Circulating proteomic biomarkers for diagnosing sporadic amyotrophic lateral sclerosis:a cross-sectional study

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.

Quantitative proteomics provides insight into the response of the marine dinoflagellate Prorocentrum donghaiense to changes in ambient phosphorus

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.

miRNA-451 regulates rhesus choroid-retinal endothelial cell function and proteome profile

AIM:To evaluate the effect of miRNA-451 on rhesus macaque choroid-retinal endothelial(RF/6A)cell function and proteome profile.METHODS:The RF/6A cells were transfected with miRNA-451 mimic and inhibitor.The role of miRNA-451 on proliferation ability was evaluated by CCK-8 assay.Furthermore,iTRAQ quantitative proteomic analysis was applied to comprehensively illuminate the change of cellular proteins and biological function between different groups.RESULTS:In miRNA-451 overexpression group,cell proliferation of RF/6A decreased both at 24 h and 48 h;while in miRNA-451 inhibition group,on the contrary,RF/6A cell proliferation was increased at 48 h.Based on iTRAQ quantitative proteomic analysis,23 differentially expressed proteins(DEPs)were detected in the comparison of miRNA-451 mimic and mimic control-transfected RF/6A cells,and 30 DEPs were identified in the comparison of RF/6A cells transfected with miRNA-451 inhibitor and inhibitor control.DEPs such as GORASP2,KRT1,SLC7 A2,RIC8 A,DDX42,CAP1,PCBP2 might be closely related to the inhibitory effect of miRNA-451 on RF/6A cell proliferation,while PCYT1 A,MGAT1,TUBB,MCU,SIL1,BID,MSH6 might account for the positive effect of miRNA-451 inhibitor on RF/6A cell growth.PTPN1,as the only protein exhibiting an opposite trend between miRNA-451 mimic and inhibitortransfected cells,was most likely accountable for the inhibition of miRNA-451 mimic on RF/6A cell growth,and the promotion of miRNA-451 inhibitor on RF/6A cell proliferation.CONCLUSION:miRNA-451 overexpression can suppress the growth of RF/6A cells while knockdown of miRNA-451 can promote RF/6A cell viability.Among all DEPs,increased PTPN1 is most likely to account for the negative regulation of miRNA-451 on RF/6A proliferation.miRNA-451 can be a protective factor for neovascular disease of fundus via regulating choroid retinal endothelial cell function.

Quantitative Proteomics Analysis Identifies the Potential Mechanism Underlying Yellow-Green Leave Mutant in Wheat

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.

Gehua Jiejiu Dizhi decoction(葛花解酒涤脂汤)ameliorates alcoholic fatty liver in mice by regulating lipid and bile acid metabolism and with exertion of antioxidant stress based on 4DLabel-free quantitative proteomic study

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.

Identification of antimalarial targets of chloroquine by a combined deconvolution strategy of ABPP and MS-CETSA

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.

Remote ischemic conditioning-induced hyperacute and acute responses of plasma proteome in healthy young male adults:a quantitative proteomic analysis

Background: Long-term remote ischemic conditioning (RIC) has been proven to be beneficial in multiple diseases, such as cerebral and cardiovascular diseases. However, the hyperacute and acute effects of a single RIC stimulus are still not clear. Quantitative proteomic analyses of plasma proteins following RIC application have been conducted in preclinical and clinical studies but exhibit high heterogeneity in results due to wide variations in experimental setups and sampling procedures. Hence, this study aimed to explore the immediate effects of RIC on plasma proteome in healthy young adults to exclude confounding factors of disease entity, such as medications and gender. Methods: Young healthy male participants were enrolled after a systematic physical examination and 6-month lifestyle observation. Individual RIC sessions included five cycles of alternative ischemia and reperfusion, each lasting for 5 min in bilateral forearms. Blood samples were collected at baseline, 5 min after RIC, and 2 h after RIC, and then samples were processed for proteomic analysis using liquid chromatography-tandem mass spectrometry method. Results: Proteins related to lipid metabolism (e.g., Apolipoprotein F), coagulation factors (hepatocyte growth factor activator preproprotein), members of complement cascades (mannan-binding lectin serine protease 1 isoform 2 precursor), and inflammatory responses (carboxypeptidase N catalytic chain precursor) were differentially altered at their serum levels following the RIC intervention. The most enriched pathways were protein glycosylation and complement/coagulation cascades. Conclusions: One-time RIC stimulus may induce instant cellular responses like anti-inflammation, coagulation, and fibrinolysis balancing, and lipid metabolism regulation which are protective in different perspectives. Protective effects of single RIC in hyperacute and acute phases may be exploited in clinical emergency settings due to apparently beneficial alterations in plasma proteome profile. Furthermore, the beneficial effects of long-term (repeated) RIC interventions in preventing chronic cardiovascular diseases among general populations can also be expected based on our study findings.

SIRT1 facilitates amyloid beta peptide degradation by upregulating lysosome number in primary astrocytes

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.

Comparative proteomic analysis reveals the effects of different fatty acid forms on high-fat diet mice

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.

Functional annotation and enrichment analysis of differentially expressed serum proteins in patients with type 2 diabetes after dapagliflozin

BACKGROUND Only 50% of patients with type 2 diabetes mellitus(T2DM) can control their blood glucose levels. Dapagliflozin is a selective inhibitor of sodium-glucose cotransporter 2(SGLT-2) that improves the insulin sensitivity of the liver and peripheral tissues. Many studies confirmed that SGLT2 inhibitors reduce blood glucose and have multiple beneficial effects such as weight loss, lipid regulation, and kidney protection. Nevertheless, the mechanisms of the renal and cardiovascular protective effects of dapagliflozin from the perspective of differentially expressed proteins in the serum of T2DM patients have not been intensively explored so far.AIM To identify differentially expressed proteins associated with dapagliflozin treatment in patients with T2DM.METHODS Twenty T2DM patients [hemoglobin A1c(HbA1c) 7.0%-10.0%] were enrolled at The Affiliated Hospital of Inner Mongolia Medical University between January 1, 2017 and December 1, 2018. They received dapagliflozin(10 mg/d) for 3 mo, and the HbA1c < 7.0% target was achieved. The changes in clinical indexes were compared before and after treatments. Label-free quantitative proteomics was used to identify differentially expressed proteins using the serum samples of five patients. The identified differentially expressed proteins were analyzed using various bioinformatics tools.RESULTS Dapagliflozin significantly improved the clinical manifestation of the patients. There were 18 downregulated proteins and one upregulated protein in the serum samples of patients after dapagliflozin administration. Bioinformatics analyses, including subcellular localization, Eu Karyotic Orthologous Groups, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes annotations, were used to profile the biological characteristics of the 19 differentially expressed proteins. Based on the literature and function enrichment analysis, two downregulated proteins, myeloperoxidase(MPO) and alpha Ⅱ B integrin(ITGA2B), and one upregulated protein, podocalyxin(PCX), were selected for enzyme linked immunosorbent assay validation. These validated differentially expressed proteins had multiple correlations with clinical indexes, including Hb Ac1 and fasting C-peptide.CONCLUSION Dapagliflozin has hypoglycemic effects and regulates the serum expressions of MPO, ITGA2B, and PCX, possibly contributing to the effects of dapagliflozin on oxidative stress, insulin resistance, and lipid metabolism.

Quantitative proteomics reveals key pathways in the symbiotic interface and the likely extracellular property of soybean symbiosome

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.

Quantitative mitochondrial proteome of pancreatic INS-1β cells stimulated with prolonged high glucose using SILAC

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)

Integrative cytology and proteome alterations unravel the multitarget effect of a novel alkaloid antofine against Penicillium italicum

Penicillium italicum is the causal agent of citrus blue mold,which is a major threat to the global citrus fruit industry.Antofine,a natural phenanthroindolizidine alkaloid,is water-soluble and exhibits a broad range of biological activities.However,whether it can inhibit P italicum growth and the potential inhibitory mechanism remains to be elucidated.This study aimed to investigate the antifungal mechanism of antofine against P italicum using scanning electron microscopy,transmission electron microscopy(TEM),propidium iodide staining,and tandem mass tag-labeled quantitative proteomic analysis.Antofine was found to exhibit its preeminent antifungal activity against P italicum with a minimum inhibitory concentration of 1.56 mg/L and a minimum fungicidal concentration of 6.25 mg/L.The challenge test revealed that antofine inhibited the development of citrus blue mold during a 6-d P italicum-infected period.Antofine acted on its potential multitargets to inhibit P italicum growth by synergistically activating oxidative stress through accumulating excess reactive oxygen species,impairing membrane integrity.inducing membrane lipid peroxidation,and disrupting mitochondrial function,thereby disrupting the membrane system and reducing cell via-bility.Moreover,antofine treatment downregulated most differentially expressed proteins involved in carbon metabolism,pyruvate metabolism,and the tricarboxylic acid cycle(TCA)in P italicum mycelia,which may explain the mitochondrial decomposition observed by TEM and the de-clines in ATP levels as well as the activities of TCA-related enzymes.These results indicate that antofine treatment inhibited P italicum growth by targeting the cell membrane and mitochondria.

Anemoside B4 inhibits SARS-CoV-2 replication in vitro and in vivo

Objective: Anemoside B4(AB4), the most abundant triterpenoidal saponin isolated from Pulsatilla chinensis, inhibited influenza virus FM1 or Klebsiella pneumoniae-induced pneumonia. However, the anti-SARS-CoV-2 effect of AB4 has not been unraveled. Therefore, this study aimed to determine the antiviral activity and potential mechanism of AB4 in inhibiting human coronavirus SARS-CoV-2 in vivo and in vitro.Methods: The cytotoxicity of AB4 was evaluated using the Cell Counting Kit-8(CCK8) assay. SARS-CoV-2 infected HEK293T, HPAEpiC, and Vero E6 cells were used for in vitro assays. The antiviral effect of AB4 in vivo was evaluated by SARS-CoV-2-infected hACE2-IRES-luc transgenic mouse model. Furthermore,label-free quantitative proteomics and bioinformatic analysis were performed to explore the potential antiviral mechanism of action of AB4. Type Ⅰ IFN signaling-associated proteins were assessed using Western blotting or immumohistochemical staining.Results: The data showed that AB4 reduced the propagation of SARS-CoV-2 along with the decreased Nucleocapsid protein(N), Spike protein(S), and 3C-like protease(3CLpro) in HEK293T cells. In vivo antiviral activity data revealed that AB4 inhibited viral replication and relieved pneumonia in a SARS-CoV-2 infected mouse model. We further disclosed that the antiviral activity of AB4 was associated with the enhanced interferon(IFN)-β response via the activation of retinoic acid-inducible gene Ⅰ(RIG-1) like receptor(RLP) pathways. Additionally, label-free quantitative proteomic analyses discovered that 17 proteins were significantly altered by AB4 in the SARS-CoV-2 coronavirus infections cells. These proteins mainly clustered in RNA metabolism.Conclusion: Our results indicated that AB4 inhibited SARS-CoV-2 replication through the RLR pathways and moderated the RNA metabolism, suggesting that it would be a potential lead compound for the development of anti-SARS-CoV-2 drugs.

Quantitative Proteomics Using Isobaric Labeling:A Practical Guide

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.

Quantitative and Functional Phosphoproteomic Analysis Reveals that Ethylene Regulates Water Transport via the C-Terminal Phosphorylation of Aquaporin PIP2;1 in Arabidopsis

Ethylene participates in the regulation of numerous cellular events and biological processes, including wa- ter loss, during leaf and flower petal wilting. The diverse ethylene responses may be regulated via dynamic interplays between protein phosphorylation/dephosphorylation and ubiquitin/26S proteasome-mediated protein degradation and protease cleavage. To address how ethylene alters protein phosphorylation through multi-furcated signaling pathways, we performed a lSN stable isotope labelling-based, differential, and quantitative phosphoproteomics study on air- and ethylene-treated ethylene-insensitive Arabidopsis double loss-of-function mutant ein3-1/eill-1. Among 535 non-redundant phosphopeptides identified, two and four phosphopeptides were up- and downregulated by ethylene, respectively. Ethylene- regulated phosphorylation of aquaporin PIP2;1 is positively correlated with the water flux rate and water loss in leaf. Genetic studies in combination with quantitative proteomics, immunoblot analysis, protoplast swelling/shrinking experiments, and leaf water loss assays on the transgenic plants expressing both the wild-type and S280A/S283A-mutated PIP2;1 in the both Col-O and ein3eill genetic backgrounds suggest that ethylene increases water transport rate in Arabidopsis cells by enhancing S280/S283 phosphorylation at the C terminus of PIP2;1. Unknown kinase and/or phosphatase activities may participate in the initial up- regulation independent of the cellular functions of EIN3/EIL1. This finding contributes to our understanding of ethylene-regulated leaf wilting that is commonly observed during post-harvest storage of plant organs.

Label-free quantitative proteomics reveals fibrinopeptide B and heparin cofactorⅡas potential serum biomarkers in respiratory syncytial virus-infected mice treated with Qingfei oral liquid formula

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.

Quantitative proteomics revealed extensive microenvironmental changes after stem cell transplantation in ischemic stroke

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.

An integrated quantitative proteomics strategy reveals the dual mechanisms of celastrol against acute inflammation

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.

Exploring the Nicotinic Acetylcholine Receptor-associated Proteome with iTRAQ and Transgenic Mice

Neuronal nicotinic acetylcholine receptors （nAChRs） containing Gt4 and 132 subunits are the principal receptors in the mammalian central nervous system that bind nicotine with high affin- ity. These nAChRs are involved in nicotine dependence, mood disorders, neurodegeneration and neuroprotection. However, our understanding of the interactions between a4β2-containing （a4β2） nAChRs and other proteins remains limited. In this study, we identified proteins that inter- act with ct4β2 nAChRs in a gene-dose dependent pattern by immunopurifying β2 nAChRs from mice that differ in ct4 and β2 subunit expression and performing proteomic analysis using isobaric tags for relative and absolute quantitation （iTRAQ）. Reduced expression of either the a4 or the β2 subunit results in a correlated decline in the expression of a number of putative interacting proteins. We identified 208 proteins co-imrnunoprecipitated with these nAChRs. Furthermore, stratified lin- ear regression analysis indicated that levels of 17 proteins was correlated significantly with expres- sion of at4β2 nAChRs, including proteins involved in cytoskeletal rearrangement and calcium signaling. These findings represent the first application of quantitative proteomics to produce a β2 nAChR interactome and describe a novel technique used to discover potential targets for pharma- cological manipulation of a4β2 nAChRs and their downstream signaling mechanisms.