds are significantly higher in the three wild rice species (Oryza rufipogon Grill., Oryza officinalis Wall. and Oryza meyeriana Baill.) than in the cultivated rice (Oryza sativa L.). However, there is still no report regarding a systematic proteomic analysis of seed proteins in the wild rice species. Also, the relationship between the contents of seed total proteins and rice nutritional quality has not been thoroughly investigated. RESULTS: The total seed protein contents, especially the glutelin contents, of the three wild rice species were higher than those of the two cultivated rice materials. Based on the protein banding patterns of SDS-PAGE, O. rufipogon was similar to the two cultivated rice materials, followed by O. officinalis, while O. meyeriana exhibited notable differences. Interestingly, O. meyeriana had high contents of glutelin and low contents of prolamine, and lacked 26 kDa globulin band and appeared a new 28 kDa protein band. However, for O. officinali a 16 kDa protein band was absent and a row of unique 32 kDa proteins appeared. In addition, we found that 13 kDa prolamine band disappeared while special 14 kDa and 12 kDa protein bands were present in O. officinalis. Two-dimensional gel electrophoresis (2-DE) analysis revealed remarkable differences in protein profiles of the wild rice species and the two cultivated rice materials. Also, the numbers of detected protein spots of the three wild rice species were significantly higher than those of two cultivated rice. A total of 35 differential protein spots were found for glutelin acidic subunits, glutelin precursors and glutelin basic subunits in wild rice species. Among those, 18 protein spots were specific and 17 major spots were elevated. Six differential protein spots for glutelin acidic subunits were identified, including a glutelin type-A 2 precursor and five hypothetical proteins. CONCLUSION: This was the first report on proteomic analysis of the three wild rice species. Overall results suggest that there were many new types of glutelin subunits and precursor in the three wild rice species. Hence, wild rice species are important genetic resources for improving nutritional quality to rice.
New insights in the composition of extracellular vesicles from pancreatic cancer cells: implications for biomarkers and functions.
Klein-Scory S, Tehrani MM, Eilert-Micus C … +6 more , Adamczyk KA, Wojtalewicz N, Schnölzer M, Hahn SA, Schmiegel W, Schwarte-Waldhoff I
Proteome Sci · 2014 · PMID 25469109 · Full text
BACKGROUND: Pancreatic cancer development is associated with characteristic alterations like desmoplastic reaction and immune escape which are mediated by the cell-cell communication mechanism and by the microenvironment...
BACKGROUND: Pancreatic cancer development is associated with characteristic alterations like desmoplastic reaction and immune escape which are mediated by the cell-cell communication mechanism and by the microenvironment of the cells. The whole of released components are important determinants in these processes. Especially the extracellular vesicles released by pancreatic cancer cells play a role in cell communication and modulate cell growth and immune responses. RESULTS: Here, we present the proteomic description of affinity purified extracellular vesicles from pancreatic tumour cells, compared to the secretome, defined as the whole of the proteins released by pancreatic cancer cells. The proteomic data provide comprehensive catalogues of hundreds of proteins, and the comparison reveals a special proteomic composition of pancreatic cancer cell derived extracellular vesicles. The functional analysis of the protein composition displayed that membrane proteins, glycoproteins, small GTP binding proteins and a further, heterogeneous group of proteins are enriched in vesicles, whereas proteins derived from proteasomes and ribosomes, as well as metabolic enzymes, are not components of the vesicles. Furthermore proteins playing a role in carcinogenesis and modulators of the extracellular matrix (ECM) or cell-cell interactions are components of affinity purified extracellular vesicles. CONCLUSION: The data deepen the knowledge of extracellular vesicle composition by hundreds of proteins that have not been previously described as vesicle components released by pancreatic cancer cells. Extracellular vesicles derived from pancreatic cancer cells show common proteins shared with other vesicles as well as cell type specific proteins indicating biomarker candidates and suggesting functional roles in cancer cell stroma interactions.
Proteomic analysis of rat cartilage: the identification of differentially expressed proteins in the early stages of osteoarthritis.
Parra-Torres NM, Cázares-Raga FE, Kouri JB
Proteome Sci · 2014 · PMID 25435813 · Full text
BACKGROUND: Osteoarthritis (OA) is a chronic degenerative disease of the articular cartilage, and its diagnosis is based on symptoms and radiological signs that are only present in the late stages of the disease. Due to...
BACKGROUND: Osteoarthritis (OA) is a chronic degenerative disease of the articular cartilage, and its diagnosis is based on symptoms and radiological signs that are only present in the late stages of the disease. Due to the limitations in diagnosing OA before the onset of symptoms, such as pain, little is known about the molecular mechanisms involved in the pathogenesis of OA. Experimental OA models are often used to study the kinetics of the progression of this disease. In this report, we conducted a proteomic study of osteoarthritic cartilage during the early stages of OA using an experimental rat model. RESULTS: Ten proteins that are differentially expressed under early OA conditions were identified by 2-DE and MALDI-TOF/MS. These proteins mediated many processes, such as glycolysis and energy production (Nme2 and Pnp), cartilage matrix (Col2a1), transcription and protein synthesis (Eef1a1 and DJ-1), signal transduction (CaM and Pebp1), transport (Alb and Hba1), and latexin (Lxn). In addition, changes in Lxn expression in early OA were observed and validated by western blot and immunofluorescence analysis. CONCLUSIONS: The proteins that we identified indicate that energy metabolism, cartilage matrix remodelling, and protective cellular mechanisms are associated with early OA. In addition, latexin expression during the early stages of OA could be implicated in cartilage repair.
Unravelling associations between unassigned mass spectrometry peaks with frequent itemset mining techniques.
Vu TN, Mrzic A, Valkenborg D … +4 more , Maes E, Lemière F, Goethals B, Laukens K
Proteome Sci · 2014 · PMID 25429250 · Full text
BACKGROUND: Mass spectrometry-based proteomics experiments generate spectra that are rich in information. Often only a fraction of this information is used for peptide/protein identification, whereas a significant propor...
BACKGROUND: Mass spectrometry-based proteomics experiments generate spectra that are rich in information. Often only a fraction of this information is used for peptide/protein identification, whereas a significant proportion of the peaks in a spectrum remain unexplained. In this paper we explore how a specific class of data mining techniques termed "frequent itemset mining" can be employed to discover patterns in the unassigned data, and how such patterns can help us interpret the origin of the unexpected/unexplained peaks. RESULTS: First a model is proposed that describes the origin of the observed peaks in a mass spectrum. For this purpose we use the classical correlative database search algorithm. Peaks that support a positive identification of the spectrum are termed explained peaks. Next, frequent itemset mining techniques are introduced to infer which unexplained peaks are associated in a spectrum. The method is validated on two types of experimental proteomic data. First, peptide mass fingerprint data is analyzed to explain the unassigned peaks in a full scan mass spectrum. Interestingly, a large numbers of experimental spectra reveals several highly frequent unexplained masses, and pattern mining on these frequent masses demonstrates that subsets of these peaks frequently co-occur. Further evaluation shows that several of these co-occurring peaks indeed have a known common origin, and other patterns are promising hypothesis generators for further analysis. Second, the proposed methodology is validated on tandem mass spectrometral data using a public spectral library, where associations within the mass differences of unassigned peaks and peptide modifications are explored. The investigation of the found patterns illustrates that meaningful patterns can be discovered that can be explained by features of the employed technology and found modifications. CONCLUSIONS: This simple approach offers opportunities to monitor accumulating unexplained mass spectrometry data for emerging new patterns, with possible applications for the development of mass exclusion lists, for the refinement of quality control strategies and for a further interpretation of unexplained spectral peaks in mass spectrometry and tandem mass spectrometry.
Promoter trapping method: transcription factor purification using human telomerase reverse transcriptase promoter.
Nagore LI, Zhou Y, Nadeau RJ … +2 more , Jia Y, Jarrett HW
Proteome Sci · 2014 · PMID 25425973 · Full text
BACKGROUND: Transcription factors bind to response elements on the promoter regions of genes to regulate transcriptional activity. One of the major problems with identifying transcription factors is their low abundance r...
BACKGROUND: Transcription factors bind to response elements on the promoter regions of genes to regulate transcriptional activity. One of the major problems with identifying transcription factors is their low abundance relative to other proteins in the cell. Developing a purification technique specific for transcription factors is crucial to the understanding of gene regulation. Promoter trapping is a method developed that uses the promoter regions as bait to trap proteins of interest and then purified using column chromatography. Here we utilize this technique to study the telomerase promoter, which has increased transcriptional activity in cancer cells. Gaining insight on how to control the enzyme at the promoter level may give new routes towards cancer treatments. RESULTS: Our findings show that the telomerase promoter (-170 - +91) and Promoter Trapping isolate a transcriptionally active and reproducible complex, when analyzed by liquid chromatography tandem mass spectrometry. We were also able to identify transcription factors, including AP-2 and SP1 known to bind this promoter, as well as show that these two proteins can bind to each other's response element. CONCLUSION: Here we focus on verifying the ability and versatility of Promoter Trapping coupled with additional well-characterized methods to identify already known factors responsible for telomerase transcriptional regulation.
Impact of three commercial feed formulations on farmed gilthead sea bream (Sparus aurata, L.) metabolism as inferred from liver and blood serum proteomics.
Ghisaura S, Anedda R, Pagnozzi D … +7 more , Biosa G, Spada S, Bonaglini E, Cappuccinelli R, Roggio T, Uzzau S, Addis MF
Proteome Sci · 2014 · PMID 25342931 · Full text
BACKGROUND: The zootechnical performance of three different commercial feeds and their impact on liver and serum proteins of gilthead sea bream (Sparus aurata, L.) were assessed in a 12 week feeding trial. The three feed...
BACKGROUND: The zootechnical performance of three different commercial feeds and their impact on liver and serum proteins of gilthead sea bream (Sparus aurata, L.) were assessed in a 12 week feeding trial. The three feeds, named A, B, and C, were subjected to lipid and protein characterization by gas chromatography (GC) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively. RESULTS: Feed B was higher in fish-derived lipids and proteins, while feeds C and A were higher in vegetable components, although the largest proportion of feed C proteins was represented by pig hemoglobin. According to biometric measurements, the feeds had significantly different impacts on fish growth, producing a higher average weight gain and a lower liver somatic index in feed B over feeds A and C, respectively. 2D DIGE/MS analysis of liver tissue and Ingenuity pathways analysis (IPA) highlighted differential changes in proteins involved in key metabolic pathways of liver, spanning carbohydrate, lipid, protein, and oxidative metabolism. In addition, serum proteomics revealed interesting changes in apolipoproteins, transferrin, warm temperature acclimation-related 65 kDa protein (Wap65), fibrinogen, F-type lectin, and alpha-1-antitrypsin. CONCLUSIONS: This study highlights the contribution of proteomics for understanding and improving the metabolic compatibility of feeds for marine aquaculture, and opens new perspectives for its monitoring with serological tests.
Mass Spectrometric Immunoassay for the qualitative and quantitative analysis of the cytokine Macrophage Migration Inhibitory Factor (MIF).
Sherma ND, Borges CR, Trenchevska O … +5 more , Jarvis JW, Rehder DS, Oran PE, Nelson RW, Nedelkov D
Proteome Sci · 2014 · PMID 25328446 · Full text
BACKGROUND: The cytokine MIF (Macrophage Migration Inhibitory Factor) has diverse physiological roles and is present at elevated concentrations in numerous disease states. However, its molecular heterogeneity has not bee...
BACKGROUND: The cytokine MIF (Macrophage Migration Inhibitory Factor) has diverse physiological roles and is present at elevated concentrations in numerous disease states. However, its molecular heterogeneity has not been previously investigated in biological samples. Mass Spectrometric Immunoassay (MSIA) may help elucidate MIF post-translational modifications existing in vivo and provide additional clarity regarding its relationship to diverse pathologies. RESULTS: In this work, we have developed and validated a fully quantitative MSIA assay for MIF, and used it in the discovery and quantification of different proteoforms of MIF in serum samples, including cysteinylated and glycated MIF. The MSIA assay had a linear range of 1.56-50 ng/mL, and exhibited good precision, linearity, and recovery characteristics. The new assay was applied to a small cohort of human serum samples, and benchmarked against an MIF ELISA assay. CONCLUSIONS: The quantitative MIF MSIA assay provides a sensitive, precise and high throughput method to delineate and quantify MIF proteoforms in biological samples.
Serum peptidome based biomarkers searching for monitoring minimal residual disease in adult acute lymphocytic leukemia.
Bai J, He A, Huang C … +7 more , Yang J, Zhang W, Wang J, Yang Y, Zhang P, Zhang Y, Zhou F
Proteome Sci · 2014 · PMID 25317080 · Full text
BACKGROUND: The persistence of minimal residual disease (MRD) during therapy is the strongest adverse prognostic factor in acute lymphocytic leukemia (ALL). This study was to identify serum candidate peptides for monitor...
BACKGROUND: The persistence of minimal residual disease (MRD) during therapy is the strongest adverse prognostic factor in acute lymphocytic leukemia (ALL). This study was to identify serum candidate peptides for monitoring MRD in adult ALL. RESULTS: A total of 33 peptides in the molecular weight range of 1000-10000 Da were detected using ClinProt system and statistically different between adult patients with ALL and healthy controls. Quick classifier (QC) algorithm was used to obtain a diagnostic model consisting of five peptides that could discriminate patients with ALL from controls with a high sensitivity (100%) and specificity (96.67%). The peptides in the QC model were identified as fibrinogen alpha chain (FGA), glutathione S-transferase P1 (GSTP1), isoform 1 of fibrinogen alpha chain precursor, platelet factor 4 (PF4) by high pressure/performance liquid chromatography mass spectrometry/mass spectrometry. Relative intensities of the five peptides were compared among ALL different groups for the potential importance of MRD evaluation in ALL. The peptides with increased relative intensities in newly diagnosed (ND) ALL patients were found to be decreased in their relative intensities after complete remission (CR) of adult ALL. When ALL patients were refractory & relapsed (RR), relative intensities of the peptides were elevated again. Peptides with decreased relative intensities in ND and RR ALL patients were found to be increased in their relative intensities when ALL patients achieved CR. The findings were validated by ELISA and western blot. Further linear regression analyses were performed to eliminate the influence of platelet and white blood cell counts on serum protein contents and indicated that there were no correlations between the contents of all four proteins (PF4, connective tissue active peptide III, FGA and GSTP1) and white blood cell or platelet counts in ALL different groups and healthy control. CONCLUSIONS: We speculate the five peptides, FGA, isoform 1 of fibrinogen alpha chain precursor, GSTP1, PF4 and connective tissue active peptide III would be potential biomarkers for forecasting relapse, monitoring MRD and evaluating therapeutic response in adult ALL.
Potential serum biomarkers for glioblastoma diagnostic assessed by proteomic approaches.
Popescu ID, Codrici E, Albulescu L … +4 more , Mihai S, Enciu AM, Albulescu R, Tanase CP
Proteome Sci · 2014 · PMID 25298751 · Full text
BACKGROUND: The rapid progress of proteomics over the past years has allowed the discovery of a large number of potential biomarker candidates to improve early tumor diagnosis and therapeutic response, thus being further...
BACKGROUND: The rapid progress of proteomics over the past years has allowed the discovery of a large number of potential biomarker candidates to improve early tumor diagnosis and therapeutic response, thus being further integrated into clinical environment. High grade gliomas represent one of the most aggressive and treatment-resistant types of human brain cancer, with approximately 9-12 months median survival rate for patients with grade IV glioma (glioblastoma). Using state-of-the-art proteomics technologies, we have investigated the proteome profile for glioblastoma patients in order to identify a novel protein biomarker panel that could discriminate glioblastoma patients from controls and increase diagnostic accuracy. RESULTS: In this study, SELDI-ToF MS technology was used to screen potential protein patterns in glioblastoma patients serum; furthermore, LC-MS/MS technology was applied to identify the candidate biomarkers peaks. Through these proteomic approaches, three proteins S100A8, S100A9 and CXCL4 were selected as putative biomarkers and confirmed by ELISA. Next step was to validate the above mentioned molecules as biomarkers through identification of protein expression by Western blot in tumoral versus peritumoral tissue. CONCLUSIONS: Proteomic technologies have been used to investigate the protein profile of glioblastoma patients and established several potential diagnostic biomarkers. While it is unlikely for a single biomarker to be highly effective for glioblastoma diagnostic, our data proposed an alternative and efficient approach by using a novel combination of multiple biomarkers.
Comparative proteomics and glycoproteomics of plasma proteins in Indian visceral leishmaniasis.
Bag AK, Saha S, Sundar S … +3 more , Saha B, Chakrabarti A, Mandal C
Proteome Sci · 2014 · PMID 25276097 · Full text
BACKGROUND: Visceral leishmaniasis (VL) is a deadly parasitic diseases caused by Leishmania donovani; it is a major health problem in many countries. A lack of proper understanding of the disease biology, poor diagnostic...
BACKGROUND: Visceral leishmaniasis (VL) is a deadly parasitic diseases caused by Leishmania donovani; it is a major health problem in many countries. A lack of proper understanding of the disease biology, poor diagnostic methods and increasing drug resistance are the main reasons for the growing burden of VL infection. Comparative plasma proteomics are a relatively useful technique that can be used to investigate disease-associated alterations that can help in understanding host responses against pathogens, and might be useful in disease management and diagnosis. RESULT: In this study, a comparative proteomics and glycoproteomics approach using 2DE and 2D-DIGE was employed between early diagnosed VL patients of all age groups and healthy endemic and non-endemic controls in order to aid the recognition of disease-associated alterations in host plasma. Comparative proteomics was performed by the depletion of seven highly abundant plasma proteins. Comparative glycoproteomics was performed by the depletion of albumin and IgG, followed by purification of plasma glycoproteins using a multi lectin affinity column. From these two approaches, 39 differentially expressed protein spots were identified and sequenced using MALDI-TOF/TOF mass spectrometry. This revealed ten distinct proteins that appeared in multiple spots, suggesting micro-heterogeneity. Among these proteins, alpha-1-antitrypsin, alpha-1-B glycoprotein and amyloid-A1 precursor were up-regulated, whereas vitamin-D binding protein, apolipoprotein-A-I and transthyretin were down-regulated in VL. Alterations in the levels of these proteins in VL-infected plasma were further confirmed by western blot and ELISA. CONCLUSIONS: These proteins may be involved in the survival of parasites, resisting neutrophil elastase, and in their multiplication in macrophages, potentially maintaining endogenous anti-inflammatory and immunosuppressive conditions. Consequently, the results of this study may help in understanding the host response against L.donovani, which could help in the discovery of new drugs and disease management. Finally, these alterations on protein levels might be beneficial in improving early diagnosis considering those as biomarkers in Indian VL.
Two dimensional gel phosphoproteome of peripheral blood mononuclear cells: comparison between two enrichment methods.
Rocchetti MT, Alfarano M, Varraso L … +5 more , Di Paolo S, Papale M, Ranieri E, Grandaliano G, Gesualdo L
Proteome Sci · 2014 · PMID 25276096 · Full text
BACKGROUND: Protein phosphorylation is considered a key event in signal transduction. Peripheral blood mononuclear cells (PBMCs) are a critical component of the immune system. The analysis of PBMCs phosphoproteome might...
BACKGROUND: Protein phosphorylation is considered a key event in signal transduction. Peripheral blood mononuclear cells (PBMCs) are a critical component of the immune system. The analysis of PBMCs phosphoproteome might help elucidate the signaling pathways essential to their biological role in health, immunological diseases and cancer. Enrichment of phosphoproteins becomes a prerequisite for phosphoproteome analysis and conventionally requires a multi-step procedure and sophisticated equipments. In this study, we standardized 2D-PAGE phosphoproteome analysis of PBMCs and compared two phosphoprotein enrichment methods, lanthanum chloride precipitation and affinity micro-column. Further, the different specificity for PBMCs phosphorylated proteins of each method was investigated. RESULTS: PBMCs were isolated from fresh whole blood of ten healthy donors. PBMCs phosphoproteins were enriched either by phosphoprotein precipitation using lanthanum chloride, with an overall yield of 8.9 ± 4.7%, or by using an affinity micro-column, with a lower yield of 3.2 ± 1.6% (p = 0.05). Image analysis of Sypro-stained analytical 2D-PAGE gels detected 554 ± 68 protein spots for the lanthanum pattern [inter-assay coefficient of variation (CV) = 27.0%, intra-assay CV = 10.7%] and 575 ± 35 protein spots for the micro-column pattern (inter-assay CV = 26.8%; intra-assay CV = 11.0%) (p = 0.6), with 57% match of the spots detected by the 2 approaches. 1D gel electrophoresis and western blot analyses of the supernatants suggested a better lanthanum ions capability to deplete phosphoproteins in a PBMCs protein lysate compared to the affinity micro-column. On the other hand, 1D gel electrophoresis analysis of dephosphorylated PBMCs protein lysate revealed a relatively higher unspecificity for the lanthanum ions compared to affinity micro-column. Filamin-A, coronin 1A, pyruvate kinase isozymes M1/M2 and ficolin-1 were considerably more expressed in the lanthanum phosphoprotein pattern. Interestingly, ficolin-1 had not been reported in 2DE-PBMCs proteome profiles so far. CONCLUSION: Our results describe the differences and the validity of phosphoprotein enrichment methods and provide two successful and complementary approaches for the 2DE phosphoproteome analysis of PBMCs.
Proteomic study of sporadic inclusion body myositis.
Li K, Pu C, Huang X … +3 more , Liu J, Mao Y, Lu X
Proteome Sci · 2014 · PMID 25253997 · Full text
BACKGROUND: Sporadic inclusion body myositis (s-IBM) is the most commonly occurring acquired inflammatory myopathy in elderly people (>45 years); however, pathogenic mechanisms are poorly understood and diagnostic tools...
BACKGROUND: Sporadic inclusion body myositis (s-IBM) is the most commonly occurring acquired inflammatory myopathy in elderly people (>45 years); however, pathogenic mechanisms are poorly understood and diagnostic tools are limited. In view of this, new therapeutic and diagnostic molecular markers for s-IBM need to be identified. EXPERIMENTAL DESIGN: In this study, the proteomes from three s-IBM cases were compared with those from three cases of neurogenic muscular atrophy (control). Proteins were separated by 2-dimensional polyacrylamide gel electrophoresis and profiled by mass spectrometric sequencing and subsequently validated by western blot. RESULTS: Differential expression was noted in 29 proteins (16 upregulated and 13 downregulated) in s-IBM compared with the control group. Functions of these proteins include oxidative stress response, regulation of apoptosis, signal transduction, and cytoskeleton. Expression of both amyloid precursor protein (APP) and αB-crystallin was increased in s-IBM cases. CONCLUSIONS: Our study reveals a unique pattern of protein expression in s-IBM, which should be further investigated in a wider cohort of IBM patients to fully realize the potential diagnostic or therapeutic benefits.
About
- Frequency
- Sun
- Papers found
- 200
- RSS feed
- Subscribe