Adenine is commonly used to establish the animal models for chronic kidney injury and its renal interstitial fibrosis. As an endogenous substance, adenine-induced kidney damage has not yet been fully studied and eluci...Adenine is commonly used to establish the animal models for chronic kidney injury and its renal interstitial fibrosis. As an endogenous substance, adenine-induced kidney damage has not yet been fully studied and elucidated, except for inflammatory reaction. Here we analyzed the proteomics of kidney of rats after adenine overloading using LS-MS/MS assay, and observed the role of anemoside B4(B4). The results showed that adenine could down-regulate 285 proteins and up-regulate 164 proteins in rat kidney tissue compared with the normal group. Down-regulated proteins mainly affected related pathways, such as energy metabolism, while up-regulated proteins affected inflammatory response pathways and metabolic pathways. B4 could significantly reverse the down-regulation of about 40 proteins, which were involved in mitochondria, redox processes, extracellular exosomes, acetylation and other signaling pathways. Simultaneously, B4 could inhibit the up-regulation of five proteins caused by adenine, which were involved in cell cycle, oocyte meiosis, PI3 K-Akt and other signaling pathways. Further experimental results of mRNA expression using real-time PCR assay supported the proteomic analysis. Therefore, we proposed that the damage of rat kidney caused by adenine was more complicated, not only with an inflammatory reaction, but also with extensive effects to various metabolic processes in the body. This work provided a valuable clue for comprehensive understanding of adenine-induced renal damage.展开更多
AIM:To identify different metabolites,proteins and related pathways to elucidate the causes of proliferative diabetic retinopathy(PDR)and resistance to anti-vascular endothelial growth factor(VEGF)drugs,and to provide...AIM:To identify different metabolites,proteins and related pathways to elucidate the causes of proliferative diabetic retinopathy(PDR)and resistance to anti-vascular endothelial growth factor(VEGF)drugs,and to provide biomarkers for the diagnosis and treatment of PDR.METHODS:Vitreous specimens from patients with diabetic retinopathy were collected and analyzed by Liquid Chromatography-Mass Spectrometry(LC-MS/MS)analyses based on 4D label-free technology.Statistically differentially expressed proteins(DEPs),Gene Ontology(GO),Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway representation and protein interactions were analyzed.RESULTS:A total of 12 samples were analyzed.The proteomics results showed that a total of 58 proteins were identified as DEPs,of which 47 proteins were up-regulated and 11 proteins were down-regulated.We found that C1q and tumor necrosis factor related protein 5(C1QTNF5),Clusterin(CLU),tissue inhibitor of metal protease 1(TIMP1)and signal regulatory protein alpha(SIRPα)can all be specifically regulated after aflibercept treatment.GO functional analysis showed that some DEPs are related to changes in inflammatory regulatory pathways caused by PDR.In addition,protein-protein interaction(PPI)network evaluation revealed that TIMP1 plays a central role in neural regulation.In addition,CD47/SIRPαmay become a key target to resolve anti-VEGF drug resistance in PDR.CONCLUSION:Proteomic analysis is an approach of choice to explore the molecular mechanisms of PDR.Our data show that multiple proteins are differentially changed in PDR patients after intravitreal injection of aflibercept,among which C1QTNF5,CLU,TIMP1 and SIRPαmay become targets for future treatment of PDR and resolution of anti-VEGF resistance.展开更多
AIM:To identify metabolites,proteins,and related pathways involved in the etiology of rhegmatogenous retinal detachment(RRD)for use as biomarkers in diagnosing and treating RRD.METHODS:Vitreous specimens were collecte...AIM:To identify metabolites,proteins,and related pathways involved in the etiology of rhegmatogenous retinal detachment(RRD)for use as biomarkers in diagnosing and treating RRD.METHODS:Vitreous specimens were collected and liquid chromatography-tandem mass spectrometry analysis was per formed using the four-dimensional label-free technique.Statistically significant differentially expressed proteins,gene ontology(GO)terms,Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway representations,and protein interactions were analyzed.RESULTS:Nine specimens were subjected to proteomic analysis.In total,161 proteins were identified as differentially expressed proteins(DEPs),including 53 upregulated proteins and 108 downregulated proteins.GO functional analysis revealed that some DEPs were enriched in neuron-related terms and membrane protein terms.Moreover,KEGG analysis indicated that the cell adhesion molecule metabolic pathway was associated with the greatest number of DEPs.Finally,the evaluation of protein-protein interaction network revealed that DEPs were clustered in neuronal adhesion,apoptosis,inflammation and immune responses,correct protein folding,and glycolysis.CONCLUSION:Proteomic profiling is useful for the exploration of molecular mechanisms that underlie RRD.This study reveals increased expression levels of proteins related to heat shock protein content,glycolysis,and inflammatory responses in RRD.Knowledge regarding biomarkers of RRD pathogenesis may help to prevent the occurrence of RRD in the future.展开更多
Apis mellifera filamentous virus(Am FV)is a large DNA virus that is endemic in honeybee colonies.The genome sequence of the Am FV Swiss isolate(Am FV CH–C05)has been reported,but so far very few molecular studies hav...Apis mellifera filamentous virus(Am FV)is a large DNA virus that is endemic in honeybee colonies.The genome sequence of the Am FV Swiss isolate(Am FV CH–C05)has been reported,but so far very few molecular studies have been conducted on this virus.In this study,we isolated and purified Am FV(Am FV CN)from Chinese honeybee(Apis mellifera)colonies and elucidated its genomics and proteomics.Electron microscopy showed ovoid purified virions with dimensions of 300–500×210–285 nm,wrapping a 3165×40 nm filamentous nucleocapsid in three figure-eight loops.Unlike Am FV CH–C05,which was reported to have a circular genome,our data suggest that Am FV CN has a linear genome of approximately 493 kb.A total of 197 ORFs were identified,among which36 putative genes including 18 baculoviral homologs were annotated.The overall nucleotide similarity between the CN and CH–C05 isolates was 96.9%.Several ORFs were newly annotated in Am FV CN,including homologs of per os infectivity factor 4(PIF4)and a putative integrase.Phylogenomic analysis placed Am FVs on a separate branch within the newly proposed virus class Naldaviricetes.Proteomic analysis revealed 47 Am FV virionassociated proteins,of which 14 had over 50%sequence coverage,suggesting that they are likely to be main structural proteins.In addition,all six of the annotated PIFs(PIF-0–5)were identified by proteomics,suggesting that they may function as entry factors in Am FV infection.This study provides fundamental information regarding the molecular biology of Am FV.展开更多
OBJECTIVE:To analyze the effect and molecular mechanism of Gehua Jiejiu Dizhi decoction(葛花解酒涤脂汤,GJDD)on alcoholic fatty live disease(AFLD)by using proteomic methods.METHODS:The male C57BL/6J mouse were randomly...OBJECTIVE:To analyze the effect and molecular mechanism of Gehua Jiejiu Dizhi decoction(葛花解酒涤脂汤,GJDD)on alcoholic fatty live disease(AFLD)by using proteomic methods.METHODS:The male C57BL/6J mouse were randomly divided into four groups:control group,model group,GJDD group and resveratrol group.After the AFLD model was successfully prepared by intragastric administration of alcohol once on the basis of the Lieber-DeCarli classical method,the GJDD group and resveratrol group were intragastrically administered with GJDD(4900 mg/kg)and resveratrol(400 mg/kg)respectively,once a day for 9 d.The fat deposition of liver tissue was observed and evaluated by oil red O(ORO)staining.4DLabel-free quantitative proteome method was used to determine and quantify the protein expression in liver tissue of each experimental group.The differentially expressed proteins were screened according to protein expression differential multiples,and then analyzed by Gene ontology classification and Kyoto Encyclopedia of Genes and Genomes pathway enrichment.Finally,expression validation of the differentially co-expressed proteins from control group,model group and GJDD group were verified by targeted proteomics quantification techniques.RESULTS:In semiquantitative analyses of ORO,all kinds of steatosis(ToS,MaS,and MiS)were evaluated higher in AFLD mice compared to those in GJDD or resveratroltreated mice.4DLabel-free proteomics analysis results showed that a total of 4513 proteins were identified,of which 3763 proteins were quantified and 946 differentially expressed proteins were screened.Compared with the control group,145 proteins were up-regulated and 148 proteins were down-regulated in the liver tissue of model group.In addition,compared with the model group,92 proteins were up-regulated and 135 proteins were downregulated in the liver tissue of the GJDD group.15 differentially co-expressed proteins were found between every two groups(model group vs control group,GJDD group vs model group and GJDD group vs control group),which were involved in many biological processes.Among them,11 differentially co-expressed key proteins(Aox3,H1-5,Fabp5,Ces3a,Nudt7,Serpinb1a,Fkbp11,Rpl22l1,Keg1,Acss2 and Slco1a1)were further identified by targeted proteomic quantitative technology and their expression patterns were consistent with the results of 4D label-free proteomic analysis.CONCLUSIONS:Our study provided proteomics-based evidence that GJDD alleviated AFLD by modulating liver protein expression,likely through the modulation of lipid metabolism,bile acid metabolism and with exertion of antioxidant stress.展开更多
BACKGROUND： To date, a complete protein expression profile of the midbrain substantia nigra in a mouse model of chronic Parkinson＇s disease, induced by 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine （MPTP）, does ...BACKGROUND： To date, a complete protein expression profile of the midbrain substantia nigra in a mouse model of chronic Parkinson＇s disease, induced by 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine （MPTP）, does not exist. In addition, there are no reports of analysis of differential protein expression. OBJECTIVE： To separate and evaluate MPTP-induced differential protein expression through the use of proteomics in the substantia nigra of a mouse model of chronic Parkinson＇s disease. DESIGN： Randomized controlled animal study. SETTING： Department of Neurology, the First Affiliated Hospital, Chongqing Medical University. MATERIALS： Sixteen 8-10-week old, healthy, male, C57BL mice, weighing 20-25 g, and of clean grade, were provided by the Experimental Animal Center of Chongqing Medical University. The experimental animals were disposed according to ethical criteria. MPTP was provided by Sigma Company, USA; Pdquest 2D image analysis software and gelatum/irradiance image analysis system （ChemiDoc XRS） by Bio-Rad, USA; and Voyager DE-PROMALD1-TOF-MS mass spectroscopy analyzer by AB1 Company, USA. METHODS： This study was performed in Chongqing Neurological Laboratory between November 2006 and July 2007. Mice were randomly divided into model and control groups, with 8 mice in each group. Mice in the model group were received a subcutaneous injection of MPTP （25 mg＆g）, twice a week, for five successive weeks, to establish a chronic Parkinson＇s disease model. Mice in the control group received the same volume of a subcutaneous saline injection at the same time points. Mice were sacrificed by anesthesia to rapidly obtain the midbrain for protein separation of the substantia nigra. MAIN OUTCOME MEASURES： （1） 2-ED handbook （Bio-Rad Company） was referenced for two-dimensional electrophoresis, （2） PDQUEST8,0 analytical electrophoresis pattern was adopted to evaluate differential protein expression. （3） Peptide mass finger print map and data were retrieved on http：//www.prospector.ucsf.edu to compare differential substantia nigral protein expression in the two groups. RESULTS： Two-dimensional gel electrophoresis of substantia nigra tissue indicated that there were 33 differential protein expressions between the two groups. Three new proteins were evaluated, including α -enolase, which exhibited regulated expression, tumor necrosis factor ligand superfamily member 4, and cyclin-dependent kinase inhibitor 1B. CONCLUSION： There are three proteins that exhibit differential expression in the substantia nigra- α -enolase, tumor necrosis factor ligand superfamily member 4, and cyclin-dependent kinase inhibitor 1B.展开更多
AIM:To develop lymph node metastasis(LNM)-associated biomarkers for colorectal cancer(CRC) using quantitative proteome analysis.METHODS:Differences in protein expression between primary CRC with LNM(LNM CRC) and witho...AIM:To develop lymph node metastasis(LNM)-associated biomarkers for colorectal cancer(CRC) using quantitative proteome analysis.METHODS:Differences in protein expression between primary CRC with LNM(LNM CRC) and without LNM(non-LNM CRC) were assessed using methyl esterification stable isotope labeling coupled with 2D liquid chromatography followed by tandem mass spectrometry(2D-LC-MS/MS).The relationship to clinicopathological parameters and prognosis of candidate biomarkers was examined using an independent sample set.RESULTS:Forty-three proteins were found to be differentially expressed by at least 2.5-fold in two types of CRC.S100A4 was significantly upregulated in LNM CRC compared with non-LNM CRC,which was confirmed by Western blotting,immunohistochemistry and real-time quantitative polymerase chain reaction.Further immunohistochemistry on another 112 CRC cases showed that overexpression of S100A4 frequently existed in LNM CRC compared with non-LNM CRC(P < 0.001).Overexpression of S100A4 was significantly associated with LNM(P < 0.001),advanced TNM stage(P < 0.001),increased 5-year recurrence rate(P < 0.001) and decreased 5-year overall survival rate(P < 0.001).Univariate and multivariate analyses indicated that S100A4 expression was an independent prognostic factor for recurrence and survival of CRC patients(P < 0.05).CONCLUSION:S100A4 might serve as a powerful biomarker for LNM and a prognostic factor in CRC.展开更多
Non-small cell lung cancer(NSCLC)is a malignant tumor with high incidence worldwide.Triptolide(TP),extracted from Tripterygium wilfordii Hook F,exhibits potent broad-spectrum antitumor activity.Although some mechanism...Non-small cell lung cancer(NSCLC)is a malignant tumor with high incidence worldwide.Triptolide(TP),extracted from Tripterygium wilfordii Hook F,exhibits potent broad-spectrum antitumor activity.Although some mechanisms through which TP inhibits NSCLC are well understood,those that involve ribosomal proteins remain yet to be understood.In this study,the transcriptome and proteome were integrated and analyzed.Our data indicated ribosomal protein L4(RPL4)to be a core hub protein in the protein-protein interaction network.RPL4 is overexpressed in NSCLC tissues and cells.Transfection with siRPL4 or TP treatment alone arrested the cell cycle in the G1 phase,induced cell apoptosis,and repressed cell invasion.Compared to treating cells with TP alone or siRPL4,treating them with siRPL4–TP enhanced the inhibition of NSCLC cells.Reduced RPL4 expression reinforced the inhibitory effects of TP on NSCLC cells by disrupting the MDM2-P53 pathway and by altering the expression of PARP1/Snail/cyclin D1.In vivo assays verified that TP induced cell apoptosis and reduced RPL4 expression in xenografts.These findings provide clues to facilitate the development of effective TP-based therapeutic strategies to kill NSCLC cells.展开更多
AIM:To explore the therapeutic effect and main molecular mechanisms of acteoside in a glaucoma model in DBA/2J mice.METHODS:Proteomics was used to compare the differentially expressed proteins of C57 and DBA/2J mice.A...AIM:To explore the therapeutic effect and main molecular mechanisms of acteoside in a glaucoma model in DBA/2J mice.METHODS:Proteomics was used to compare the differentially expressed proteins of C57 and DBA/2J mice.After acteoside administration in DBA/2J mice,anterior segment observation,intraocular pressure(IOP)monitoring,electrophysiology examination,and hematoxylin and eosin staining were used to analyze any potential effects.Immunohistochemistry(IHC)assays were used to verify the proteomics results.Furthermore,retinal ganglion cell 5(RGC5)cell proliferation was assessed with cell counting kit-8(CCK-8)assays.Serta domain-containing protein 4(Sertad4)mRNA and protein expression levels were measured by qRT-PCR and Western blot analysis,respectively.RESULTS:Proteomics analysis suggested that Sertad4 was the most significantly differentially expressed protein.Compared with the saline group,the acteoside treatment group showed decreased IOP,improved N1-P1 wave amplitudes,thicker retina,and larger numbers of cells in the ganglion cell layer(GCL).The IHC results showed that Sertad4 expression levels in DBA/2J mice treated with acteoside were significantly lower than in the saline group.Acteoside treatment could improve RGC5 cell survival and reduce the Sertad4 mRNA and protein expression levels after glutamate injury.CONCLUSION:Sertad4 is differentially expressed in DBA/2J mice.Acteoside can protect RGCs from damage,possibly through the downregulation of Sertad4,and has a potential use in glaucoma treatment.展开更多
In plants,heteromorphic self-incompatibility(HetSI)is a strategy for avoiding self-pollination and promoting outcrossing,and during this process,numerous protein-protein interaction events occur between the pistil and...In plants,heteromorphic self-incompatibility(HetSI)is a strategy for avoiding self-pollination and promoting outcrossing,and during this process,numerous protein-protein interaction events occur between the pistil and pollen.Previous studies in Primula and Fagopyrum that focused on HetSI systems have provided interesting insights;however,the molecular mechanism underlying HetSI remains largely unknown.In this study,we profiled the proteome of Plumbago auriculata stigmas before and after self-incompatible(SI)and self-compatible(SC)pollination.Comparative analyses were conducted by 4D-DIA(Four-dimensional data independent acquisition),a promising technology that increases the sensitivity and reduces the spectral complexity of proteomic analysis by adding a fourth dimension,ion mobility.The results revealed 33387 peptides and 5311 proteins in all samples.The pathways in which the differentially expressed proteins(DEPs)identified in the P×P(Pin style self-pollinated with pin pollen)vs.PS(Pin style)and T×T(Thrum style self-pollinated with thrum pollen)vs.TS(Thrum style)comparisons were significantly enriched were biosynthesis of secondary metabolites and pentose and glucuronate interconversions.In the P×T(Pin style cross-pollinated with thrum pollen)vs.PS and T×P(Thrum style cross-pollinated with pin pollen)vs.TS comparison,the top three pathways were biosynthesis of secondary metabolites,pentose and glucuronate interconversions,and phenylpropanoid biosynthesis.The phenylpropanoid biosynthesis,cutin,suberine and wax biosynthesis,and flavonoid biosynthesis pathways were enriched in the P×T vs.P×P comparison,and starch and sucrose metabolism,glycerophospholipid metabolism,and alpha-linolenic acid metabolism were abundant in the T×T vs.T×P comparison.The enriched pathways between PS and TS were the biosynthesis of secondary metabolites,phenylpropanoid biosynthesis,and pentose and glucuronate interconversion.Self-incompatibility protein S1(SI S1),Mitogen-activated protein kinase 3/4(MPK3/4),Mitogen-activated protein kinase kinase 2/3(M2K2/3),Exocyst complex component EXO70A1(E70A1)and Thioredoxin H1/2(TRXH1/2)were found to be HetSI-related candidates,and O-fucosyltransferase 23(OFT23),3-ketoacyl-CoA synthase 6(KCS6),Receptor-like protein kinase FERONIA(FERON),Fimbrin-5(FIMB5),Pollen-specific leucine-rich repeat extensin-like protein 4(PLRX4),Transcription initiation factor IIB-2(TF2B2)and Pectinesterase 1(AL11A),etc.,were identified as other regulatory transducers.These findings combined with our morphological and reactive oxygen species(ROS)intensity analyses indicate that P.auriculata has typical dry-stigmas and that the HetSI mechanism might differ between the pin and thrum.SI S1 might be the key factor in HetSI,and ROS are overexpressed during SC pollination to rapidly activate the mitogen-activated protein kinase(MAPK)-mediated phosphorylation of E70A1 to maintain stigma receptivity in plants with HetSI.展开更多
Studying the genetic basis and regulatory mechanism of chrysanthemum lateral bud outgrowth is of great significance for reduction the production cost of cut chrysanthemum.To clarify the molecular basis of lateral bud ...Studying the genetic basis and regulatory mechanism of chrysanthemum lateral bud outgrowth is of great significance for reduction the production cost of cut chrysanthemum.To clarify the molecular basis of lateral bud elongation after removal of apical dominance in chrysanthemum,label-free quantification analysis was used to analyze the proteome changes after apical bud removal.Quantitative real-time PCR(qPCR)was used to analyze the changes in the expression of three plant hormone-related genes.A total of 440 differentially expressed proteins were successfully identified at three time points during the lateral bud elongation.The number of differentially expressed proteins in the three stages(24 h/0 h,48 h/0 h,48 h/24 h)were 219,332,and 97,respectively.The difference in expressed proteins in the three comparison stages mainly involves RNA processing and modification;translation,ribosomal structure and biogenesis;Posttranslational modification,protein turnover,and chaperones.Path analysis showed that there was various physiological activities in the process of lateral bud dormancy breaking and elongation,which involved energy metabolism,biosynthesis,signal transduction and stress response in the growth process of lateral buds.qPCR indicated that the expression of cytokinin synthesis related gene was significantly increased after the removal of apical dominance,while the expression of strigolactones synthesis related gene experiences a dramatic fall to promote the development of the lateral buds.However,there was a drop before a slight increase in the expression of the auxin synthesis related gene,which was mainly due to the removal of apical dominance that led to the loss of indoleacetic acid in the main stem.However,with formation of the new apical source,indoleacetic acid can be released again.展开更多
In order to explore the salt tolerance mechanism of Bacillus cereus LBR-4 with salinity of 14%NaCl,differential proteomic analysis of the whole protein of LBR-4 strain expressed under 14%NaCl high salinity condition a...In order to explore the salt tolerance mechanism of Bacillus cereus LBR-4 with salinity of 14%NaCl,differential proteomic analysis of the whole protein of LBR-4 strain expressed under 14%NaCl high salinity condition and normalculture condition(1%NaCl)was studied by two-dimensional electrophoresis and mass spectrometry.The isoelectric point of most detected proteins was between pH 4-7 and the molecular weight distribution was 10-70 ku.Compared with the normal culture condition,the expression level of 118 protein spots in the whole protein expression map changed significantly(accounting for 25.2%of the total protein spots).The expression level of 78 protein spots increased significantly,including 22 new protein spots that appeared under high salt stress.The expression levels of 40 protein spots decreased significantly,including 18 protein spots that disappeared under high salt stress.By mass spectrometry,six distinct differentially expressed protein spotswere dihydroxy acid dehydratase,cell division protein FtsZ,iron sulfur cluster synthesis protein SufD,unknown carboxylase YngE,hypothetical acetaldehyde dehydrogenase DhaS and phenylalanine acid tRNA ligase alpha subunit.It was speculated that under high salt stress,the cells had protective measures and the secretion of intracellular compatible solutes increased.The iron and sulfur clusters involved in various physiological reactions also activated the stressful suf synthesis pathway,and therate of cell division and reproduction was also slowed down and ensured the normal progress of physiological reactions inthe cells.展开更多
基金National Innovative Drugs 13th Five-Year Major Special Project of China(Grant No.2018ZX09301030-002)
文摘Adenine is commonly used to establish the animal models for chronic kidney injury and its renal interstitial fibrosis. As an endogenous substance, adenine-induced kidney damage has not yet been fully studied and elucidated, except for inflammatory reaction. Here we analyzed the proteomics of kidney of rats after adenine overloading using LS-MS/MS assay, and observed the role of anemoside B4(B4). The results showed that adenine could down-regulate 285 proteins and up-regulate 164 proteins in rat kidney tissue compared with the normal group. Down-regulated proteins mainly affected related pathways, such as energy metabolism, while up-regulated proteins affected inflammatory response pathways and metabolic pathways. B4 could significantly reverse the down-regulation of about 40 proteins, which were involved in mitochondria, redox processes, extracellular exosomes, acetylation and other signaling pathways. Simultaneously, B4 could inhibit the up-regulation of five proteins caused by adenine, which were involved in cell cycle, oocyte meiosis, PI3 K-Akt and other signaling pathways. Further experimental results of mRNA expression using real-time PCR assay supported the proteomic analysis. Therefore, we proposed that the damage of rat kidney caused by adenine was more complicated, not only with an inflammatory reaction, but also with extensive effects to various metabolic processes in the body. This work provided a valuable clue for comprehensive understanding of adenine-induced renal damage.
基金Supported by Tianjin Key Medical Discipline Specialty Construction Project(No.TJYXZDXK-016A)Henan Provincial Department of Science and Technology(No.LHGJ20200802).
文摘AIM:To identify different metabolites,proteins and related pathways to elucidate the causes of proliferative diabetic retinopathy(PDR)and resistance to anti-vascular endothelial growth factor(VEGF)drugs,and to provide biomarkers for the diagnosis and treatment of PDR.METHODS:Vitreous specimens from patients with diabetic retinopathy were collected and analyzed by Liquid Chromatography-Mass Spectrometry(LC-MS/MS)analyses based on 4D label-free technology.Statistically differentially expressed proteins(DEPs),Gene Ontology(GO),Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway representation and protein interactions were analyzed.RESULTS:A total of 12 samples were analyzed.The proteomics results showed that a total of 58 proteins were identified as DEPs,of which 47 proteins were up-regulated and 11 proteins were down-regulated.We found that C1q and tumor necrosis factor related protein 5(C1QTNF5),Clusterin(CLU),tissue inhibitor of metal protease 1(TIMP1)and signal regulatory protein alpha(SIRPα)can all be specifically regulated after aflibercept treatment.GO functional analysis showed that some DEPs are related to changes in inflammatory regulatory pathways caused by PDR.In addition,protein-protein interaction(PPI)network evaluation revealed that TIMP1 plays a central role in neural regulation.In addition,CD47/SIRPαmay become a key target to resolve anti-VEGF drug resistance in PDR.CONCLUSION:Proteomic analysis is an approach of choice to explore the molecular mechanisms of PDR.Our data show that multiple proteins are differentially changed in PDR patients after intravitreal injection of aflibercept,among which C1QTNF5,CLU,TIMP1 and SIRPαmay become targets for future treatment of PDR and resolution of anti-VEGF resistance.
文摘AIM:To identify metabolites,proteins,and related pathways involved in the etiology of rhegmatogenous retinal detachment(RRD)for use as biomarkers in diagnosing and treating RRD.METHODS:Vitreous specimens were collected and liquid chromatography-tandem mass spectrometry analysis was per formed using the four-dimensional label-free technique.Statistically significant differentially expressed proteins,gene ontology(GO)terms,Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway representations,and protein interactions were analyzed.RESULTS:Nine specimens were subjected to proteomic analysis.In total,161 proteins were identified as differentially expressed proteins(DEPs),including 53 upregulated proteins and 108 downregulated proteins.GO functional analysis revealed that some DEPs were enriched in neuron-related terms and membrane protein terms.Moreover,KEGG analysis indicated that the cell adhesion molecule metabolic pathway was associated with the greatest number of DEPs.Finally,the evaluation of protein-protein interaction network revealed that DEPs were clustered in neuronal adhesion,apoptosis,inflammation and immune responses,correct protein folding,and glycolysis.CONCLUSION:Proteomic profiling is useful for the exploration of molecular mechanisms that underlie RRD.This study reveals increased expression levels of proteins related to heat shock protein content,glycolysis,and inflammatory responses in RRD.Knowledge regarding biomarkers of RRD pathogenesis may help to prevent the occurrence of RRD in the future.
基金the Open Research Fund Program of the State Key Laboratory of Virology of China(Grant No.2019IOV004)the key Research Program of Frontier Sciences of Chinese Academy of Sciences(Grant No.QYZDJ-SSW-SMC021)the National Natural Science Foundation of China(Grant No.31900154 and 31572471)。
文摘Apis mellifera filamentous virus(Am FV)is a large DNA virus that is endemic in honeybee colonies.The genome sequence of the Am FV Swiss isolate(Am FV CH–C05)has been reported,but so far very few molecular studies have been conducted on this virus.In this study,we isolated and purified Am FV(Am FV CN)from Chinese honeybee(Apis mellifera)colonies and elucidated its genomics and proteomics.Electron microscopy showed ovoid purified virions with dimensions of 300–500×210–285 nm,wrapping a 3165×40 nm filamentous nucleocapsid in three figure-eight loops.Unlike Am FV CH–C05,which was reported to have a circular genome,our data suggest that Am FV CN has a linear genome of approximately 493 kb.A total of 197 ORFs were identified,among which36 putative genes including 18 baculoviral homologs were annotated.The overall nucleotide similarity between the CN and CH–C05 isolates was 96.9%.Several ORFs were newly annotated in Am FV CN,including homologs of per os infectivity factor 4(PIF4)and a putative integrase.Phylogenomic analysis placed Am FVs on a separate branch within the newly proposed virus class Naldaviricetes.Proteomic analysis revealed 47 Am FV virionassociated proteins,of which 14 had over 50%sequence coverage,suggesting that they are likely to be main structural proteins.In addition,all six of the annotated PIFs(PIF-0–5)were identified by proteomics,suggesting that they may function as entry factors in Am FV infection.This study provides fundamental information regarding the molecular biology of Am FV.
基金National Science Foundation-funded Project:the Study on the Changes of Energy Metabolism and Molecular Regulation Mechanism of Alcoholic Fatty Liver based on Sirtuins1-Adenosine Monophosphate-Activated Protein Kinase Signal System and the Intervention of Gehua Jiejiu dizhi decoction(No.81660752)Basic Research Project of Guizhou Provincial Science and Technology Plan:Study on the Mechanism of Sirtuins1 Mediated Deacetylation in the Regulation of Alcoholic Fatty Liver Metabolism and the Intervention of Gehua Jiejiu Dizhi Tang[QianKeHe Fundamentals-ZK[2023]General 410]。
文摘OBJECTIVE:To analyze the effect and molecular mechanism of Gehua Jiejiu Dizhi decoction(葛花解酒涤脂汤,GJDD)on alcoholic fatty live disease(AFLD)by using proteomic methods.METHODS:The male C57BL/6J mouse were randomly divided into four groups:control group,model group,GJDD group and resveratrol group.After the AFLD model was successfully prepared by intragastric administration of alcohol once on the basis of the Lieber-DeCarli classical method,the GJDD group and resveratrol group were intragastrically administered with GJDD(4900 mg/kg)and resveratrol(400 mg/kg)respectively,once a day for 9 d.The fat deposition of liver tissue was observed and evaluated by oil red O(ORO)staining.4DLabel-free quantitative proteome method was used to determine and quantify the protein expression in liver tissue of each experimental group.The differentially expressed proteins were screened according to protein expression differential multiples,and then analyzed by Gene ontology classification and Kyoto Encyclopedia of Genes and Genomes pathway enrichment.Finally,expression validation of the differentially co-expressed proteins from control group,model group and GJDD group were verified by targeted proteomics quantification techniques.RESULTS:In semiquantitative analyses of ORO,all kinds of steatosis(ToS,MaS,and MiS)were evaluated higher in AFLD mice compared to those in GJDD or resveratroltreated mice.4DLabel-free proteomics analysis results showed that a total of 4513 proteins were identified,of which 3763 proteins were quantified and 946 differentially expressed proteins were screened.Compared with the control group,145 proteins were up-regulated and 148 proteins were down-regulated in the liver tissue of model group.In addition,compared with the model group,92 proteins were up-regulated and 135 proteins were downregulated in the liver tissue of the GJDD group.15 differentially co-expressed proteins were found between every two groups(model group vs control group,GJDD group vs model group and GJDD group vs control group),which were involved in many biological processes.Among them,11 differentially co-expressed key proteins(Aox3,H1-5,Fabp5,Ces3a,Nudt7,Serpinb1a,Fkbp11,Rpl22l1,Keg1,Acss2 and Slco1a1)were further identified by targeted proteomic quantitative technology and their expression patterns were consistent with the results of 4D label-free proteomic analysis.CONCLUSIONS:Our study provided proteomics-based evidence that GJDD alleviated AFLD by modulating liver protein expression,likely through the modulation of lipid metabolism,bile acid metabolism and with exertion of antioxidant stress.
基金the National Natural Science Foundation of China, No. 30370499
文摘BACKGROUND： To date, a complete protein expression profile of the midbrain substantia nigra in a mouse model of chronic Parkinson＇s disease, induced by 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine （MPTP）, does not exist. In addition, there are no reports of analysis of differential protein expression. OBJECTIVE： To separate and evaluate MPTP-induced differential protein expression through the use of proteomics in the substantia nigra of a mouse model of chronic Parkinson＇s disease. DESIGN： Randomized controlled animal study. SETTING： Department of Neurology, the First Affiliated Hospital, Chongqing Medical University. MATERIALS： Sixteen 8-10-week old, healthy, male, C57BL mice, weighing 20-25 g, and of clean grade, were provided by the Experimental Animal Center of Chongqing Medical University. The experimental animals were disposed according to ethical criteria. MPTP was provided by Sigma Company, USA; Pdquest 2D image analysis software and gelatum/irradiance image analysis system （ChemiDoc XRS） by Bio-Rad, USA; and Voyager DE-PROMALD1-TOF-MS mass spectroscopy analyzer by AB1 Company, USA. METHODS： This study was performed in Chongqing Neurological Laboratory between November 2006 and July 2007. Mice were randomly divided into model and control groups, with 8 mice in each group. Mice in the model group were received a subcutaneous injection of MPTP （25 mg＆g）, twice a week, for five successive weeks, to establish a chronic Parkinson＇s disease model. Mice in the control group received the same volume of a subcutaneous saline injection at the same time points. Mice were sacrificed by anesthesia to rapidly obtain the midbrain for protein separation of the substantia nigra. MAIN OUTCOME MEASURES： （1） 2-ED handbook （Bio-Rad Company） was referenced for two-dimensional electrophoresis, （2） PDQUEST8,0 analytical electrophoresis pattern was adopted to evaluate differential protein expression. （3） Peptide mass finger print map and data were retrieved on http：//www.prospector.ucsf.edu to compare differential substantia nigral protein expression in the two groups. RESULTS： Two-dimensional gel electrophoresis of substantia nigra tissue indicated that there were 33 differential protein expressions between the two groups. Three new proteins were evaluated, including α -enolase, which exhibited regulated expression, tumor necrosis factor ligand superfamily member 4, and cyclin-dependent kinase inhibitor 1B. CONCLUSION： There are three proteins that exhibit differential expression in the substantia nigra- α -enolase, tumor necrosis factor ligand superfamily member 4, and cyclin-dependent kinase inhibitor 1B.
基金Supported by Shanghai Momentous Program,Grant No.07dz19505Shanghai Rising-star Program from the Science and Technology Commission of Shanghai Municipality,No.10QA1401400,China
文摘AIM:To develop lymph node metastasis(LNM)-associated biomarkers for colorectal cancer(CRC) using quantitative proteome analysis.METHODS:Differences in protein expression between primary CRC with LNM(LNM CRC) and without LNM(non-LNM CRC) were assessed using methyl esterification stable isotope labeling coupled with 2D liquid chromatography followed by tandem mass spectrometry(2D-LC-MS/MS).The relationship to clinicopathological parameters and prognosis of candidate biomarkers was examined using an independent sample set.RESULTS:Forty-three proteins were found to be differentially expressed by at least 2.5-fold in two types of CRC.S100A4 was significantly upregulated in LNM CRC compared with non-LNM CRC,which was confirmed by Western blotting,immunohistochemistry and real-time quantitative polymerase chain reaction.Further immunohistochemistry on another 112 CRC cases showed that overexpression of S100A4 frequently existed in LNM CRC compared with non-LNM CRC(P < 0.001).Overexpression of S100A4 was significantly associated with LNM(P < 0.001),advanced TNM stage(P < 0.001),increased 5-year recurrence rate(P < 0.001) and decreased 5-year overall survival rate(P < 0.001).Univariate and multivariate analyses indicated that S100A4 expression was an independent prognostic factor for recurrence and survival of CRC patients(P < 0.05).CONCLUSION:S100A4 might serve as a powerful biomarker for LNM and a prognostic factor in CRC.
基金supported by the National Natural Science Foundation of China(Grant Nos.82004007 and 81774026).
文摘Non-small cell lung cancer(NSCLC)is a malignant tumor with high incidence worldwide.Triptolide(TP),extracted from Tripterygium wilfordii Hook F,exhibits potent broad-spectrum antitumor activity.Although some mechanisms through which TP inhibits NSCLC are well understood,those that involve ribosomal proteins remain yet to be understood.In this study,the transcriptome and proteome were integrated and analyzed.Our data indicated ribosomal protein L4(RPL4)to be a core hub protein in the protein-protein interaction network.RPL4 is overexpressed in NSCLC tissues and cells.Transfection with siRPL4 or TP treatment alone arrested the cell cycle in the G1 phase,induced cell apoptosis,and repressed cell invasion.Compared to treating cells with TP alone or siRPL4,treating them with siRPL4–TP enhanced the inhibition of NSCLC cells.Reduced RPL4 expression reinforced the inhibitory effects of TP on NSCLC cells by disrupting the MDM2-P53 pathway and by altering the expression of PARP1/Snail/cyclin D1.In vivo assays verified that TP induced cell apoptosis and reduced RPL4 expression in xenografts.These findings provide clues to facilitate the development of effective TP-based therapeutic strategies to kill NSCLC cells.
基金Supported by Tianjin Key Medical Discipline(Specialty)Construction Project(No.TJYXZDXK-037A).
文摘AIM:To explore the therapeutic effect and main molecular mechanisms of acteoside in a glaucoma model in DBA/2J mice.METHODS:Proteomics was used to compare the differentially expressed proteins of C57 and DBA/2J mice.After acteoside administration in DBA/2J mice,anterior segment observation,intraocular pressure(IOP)monitoring,electrophysiology examination,and hematoxylin and eosin staining were used to analyze any potential effects.Immunohistochemistry(IHC)assays were used to verify the proteomics results.Furthermore,retinal ganglion cell 5(RGC5)cell proliferation was assessed with cell counting kit-8(CCK-8)assays.Serta domain-containing protein 4(Sertad4)mRNA and protein expression levels were measured by qRT-PCR and Western blot analysis,respectively.RESULTS:Proteomics analysis suggested that Sertad4 was the most significantly differentially expressed protein.Compared with the saline group,the acteoside treatment group showed decreased IOP,improved N1-P1 wave amplitudes,thicker retina,and larger numbers of cells in the ganglion cell layer(GCL).The IHC results showed that Sertad4 expression levels in DBA/2J mice treated with acteoside were significantly lower than in the saline group.Acteoside treatment could improve RGC5 cell survival and reduce the Sertad4 mRNA and protein expression levels after glutamate injury.CONCLUSION:Sertad4 is differentially expressed in DBA/2J mice.Acteoside can protect RGCs from damage,possibly through the downregulation of Sertad4,and has a potential use in glaucoma treatment.
基金Scientific Research Foundation of Science&Technology Department of Sichuan Province(2021YJ0497).
文摘In plants,heteromorphic self-incompatibility(HetSI)is a strategy for avoiding self-pollination and promoting outcrossing,and during this process,numerous protein-protein interaction events occur between the pistil and pollen.Previous studies in Primula and Fagopyrum that focused on HetSI systems have provided interesting insights;however,the molecular mechanism underlying HetSI remains largely unknown.In this study,we profiled the proteome of Plumbago auriculata stigmas before and after self-incompatible(SI)and self-compatible(SC)pollination.Comparative analyses were conducted by 4D-DIA(Four-dimensional data independent acquisition),a promising technology that increases the sensitivity and reduces the spectral complexity of proteomic analysis by adding a fourth dimension,ion mobility.The results revealed 33387 peptides and 5311 proteins in all samples.The pathways in which the differentially expressed proteins(DEPs)identified in the P×P(Pin style self-pollinated with pin pollen)vs.PS(Pin style)and T×T(Thrum style self-pollinated with thrum pollen)vs.TS(Thrum style)comparisons were significantly enriched were biosynthesis of secondary metabolites and pentose and glucuronate interconversions.In the P×T(Pin style cross-pollinated with thrum pollen)vs.PS and T×P(Thrum style cross-pollinated with pin pollen)vs.TS comparison,the top three pathways were biosynthesis of secondary metabolites,pentose and glucuronate interconversions,and phenylpropanoid biosynthesis.The phenylpropanoid biosynthesis,cutin,suberine and wax biosynthesis,and flavonoid biosynthesis pathways were enriched in the P×T vs.P×P comparison,and starch and sucrose metabolism,glycerophospholipid metabolism,and alpha-linolenic acid metabolism were abundant in the T×T vs.T×P comparison.The enriched pathways between PS and TS were the biosynthesis of secondary metabolites,phenylpropanoid biosynthesis,and pentose and glucuronate interconversion.Self-incompatibility protein S1(SI S1),Mitogen-activated protein kinase 3/4(MPK3/4),Mitogen-activated protein kinase kinase 2/3(M2K2/3),Exocyst complex component EXO70A1(E70A1)and Thioredoxin H1/2(TRXH1/2)were found to be HetSI-related candidates,and O-fucosyltransferase 23(OFT23),3-ketoacyl-CoA synthase 6(KCS6),Receptor-like protein kinase FERONIA(FERON),Fimbrin-5(FIMB5),Pollen-specific leucine-rich repeat extensin-like protein 4(PLRX4),Transcription initiation factor IIB-2(TF2B2)and Pectinesterase 1(AL11A),etc.,were identified as other regulatory transducers.These findings combined with our morphological and reactive oxygen species(ROS)intensity analyses indicate that P.auriculata has typical dry-stigmas and that the HetSI mechanism might differ between the pin and thrum.SI S1 might be the key factor in HetSI,and ROS are overexpressed during SC pollination to rapidly activate the mitogen-activated protein kinase(MAPK)-mediated phosphorylation of E70A1 to maintain stigma receptivity in plants with HetSI.
基金This work was supported by grants from the National Natural Science Foundation of China(Grant No.31800601).
文摘Studying the genetic basis and regulatory mechanism of chrysanthemum lateral bud outgrowth is of great significance for reduction the production cost of cut chrysanthemum.To clarify the molecular basis of lateral bud elongation after removal of apical dominance in chrysanthemum,label-free quantification analysis was used to analyze the proteome changes after apical bud removal.Quantitative real-time PCR(qPCR)was used to analyze the changes in the expression of three plant hormone-related genes.A total of 440 differentially expressed proteins were successfully identified at three time points during the lateral bud elongation.The number of differentially expressed proteins in the three stages(24 h/0 h,48 h/0 h,48 h/24 h)were 219,332,and 97,respectively.The difference in expressed proteins in the three comparison stages mainly involves RNA processing and modification;translation,ribosomal structure and biogenesis;Posttranslational modification,protein turnover,and chaperones.Path analysis showed that there was various physiological activities in the process of lateral bud dormancy breaking and elongation,which involved energy metabolism,biosynthesis,signal transduction and stress response in the growth process of lateral buds.qPCR indicated that the expression of cytokinin synthesis related gene was significantly increased after the removal of apical dominance,while the expression of strigolactones synthesis related gene experiences a dramatic fall to promote the development of the lateral buds.However,there was a drop before a slight increase in the expression of the auxin synthesis related gene,which was mainly due to the removal of apical dominance that led to the loss of indoleacetic acid in the main stem.However,with formation of the new apical source,indoleacetic acid can be released again.
基金Supported by Heilongjiang Province National Science Foundation(LH2020C007)。
文摘In order to explore the salt tolerance mechanism of Bacillus cereus LBR-4 with salinity of 14%NaCl,differential proteomic analysis of the whole protein of LBR-4 strain expressed under 14%NaCl high salinity condition and normalculture condition(1%NaCl)was studied by two-dimensional electrophoresis and mass spectrometry.The isoelectric point of most detected proteins was between pH 4-7 and the molecular weight distribution was 10-70 ku.Compared with the normal culture condition,the expression level of 118 protein spots in the whole protein expression map changed significantly(accounting for 25.2%of the total protein spots).The expression level of 78 protein spots increased significantly,including 22 new protein spots that appeared under high salt stress.The expression levels of 40 protein spots decreased significantly,including 18 protein spots that disappeared under high salt stress.By mass spectrometry,six distinct differentially expressed protein spotswere dihydroxy acid dehydratase,cell division protein FtsZ,iron sulfur cluster synthesis protein SufD,unknown carboxylase YngE,hypothetical acetaldehyde dehydrogenase DhaS and phenylalanine acid tRNA ligase alpha subunit.It was speculated that under high salt stress,the cells had protective measures and the secretion of intracellular compatible solutes increased.The iron and sulfur clusters involved in various physiological reactions also activated the stressful suf synthesis pathway,and therate of cell division and reproduction was also slowed down and ensured the normal progress of physiological reactions inthe cells.
