Proteome Science[JOURNAL]
Sun
200 papers
Label-free quantitative mass spectrometry analysis of differential protein expression in the developing cochlear sensory epithelium.
Darville LNF, Sokolowski BHA
Proteome Sci · 2018 · PMID 30127667 · Full text
BACKGROUND: The sensory epithelium of the inner ear converts the mechanical energy of sound to electro-chemical energy recognized by the central nervous system. This process is mediated by receptor cells known as hair ce...
BACKGROUND: The sensory epithelium of the inner ear converts the mechanical energy of sound to electro-chemical energy recognized by the central nervous system. This process is mediated by receptor cells known as hair cells that express proteins in a timely fashion with the onset of hearing. METHODS: The proteomes of 3, 14, and 30 day-old mice cochlear sensory epithelia were revealed, using label-free quantitative mass spectrometry (LTQ-Orbitrap). Statistical analysis using a one-way ANOVA followed by Bonferroni's test was used to show significant differences in protein expression. Ingenuity Pathway Analysis was used to observe networks of differentially expressed proteins, their biological processes, and associated diseases, while Cytoscape software was used to determine putative interactions with select biomarker proteins. These candidate biomarkers were further verified using Western blotting, while coimmunoprecipitation was used to verify putative partners determined using bioinformatics. RESULTS: We show that a comparison across all three proteomes shows that there are 447 differentially expressed proteins, with 387 differentially expressed between postnatal day 3 and 30. Ingenuity Pathway Analysis revealed ~ 62% of postnatal day 3 downregulated proteins are involved in neurological diseases. Several proteins are expressed exclusively on P3, including Parvin α, Drebrin1 (Drb1), Secreted protein acidic and cysteine rich (SPARC), Transmembrane emp24 domain-containing protein 10 (Tmed10). Coimmunoprecipitations showed that Parvin and SPARC interact with integrin-linked protein kinase and the large conductance calcium-activated potassium channel, respectively. CONCLUSIONS: Quantitative mass spectrometry revealed the identification of numerous differentially regulated proteins over three days of postnatal development. These data provide insights into functional pathways regulating normal sensory and supporting cell development in the cochlea that include potential biomarkers. Interacting partners of two of these markers suggest the importance of these complexes in regulating cellular structure and synapse development.
Comparative iTRAQ proteomics revealed proteins associated with horn development in yak.
Li M, Wu X, Guo X … +5 more , Bao P, Ding X, Chu M, Liang C, Yan P
Proteome Sci · 2018 · PMID 30061793 · Full text
BACKGROUND: The practice of dehorning yak raises animal safety concerns, which have been addressed by selective breeding to obtain genetically hornless yak. The POLLED locus in yak has been studied extensively; however,...
BACKGROUND: The practice of dehorning yak raises animal safety concerns, which have been addressed by selective breeding to obtain genetically hornless yak. The POLLED locus in yak has been studied extensively; however, little is known regarding the proteins that regulate horn bud development. METHODS: A differential proteomic analysis was performed to compare the skin from the horn bud region of polled yak fetuses and the horn bud tissue of horned yak fetuses using isobaric tags for relative and absolute quantitation (iTRAQ) technology coupled with 2D LC-MS/MS. RESULTS: One hundred differentially abundant proteins (DAPs) were identified. Of these, 29 were up-regulated and 71 were down-regulated in skin from the horn bud region of polled fetuses when compared to the horn bud tissue of horned fetuses. Bioinformatics analyses showed that the up-regulated DAPs were mainly associated with metabolic activities, while the down-regulated DAPs were significantly enriched in cell adhesion and cell movement activities. CONCLUSIONS: We concluded that some important proteins were associated with cell adhesion, cell motility, keratinocyte differentiation, cytoskeleton organization, osteoblast differentiation, and fatty acid metabolism during horn bud development. These results advance our understanding of the molecular mechanisms underlying horn development.
Correction to: Proteomic identification and characterization of hepatic glyoxalase 1 dysregulation in non-alcoholic fatty liver disease.
Spanos C, Maldonado EM, Fisher CP … +17 more , Leenutaphong P, Oviedo-Orta E, Windridge D, Salguero FJ, Bermúdez-Fajardo A, Weeks ME, Evans C, Corfe BM, Rabbani N, Thornalley PJ, Miller MH, Wang H, Dillon JF, Quaglia A, Dhawan A, Fitzpatrick E, Moore JB
Proteome Sci · 2018 · PMID 29983642 · Full text
[This corrects the article DOI: 10.1186/s12953-018-0131-y.].
[This corrects the article DOI: 10.1186/s12953-018-0131-y.].
In-depth proteomic analyses of (greenlip abalone) nacre and prismatic organic shell matrix.
Mann K, Cerveau N, Gummich M … +3 more , Fritz M, Mann M, Jackson DJ
Proteome Sci · 2018 · PMID 29983641 · Full text
BACKGROUND: The shells of various species have served as models of invertebrate biomineralization and physical shell properties for more than 20 years. A focus of this research has been the nacreous inner layer of the s...
BACKGROUND: The shells of various species have served as models of invertebrate biomineralization and physical shell properties for more than 20 years. A focus of this research has been the nacreous inner layer of the shell with its conspicuous arrangement of aragonite platelets, resembling in cross-section a brick-and-mortar wall. In comparison, the outer, less stable, calcitic prismatic layer has received much less attention. One of the first molluscan shell proteins to be characterized at the molecular level was Lustrin A, a component of the nacreous organic matrix of . This was soon followed by the C-type lectin perlucin and the growth factor-binding perlustrin, both isolated from nacre, and the crystal growth-modulating AP7 and AP24, isolated from nacre. Mass spectrometry-based proteomics was subsequently applied to to biomineralization research with the analysis of the shell matrix and yielded 14 different shell-associated proteins. That study was the most comprehensive for a species to date. METHODS: The shell proteomes of nacre and prismatic layer of the marine gastropod were analyzed combining mass spectrometry-based proteomics and next generation sequencing. RESULTS: We identified 297 proteins from the nacreous shell layer and 350 proteins from the prismatic shell layer from the green lip abalone . Considering the overlap between the two sets we identified a total of 448 proteins. Fifty-one nacre proteins and 43 prismatic layer proteins were defined as major proteins based on their abundance at more than 0.2% of the total. The remaining proteins occurred at low abundance and may not play any significant role in shell fabrication. The overlap of major proteins between the two shell layers was 17, amounting to a total of 77 major proteins. CONCLUSIONS: The shell proteome shares moderate sequence similarity at the protein level with other gastropod, bivalve and more distantly related invertebrate biomineralising proteomes. Features conserved in and other molluscan shell proteomes include short repetitive sequences of low complexity predicted to lack intrinsic three-dimensional structure, and domains such as tyrosinase, chitin-binding, and carbonic anhydrase. This catalogue of shell proteins represents the most comprehensive for a haliotid and should support future efforts to elucidate the molecular mechanisms of shell assembly.
iTRAQ-Based Proteomic Analysis reveals possible target-related proteins and signal networks in human osteoblasts overexpressing FGFR2.
Cai T, Wu B, Tang X … +4 more , Zhou Z, Yang J, Ke R, Mu X
Proteome Sci · 2018 · PMID 29950929 · Full text
BACKGROUND: Fibroblast growth factor receptor 2 (FGFR2) play a vital role in skeletogenesis. However, the molecular mechanisms triggered by FGFR2 in osteoblasts are still not fully understood. In this study, proteomics a...
BACKGROUND: Fibroblast growth factor receptor 2 (FGFR2) play a vital role in skeletogenesis. However, the molecular mechanisms triggered by FGFR2 in osteoblasts are still not fully understood. In this study, proteomics and bioinformatics analysis were performed to investigate changes in the protein profiles regulated by FGFR2, with the goal of characterizing the molecular mechanisms of FGFR2 function in osteoblasts. METHODS: In this study, FGFR2-overexpression cell line was established using the lentivirus-packaging vector in human osteoblasts (hFOB1.19). Next, the isobaric tags for relative and absolute quantitation (iTRAQ) in combination with the liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was used to compare the proteomic changes between control and FGFR2-overexpression cells. Thresholds (fold-change of ≥ 1.5 and a -value of < 0.05) were selected to determine differentially expressed proteins (DEPs). The bioinformatics analysis including GO and pathway analysis were done to identify the key pathways underlying the molecular mechanism. RESULTS: A Total of 149 DEPs was identified. The DEPs mainly located within organelles and involved in protein binding and extracellular regulation of signal transduction. ColI, TNC, FN1 and CDKN1A were strikingly downregulated while UBE2E3, ADNP2 and HSP70 were significantly upregulated in FGFR2-overexpression cells. KEEG analysis suggested the key pathways included cell death, PI3K-Akt signaling, focal adhesion and cell cycle. CONCLUSIONS: To our knowledge, this is the first protomic research to investigate alterations in protein levels and affected pathways in FGFR2-overexpression osteoblasts. Thus, this study not only provides a comprehensive dataset on overall protein changes regulated by FGFR2, but also shed light on its potential molecular mechanism in human osteoblasts.
Correction to: 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 · 2018 · PMID 29875618 · Full text
[This corrects the article DOI: 10.1186/s12953-015-0063-8.].
[This corrects the article DOI: 10.1186/s12953-015-0063-8.].
Proteomic analysis of buccal gland secretion from fasting and feeding lampreys ().
Li B, Gou M, Han J … +6 more , Yuan X, Li Y, Li T, Jiang Q, Xiao R, Li Q
Proteome Sci · 2018 · PMID 29796011 · Full text
BACKGROUND: Previous studies have shown that lamprey buccal glands contain some regulators related to anticoagulation, nociception, and immune responses due to the blood sucking habit. Regrettably, the protein expression...
BACKGROUND: Previous studies have shown that lamprey buccal glands contain some regulators related to anticoagulation, nociception, and immune responses due to the blood sucking habit. Regrettably, the protein expression profile in the buccal glands of feeding lampreys has never been reported yet. The present study was performed in order to further identify more proteins which are closely associated with lamprey feeding process. METHODS: 2D-PAGE, NanoLC-MS/MS with higher resolution, Ensembl lamprey and NCBI protein databases, as well as western blot was used to compare the proteomics of buccal gland secretion from China northeast lampreys () which had been fed for 0, 10, and 60 min, respectively. RESULTS: In the present study, the number of identified protein species in the buccal glands of feeding groups (60 min) was increased significantly, nearly ten times of that in the fasting group. During the feeding stage, novel proteins emerged in the buccal gland secretion of lampreys. According to gene ontology (GO) analysis and function predictions, these proteins were summarized and discussed based on their potential roles during feeding process. Furthermore, some of the identified proteins were confirmed to express during the feeding time of lampreys. CONCLUSION: When lampreys attack host fishes to suck blood and flesh, their buccal glands could secrete enough proteins to suppress blood coagulation, nociception, oxidative stress, immune response, as well as other adverse effects encountered during their parasitic lives. The present study would provide clues to clarify the feeding mechanism of the bloodsucking lampreys.
In vitro gentamicin exposure alters caveolae protein profile in cochlear spiral ligament pericytes.
Ghelfi E, Grondin Y, Millet EJ … +6 more , Bartos A, Bortoni M, Oliveira Gomes Dos Santos C, Trevino-Villarreal HJ, Sepulveda R, Rogers R
Proteome Sci · 2018 · PMID 29760588 · Full text
BACKGROUND: The aminoglycoside antibiotic gentamicin is an ototoxic drug and has been used experimentally to investigate cochlear damage induced by noise.We have investigated the changes in the protein profile associated...
BACKGROUND: The aminoglycoside antibiotic gentamicin is an ototoxic drug and has been used experimentally to investigate cochlear damage induced by noise.We have investigated the changes in the protein profile associated with caveolae in gentamicin treated and untreated spiral ligament (SL) pericytes, specialized cells in the blood labyrinth barrier of the inner ear microvasculature. Pericytes from various microvascular beds express caveolae, protein and cholesterol rich microdomains, which can undergo endocytosis and transcytosis to transport small molecules in and out the cells. A different protein profile in transport-specialized caveolae may induce pathological changes affecting the integrity of the blood labyrinth barrier and ultimately contributing to hearing loss. METHOD: Caveolae isolation from treated and untreated cells is achieved through ultracentrifugation of the lysates in discontinuous gradients. Mass spectrometry (LC-MS/MS) analysis identifies the proteins in the two groups. Proteins segregating with caveolae isolated from untreated SL pericytes are then compared to caveolae isolated from SL pericytes treated with the gentamicin for 24 h. Data are analyzed using bioinformatic tools. RESULTS: The caveolae proteome in gentamicin treated cells shows that 40% of total proteins are uniquely associated with caveolae during the treatment, and 15% of the proteins normally associated with caveolae in untreated cell are suppressed. Bioinformatic analysis of the data shows a decreased expression of proteins involved in genetic information processing, and an increase in proteins involved in metabolism, vesicular transport and signal transduction in gentamicin treated cells. Several Rab GTPases proteins, ubiquitous transporters, uniquely segregate with caveolae and are significantly enriched in gentamicin treated cells. CONCLUSION: We report that gentamicin exposure modifies protein profile of caveolae from SL pericytes. We identified a pool of proteins which are uniquely segregating with caveolae during the treatment, mainly participating in metabolic and biosynthetic pathways, in transport pathways and in genetic information processing. Finally, we show for the first time proteins associated with caveolae SL pericytes linked to nonsyndromic hearing loss.
ITRAQ-based quantitative proteomic analysis of processed L. for reducing the intestinal toxicity.
Zhang Y, Wang Y, Li S … +5 more , Zhang X, Li W, Luo S, Sun Z, Nie R
Proteome Sci · 2018 · PMID 29692685 · Full text
BACKGROUND: L., a Traditional Chinese medicine (TCM), is commonly used for the treatment of hydropsy, ascites, constipation, amenorrhea, and scabies. Semen Euphorbiae Pulveratum, which is another type of that is common...
BACKGROUND: L., a Traditional Chinese medicine (TCM), is commonly used for the treatment of hydropsy, ascites, constipation, amenorrhea, and scabies. Semen Euphorbiae Pulveratum, which is another type of that is commonly used in TCM practice and is obtained by removing the oil from the seed that is called paozhi, has been known to ease diarrhea. Whereas, the mechanisms of reducing intestinal toxicity have not been clearly investigated yet. METHODS: In this study, the isobaric tags for relative and absolute quantitation (iTRAQ) in combination with the liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomic method was applied to investigate the effects of L. on the protein expression involved in intestinal metabolism, in order to illustrate the potential attenuated mechanism of L. processing. Differentially expressed proteins (DEPs) in the intestine after treated with Semen Euphorbiae (SE), Semen Euphorbiae Pulveratum (SEP) and Euphorbiae Factor 1 (EFL) were identified. The bioinformatics analysis including GO analysis, pathway analysis, and network analysis were done to analyze the key metabolic pathways underlying the attenuation mechanism through protein network in diarrhea. Western blot were performed to validate selected protein and the related pathways. RESULTS: A number of differentially expressed proteins that may be associated with intestinal inflammation were identified. They mainly constituted by part of the cell. The expression sites of them located within cells and organelles. G protein and Eph/Ephrin signal pathway were controlled jointly by SEP and SE. After processing, the extraction of SEP were mainly reflected in the process of cytoskeleton, glycolysis and gluconeogenesis. CONCLUSIONS: These findings suggest that SE induced an inflammatory response, and activated the Interleukin signaling pathway, such as the Ang/Tie 2 and JAK2/ STAT signaling pathways, which may eventually contribute to injury result from intestinal inflammatory, while SEP could alleviate this injury by down-regulating STAT1 and activating Ang-4 that might reduce the inflammatory response. Our results demonstrated the importance of Ang-4 and STAT1 expression, which are the target proteins in the attenuated of SE after processing based on proteomic investigation. Thus iTRAQ might be a novel candidate method to study scientific connotation of hypothesis that the attenuated of SE after processing expressed lower toxicity from cellular levels.
Effects of the complete replacement of fish oil with linseed oil on growth, fatty acid composition, and protein expression in the Chinese mitten crab ().
Wei B, Yang Z, Cheng Y … +2 more , Wang J, Zhou J
Proteome Sci · 2018 · PMID 29568239 · Full text
BACKGROUND: The finite marine resources make it difficult for us to obtain enough fish oil (FO) used in aquatic feeds. Another sustainable ingredients should be found to substitute FO. The effects of replacing FO with ve...
BACKGROUND: The finite marine resources make it difficult for us to obtain enough fish oil (FO) used in aquatic feeds. Another sustainable ingredients should be found to substitute FO. The effects of replacing FO with vegetable oil have been studied in a variety of crustaceans, but most studies have focused on the phenotypic effects. Little is known about the mechanisms of the effects. METHODS: To understand the molecular responses during the replacement of FO in , we investigated the effects of feeding FO or linseed oil (LO) on growth performance, digestive enzyme activity, fatty acid composition and protein expression in . Twenty-four juvenile crabs were fed diets containing FO or LO for 112 days. Weight, carapace length and width were recorded. Fatty acid composition of the diets and the hepatopancreas and protein expression in the hepatopancreas were analyzed. RESULTS: Growth performance and molting interval were unchanged by diet. Crabs fed FO and LO had same activity of lipase and amylase, but comparing with crabs fed LO, crabs fed FO had higher trypsin activity and lower pepsin activity. Hepatopancreas fatty acid composition changed to reflect the fatty acid composition of the diets. In total, 194 proteins were differentially expressed in the hepatopancreas between the diets. Expression of heat shock proteins was higher in crabs fed LO. Expression of fatty acid synthase, long-chain fatty acid transport protein 4, acyl-CoA delta-9 desaturase, and fatty acid-binding protein 1, was higher in crabs fed FO. CONCLUSIONS: The substitution of FO with LO didn't have any effects on the growth and molting of mitten crab, but could significantly decrease the ability of mitten crab to cope with stress. The high content of HUFAs in the hepatopancreas of mitten crab fed FO is due to the high abundance of the proteins relative to the transport of the HUFAs. These findings provide a reason of the high content of EPA and DHA in crabs fed with FO, and provide new information for the replacement of FO in diets of mitten crab.
Profiling the interactome of protein kinase C ζ by proteomics and bioinformatics.
Hou C, Li Y, Liu H … +4 more , Dang M, Qin G, Zhang N, Chen R
Proteome Sci · 2018 · PMID 29491746 · Full text
BACKGROUND: Protein kinase C ζ (PKCζ), an isoform of the atypical protein kinase C, is a pivotal regulator in cancer. However, the molecular and cellular mechanisms whereby PKCζ regulates tumorigenesis and metastasis are...
BACKGROUND: Protein kinase C ζ (PKCζ), an isoform of the atypical protein kinase C, is a pivotal regulator in cancer. However, the molecular and cellular mechanisms whereby PKCζ regulates tumorigenesis and metastasis are still not fully understood. In this study, proteomics and bioinformatics analyses were performed to establish a protein-protein interaction (PPI) network associated with PKCζ, laying a stepping stone to further understand the diverse biological roles of PKCζ. METHODS: Protein complexes associated with PKCζ were purified by co-immunoprecipitation from breast cancer cell MDA-MB-231 and identified by LC-MS/MS. Two biological replicates and two technical replicates were analyzed. The observed proteins were filtered using the CRAPome database to eliminate the potential false positives. The proteomics identification results were combined with PPI database search to construct the interactome network. Gene ontology (GO) and pathway analysis were performed by PANTHER database and DAVID. Next, the interaction between PKCζ and protein phosphatase 2 catalytic subunit alpha (PPP2CA) was validated by co-immunoprecipitation, Western blotting and immunofluorescence. Furthermore, the TCGA database and the COSMIC database were used to analyze the expressions of these two proteins in clinical samples. RESULTS: The PKCζ centered PPI network containing 178 nodes and 1225 connections was built. Network analysis showed that the identified proteins were significantly associated with several key signaling pathways regulating cancer related cellular processes. CONCLUSIONS: Through combining the proteomics and bioinformatics analyses, a PKCζ centered PPI network was constructed, providing a more complete picture regarding the biological roles of PKCζ in both cancer regulation and other aspects of cellular biology.
Proteomic identification and characterization of hepatic glyoxalase 1 dysregulation in non-alcoholic fatty liver disease.
Spanos C, Maldonado EM, Fisher CP … +17 more , Leenutaphong P, Oviedo-Orta E, Windridge D, Salguero FJ, Bermúdez-Fajardo A, Weeks ME, Evans C, Corfe BM, Rabbani N, Thornalley PJ, Miller MH, Wang H, Dillon JF, Quaglia A, Dhawan A, Fitzpatrick E, Moore JB
Proteome Sci · 2018 · PMID 29456458 · Full text
BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease worldwide. However, its molecular pathogenesis is incompletely characterized and clinical biomarkers remain scarce. The aims of these...
BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease worldwide. However, its molecular pathogenesis is incompletely characterized and clinical biomarkers remain scarce. The aims of these experiments were to identify and characterize liver protein alterations in an animal model of early, diet-related, liver injury and to assess novel candidate biomarkers in NAFLD patients. METHODS: Liver membrane and cytosolic protein fractions from high fat fed apolipoprotein E knockout (ApoE) animals were analyzed by quantitative proteomics, utilizing isobaric tags for relative and absolute quantitation (iTRAQ) combined with nano-liquid chromatography and tandem mass spectrometry (nLC-MS/MS). Differential protein expression was confirmed independently by immunoblotting and immunohistochemistry in both murine tissue and biopsies from paediatric NAFLD patients. Candidate biomarkers were analyzed by enzyme-linked immunosorbent assay in serum from adult NAFLD patients. RESULTS: Through proteomic profiling, we identified decreased expression of hepatic glyoxalase 1 (GLO1) in a murine model. GLO1 protein expression was also found altered in tissue biopsies from paediatric NAFLD patients. In vitro experiments demonstrated that, in response to lipid loading in hepatocytes, GLO1 is first hyperacetylated then ubiquitinated and degraded, leading to an increase in reactive methylglyoxal. In a cohort of 59 biopsy-confirmed adult NAFLD patients, increased serum levels of the primary methylglyoxal-derived advanced glycation endproduct, hydroimidazolone (MG-H1) were significantly correlated with body mass index ( = 0.520, < 0.0001). CONCLUSION: Collectively these results demonstrate the dysregulation of GLO1 in NAFLD and implicate the acetylation-ubquitination degradation pathway as the functional mechanism. Further investigation of the role of GLO1 in the molecular pathogenesis of NAFLD is warranted.
Effect of ovarian cancer ascites on SKOV-3 cells proteome: new proteins associated with aggressive phenotype in epithelial ovarian cancer.
Toledo-Leyva A, Villegas-Pineda JC, Encarnación-Guevara S … +2 more , Gallardo-Rincón D, Talamás-Rohana P
Proteome Sci · 2018 · PMID 29456457 · Full text
BACKGROUND: Epithelial ovarian cancer is the second most lethal gynecological cancer worldwide. Ascites can be found in all clinical stages, however in advanced disease stages IIIC and IV it is more frequent and could be...
BACKGROUND: Epithelial ovarian cancer is the second most lethal gynecological cancer worldwide. Ascites can be found in all clinical stages, however in advanced disease stages IIIC and IV it is more frequent and could be massive, associated with worse prognosis. Due to the above, it was our interest to understanding how the ascites of ovarian cancer patients induces the mechanisms by which the cells present in it acquire a more aggressive phenotype and to know new proteins associated to this process. METHODS: A proteomic analysis of SKOV-3 cells treated with five different EOC ascites was performed by two-dimensional electrophoresis coupled to MALDI-TOF. The level of expression of the proteins of interest was validated by RT-PCR because several of these proteins have only been reported at the messenger level. RESULTS: Among the proteins identified that increased their expression in ascites-treated SKOV-3 cells, were Ran GTPase, ZNF268, and Synaptotagmin like-3. On the other hand, proteins that were negatively regulated by ascites were HLA-I, HSPB1, ARF1, Synaptotagmin 1, and hnRNPH1, among others. Furthermore, an interactome for every one of these proteins was done in order to identify biological processes, molecular actions, and cellular components in which they may participate. CONCLUSIONS: Identified proteins participate in cellular processes highly relevant to the aggressive phenotype such as nuclear transport, regulation of gene expression, vesicular trafficking, evasion of the immune response, invasion, metastasis, and in resistance to chemotherapy. These proteins may represent a source of information which has the potential to be evaluated for the design of therapies directed against these malignant cells that reside on ovarian cancer ascites.
Proteomic identification of moesin upon exposure to acrolein.
Lee PH, Kim BG, Lee SH … +2 more , Leikauf GD, Jang AS
Proteome Sci · 2018 · PMID 29375273 · Full text
BACKGROUND: Acrolein (allyl Aldehyde) as one of smoke irritant exacerbates chronic airway diseases and increased in sputum of patients with asthma and chronic obstructive lung disease. But underlying mechanism remains un...
BACKGROUND: Acrolein (allyl Aldehyde) as one of smoke irritant exacerbates chronic airway diseases and increased in sputum of patients with asthma and chronic obstructive lung disease. But underlying mechanism remains unresolved. The aim of study was to identify protein expression in human lung microvascular endothelial cells (HMVEC-L) exposed to acrolein. METHODS: A proteomic approach was used to determine the different expression of proteins at 8 h and 24 h after treatment of acrolein 30 nM and 300 nM to HMVEC-L. Treatment of HMVEC-L with acrolein 30 nM and 300 nM altered 21 protein spots on the two-dimensional gel, and these were then analyzed by MALDI-TOF MS. RESULTS: These proteins included antioxidant, signal transduction, cytoskeleton, protein transduction, catalytic reduction. The proteins were classified into four groups according to the time course of their expression patterns such as continually increasing, transient increasing, transient decreasing, and continually decreasing. For validation immunohistochemical staining and Western blotting was performed on lung tissues from acrolein exposed mice. Moesin was expressed in endothelium, epithelium, and inflammatory cells and increased in lung tissues of acrolein exposed mice compared with sham treated mice. CONCLUSIONS: These results indicate that some of proteins may be an important role for airway disease exacerbation caused by acrolein exposure.
Chemical proteomics, an integrated research engine for exploring drug-target-phenotype interactions.
Kwon HJ, Karuso P
Proteome Sci · 2018 · PMID 29339928 · Full text
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Comparative proteomic analysis between nitrogen supplemented and starved conditions in .
Oh Y, Robertson SL, Parker J … +2 more , Muddiman DC, Dean RA
Proteome Sci · 2017 · PMID 29158724 · Full text
BACKGROUND: Fungi are constantly exposed to nitrogen limiting environments, and thus the efficient regulation of nitrogen metabolism is essential for their survival, growth, development and pathogenicity. To understand h...
BACKGROUND: Fungi are constantly exposed to nitrogen limiting environments, and thus the efficient regulation of nitrogen metabolism is essential for their survival, growth, development and pathogenicity. To understand how the rice blast pathogen copes with limited nitrogen availability, a global proteome analysis under nitrogen supplemented and nitrogen starved conditions was completed. METHODS: strain 70-15 was cultivated in liquid minimal media and transferred to media with nitrate or without a nitrogen source. Proteins were isolated and subjected to unfractionated gel-free based liquid chromatography-tandem mass spectrometry (LC-MS/MS). The subcellular localization and function of the identified proteins were predicted using bioinformatics tools. RESULTS: A total of 5498 proteins were identified. Comparative analysis of protein expression showed 363 proteins and 266 proteins significantly induced or uniquely expressed under nitrogen starved or nitrogen supplemented conditions, respectively. A functional analysis of differentially expressed proteins revealed that during nitrogen starvation nitrogen catabolite repression, melanin biosynthesis, protein degradation and protein translation pathways underwent extensive alterations. In addition, nitrogen starvation induced accumulation of various extracellular proteins including small extracellular proteins consistent with observations of a link between nitrogen starvation and the development of pathogenicity in . CONCLUSION: The results from this study provide a comprehensive understanding of fungal responses to nitrogen availability.
Proteomic analysis of early salt stress responsive proteins in alfalfa roots and shoots.
Xiong J, Sun Y, Yang Q … +4 more , Tian H, Zhang H, Liu Y, Chen M
Proteome Sci · 2017 · PMID 29093645 · Full text
BACKGROUND: Alfalfa () is the most extensively cultivated forage legume in the world, and salinity stress is the most problematic environmental factors limiting alfalfa production. To evaluate alfalfa tissue variations i...
BACKGROUND: Alfalfa () is the most extensively cultivated forage legume in the world, and salinity stress is the most problematic environmental factors limiting alfalfa production. To evaluate alfalfa tissue variations in response to salt stress, comparative physiological and proteomic analyses were made of salt responses in the roots and shoots of the alfalfa. METHOD: A two-dimensional gel electrophoresis (2-DE)-based proteomic technique was employed to identify the differentially abundant proteins (DAPs) from salt-treated alfalfa roots and shoots of the salt tolerance cultivars Zhongmu No 1 cultivar, which was subjected to a range of salt stress concentrations for 9 days. In parallel, REL, MAD and HO contents, and the activities of antioxidant enzymes of shoots and roots were determinand. RESULT: Twenty-seven spots in the shoots and 36 spots in the roots that exhibited showed significant abundance variations were identified by MALDI-TOF-TOF MS. These DAPs are mainly involved in the biological processes of photosynthesis, stress and defense, carbohydrate and energy metabolism, second metabolism, protein metabolism, transcriptional regulation, cell wall and cytoskeleton metabolism, ion transpor, signal transduction. In parallel, physiological data were correlated well with our proteomic results. It is worth emphasizing that some novel salt-responsive proteins were identified, such as CP12, pathogenesis-related protein 2, harvest-induced protein, isoliquiritigenin 2'-O-methyltransferase. qRT-PCR was used to study the gene expression levels of the four above-mentioned proteins; four patterns are consistent with those of induced protein. CONCLUSION: The primary mechanisms underlying the ability of alfalfa seedlings to tolerate salt stress were photosynthesis, detoxifying and antioxidant, secondary metabolism, and ion transport. And it also suggests that the different tissues responded to salt-stress in different ways.
Iron overload down-regulates the expression of the HIV-1 Rev cofactor eIF5A in infected T lymphocytes.
Mancone C, Grimaldi A, Refolo G … +8 more , Abbate I, Rozera G, Benelli D, Fimia GM, Barnaba V, Tripodi M, Piacentini M, Ciccosanti F
Proteome Sci · 2017 · PMID 28785172 · Full text
BACKGROUND: Changes in iron metabolism frequently accompany HIV-1 infection. However, while many clinical and in vitro studies report iron overload exacerbates the development of infection, many others have found no corr...
BACKGROUND: Changes in iron metabolism frequently accompany HIV-1 infection. However, while many clinical and in vitro studies report iron overload exacerbates the development of infection, many others have found no correlation. Therefore, the multi-faceted role of iron in HIV-1 infection remains enigmatic. METHODS: RT-qPCR targeting the LTR region, , and were performed to measure the levels of viral RNAs in response to iron overload. Spike-in SILAC proteomics comparing i) iron-treated, ii) HIV-1-infected and iii) HIV-1-infected/iron treated T lymphocytes was performed to define modifications in the host cell proteome. Data from quantitative proteomics were integrated with the HIV-1 Human Interaction Database for assessing any viral cofactors modulated by iron overload in infected T lymphocytes. RESULTS: Here, we demonstrate that the iron overload down-regulates HIV-1 gene expression by decreasing the levels of viral RNAs. In addition, we found that iron overload modulates the expression of many viral cofactors. Among them, the downregulation of the REV cofactor eIF5A may correlate with the iron-induced inhibition of HIV-1 gene expression. Therefore, we demonstrated that eiF5A downregulation by shRNA resulted in a significant decrease of Nef levels, thus hampering HIV-1 replication. CONCLUSIONS: Our study indicates that HIV-1 cofactors influenced by iron metabolism represent potential targets for antiretroviral therapy and suggests eIF5A as a selective target for drug development.
Examining the influence of specificity ligands and ATP-competitive ligands on the overall effectiveness of bivalent kinase inhibitors.
Wong ML, Murphy J, Harrington E … +4 more , Gower CM, Jain RK, Schirle M, Thomas JR
Proteome Sci · 2016 · PMID 28725163 · Full text
BACKGROUND: Identifying selective kinase inhibitors remains a major challenge. The design of bivalent inhibitors provides a rational strategy for accessing potent and selective inhibitors. While bivalent kinase inhibitor...
BACKGROUND: Identifying selective kinase inhibitors remains a major challenge. The design of bivalent inhibitors provides a rational strategy for accessing potent and selective inhibitors. While bivalent kinase inhibitors have been successfully designed, no comprehensive assessment of affinity and selectivity for a series of bivalent inhibitors has been performed. Here, we present an evaluation of the structure activity relationship for bivalent kinase inhibitors targeting ABL1. METHODS: Various SNAPtag constructs bearing different specificity ligands were expressed in vitro. Bivalent inhibitor formation was accomplished by synthesizing individual ATP-competitive kinase inhibitors containing a SNAPtag targeting moiety, enabling the spontaneous self-assembly of the bivalent inhibitor. Assembled bivalent inhibitors were incubated with K562 lysates, and then subjected to affinity enrichment using various ATP-competitive inhibitors immobilized to sepharose beads. Resulting eluents were analyzed using Tandem Mass Tag (TMT) labeling and two-dimensional liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS). Relative binding affinity of the bivalent inhibitor was determined by calculating the concentration at which 50% of a given kinase remained bound to the affinity matrix. RESULTS: The profiling of three parental ATP-competitive inhibitors and nine SNAPtag conjugates led to the identification of 349 kinase proteins. In all cases, the bivalent inhibitors exhibited enhanced binding affinity and selectivity for ABL1 when compared to the parental compound conjugated to SNAPtag alone. While the rank order of binding affinity could be predicted by considering the binding affinities of the individual specificity ligands, the resulting affinity of the assembled bivalent inhibitor was not predictable. The results from this study suggest that as the potency of the ATP-competitive ligand increases, the contribution of the specificity ligand towards the overall binding affinity of the bivalent inhibitor decreases. However, the affinity of the specificity components in its interaction with the target is essential for achieving selectivity. CONCLUSION: Through comprehensive chemical proteomic profiling, this work provides the first insight into the influence of ATP-competitive and specificity ligands binding to their intended target on a proteome-wide scale. The resulting data suggest a subtle interplay between the ATP-competitive and specificity ligands that cannot be accounted for by considering the specificity or affinity of the individual components alone.
Daptomycin, a last-resort antibiotic, binds ribosomal protein S19 in humans.
Gotsbacher MP, Cho S, Kwon HJ … +1 more , Karuso P
Proteome Sci · 2016 · PMID 28680364 · Full text
BACKGROUND: Daptomycin is a recently introduced, last-resort antibiotic that displays a unique mode of action against Gram-positive bacteria that is not fully understood. Several bacterial targets have been proposed but...
BACKGROUND: Daptomycin is a recently introduced, last-resort antibiotic that displays a unique mode of action against Gram-positive bacteria that is not fully understood. Several bacterial targets have been proposed but no human binding partner is known. METHODS: In the present study we tested daptomycin in cell viability and proliferation assays against six human cell lines, describe the synthesis of biotinylated and fluorescently labeled analogues of daptomycin. Biotinylated daptomycin was used as bait to isolate the human binding partner by the application of reverse chemical proteomics using T7 phage display of five human tumor cDNA libraries. The interaction between the rescued protein and daptomycin was validated via siRNA knockdown, DARTS assay and immunocytochemistry. RESULTS: We have found that daptomycin possesses selective growth inhibition of some cancer cell lines, especially MCF7. The unbiased interrogation of human cDNA libraries, displayed on bacteriophage T7, revealed a single human target of daptomycin; ribosomal protein S19. Using a drug affinity responsive target stability (DARTS) assay , we show that daptomycin stabilizes RPS19 toward pronase. Fluorescently labeled daptomycin stained specific structures in HeLa cells and co-localized with a RPS19 antibody. CONCLUSION: This study provides, for the first time, a human protein target of daptomycin and identifies RPS19 as a possible anticancer drug target for the development of new pharmacological applications and research.
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