Sini Decoction(SNT)is a traditional formula recognized for its efficacy in warming the spleen and stomach and dispersing cold.However,elucidating the mechanism of action of SNT remains challenging due to its complex m...Sini Decoction(SNT)is a traditional formula recognized for its efficacy in warming the spleen and stomach and dispersing cold.However,elucidating the mechanism of action of SNT remains challenging due to its complex multiple components.This study utilized a synergistic approach combining two-dimensional fluorescence difference in gel electrophoresis(2D-DIGE)-based drug affinity responsive target stability(DARTS)with label-free quantitative proteomics techniques to identify the direct and indirect protein targets of SNT in myocardial infarction.The analysis identified 590 proteins,with 30 proteins showing significant upregulation and 51 proteins showing downregulation when comparing the SNT group with the model group.Through the integration of 2D-DIGE DARTS with proteomics data and pharmacological assessments,the findings indicate that protein disulfide-isomerase A3(PDIA3)may serve as a potential protein target through which SNT provides protective effects on myocardial cells during myocardial infarction.展开更多
An effective symbiosis between legumes and rhizobia relies largely on diverse proteins at the plantrhizobium interface for material transportation and signal transduction during symbiotic nitrogen fixation.Here,we rep...An effective symbiosis between legumes and rhizobia relies largely on diverse proteins at the plantrhizobium interface for material transportation and signal transduction during symbiotic nitrogen fixation.Here,we report a comprehensive proteome atlas of the soybean symbiosome membrane(SM),peribacteroid space(PBS),and root microsomal fraction(RMF)using state-of-the-art label-free quantitative proteomic technology.In total,1759 soybean proteins with diverse functions are detected in the SM,and 1476 soybean proteins and 369 rhizobial proteins are detected in the PBS.The diversity of SM proteins detected suggests multiple origins of the SM.Quantitative comparative analysis highlights amino acid metabolism and nutrient uptake in the SM,indicative of the key pathways in nitrogen assimilation.The detection of soybean secretory proteins in the PBS and receptor-like kinases in the SM provides evidence for the likely extracellular property of the symbiosome and the potential signaling communication between both symbionts at the symbiotic interface.Our proteomic data provide clues for how some of the sophisticated regulation between soybean and rhizobium at the symbiotic interface is achieved,and suggest approaches for symbiosis engineering.展开更多
Respiratory syncytial virus(RSV) is a leading cause of acute lower respiratory tract infections. Qingfei oral liquid(QFOL), a traditional Chinese medicine, is widely used in clinical treatment for RSV-induced pneumoni...Respiratory syncytial virus(RSV) is a leading cause of acute lower respiratory tract infections. Qingfei oral liquid(QFOL), a traditional Chinese medicine, is widely used in clinical treatment for RSV-induced pneumonia. The present study was designed to reveal the potential targets and mechanism of action for QFOL by exploring its influence on the host cellular network following RSV infection. We investigated the serum proteomic changes and potential biomarkers in an RSV-infected mouse pneumonia model treated with QFOL. Eighteen BALB/c mice were randomly divided into three groups: RSV pneumonia model group(M), QFOL-treated group(Q) and the control group(C). Serum proteomes were analyzed and compared using a label-free quantitative LC-MS/MS approach. A total of 172 protein groups, 1009 proteins, and 1073 unique peptides were successfully identified. 51 differentially expressed proteins(DEPs) were identified(15 DEPs when M/C and 43 DEPs when Q/M; 7 DEPs in common). Classification and interaction network showed that these proteins participated in various biological processes including immune response, blood coagulation, complement activation, and so forth. Particularly, fibrinopeptide B(FpB) and heparin cofactor Ⅱ(HCII) were evaluated as important nodes in the interaction network, which was closely involved in coagulation and inflammation. Further, the Fp B level was increased in Group M but decreased in Group Q, while the HCII level exhibited the opposite trend. These findings not only indicated FpB and HCII as potential biomarkers and targets of QFOL in the treatment of RSV pneumonia, but also suggested a regulatory role of QFOL in the RSV-induced disturbance of coagulation and inflammation-coagulation interactions.展开更多
Inflammation is a defense mechanism associated with a wide range of diseases.Celastrol is a small molecule isolated from traditional Chinese medicine with potent anti-inflammation activity.In this study,we established...Inflammation is a defense mechanism associated with a wide range of diseases.Celastrol is a small molecule isolated from traditional Chinese medicine with potent anti-inflammation activity.In this study,we established an integrated quantitative proteomics strategy to investigate the acute response to celastrol treatment in a rat macrophage cell line challenged with lipopolysaccharide(LPS).Both stableisotopic based non-targeted quantitative profiling and PRM-based targeted quantitation methods were employed.Dimethyl-labeling based non-targeted profiling revealed 28 and 52 proteins that significantly up-and down-regulated by celastrol.Bioinformatics analysis pinpoint key signaling pathways affected.Seven proteins were selected for examining their time-dependent regulatory pattern in response to celastrol using targeted PRM quantitation.The abundance of mRNA at multiple time-points of selected proteins was also examined.Celastrol induced an acute response of selected key transcriptional factors in terms of mRNA or protein abundance within one hour.Interestingly,regulatory trend of mRNA and protein abundance suggested a novel dual mechanism of celastrol in the terms of acute antiinflammation.The integrated quantitative proteomic strategy established in this study constitutes an efficient workflow to characterize key components and their time-dependent regulatory pattern for monitoring drug response.展开更多
Dinofl agellates are the major causative agents of harmful algal blooms in the global ocean and they usually form blooms under conditions of very low dissolved inorganic phosphorus(DIP).However,the mechanisms underpin...Dinofl agellates are the major causative agents of harmful algal blooms in the global ocean and they usually form blooms under conditions of very low dissolved inorganic phosphorus(DIP).However,the mechanisms underpinning the dinofl agellate blooms remain unclear.Here,we quantitatively compared protein expression profi les of a marine dinofl agellate,Prorocentrum donghaiense,grown in inorganic P-replete,P-defi cient,and DIP-and dissolved organic phosphorus(DOP)-resupplied conditions by employing a Tandem Mass Tag(TMT)-based quantitative proteomic approach.Proteins involved in intracellular P reallocation,organic P,and non-P lipid utilization were up-regulated under the P-defi cient condition,while inorganic phosphate transporters varied insignifi cantly.In response to the P resupplementation,nitrogen metabolism,ribosome,porphyrin,and chlorophyll metabolism were up-regulated,while lysosome,and starch and sucrose metabolism were down-regulated.Notably,photosynthesis was up-regulated and secondary metabolism was down-regulated only in the DIP-resupplied cells,whereas amino acid metabolism and vitamin B6 metabolism were up-regulated in the DOP-resupplied cells,indicating diff erential response mechanisms of P.donghaiense to DIP or DOP resupplementation.Our results indicated that P.donghaiense initiated multiple strategies in response to an ambient inorganic P-defi ciency,and its efficient DOP assimilation by providing both P and carbon sources might be a key factor driving bloom formations of P.donghaiense in a low DIP environment.展开更多
Enhancing photosynthesis efficiency is considered as one of the most crucial targets during wheat breeding.However,the molecular basis underlying high photosynthesis efficiency is not well understood up to now.In this...Enhancing photosynthesis efficiency is considered as one of the most crucial targets during wheat breeding.However,the molecular basis underlying high photosynthesis efficiency is not well understood up to now.In this study,we investigated the protein expression profile of wheat Jimai5265yg mutant,which is a yellow-green mutant with chlorophylls b deficiency but high photosynthesis efficiency.Though TMT-labeling quantitative proteomics analysis,a total of 72 differential expressed proteins(DEPs)were obtained between the mutant and wild type(WT).GO analysis found that they significantly enriched in thylakoid membrane,pigment binding,magnesium chelatase activity and response to light intensity.KEGG analysis showed that they involved in photosynthesis-antenna protein as well as porphyrin and chlorophyll metabolism.Finally,118 RNA editing events were found between mutant and WT genotype.The A to C editing in the 3-UTR of TraesCS6D02G401500 lead to its high expression in mutant through removing the inhibition of tae-miR9781,which might have vital role in regulating the yellow-green mutant.This study provided some useful clues about the molecular basis of Jimai5265yg mutant as well as chlorophylls metabolism in wheat.展开更多
In the past decade,relative proteomic quantification using isobaric labeling technology has developed into a key tool for comparing the expression of proteins in biological samples.Although its multiplexing capacity a...In the past decade,relative proteomic quantification using isobaric labeling technology has developed into a key tool for comparing the expression of proteins in biological samples.Although its multiplexing capacity and flexibility make this a valuable technology for addressing various biological questions,its quantitative accuracy and precision still pose significant challenges to the reliability of its quantification results.Here,we give a detailed overview of the different kinds of isobaric mass tags and the advantages and disadvantages of the isobaric labeling method.We also discuss which precautions should be taken at each step of the isobaric labeling workflow,to obtain reliable quantification results in large-scale quantitative proteomics experiments.In the last section,we discuss the broad applications of the isobaric labeling technology in biological and clinical studies,with an emphasis on thermal proteome profiling and proteogenomics.展开更多
The local microenvironment is essential to stem cell-based therapy for ischemic stroke,and spatiotemporal changes of the microenvironment in the pathological process provide vital clues for understanding the therapeut...The local microenvironment is essential to stem cell-based therapy for ischemic stroke,and spatiotemporal changes of the microenvironment in the pathological process provide vital clues for understanding the therapeutic mechanisms.However,relevant studies on microenvironmental changes were mainly confined in the acute phase of stroke,and long-term changes remain unclear.This study aimed to investigate the microenvironmental changes in the subacute and chronic phases of ischemic stroke after stem cell transplantation.Herein,induced pluripotent stem cells(iPSCs)and neural stem cells(NSCs)were transplanted into the ischemic brain established by middle cerebral artery occlusion surgery.Positron emission tomography imaging and neurological tests were applied to evaluate the metabolic and neurofunctional alterations of rats transplanted with stem cells.Quantitative proteomics was employed to investigate the protein expression profiles in iPSCs-transplanted brain in the subacute and chronic phases of stroke.Compared with NSCs-transplanted rats,significantly increased glucose metabolism and neurofunctional scores were observed in iPSCs-transplanted rats.Subsequent proteomic data of iPSCs-transplanted rats identified a total of 39 differentially expressed proteins in the subacute and chronic phases,which are involved in various ischemic stroke-related biological processes,including neuronal survival,axonal remodeling,antioxidative stress,and mitochondrial function restoration.Taken together,our study indicated that iPSCs have a positive therapeutic effect in ischemic stroke and emphasized the wide-ranging microenvironmental changes in the subacute and chronic phases.展开更多
High-sensitivity mass spectrometry approaches using selected reaction monitoring(SRM)or multiple reaction monitoring(MRM)methods are powerful tools for targeted quantitative proteomics-based investigation of dynamics ...High-sensitivity mass spectrometry approaches using selected reaction monitoring(SRM)or multiple reaction monitoring(MRM)methods are powerful tools for targeted quantitative proteomics-based investigation of dynamics in specific biological systems.Both high-sensitivity detection of lowabundance proteins and their quantification using this technique employ stable isotope-labeled peptide internal standards.Currently,there are various ways for preparing standards,including chemical peptide synthesis,cellular protein expression,and cell-free protein or peptide synthesis.Cell-free protein synthesis(CFPS)or in vitro translation(IVT)systems in particular provide high-throughput and low-cost preparation methods,and various cell types and reconstituted forms are now commercially available.Herein,we review the use of such systems for precise and reliable protein quantification.展开更多
The msh homeobox 1(Msx1)and msh homeobox 2(Msx2)coordinate in myoblast differentiation and also contribute to muscle defects if altered during development.Deciphering the downstream signaling networks of Msx1 and Msx2...The msh homeobox 1(Msx1)and msh homeobox 2(Msx2)coordinate in myoblast differentiation and also contribute to muscle defects if altered during development.Deciphering the downstream signaling networks of Msx1 and Msx2 in myoblast differentiation will help us to understand the molecular events that contribute to muscle defects.Here,the proteomics characteristics in Msx1-and Msx2-mediated myoblast differentiation was evaluated using isobaric tags for the relative and absolute quantification labeling technique(iTRAQ).The downstream regulatory proteins of Msx1-and Msx2-mediated differentiation were identified.Bioinformatics analysis revealed that these proteins were primarily associated with xenobiotic metabolism by cytochrome P450,fatty acid degradation,glycolysis/gluconeogenesis,arginine and proline metabolism,and apoptosis.In addition,our data show Acta1 was probably a core of the downstream regulatory networks of Msx1 and Msx2 in myoblast differentiation.展开更多
Drug resistance of sorafenib seriously affects the treatment effect of late-stage hepatocellular carcinoma(HCC)patients.However,the precise mechanism of resistance to sorafenib remains unclear.Therefore,to obtain a de...Drug resistance of sorafenib seriously affects the treatment effect of late-stage hepatocellular carcinoma(HCC)patients.However,the precise mechanism of resistance to sorafenib remains unclear.Therefore,to obtain a deep understand of sorafenib resistance mechanisms and find potential therapeutic targets are very important for improving the clinical prognosis of HCC patients.In this study,a label-free quantitative proteomics method was performed to investigate the proteins differentially expressed between HepG2 and the sorafenib-acquired resistance HepG2(HepG2-R)cells.In total,84 differential expressed proteins were identified between the two cell lines.Bioinformatics analysis results demonstrated the dysregulated metabolic processes have a significant impact on the drug resistance of HepG2-R cells.Among them,the expression of Microsomal glutathione S-transferase 1(MGST1)in two cell lines was further confirmed by western blot method.Moreover,colony formation assay and trypan blue dye assay results revealed that MGST1 is closely connected with the sorafenib resistance of HepG2-R cells,and the knockdown of MGST1 increased the sensitivity of sorafenib resistance HepG2-R cells to sorafenib treatment.In conclusion,these results lay a foundation for deciphering the mechanism for HCC sorafenib resistance and present a possibility of MGST1 serving as a therapeutic target for the treatment of sorafenib resistance HCC.展开更多
OBJECTIVE:To explore the novel biomarkers and therapeutic target candidates related to the stasis-heat syndrome of acute intracerebral hemorrhage(AICH).METHODS:Applying an isobaric tagging for relative and absolute qu...OBJECTIVE:To explore the novel biomarkers and therapeutic target candidates related to the stasis-heat syndrome of acute intracerebral hemorrhage(AICH).METHODS:Applying an isobaric tagging for relative and absolute quantitation-(i TRAQ-)based quantitative proteomic approach,plasma samples from AICH patients with stasis-heat,and AICH patients with non-stasis-heat and healthy control subjects were collected and analyzed to distinguish differentially expressed proteins(DEPs)correlated to AICH with stasis-heat in this block design.The standard Western blot was applied to verify DEPs.Additionally,DEPs were analyzed via bioinformatic platforms and further approved via Ingenuity Pathway Analysis(IPA).RESULTS:A total of 26 DEPs were found among AICH with the stasis-heat,AICH with non-stasis-heat,and healthy control group.The seven DEPs compared with the non-stasis-heat group are closely related to the pathogenesis of stasis heat.These proteins showed three different protein expression patterns.The alpha-1-b glycoprotein(A1 BG)and copper-protein(CP)were upregulated in the stasis-heat group,but down-regulated in the non-stasis-heat group.Compared with the non-stasisheat group,the expression abundance of actinin,alpha 1(ACTN1),carbonic anhydrase I(CA1),peroxiredoxin 2(PRDX2),and vinculin(VCL)is higher in the stasis-heat group,while the CD44 is the opposite.These differences reflect that stasis-heat syndrome has more severe inflammatory immune response,coagulation disorders and damage.Bioinformatics analysis revealed that a wide variety of cellular and metabolic processes and some signaling pathways were involved in the pathophysiology of AICH with stasis-heat.AICH with stasis-heat syndrome showed more severe inflammatory reactions,tissue damage,and coagulation disorders than non-stasis heat syndrome.CONCLUSIONS:There are differences in the protein expression patterns between the stasis-heat syndrome and non-stasis-heat syndrome.These differences reflect that stasis-heat syndrome has more severe damage.CD44,CP,ACTN1,CA1,VCL,PRDX2,and A1 BG could be the potential biomarkers and therapeutic target candidates of the stasis-heat subtype.This study provides a reasonable explaination for Liangxue Tongyu decoction through anti-inflammatory and brain protection treatment.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
Dengue virus(DENV)infection is a worldwide public health threat.To date,the knowledge about the pathogenesis and progression of DENV infection is still limited.Combining global profiling based on proteomic analysis to...Dengue virus(DENV)infection is a worldwide public health threat.To date,the knowledge about the pathogenesis and progression of DENV infection is still limited.Combining global profiling based on proteomic analysis together with functional verification analysis is a powerful strategy to investigate the interplay between the virus and host cells.In the present study,quantitative proteomics has been applied to evaluate host responses(as indicated by altered proteins and modifications)in human cells(using K562 cell line)upon DENV-2 infection,as DENV-2 spreads most widely among all DENV serotypes.Comparative analysis was performed to define differentially expressed proteins in the infected cells compared to the mock-control,and it revealed critical pathogen-induced changes covering a broad spectrum of host cellular compartments and processes.We also discovered more dramatic changes(>20%,160 regulated phosphoproteins)in protein phosphorylation compared to protein expression(14%,321 regulated proteins).Most of these proteins/phosphoproteins were involved in transcription regulation,RNA splicing and processing,immune system,cellular response to stimulus,and macromolecule biosynthesis.Western blot analysis was also performed to confirm the proteomic data.Potential roles of these altered proteins were discussed.The present study provides valuable large-scale protein-related information for elucidating the functional emphasis of host cell proteins and their post-translational modifications in virus infection,and also provides insight and protein evidence for understanding the general pathogenesis and pathology of DENV.展开更多
OBJECTIVE To explore the hypolipidemic mechanisms of the total phenylpropanoid glycosides fromLigustrum robustum(Roxb.) Blume(LRTPG) in hamsters using proteomics technique.METHODS The hamsters were fed with a high fat...OBJECTIVE To explore the hypolipidemic mechanisms of the total phenylpropanoid glycosides fromLigustrum robustum(Roxb.) Blume(LRTPG) in hamsters using proteomics technique.METHODS The hamsters were fed with a high fat diet to induce hyperlipidemia.Then LRTPG of high(1.2 g·kg^(-1)),medium(0.6 g·kg^(-1)) and low(0.3 g·kg^(-1)) doses were administrated daily for 4 weeks.Then the concentrations of plasma and hepatic lipids were determined using enzymic methods.The total protein was extracted from livers of the model group and the group treated with the high dose of LRTPG for label-free quantitative proteomics.RESULTS LRTPG significantly reduced the concentrations of plasma and hepatic lipids in hamsters fed a high fat diet.The proteomics data showed that a total of 2231 proteins were identified,and 549 proteins were found to be differentially expressed between the model group and the group treated with LRTPG.Among the 549 proteins,93 proteins were up-regulated and 59 proteins were down-regulated,and 397 proteins were absent or not.And some of these proteins were much related to the lipid metabolism.Further,gene ontology(GO) analysis indicated metabolic process,transport,oxidation-reduction process,phosphorylation,signal transduction,lipid metabolic process were the main biological processes that those differentially expressed proteins participated.KEGG pathway analysis showed that those proteins were involved in several metabolic pathways including oxidative phosphorylation,non-alcoholic fatty liver disease(NAFLD),PI3K-Akt signaling pathway,cAMP signaling pathway,cGMP-PKG signaling pathway.CONCLUSION The proteomics study could provide valuable clues to help us to understand the hypolipidemic mechanisms of LRTPG much better.展开更多
Biomarke rs are required for the early detection,prognosis prediction,and monitoring of amyotrophic lateral sclerosis,a progressive disease.Proteomics is an unbiased and quantitative method that can be used to detect ...Biomarke rs are required for the early detection,prognosis prediction,and monitoring of amyotrophic lateral sclerosis,a progressive disease.Proteomics is an unbiased and quantitative method that can be used to detect neurochemical signatures to aid in the identification of candidate biomarke rs.In this study,we used a label-free quantitative proteomics approach to screen for substantially differentially regulated proteins in ten patients with sporadic amyotrophic lateral scle rosis compared with five healthy controls.Su bstantial upregulation of serum proteins related to multiple functional clusters was observed in patients with spo radic amyotrophic lateral sclerosis.Potential biomarke rs were selected based on functionality and expression specificity.To validate the proteomics profiles,blood samples from an additional cohort comprising 100 patients with sporadic amyotrophic lateral sclerosis and 100 healthy controls were subjected to enzyme-linked immunosorbent assay.Eight substantially upregulated serum proteins in patients with spora dic amyotrophic lateral sclerosis were selected,of which the cathelicidin-related antimicrobial peptide demonstrated the best discriminative ability between patients with sporadic amyotrophic lateral sclerosis and healthy controls(area under the curve[AUC]=0.713,P<0.0001).To further enhance diagnostic accuracy,a multi-protein combined discriminant algorithm was developed incorporating five proteins(hemoglobin beta,cathelicidin-related antimicrobial peptide,talin-1,zyxin,and translationally-controlled tumor protein).The algo rithm achieved an AUC of 0.811 and a P-value of<0.0001,resulting in 79%sensitivity and 71%specificity for the diagnosis of sporadic amyotrophic lateral scle rosis.Subsequently,the ability of candidate biomarkers to discriminate between early-stage amyotrophic lateral sclerosis patients and controls,as well as patients with different disease severities,was examined.A two-protein panel comprising talin-1 and translationally-controlled tumor protein effectively distinguished early-stage amyotrophic lateral sclerosis patients from controls(AUC=0.766,P<0.0001).Moreove r,the expression of three proteins(FK506 binding protein 1A,cathelicidin-related antimicrobial peptide,and hemoglobin beta-1)was found to increase with disease progression.The proteomic signatures developed in this study may help facilitate early diagnosis and monitor the progression of sporadic amyotrophic lateral sclerosis when used in co mbination with curre nt clinical-based parameters.展开更多
Most type 2 diabetics are accompanied with deficiency of insulin secretion and hyperglycemia. It has reported that glucose-stimulated insulin secretion of β cell (GSIS)
Long-chain omega-3 polyunsaturated fatty acids(LC-PUFAs),known for having many health benefits,are usually present in three forms:triglycerides(TG),ethyl esters(EE),and phospholipid(PL).In this study,the effects of th...Long-chain omega-3 polyunsaturated fatty acids(LC-PUFAs),known for having many health benefits,are usually present in three forms:triglycerides(TG),ethyl esters(EE),and phospholipid(PL).In this study,the effects of these three LC-PUFAs forms(fish oil for TG and EE,krill oil for PL)on the obese mice were compared,and the proteomic changes that focused on lipid metabolism were evaluated via label-free quantitative proteomics analysis.Compared with the model group,all three of the LC-PUFA form supplementations(labeled as the FO-TG group,FO-EE group and KO-PL groups)could significantly reduce body weight gain(P<0.01).Low-density lipoprotein cholesterol levels were significantly decreased,whereas high-density lipoprotein cholesterol levels were significantly increased in the FO-TG group and FO-EE group(P<0.01),and especially in the PL group(P<0.001).Furthermore,proteomics analysis results suggested that some differentially expressed genes involved in the fatty acid degradation and oxidation pathways had a higher expression fold in the KO-PL group than in the FO-TG or FO-EE groups.Our results showed that dietary LC-PUFAs can reduce fat deposition and inhibit lipogenesis in the liver by upregulating the expression of proteins that are involved in the fatty acid degradation and oxidation pathways.Additionally,KO-PL elicits stronger effects than FO-TG or FO-EE.展开更多
Previous studies have shown that sirtuin 1（SIRT1） reduces the production of neuronal amyloid beta（Aβ） and inhibits the inflammatory response of glial cells, thereby generating a neuroprotective effect against Aβ...Previous studies have shown that sirtuin 1（SIRT1） reduces the production of neuronal amyloid beta（Aβ） and inhibits the inflammatory response of glial cells, thereby generating a neuroprotective effect against Aβ neurotoxicity in animal models of Alzheimer＇s disease. However, the protective effect of SIRT1 on astrocytes is still under investigation. This study established a time point model for the clearance of Aβ in primary astrocytes. Results showed that 12 hours of culture was sufficient for endocytosis of oligomeric Aβ, and 36 hours sufficient for effective degradation. Immunofluorescence demonstrated that Aβ degradation in primary astrocytes relies on lysosome function. Enzymatic agonists or SIRT1 inhibitors were used to stimulate cells over a concentration gradient. Aβ was co-cultured for 36 hours in medium. Western blot assay results under different conditions revealed that SIRT1 relies on its deacetylase activity to promote intracellular Aβ degradation. The experiment further screened SIRT1 using quantitative proteomics to investigate downstream, differentially expressed proteins in the Aβ degradation pathway and selected the ones related to enzyme activity of SIRT1. Most of the differentially expressed proteins detected are close to the primary astrocyte lysosomal pathway. Immunofluorescence staining demonstrated that SIRT1 relies on its deacetylase activity to upregulate lysosome number in primary astrocytes. Taken together, these findings confirm that SIRT1 relies on its deacetylase activity to upregulate lysosome number, thereby facilitating oligomeric Aβ degradation in primary astrocytes.展开更多
Background: Malaria is a devastating infectious disease that disproportionally threatens hundreds of millions of people in developing countries. In the history of anti-malaria campaign, chloroquine(CQ) has played an i...Background: Malaria is a devastating infectious disease that disproportionally threatens hundreds of millions of people in developing countries. In the history of anti-malaria campaign, chloroquine(CQ) has played an indispensable role, however, its mechanism of action(MoA) is not fully understood.Methods: We used the principle of photo-affinity labeling and click chemistry-based functionalization in the design of a CQ probe and developed a combined deconvolution strategy of activity-based protein profiling(ABPP) and mass spectrometry-coupled cellular thermal shift assay(MS-CETSA) that identified the protein targets of CQ in an unbiased manner in this study. The interactions between CQ and these identified potential protein hits were confirmed by biophysical and enzymatic assays.Results: We developed a novel clickable, photo-affinity chloroquine analog probe(CQP) which retains the antimalarial activity in the nanomole range, and identified a total of 40 proteins that specifically interacted and photocrosslinked with CQP which was inhibited in the presence of excess CQ. Using MS-CETSA, we identified 83 candidate interacting proteins out of a total of 3375 measured parasite proteins. At the same time, we identified 8 proteins as the most potential hits which were commonly identified by both methods.Conclusions: We found that CQ could disrupt glycolysis and energy metabolism of malarial parasites through direct binding with some of the key enzymes, a new mechanism that is different from its well-known inhibitory effect of hemozoin formation. This is the first report of identifying CQ antimalarial targets by a parallel usage of labeled(ABPP)and label-free(MS-CETSA) methods.展开更多
基金supported by the National Natural Science Foundation of China(Nos.82073814,82122066,and 82104328)the"Dawn"Program of the Shanghai Education Commission(No.22SG34)+1 种基金the National Key Research and Development Program of the Ministry of China(No.2022YFC2704603)Shanghai Sailing Program(No.20YF1458900).
文摘Sini Decoction(SNT)is a traditional formula recognized for its efficacy in warming the spleen and stomach and dispersing cold.However,elucidating the mechanism of action of SNT remains challenging due to its complex multiple components.This study utilized a synergistic approach combining two-dimensional fluorescence difference in gel electrophoresis(2D-DIGE)-based drug affinity responsive target stability(DARTS)with label-free quantitative proteomics techniques to identify the direct and indirect protein targets of SNT in myocardial infarction.The analysis identified 590 proteins,with 30 proteins showing significant upregulation and 51 proteins showing downregulation when comparing the SNT group with the model group.Through the integration of 2D-DIGE DARTS with proteomics data and pharmacological assessments,the findings indicate that protein disulfide-isomerase A3(PDIA3)may serve as a potential protein target through which SNT provides protective effects on myocardial cells during myocardial infarction.
基金the grant support to W.-C.Y.from the MOST(2016YFA0500502)NSFC(31161130534),ChinaY.L.from the Chinese Academy of Sciences(YSBR-011,ZDRW-ZS2019-2,KFZD-SW-112-02-05)。
文摘An effective symbiosis between legumes and rhizobia relies largely on diverse proteins at the plantrhizobium interface for material transportation and signal transduction during symbiotic nitrogen fixation.Here,we report a comprehensive proteome atlas of the soybean symbiosome membrane(SM),peribacteroid space(PBS),and root microsomal fraction(RMF)using state-of-the-art label-free quantitative proteomic technology.In total,1759 soybean proteins with diverse functions are detected in the SM,and 1476 soybean proteins and 369 rhizobial proteins are detected in the PBS.The diversity of SM proteins detected suggests multiple origins of the SM.Quantitative comparative analysis highlights amino acid metabolism and nutrient uptake in the SM,indicative of the key pathways in nitrogen assimilation.The detection of soybean secretory proteins in the PBS and receptor-like kinases in the SM provides evidence for the likely extracellular property of the symbiosome and the potential signaling communication between both symbionts at the symbiotic interface.Our proteomic data provide clues for how some of the sophisticated regulation between soybean and rhizobium at the symbiotic interface is achieved,and suggest approaches for symbiosis engineering.
基金supported by the National Natural Science Foundation of China(No.81574025)the Open Project Program of Jiangsu Key Laboratory of Pediatric Respiratory Disease,Nanjing University of Chinese Medicine(No.JKLPRD201410)
文摘Respiratory syncytial virus(RSV) is a leading cause of acute lower respiratory tract infections. Qingfei oral liquid(QFOL), a traditional Chinese medicine, is widely used in clinical treatment for RSV-induced pneumonia. The present study was designed to reveal the potential targets and mechanism of action for QFOL by exploring its influence on the host cellular network following RSV infection. We investigated the serum proteomic changes and potential biomarkers in an RSV-infected mouse pneumonia model treated with QFOL. Eighteen BALB/c mice were randomly divided into three groups: RSV pneumonia model group(M), QFOL-treated group(Q) and the control group(C). Serum proteomes were analyzed and compared using a label-free quantitative LC-MS/MS approach. A total of 172 protein groups, 1009 proteins, and 1073 unique peptides were successfully identified. 51 differentially expressed proteins(DEPs) were identified(15 DEPs when M/C and 43 DEPs when Q/M; 7 DEPs in common). Classification and interaction network showed that these proteins participated in various biological processes including immune response, blood coagulation, complement activation, and so forth. Particularly, fibrinopeptide B(FpB) and heparin cofactor Ⅱ(HCII) were evaluated as important nodes in the interaction network, which was closely involved in coagulation and inflammation. Further, the Fp B level was increased in Group M but decreased in Group Q, while the HCII level exhibited the opposite trend. These findings not only indicated FpB and HCII as potential biomarkers and targets of QFOL in the treatment of RSV pneumonia, but also suggested a regulatory role of QFOL in the RSV-induced disturbance of coagulation and inflammation-coagulation interactions.
基金supported by grants from the National Natural Science Foundation of China(No.21705137)China and donation from Kwok Chung Bo Fun Charitable Fund for the establishment of the Kwok Yat Wai Endowed Chair of Environmental and Biological Analysis。
文摘Inflammation is a defense mechanism associated with a wide range of diseases.Celastrol is a small molecule isolated from traditional Chinese medicine with potent anti-inflammation activity.In this study,we established an integrated quantitative proteomics strategy to investigate the acute response to celastrol treatment in a rat macrophage cell line challenged with lipopolysaccharide(LPS).Both stableisotopic based non-targeted quantitative profiling and PRM-based targeted quantitation methods were employed.Dimethyl-labeling based non-targeted profiling revealed 28 and 52 proteins that significantly up-and down-regulated by celastrol.Bioinformatics analysis pinpoint key signaling pathways affected.Seven proteins were selected for examining their time-dependent regulatory pattern in response to celastrol using targeted PRM quantitation.The abundance of mRNA at multiple time-points of selected proteins was also examined.Celastrol induced an acute response of selected key transcriptional factors in terms of mRNA or protein abundance within one hour.Interestingly,regulatory trend of mRNA and protein abundance suggested a novel dual mechanism of celastrol in the terms of acute antiinflammation.The integrated quantitative proteomic strategy established in this study constitutes an efficient workflow to characterize key components and their time-dependent regulatory pattern for monitoring drug response.
基金Supported by the National Key Research Development Program of China(No.2017YFC1404302)the National Natural Science Foundation of China(Nos.41425021,41706131)+1 种基金the Open Fund of CAS Key Laboratory of Marine Ecology and Environmental Sciences,Institute of Oceanology,Chinese Academy of Sciences(No.KLMEES201806)supported by the“Ten-Thousand Talents Program”for leading talents in science and technological innovation。
文摘Dinofl agellates are the major causative agents of harmful algal blooms in the global ocean and they usually form blooms under conditions of very low dissolved inorganic phosphorus(DIP).However,the mechanisms underpinning the dinofl agellate blooms remain unclear.Here,we quantitatively compared protein expression profi les of a marine dinofl agellate,Prorocentrum donghaiense,grown in inorganic P-replete,P-defi cient,and DIP-and dissolved organic phosphorus(DOP)-resupplied conditions by employing a Tandem Mass Tag(TMT)-based quantitative proteomic approach.Proteins involved in intracellular P reallocation,organic P,and non-P lipid utilization were up-regulated under the P-defi cient condition,while inorganic phosphate transporters varied insignifi cantly.In response to the P resupplementation,nitrogen metabolism,ribosome,porphyrin,and chlorophyll metabolism were up-regulated,while lysosome,and starch and sucrose metabolism were down-regulated.Notably,photosynthesis was up-regulated and secondary metabolism was down-regulated only in the DIP-resupplied cells,whereas amino acid metabolism and vitamin B6 metabolism were up-regulated in the DOP-resupplied cells,indicating diff erential response mechanisms of P.donghaiense to DIP or DOP resupplementation.Our results indicated that P.donghaiense initiated multiple strategies in response to an ambient inorganic P-defi ciency,and its efficient DOP assimilation by providing both P and carbon sources might be a key factor driving bloom formations of P.donghaiense in a low DIP environment.
基金supported by the National Key Research and Development Plan[2017YFD0100706]National Natural Science Foundation of China[31871618].
文摘Enhancing photosynthesis efficiency is considered as one of the most crucial targets during wheat breeding.However,the molecular basis underlying high photosynthesis efficiency is not well understood up to now.In this study,we investigated the protein expression profile of wheat Jimai5265yg mutant,which is a yellow-green mutant with chlorophylls b deficiency but high photosynthesis efficiency.Though TMT-labeling quantitative proteomics analysis,a total of 72 differential expressed proteins(DEPs)were obtained between the mutant and wild type(WT).GO analysis found that they significantly enriched in thylakoid membrane,pigment binding,magnesium chelatase activity and response to light intensity.KEGG analysis showed that they involved in photosynthesis-antenna protein as well as porphyrin and chlorophyll metabolism.Finally,118 RNA editing events were found between mutant and WT genotype.The A to C editing in the 3-UTR of TraesCS6D02G401500 lead to its high expression in mutant through removing the inhibition of tae-miR9781,which might have vital role in regulating the yellow-green mutant.This study provided some useful clues about the molecular basis of Jimai5265yg mutant as well as chlorophylls metabolism in wheat.
基金supported by grants from the National Key R&D Program of China (Grant Nos. 2018YFA0507801 and 2018YFA0507103)the National Natural Science Foundation of China (Grant No. 31900925)the China Scholarship Council (CSC)
文摘In the past decade,relative proteomic quantification using isobaric labeling technology has developed into a key tool for comparing the expression of proteins in biological samples.Although its multiplexing capacity and flexibility make this a valuable technology for addressing various biological questions,its quantitative accuracy and precision still pose significant challenges to the reliability of its quantification results.Here,we give a detailed overview of the different kinds of isobaric mass tags and the advantages and disadvantages of the isobaric labeling method.We also discuss which precautions should be taken at each step of the isobaric labeling workflow,to obtain reliable quantification results in large-scale quantitative proteomics experiments.In the last section,we discuss the broad applications of the isobaric labeling technology in biological and clinical studies,with an emphasis on thermal proteome profiling and proteogenomics.
基金sponsored by the National Key Research and Development Program of China(No.2016YFA0100-900)and the Fund for Shanxi“1331 Project Key Innovative Research Team.
文摘The local microenvironment is essential to stem cell-based therapy for ischemic stroke,and spatiotemporal changes of the microenvironment in the pathological process provide vital clues for understanding the therapeutic mechanisms.However,relevant studies on microenvironmental changes were mainly confined in the acute phase of stroke,and long-term changes remain unclear.This study aimed to investigate the microenvironmental changes in the subacute and chronic phases of ischemic stroke after stem cell transplantation.Herein,induced pluripotent stem cells(iPSCs)and neural stem cells(NSCs)were transplanted into the ischemic brain established by middle cerebral artery occlusion surgery.Positron emission tomography imaging and neurological tests were applied to evaluate the metabolic and neurofunctional alterations of rats transplanted with stem cells.Quantitative proteomics was employed to investigate the protein expression profiles in iPSCs-transplanted brain in the subacute and chronic phases of stroke.Compared with NSCs-transplanted rats,significantly increased glucose metabolism and neurofunctional scores were observed in iPSCs-transplanted rats.Subsequent proteomic data of iPSCs-transplanted rats identified a total of 39 differentially expressed proteins in the subacute and chronic phases,which are involved in various ischemic stroke-related biological processes,including neuronal survival,axonal remodeling,antioxidative stress,and mitochondrial function restoration.Taken together,our study indicated that iPSCs have a positive therapeutic effect in ischemic stroke and emphasized the wide-ranging microenvironmental changes in the subacute and chronic phases.
基金This work was supported by a Grant-in-Aid in number 17H05680(YS)from Japan Society for the Promotion of Science(JSPS)the strategic programs for R&D(President's discretionary fund)of RIKEN(YS)an intramural Grant-in-Aid from the RIKEN Quantitative Biology Center(YS).
文摘High-sensitivity mass spectrometry approaches using selected reaction monitoring(SRM)or multiple reaction monitoring(MRM)methods are powerful tools for targeted quantitative proteomics-based investigation of dynamics in specific biological systems.Both high-sensitivity detection of lowabundance proteins and their quantification using this technique employ stable isotope-labeled peptide internal standards.Currently,there are various ways for preparing standards,including chemical peptide synthesis,cellular protein expression,and cell-free protein or peptide synthesis.Cell-free protein synthesis(CFPS)or in vitro translation(IVT)systems in particular provide high-throughput and low-cost preparation methods,and various cell types and reconstituted forms are now commercially available.Herein,we review the use of such systems for precise and reliable protein quantification.
基金This work was supported by the grant from the National Natural Science Foundation Grant of China to Jingqiang Wang(31972885).
文摘The msh homeobox 1(Msx1)and msh homeobox 2(Msx2)coordinate in myoblast differentiation and also contribute to muscle defects if altered during development.Deciphering the downstream signaling networks of Msx1 and Msx2 in myoblast differentiation will help us to understand the molecular events that contribute to muscle defects.Here,the proteomics characteristics in Msx1-and Msx2-mediated myoblast differentiation was evaluated using isobaric tags for the relative and absolute quantification labeling technique(iTRAQ).The downstream regulatory proteins of Msx1-and Msx2-mediated differentiation were identified.Bioinformatics analysis revealed that these proteins were primarily associated with xenobiotic metabolism by cytochrome P450,fatty acid degradation,glycolysis/gluconeogenesis,arginine and proline metabolism,and apoptosis.In addition,our data show Acta1 was probably a core of the downstream regulatory networks of Msx1 and Msx2 in myoblast differentiation.
基金supported by grants from National Natural Science Foundation(21725506,32071434)National Key Research and Development Program of China(2016YFA0501401)
文摘Drug resistance of sorafenib seriously affects the treatment effect of late-stage hepatocellular carcinoma(HCC)patients.However,the precise mechanism of resistance to sorafenib remains unclear.Therefore,to obtain a deep understand of sorafenib resistance mechanisms and find potential therapeutic targets are very important for improving the clinical prognosis of HCC patients.In this study,a label-free quantitative proteomics method was performed to investigate the proteins differentially expressed between HepG2 and the sorafenib-acquired resistance HepG2(HepG2-R)cells.In total,84 differential expressed proteins were identified between the two cell lines.Bioinformatics analysis results demonstrated the dysregulated metabolic processes have a significant impact on the drug resistance of HepG2-R cells.Among them,the expression of Microsomal glutathione S-transferase 1(MGST1)in two cell lines was further confirmed by western blot method.Moreover,colony formation assay and trypan blue dye assay results revealed that MGST1 is closely connected with the sorafenib resistance of HepG2-R cells,and the knockdown of MGST1 increased the sensitivity of sorafenib resistance HepG2-R cells to sorafenib treatment.In conclusion,these results lay a foundation for deciphering the mechanism for HCC sorafenib resistance and present a possibility of MGST1 serving as a therapeutic target for the treatment of sorafenib resistance HCC.
基金Supported by Jiangsu Province Social Development Key Research and Development Program:Construction and Application of Decision Support System of TCM Master Zhou Zhongying’s Experience Learning in Distinguishing and Treating Major Diseases based on the Intelligent Technology(No.BE2019723)the National Natural Science Foundation of China:Dynamic Measurement and Study of Biomarker on Pathogenic Unit of Stasis-Heat in Acute Intracerebral Hemorrhage(No.813735)
文摘OBJECTIVE:To explore the novel biomarkers and therapeutic target candidates related to the stasis-heat syndrome of acute intracerebral hemorrhage(AICH).METHODS:Applying an isobaric tagging for relative and absolute quantitation-(i TRAQ-)based quantitative proteomic approach,plasma samples from AICH patients with stasis-heat,and AICH patients with non-stasis-heat and healthy control subjects were collected and analyzed to distinguish differentially expressed proteins(DEPs)correlated to AICH with stasis-heat in this block design.The standard Western blot was applied to verify DEPs.Additionally,DEPs were analyzed via bioinformatic platforms and further approved via Ingenuity Pathway Analysis(IPA).RESULTS:A total of 26 DEPs were found among AICH with the stasis-heat,AICH with non-stasis-heat,and healthy control group.The seven DEPs compared with the non-stasis-heat group are closely related to the pathogenesis of stasis heat.These proteins showed three different protein expression patterns.The alpha-1-b glycoprotein(A1 BG)and copper-protein(CP)were upregulated in the stasis-heat group,but down-regulated in the non-stasis-heat group.Compared with the non-stasisheat group,the expression abundance of actinin,alpha 1(ACTN1),carbonic anhydrase I(CA1),peroxiredoxin 2(PRDX2),and vinculin(VCL)is higher in the stasis-heat group,while the CD44 is the opposite.These differences reflect that stasis-heat syndrome has more severe inflammatory immune response,coagulation disorders and damage.Bioinformatics analysis revealed that a wide variety of cellular and metabolic processes and some signaling pathways were involved in the pathophysiology of AICH with stasis-heat.AICH with stasis-heat syndrome showed more severe inflammatory reactions,tissue damage,and coagulation disorders than non-stasis heat syndrome.CONCLUSIONS:There are differences in the protein expression patterns between the stasis-heat syndrome and non-stasis-heat syndrome.These differences reflect that stasis-heat syndrome has more severe damage.CD44,CP,ACTN1,CA1,VCL,PRDX2,and A1 BG could be the potential biomarkers and therapeutic target candidates of the stasis-heat subtype.This study provides a reasonable explaination for Liangxue Tongyu decoction through anti-inflammatory and brain protection treatment.
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supported by the National Natural Science Foundation of China (31870827 to X.Zhao, 31670161 to X.Zhou., and 81873964 to Y.Q.)the Hubei Natural Science Foundation (2018CFB603 to X.Zhao)the Fundamental Research Funds for the Central Universities (2042018kf0247 to X.Zhao)
文摘Dengue virus(DENV)infection is a worldwide public health threat.To date,the knowledge about the pathogenesis and progression of DENV infection is still limited.Combining global profiling based on proteomic analysis together with functional verification analysis is a powerful strategy to investigate the interplay between the virus and host cells.In the present study,quantitative proteomics has been applied to evaluate host responses(as indicated by altered proteins and modifications)in human cells(using K562 cell line)upon DENV-2 infection,as DENV-2 spreads most widely among all DENV serotypes.Comparative analysis was performed to define differentially expressed proteins in the infected cells compared to the mock-control,and it revealed critical pathogen-induced changes covering a broad spectrum of host cellular compartments and processes.We also discovered more dramatic changes(>20%,160 regulated phosphoproteins)in protein phosphorylation compared to protein expression(14%,321 regulated proteins).Most of these proteins/phosphoproteins were involved in transcription regulation,RNA splicing and processing,immune system,cellular response to stimulus,and macromolecule biosynthesis.Western blot analysis was also performed to confirm the proteomic data.Potential roles of these altered proteins were discussed.The present study provides valuable large-scale protein-related information for elucidating the functional emphasis of host cell proteins and their post-translational modifications in virus infection,and also provides insight and protein evidence for understanding the general pathogenesis and pathology of DENV.
基金supported by the PUMC(Peking Union Medical College)Youth Fund(3332015142) National Natural Science Foundation of China(81703746)
文摘OBJECTIVE To explore the hypolipidemic mechanisms of the total phenylpropanoid glycosides fromLigustrum robustum(Roxb.) Blume(LRTPG) in hamsters using proteomics technique.METHODS The hamsters were fed with a high fat diet to induce hyperlipidemia.Then LRTPG of high(1.2 g·kg^(-1)),medium(0.6 g·kg^(-1)) and low(0.3 g·kg^(-1)) doses were administrated daily for 4 weeks.Then the concentrations of plasma and hepatic lipids were determined using enzymic methods.The total protein was extracted from livers of the model group and the group treated with the high dose of LRTPG for label-free quantitative proteomics.RESULTS LRTPG significantly reduced the concentrations of plasma and hepatic lipids in hamsters fed a high fat diet.The proteomics data showed that a total of 2231 proteins were identified,and 549 proteins were found to be differentially expressed between the model group and the group treated with LRTPG.Among the 549 proteins,93 proteins were up-regulated and 59 proteins were down-regulated,and 397 proteins were absent or not.And some of these proteins were much related to the lipid metabolism.Further,gene ontology(GO) analysis indicated metabolic process,transport,oxidation-reduction process,phosphorylation,signal transduction,lipid metabolic process were the main biological processes that those differentially expressed proteins participated.KEGG pathway analysis showed that those proteins were involved in several metabolic pathways including oxidative phosphorylation,non-alcoholic fatty liver disease(NAFLD),PI3K-Akt signaling pathway,cAMP signaling pathway,cGMP-PKG signaling pathway.CONCLUSION The proteomics study could provide valuable clues to help us to understand the hypolipidemic mechanisms of LRTPG much better.
基金supported by the grants from Shanghai Shuguang Plan Project,No.18SG15(to SC)Shanghai Outstanding Young Scholars Project+2 种基金Shanghai Talent Development Project,No.2019044(to SC)Medical-engineering cross fund of Shanghai Jiao Tong University,No.YG2022QN009(to QZ)the National Natural Science Foundation of China,No.82201558(to QZ)。
文摘Biomarke rs are required for the early detection,prognosis prediction,and monitoring of amyotrophic lateral sclerosis,a progressive disease.Proteomics is an unbiased and quantitative method that can be used to detect neurochemical signatures to aid in the identification of candidate biomarke rs.In this study,we used a label-free quantitative proteomics approach to screen for substantially differentially regulated proteins in ten patients with sporadic amyotrophic lateral scle rosis compared with five healthy controls.Su bstantial upregulation of serum proteins related to multiple functional clusters was observed in patients with spo radic amyotrophic lateral sclerosis.Potential biomarke rs were selected based on functionality and expression specificity.To validate the proteomics profiles,blood samples from an additional cohort comprising 100 patients with sporadic amyotrophic lateral sclerosis and 100 healthy controls were subjected to enzyme-linked immunosorbent assay.Eight substantially upregulated serum proteins in patients with spora dic amyotrophic lateral sclerosis were selected,of which the cathelicidin-related antimicrobial peptide demonstrated the best discriminative ability between patients with sporadic amyotrophic lateral sclerosis and healthy controls(area under the curve[AUC]=0.713,P<0.0001).To further enhance diagnostic accuracy,a multi-protein combined discriminant algorithm was developed incorporating five proteins(hemoglobin beta,cathelicidin-related antimicrobial peptide,talin-1,zyxin,and translationally-controlled tumor protein).The algo rithm achieved an AUC of 0.811 and a P-value of<0.0001,resulting in 79%sensitivity and 71%specificity for the diagnosis of sporadic amyotrophic lateral scle rosis.Subsequently,the ability of candidate biomarkers to discriminate between early-stage amyotrophic lateral sclerosis patients and controls,as well as patients with different disease severities,was examined.A two-protein panel comprising talin-1 and translationally-controlled tumor protein effectively distinguished early-stage amyotrophic lateral sclerosis patients from controls(AUC=0.766,P<0.0001).Moreove r,the expression of three proteins(FK506 binding protein 1A,cathelicidin-related antimicrobial peptide,and hemoglobin beta-1)was found to increase with disease progression.The proteomic signatures developed in this study may help facilitate early diagnosis and monitor the progression of sporadic amyotrophic lateral sclerosis when used in co mbination with curre nt clinical-based parameters.
文摘Most type 2 diabetics are accompanied with deficiency of insulin secretion and hyperglycemia. It has reported that glucose-stimulated insulin secretion of β cell (GSIS)
基金supported by the Regional Demonstration Project of Marine Economic Innovation and Development(2013 and 2016)National Natural Science Foundation of China(31800117)the K.C.Wong Magna Fund offered by the Ningbo University。
文摘Long-chain omega-3 polyunsaturated fatty acids(LC-PUFAs),known for having many health benefits,are usually present in three forms:triglycerides(TG),ethyl esters(EE),and phospholipid(PL).In this study,the effects of these three LC-PUFAs forms(fish oil for TG and EE,krill oil for PL)on the obese mice were compared,and the proteomic changes that focused on lipid metabolism were evaluated via label-free quantitative proteomics analysis.Compared with the model group,all three of the LC-PUFA form supplementations(labeled as the FO-TG group,FO-EE group and KO-PL groups)could significantly reduce body weight gain(P<0.01).Low-density lipoprotein cholesterol levels were significantly decreased,whereas high-density lipoprotein cholesterol levels were significantly increased in the FO-TG group and FO-EE group(P<0.01),and especially in the PL group(P<0.001).Furthermore,proteomics analysis results suggested that some differentially expressed genes involved in the fatty acid degradation and oxidation pathways had a higher expression fold in the KO-PL group than in the FO-TG or FO-EE groups.Our results showed that dietary LC-PUFAs can reduce fat deposition and inhibit lipogenesis in the liver by upregulating the expression of proteins that are involved in the fatty acid degradation and oxidation pathways.Additionally,KO-PL elicits stronger effects than FO-TG or FO-EE.
基金supported by the National Natural Science Foundation of China,No.31670832,31470807,31270872a grant from the National Key Research and Development Program of China,No.2016YFA0500301a grant from the State Key Laboratory of Protein and Plant Gene Research,College of Life Sciences,Peking University,China
文摘Previous studies have shown that sirtuin 1（SIRT1） reduces the production of neuronal amyloid beta（Aβ） and inhibits the inflammatory response of glial cells, thereby generating a neuroprotective effect against Aβ neurotoxicity in animal models of Alzheimer＇s disease. However, the protective effect of SIRT1 on astrocytes is still under investigation. This study established a time point model for the clearance of Aβ in primary astrocytes. Results showed that 12 hours of culture was sufficient for endocytosis of oligomeric Aβ, and 36 hours sufficient for effective degradation. Immunofluorescence demonstrated that Aβ degradation in primary astrocytes relies on lysosome function. Enzymatic agonists or SIRT1 inhibitors were used to stimulate cells over a concentration gradient. Aβ was co-cultured for 36 hours in medium. Western blot assay results under different conditions revealed that SIRT1 relies on its deacetylase activity to promote intracellular Aβ degradation. The experiment further screened SIRT1 using quantitative proteomics to investigate downstream, differentially expressed proteins in the Aβ degradation pathway and selected the ones related to enzyme activity of SIRT1. Most of the differentially expressed proteins detected are close to the primary astrocyte lysosomal pathway. Immunofluorescence staining demonstrated that SIRT1 relies on its deacetylase activity to upregulate lysosome number in primary astrocytes. Taken together, these findings confirm that SIRT1 relies on its deacetylase activity to upregulate lysosome number, thereby facilitating oligomeric Aβ degradation in primary astrocytes.
基金suppor ted by the National Key Research and Development Program of China(2020YFA0908000)the Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine(ZYYCXTD-C-202002)+2 种基金the National Natural Science Foundation of China(82074098,82003814)the CACMS Innovation Fund(CI2021A05101)the Fundamental Research Funds for the Central public welfare research institutes(ZZ14-YQ-050,ZZ14-YQ-051,ZZ14-ND-010,ZZ15-ND-10 and ZZ14-FL-002)。
文摘Background: Malaria is a devastating infectious disease that disproportionally threatens hundreds of millions of people in developing countries. In the history of anti-malaria campaign, chloroquine(CQ) has played an indispensable role, however, its mechanism of action(MoA) is not fully understood.Methods: We used the principle of photo-affinity labeling and click chemistry-based functionalization in the design of a CQ probe and developed a combined deconvolution strategy of activity-based protein profiling(ABPP) and mass spectrometry-coupled cellular thermal shift assay(MS-CETSA) that identified the protein targets of CQ in an unbiased manner in this study. The interactions between CQ and these identified potential protein hits were confirmed by biophysical and enzymatic assays.Results: We developed a novel clickable, photo-affinity chloroquine analog probe(CQP) which retains the antimalarial activity in the nanomole range, and identified a total of 40 proteins that specifically interacted and photocrosslinked with CQP which was inhibited in the presence of excess CQ. Using MS-CETSA, we identified 83 candidate interacting proteins out of a total of 3375 measured parasite proteins. At the same time, we identified 8 proteins as the most potential hits which were commonly identified by both methods.Conclusions: We found that CQ could disrupt glycolysis and energy metabolism of malarial parasites through direct binding with some of the key enzymes, a new mechanism that is different from its well-known inhibitory effect of hemozoin formation. This is the first report of identifying CQ antimalarial targets by a parallel usage of labeled(ABPP)and label-free(MS-CETSA) methods.
