Low temperature(LT)in spring has become one of the principal abiotic stresses that restrict the growth and development of wheat.Diverse analyses were performed to investigate the mechanism underlying the response of w...Low temperature(LT)in spring has become one of the principal abiotic stresses that restrict the growth and development of wheat.Diverse analyses were performed to investigate the mechanism underlying the response of wheat grain development to LT stress during booting.These included morphological observation,measurements of starch synthase activity,and determination of amylose and amylopectin content of wheat grain after exposure to treatment with LT during booting.Additionally,proteomic analysis was performed using tandem mass tags(TMT).Results showed that the plumpness of wheat grains decreased after LT stress.Moreover,the activities of sucrose synthase(SuS,EC 2.4.1.13)and ADP-glucose pyrophosphorylase(AGPase,EC 2.7.7.27)exhibited a significant reduction,leading to a significant reduction in the contents of amylose and amylopectin.A total of 509 differentially expressed proteins(DEPs)were identified by proteomics analysis.The Gene Ontology(GO)enrichment analysis showed that the protein difference multiple in the nutritional repository activity was the largest among the molecular functions,and the up-regulated seed storage protein(ssP)played an active role in the response of grains to LT stress and subsequent damage.The Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis showed that LT stress reduced the expression of DEPs such as sucrose phosphate synthase(SPS),glucose-1-phosphate adenylyltransferase(glgC),andβ-fructofuranosidase(FFase)in sucrose and starch metabolic pathways,thus affecting the synthesis of grain starch.In addition,many heat shock proteins(HsPs)were found in the protein processing in endoplasmic reticulum pathways,which can resist some damage caused by LT stress.These findings provide a new theoretical foundation for elucidating the underlying mechanism governing wheat yield developmentafterexposuretoLTstress inspring.展开更多
BACKGROUND Despite the developments in the field of kidney transplantation,the already existing diagnostic techniques for patient monitoring are considered insufficient.Protein biomarkers that can be derived from mode...BACKGROUND Despite the developments in the field of kidney transplantation,the already existing diagnostic techniques for patient monitoring are considered insufficient.Protein biomarkers that can be derived from modern approaches of proteomic analysis of liquid biopsies(serum,urine)represent a promising innovation in the monitoring of kidney transplant recipients.AIM To investigate the diagnostic utility of protein biomarkers derived from proteomics approaches in renal allograft assessment.METHODS A systematic review was conducted in accordance with PRISMA guidelines,based on research results from the PubMed and Scopus databases.The primary focus was on evaluating the role of biomarkers in the non-invasive diagnosis of transplant-related com-plications.Eligibility criteria included protein biomarkers and urine and blood samples,while exclusion criteria were language other than English and the use of low resolution and sensitivity methods.The selected research articles,were categorized based on the biological sample,condition and methodology and the significantly and reproducibly differentiated proteins were manually selected and extracted.Functional and network analysis of the selected proteins was performed.RESULTS In 17 included studies,58 proteins were studied,with the cytokine CXCL10 being the most investigated.Biological pathways related to immune response and fibrosis have shown to be enriched.Applications of biomarkers for the assessment of renal damage as well as the prediction of short-term and long-term function of the graft were reported.Overall,all studies have shown satisfactory diagnostic accuracy of proteins alone or in combination with conventional methods,as far as renal graft assessment is concerned.CONCLUSION Our review suggests that protein biomarkers,evaluated in specific biological fluids,can make a significant contribution to the timely,valid and non-invasive assessment of kidney graft.展开更多
OBJECTIVE:To observe the effects of moxibustion at Zusanli(ST36)on rats with chronic fatigue syndrome(CFS)and to analyze the mechanisms of moxibustion through hippocampal Proteomics.METHODS:Male Sprague-Dawley(SD)rats...OBJECTIVE:To observe the effects of moxibustion at Zusanli(ST36)on rats with chronic fatigue syndrome(CFS)and to analyze the mechanisms of moxibustion through hippocampal Proteomics.METHODS:Male Sprague-Dawley(SD)rats were randomly divided into three groups:control group(CON),model group(MOD),and moxibustion group(MOX),with 12 rats in each group.The MOD and MOX groups underwent chronic multi-factor stress stimulation for 35 d to establish the CFS model.After modeling,the rats in the MOX group received mild moxibustion at Zusanli(ST36)(bilateral)for 10 minutes daily for 28 d.During the treatment period,rats in both the MOD and MOX groups continued modeling,while the CON group was kept under normal breeding conditions.The general condition of the rats was monitored,and behaviors were assessed using the Open Field Test(OFT),Exhaustion Treadmill Test,and Morris Water Maze(MWM).Hematoxylin and eosin(HE)staining and transmission electron microscopy(TEM)were employed to observe morphological changes in the hippocampus.Label-free Proteomics were utilized to identify differentially expressed proteins(DEPs)in the hippocampus,followed by bioinformatics analysis.The reliability of the Proteomics results was verified using Parallel Reaction Monitoring.RESULTS:A:Moxibustion at Zusanli(ST36)significantly reduced the general condition score of CFS rats,improved their behavioral performance in OFT,treadmill and MWM,and repaired the pathological and synaptic structural damage in the hippocampus.B:We identified DEPs by applying a fold change threshold of 1.2 and a significance level of P<0.05.In the comparison between the CON and the MOD,we identified a total of 72 DEPs(31 up-regulated and 41 down-regulated)associated with the development of CFS.In the comparison between the MOX and the MOD group,we identified a total of 103 DEPs(40 up-regulated and 63 down-regulated)related to the therapeutic effects of moxibustion.Gene Ontology(GO)enrichment analysis showed that CFS and moxibustion treatment were related to multiple biological processes,molecular functions,and cellular components.Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis revealed that CFS pathogenesis was linked to base excision repair,steroid biosynthesis,and systemic lupus erythematosus,Furthermore,the treatment of CFS with moxibustion was relevant to terpenoid skeleton biosynthesis.C:Compared with the two comparison groups,we identified 16 potential biomarkers,noting that moxibustion reversed the upregulation of 14 DEPs and the down-regulation of 2 DEPs in CFS.These proteins are mainly associated with synaptic plasticity,ribosomal function,neurotransmitter secretion,glycine metabolism,and mitochondrial function.CONCLUSION:Moxibustion at Zusanli(ST36)is effective in treating CFS,the potential biomarkers identified by Proteomics confirm that the mechanisms of moxibustion involve multiple targets and pathways,which may be key to regulating the structural and functional damage in the hippocampus associated with CFS,highlighting their significant value for future research.展开更多
Natural products(NPs)have long been recognized for their therapeutic potential,especially in cancer treatment,due to an ability to interact with multiple cellular pathways.The identification of molecular targets for N...Natural products(NPs)have long been recognized for their therapeutic potential,especially in cancer treatment,due to an ability to interact with multiple cellular pathways.The identification of molecular targets for NPs is a critical step in understanding anticancer mechanisms,with chemical proteomics emerging as a powerful approach.Both label-based and-free proteomic techniques have been utilized to identify these targets,each with their own advantages and limitations.While label-based methods provide high specificity through chemical tagging,the requirement for labeling can be a limitation,potentially altering NP natural properties.Conversely,label-free techniques allow for the detection of NP-protein interactions without structural modification but may struggle with transient interactions or low-abundance targets.Recent advances in artificial intelligence(AI)have further enhanced the field by improving target prediction and streamlining data analysis.AI-driven models,especially machine learning algorithms,have proven effective in processing complex proteomic data and predicting potential NP-protein interactions.The integration of AI with chemical proteomics accelerates target identification and deepens our understanding of the molecular mechanisms underlying the anticancer effects of NPs.This review explores the application of chemical proteomics and AI in the identification of cancer-related targets for NPs,highlighting current challenges and future directions for clinical translation.展开更多
Objectives To elucidate the potential mechanisms of electroacupuncture(EA)in restoring detrusor-bladder neck dyssynergia(DBND)following suprasacral spinal cord injury(SSCI).Methods A total of 52 specific pathogen-free...Objectives To elucidate the potential mechanisms of electroacupuncture(EA)in restoring detrusor-bladder neck dyssynergia(DBND)following suprasacral spinal cord injury(SSCI).Methods A total of 52 specific pathogen-free(SPF)grade famale Sprague-Dawley(SD)rats(10-12 weeks,250-280 g)were randomly assigned to either a sham group(n=12)or a spinal cord injury model group(n=40).In the model group,DBND was induced through Hassan Shaker spinal cord transection at T10 level,with 24 rats meeting inclusion criteria and subse-quently randomized into DBND group(n=12)and EA intervention group(DBND+EA group,n=12).After spinal shock recovery(day 19 after modeling),DBND+EA group received EA treatment at Ciliao(BL32),Zhongji(RN3),and Sanyinjiao(SP6)acupoints for 20 min per ses-sion at 10/50 Hz frequencies,once daily for 10 d.Sham and DBND groups received anesthe-sia only without EA intervention.On day 29 post-modeling,all rats underwent urodynamic assessments,followed by hematoxylin and eosin(HE)staining,tandem mass tag(TMT)pro-teomics,and Western blot(WB)analysis of detrusor and bladder neck tissues.Differentially expressed proteins(DEPs)were defined as proteins with P<0.05,unique peptides≥2,and fold change>1.2 or<0.83.Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway anal-ysis was performed using KOBAS 3.0(P<0.01),and protein-protein interaction(PPI)net-works were analyzed using Search Tool for the Retrieval of Interacting Genes/Proteins(STRING)11.5 and Cytoscape 3.9.1.Results Compared with sham group,DBND group showed significantly elevated leak point pressure(LPP)and maximum cystometric capacity(MCC)(both P<0.01).EA treatment sig-nificantly reduced both LPP and MCC compared with DBND group(P<0.01 and P<0.05,re-spectively).HE staining revealed that EA reduced detrusor fibrosis and improved bladder neck inflammation.TMT proteomics identified 30 overlapping DEPs in detrusor and 59 over-lapping DEPs in bladder neck when comparing DBND+EA/DBND groups with sham group.In detrusor tissue,KEGG analysis revealed 10 significantly enriched pathways(P<0.01),in-cluding mitogen-activated protein kinase(MAPK)signaling pathway.PPI analysis showed 22 of 30 DEPs were interconnected.In bladder neck tissue,14 pathways were significantly en-riched(P<0.01),including relaxin signaling pathway,with 51 of 59 DEPs showing intercon-nections.Both TMT and WB validations demonstrated that compared with sham controls,DBND rats exhibited upregulated collagen type IV alpha 2 chain(Col4a2)and downregulated guanine nucleotide-binding protein G(z)subunit alpha(Gnaz)in detrusor tissue,while EA treatment normalized both proteins(both P<0.05).In bladder neck tissue,DBND rats showed decreased expression of smoothelin(Smtn)and calcium-activated potassium chan-nel subunit beta-1(Kcnmb1)compared with sham controls(both P<0.01),which were both upregulated following EA treatment(P<0.01 and P<0.05,respectively).Conclusion EA restores detrusor-bladder neck coordination in DBND through dual-target mechanisms.In detrusor tissue,EA modulates contraction via extracellular matrix remodel-ing,cyclic adenosine monophosphate(cAMP)signaling pathway regulation,and enhanced adenosine triphosphate(ATP)biosynthesis mediated by neurotransmitters.In bladder neck tissue,EA promotes relaxation by maintaining contractile phenotypes,reducing fibrosis,sup-pressing smooth muscle excitation,and regulating presynaptic neurotransmitter release.These findings provide mechanistic insights into EA's therapeutic role in managing DBND.展开更多
Objective:To explore the impact of exogenous chitosan on the growth and metabolism of Glycyrrhiza uralensis Fisch.(G.uralensis)and to improve the quality of cultivated G.uralensis for both medicine and food and aid in...Objective:To explore the impact of exogenous chitosan on the growth and metabolism of Glycyrrhiza uralensis Fisch.(G.uralensis)and to improve the quality of cultivated G.uralensis for both medicine and food and aid in the increase in the content of effective components in G.uralensis.Methods:In this study,whole G.uralensis plants were treated with exogenous chitosan,and compre-hensive analyses of secondary metabolites and proteins were conducted using liquid chromatography with tandem mass spectrometry and isobaric tag for relative and absolute quantitation,respectively.Effects of chitosan induction on endogenous hormones of G.uralensis were analyzed using an enzyme-linked immunosorbent assay.Gene ontology function annotation and Kyoto Encyclopedia of Genes and Genomes pathway annotation were conducted to study the effect of chitosan induction on the proteome.Results:Chitosan induction significantly increased the levels of flavonoids in G.uralensis;however,the variation in triterpenoids was not substantial.Biological processes,including photosynthesis,secondary metabolism,and abiotic stress responses,were significantly enriched.Additionally,the photosynthetic pathway,photosynthesis-antenna protein pathway,and plant hormone signal transduction pathway were significantly enriched.In the flavonoid biosynthesis pathway,the upstream-related enzyme phenylalanine ammonia-lyase(PAL)and the downstream-related enzymes chalcone synthase(CHS),polyketide reductase(PKR),chalcone isomerase(CHI),and vestitone reductase(VR)were significantly upregulated.Conclusions:Our findings suggest that chitosan induction may promote the tricarboxylic acid(TCA)cycle,and the TCA cycle enhancement significantly upregulated PAL,CHS,PKR,CHI,and VR,the five key enzymes involved in flavonoid synthesis of G.uralensis,indicating that chitosan induction activated the entire metabolic pathway associated with flavonoids in G.uralensis.Our findings provide a reference for improving the quality of cultivated G.uralensis from the perspective of pharmacodynamic components.展开更多
BACKGROUND:Community-acquired pneumonia(CAP)represents a significant public health concern due to its widespread prevalence and substantial healthcare costs.This study was to utilize an integrated proteomic and metabo...BACKGROUND:Community-acquired pneumonia(CAP)represents a significant public health concern due to its widespread prevalence and substantial healthcare costs.This study was to utilize an integrated proteomic and metabolomic approach to explore the mechanisms involved in severe CAP.METHODS:We integrated proteomics and metabolomics data to identify potential biomarkers for early diagnosis of severe CAP.Plasma samples were collected from 46 CAP patients(including27 with severe CAP and 19 with non-severe CAP)and 19 healthy controls upon admission.A comprehensive analysis of the combined proteomics and metabolomics data was then performed to elucidate the key pathological features associated with CAP severity.RESULTS:The proteomic and metabolic signature was markedly dif ferent between CAPs and healthy controls.Pathway analysis of changes revealed complement and coagulation cascades,ribosome,tumor necrosis factor(TNF)signaling pathway and lipid metabolic process as contributors to CAP.Furthermore,alterations in lipid metabolism,including sphingolipids and phosphatidylcholines(PCs),and dysregulation of cadherin binding were observed,potentially contributing to the development of severe CAP.Specifi cally,within the severe CAP group,sphingosine-1-phosphate(S1P)and apolipoproteins(APOC1 and APOA2)levels were downregulated,while S100P level was signifi cantly upregulated.CONCLUSION:The combined proteomic and metabolomic analysis may elucidate the complexity of CAP severity and inform the development of improved diagnostic tools.展开更多
AIM:To employ proteome-wide Mendelian randomization(MR)to explore novel protein and drug targets for retinal neurodegenerative diseases(RND)in individuals of European ancestry.METHODS:This study used summary data-base...AIM:To employ proteome-wide Mendelian randomization(MR)to explore novel protein and drug targets for retinal neurodegenerative diseases(RND)in individuals of European ancestry.METHODS:This study used summary data-based MR to analyze the correlation between plasma protein levels and three RND,with protein data derived from two independent large-scale proteomics datasets.Potential drug targets were identified using Bayesian colocalization,followed by MR analysis,sensitivity testing,and external validation.Drug prediction and molecular docking were conducted to evaluate the druggability of the target proteins.RESULTS:The study identified six promising protein targets,each successfully replicated at least twice.The results included three proteins related to diabetic retinopathy(ICAM1,GCKR,WARS),two proteins related to age-related macular degeneration(WARS,BRD2),and two proteins related to glaucoma(SVEP1,NPTXR).Additionally,drug prediction and molecular docking indicated that five drugs(fenofibrate,trofinetide,ticagrelor,lifitegrast,acetaminophen)effectively bound to the target proteins.CONCLUSION:This study identified six potential protein targets for RND and five existing drugs with therapeutic potential.By integrating plasma proteomics with genetic data,it provides a cost-effective framework for drug discovery.展开更多
Background:Fufang Muji Granules is a traditional Chinese medicine of the Manchu ethnic group and is thought to treat hepatitis and liver injury by inhibiting the elevation of alpha-fetoprotein.Methods:In this investig...Background:Fufang Muji Granules is a traditional Chinese medicine of the Manchu ethnic group and is thought to treat hepatitis and liver injury by inhibiting the elevation of alpha-fetoprotein.Methods:In this investigation,tandem mass tag(TMT)-based quantitative proteomics was performed to figure out the therapeutic mechanisms of Fufang Muji Granules on liver injury caused by carbon tetrachloride(CCl_(4))in rats.Results:Biochemical analyses(alanine aminotransferase;glutamate aminotransferase;aspartate aminotransferase)and histologic analyses(hematoxylin-eosin)demonstrated that FMG was effective in ameliorating liver injury.A sum of 6,208 proteins were identified and 2,475 proteins were determined as differential abundance proteins(DAPs)in rat liver treated with Fufang Muji Granules which compared to the model group.Bioinformatics analysis indicated that the DAPs are primarily enriched in multiple pathways such as rno00280(valine,leucine,and isoleucine degradation),rno00640(Propanoate metabolism),and rno00380(Tryptophan metabolism).Western blot was employed to validate the findings from the proteomic analysis.Conclusion:This study not only provides useful information on the mechanism of Fufang Muji Granules in the treatment of liver injury but also serves as a basis for further study of Fufang Muji Granules in vivo.展开更多
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
Neonatal hypoxic-ischemic encephalopathy(HIE)refers to neonatal brain damage caused by various factors during the perinatal period that lead to hypoxia and reduced cerebral blood flow[1].Globally,0.2%to 2.26%of newbor...Neonatal hypoxic-ischemic encephalopathy(HIE)refers to neonatal brain damage caused by various factors during the perinatal period that lead to hypoxia and reduced cerebral blood flow[1].Globally,0.2%to 2.26%of newborns develop HIE,with approximately 20%resulting in neonatal death and about 25%of survivors suffering from neurological impairment[2].Currently,there is a lack of highly sensitive and specific diagnostic tools for HIE,posing significant challenges to reducing HIE mortality and neurological abnormalities[3].The development of high-throughput proteomics technology based on mass spectrometry(MS)has significantly enhanced the potential to discover biomarkers in biological fluids such as plasma,cerebrospinal fluid,saliva,and urine[4].Proteomics technology has become an engine for exploring novel markers of HIE[5].This article systematically reviews the progress of proteomics technology in the study of biomarkers for the early diagnosis of HIE,elucidating its potential application value.展开更多
Objective:While immunotherapy holds great potential for triple-negative breast cancer(TNBC),the lack of non-invasive biomarkers to identify beneficiaries limits the application.Methods:Paired baseline,on-treatment,and...Objective:While immunotherapy holds great potential for triple-negative breast cancer(TNBC),the lack of non-invasive biomarkers to identify beneficiaries limits the application.Methods:Paired baseline,on-treatment,and post-treatment plasma samples were collected from 195 TNBC patients receiving anti-PD-1 immunotherapy in this retrospective study conducted at the Fudan University Shanghai Cancer Center(FUSCC)for sequential high-precision proteomic profiling.Results:ARG1,NOS3,and CD28 were identified as plasma proteins significantly associated with the response to immunotherapy in neoadjuvant settings or in advanced stages of TNBC.Matched single-cell RNA sequencing data were incorporated to correlate peripheral plasma with the tumor microenvironment.Furthermore,the Plasma Immuno Prediction Score was developed to demonstrate significant predictive power for evaluating the efficacy and prognosis of patients undergoing neoadjuvant immunotherapy.Conclusions:The results underscore the importance of systemic immunity in the immunotherapy response and support the use of plasma protein profiles as a feasible tool for enhancing personalized management of immunotherapy in breast cancer.展开更多
Tauopathies,diseases characterized by neuropathological aggregates of tau including Alzheimer's disease and subtypes of fro ntotemporal dementia,make up the vast majority of dementia cases.Although there have been...Tauopathies,diseases characterized by neuropathological aggregates of tau including Alzheimer's disease and subtypes of fro ntotemporal dementia,make up the vast majority of dementia cases.Although there have been recent developments in tauopathy biomarkers and disease-modifying treatments,ongoing progress is required to ensure these are effective,economical,and accessible for the globally ageing population.As such,continued identification of new potential drug targets and biomarkers is critical."Big data"studies,such as proteomics,can generate information on thousands of possible new targets for dementia diagnostics and therapeutics,but currently remain underutilized due to the lack of a clear process by which targets are selected for future drug development.In this review,we discuss current tauopathy biomarkers and therapeutics,and highlight areas in need of improvement,particularly when addressing the needs of frail,comorbid and cognitively impaired populations.We highlight biomarkers which have been developed from proteomic data,and outline possible future directions in this field.We propose new criteria by which potential targets in proteomics studies can be objectively ranked as favorable for drug development,and demonstrate its application to our group's recent tau interactome dataset as an example.展开更多
BACKGROUND As a well-known fact to the public,gestational diabetes mellitus(GDM)could bring serious risks for both pregnant women and infants.During this important investigation into the linkage between GDM patients a...BACKGROUND As a well-known fact to the public,gestational diabetes mellitus(GDM)could bring serious risks for both pregnant women and infants.During this important investigation into the linkage between GDM patients and their altered expression in the serum,proteomics techniques were deployed to detect the differentially expressed proteins(DEPs)of in the serum of GDM patients to further explore its pathogenesis,and find out possible biomarkers to forecast GDM occurrence.METHODS Subjects were divided into GDM and normal control groups according to the IADPSG diagnostic criteria.Serum samples were randomly selected from four cases in each group at 24-28 wk of gestation,and the blood samples were identified by applying iTRAQ technology combined with liquid chromatography-tandem mass spectrometry.Key proteins and signaling pathways associated with GDM were identified by bioinformatics analysis,and the expression of key proteins in serum from 12 wk to 16 wk of gestation was further verified using enzyme-linked immunosorbent assay (ELISA).RESULTS Forty-seven proteins were significantly differentially expressed by analyzing the serum samples between the GDMgravidas as well as the healthy ones. Among them, 31 proteins were found to be upregulated notably and the rest16 proteins were downregulated remarkably. Bioinformatic data report revealed abnormal expression of proteinsassociated with lipid metabolism, coagulation cascade activation, complement system and inflammatory responsein the GDM group. ELISA results showed that the contents of RBP4, as well as ANGPTL8, increased in the serumof GDM gravidas compared with the healthy ones, and this change was found to initiate from 12 wk to 16 wk ofgestation.CONCLUSION GDM symptoms may involve abnormalities in lipid metabolism, coagulation cascade activation, complementsystem and inflammatory response. RBP4 and ANGPTL8 are expected to be early predictors of GDM.展开更多
OBJECTIVE: To investigate the underlying protein molecular mechanisms of "Qi stagnation and blood stasis syndrome"(QS) and "Qi deficiency and blood stasis syndrome"(QD), as two subtypes of coronary...OBJECTIVE: To investigate the underlying protein molecular mechanisms of "Qi stagnation and blood stasis syndrome"(QS) and "Qi deficiency and blood stasis syndrome"(QD), as two subtypes of coronary artery disease(CAD) in Traditional Chinese Medicine(TCM),following percutaneous coronary intervention(PCI).METHODS: In this study, a total of 227 CAD patients with QS and 211 CAD patients with QD were enrolled;all participants underwent PCI. Label-free quantification proteomics were employed to analyze the changes in serum in two subtypes of CAD patients before and 6 months after PCI, aiming to elucidate the intervention mechanism of PCI in treating CAD characterized by two different TCM syndromes.RESULTS: Biochemical analysis revealed significant changes in tumor necrosis factor-α, high density lipoprotein cholesterol, blood stasis clinical symptoms observation, and Gensini levels in both patient groups post-PCI;Proteomic analysis identified 79 and 95 differentially expressed proteins in the QS and QD patient groups, respectively, compared to their control groups.complement C8 alpha chain, complement factor H,apolipoprotein H, apolipoprotein B, plasminogen,carbonic anhydrase 2, and complement factor Ⅰ were altered in both comparison groups. Furthermore,enrichment analysis demonstrated that cell adhesion and connectivity-related processes underwent changes in QS patients post-PCI, whereas lipid metabolism-related pathways, including the peroxisome proliferator-activated receptor signaling pathway and extracellular matrix receptor interaction, underwent changes in the QD group.The protein-protein interaction network analysis further enriched 52 node proteins, including apolipoprotein B,lipoprotein(a), complement C5, apolipoprotein A4,complement C8 alpha chain, complement C8 beta chain,complement C8 gamma chain, apolipoprotein H,apolipoprotein A-Ⅱ, albumin, complement C4-B,apolipoprotein C3, among others. The functional network of these proteins is posited to contribute to the pathophysiology of CAD characterized by TCM syndromes.CONCLUSION: The current quantitative proteomic study has preliminarily identified biomarkers of CAD in different TCM subtypes treated with PCI, potentially laying the groundwork for understanding the protein profiles associated with the treatment of various TCM subtypes of CAD.展开更多
In this editorial,we comment on the article by Cao et al.Through applying isobaric tags for relative and absolute quantification technology coupled with liquid chromatography-tandem mass spectrometry,the researchers o...In this editorial,we comment on the article by Cao et al.Through applying isobaric tags for relative and absolute quantification technology coupled with liquid chromatography-tandem mass spectrometry,the researchers observed significant differential expression of 47 proteins when comparing serum samples from pregnant women with gestational diabetes mellitus(GDM)to the healthy ones.GDM symptoms may involve abnormalities in inflammatory response,complement system,coagulation cascade activation,and lipid metabolism.Retinol binding protein 4 and angiopoietin like 8 are potential early indicators of GDM.GDM stands out as one of the most prevalent metabolic complications during pregnancy and is linked to severe maternal and fetal outcomes like pre-eclampsia and stillbirth.Nevertheless,none of the biomarkers discovered so far have demonstrated effectiveness in predicting GDM.Our topic was designed to foster insights into advances in the application of proteomics for early prenatal screening of GDM.展开更多
Objective Hydroquinone(HQ),one of the phenolic metabolites of benzene,is widely recognized as an important participant in benzene-induced hematotoxicity.However,there are few relevant proteomics in HQ-induced hematoto...Objective Hydroquinone(HQ),one of the phenolic metabolites of benzene,is widely recognized as an important participant in benzene-induced hematotoxicity.However,there are few relevant proteomics in HQ-induced hematotoxicity and the mechanism hasn’t been fully understood yet.Methods In this study,we treated K562 cells with 40μmol/L HQ for 72 h,examined and validated protein expression changes by Label-free proteomic analysis and Parallel reaction monitoring(PRM),and performed bioinformatics analysis to identify interaction networks.Results One hundred and eighty-seven upregulated differentially expressed proteins(DEPs)and 279 downregulated DEPs were identified in HQ-exposed K562 cells,which were involved in neutrophilmediated immunity,blood microparticle,and other GO terms,as well as the lysosome,metabolic,cell cycle,and cellular senescence-related pathways.Focusing on the 23 DEGs and 5 DEPs in erythroid differentiation-related pathways,we constructed the network of protein interactions and determined 6 DEPs(STAT1,STAT3,CASP3,KIT,STAT5B,and VEGFA)as main hub proteins with the most interactions,among which STATs made a central impact and may be potential biomarkers of HQ-induced hematotoxicity.Conclusion Our work reinforced the use of proteomics and bioinformatic approaches to advance knowledge on molecular mechanisms of HQ-induced hematotoxicity at the protein level and provide a valuable basis for further clarification.展开更多
BACKGROUND Obstructed defecation syndrome(ODS)represents the most prevalent form of chronic constipation,affecting a diverse patient population,leading to numerous complications,and imposing a significant burden on he...BACKGROUND Obstructed defecation syndrome(ODS)represents the most prevalent form of chronic constipation,affecting a diverse patient population,leading to numerous complications,and imposing a significant burden on healthcare resources.Most ODS patients have insufficient rectal propulsion,but the exact mechanism underlying the pathogenesis of ODS remains unclear.AIM To explore the molecular mechanism underlying the pathogenesis of ODS.METHODS A total of 30 pairs of rectal samples were collected from patients with ODS(ODS group)or grade IV prolapsed hemorrhoids without constipation(control group)for quantitative proteomic and bioinformatic analysis.Subsequently,50 pairs of paraffin-embedded rectal specimens were selected for immunohistochemistry and immunofluorescence studies to validate the analysis results.Human intestinal smooth cell contractile function experiments and electrophysiological experiments were conducted to verify the physiological functions of target proteins.Cellular ultrastructure was detected using transmission electron microscopy.RESULTS In comparison to the control group,the expression level of dystrophin(DMD)in rectal specimens from ODS patients was markedly reduced.This finding was corroborated using immunohistochemistry and immunofluorescence techniques.The diminished expression of DMD compromised the contractile function of intestinal smooth muscle cells.At the molecular level,nucleoporin protein 153 and L-type voltage-gated calcium channel were found to be overexpressed in intestinal smooth muscle cells exhibiting downregulated DMD expression.Electrophysiological experiments confirmed an excessive influx of calcium ions into these cells.Moreover,vacuolar-like structures which may be associated with excessive calcium influx were observed in the cells by transmission electron microscopy.CONCLUSION Decreased DMD expression in intestinal smooth muscle may upregulate L-type voltage-gated calcium channel expression,leading to excessive calcium influx which may cause a decrease in rectal propulsion,thereby contributing to the pathogenesis of ODS.展开更多
Objective:To uncover the underlying mechanisms of action of the Yinlai decoction on high-calorie dietinduced pneumonia through proteomics analysis.Methods:Based on the Gene Expression Omnibus(GEO)database,lung tissue ...Objective:To uncover the underlying mechanisms of action of the Yinlai decoction on high-calorie dietinduced pneumonia through proteomics analysis.Methods:Based on the Gene Expression Omnibus(GEO)database,lung tissue samples from normal and high-fat diet(HFD)fed mice in the GSE16377 dataset were selected as test cohorts to identify differentially expressed genes and conduct bioinformatics analyses.In the animal experiments,mice were randomly divided into the control(N),high-calorie diet pneumonia(M),and Yinlai decoction treatment(Y)groups.Mice in the M group received high-calorie feed and a 0.5 mg/mL lipopolysaccharide solution spray for 30 min for 3 d.The mice in the Y group were intragastrically administered 2 mL/10 g Yinlai decoction twice daily for 3 d.Pathological evaluation of the lung tissue was performed.Differentially expressed proteins(DEPs)in the lung tissue were identified using quantitative proteomics and bioinformatics analyses.The drug-target relationships between Yinlai decoction and core DEPs in the lung tissue were verified using AutoDock Vina and Molecular Graphics Laboratory(MGL)Tools.DEPs were verified by western blot.Results:GEO data mining showed that an HFD altered oxidative phosphorylation in mouse lung tissue.The Yinlai decoction alleviated pathological damage to lung tissue and pneumonia in mice that were fed a high-calorie diet.A total of 47 DEPs were identified between the Y and M groups.Enrichment analysis revealed their association with energy metabolism pathways such as the tricarboxylic acid cycle(TCA)and oxidative phosphorylation.The protein-protein interaction network revealed that Atp5a1,Pdha1,and Sdha were the target proteins mediating the therapeutic effects of Yinlai decoction.Molecular docking results suggested that the mechanism of the therapeutic effect of Yinlai decoction involves the binding of brassinolide,praeruptorin B,chrysoeriol,and other components in Yinlai decoction to Atp5a1.Conclusion:The Yinlai decoction alleviated lung tissue damage and pneumonia in mice that were fed a high-calorie diet by regulating the TCA and oxidative phosphorylation.Our study highlights the importance of a healthy diet for patients with pneumonia and provides a scientific basis for the prevention and treatment of pneumonia through dietary adjustments.展开更多
BACKGROUND The majority of colorectal cancer(CRC)cases develop from precursor advanced adenoma(AA).With the development of proteomics technologies,blood protein biomarkers have potential applications in the early scre...BACKGROUND The majority of colorectal cancer(CRC)cases develop from precursor advanced adenoma(AA).With the development of proteomics technologies,blood protein biomarkers have potential applications in the early screening of AA and CRC in the general population.AIM To identify serum protein biomarkers for the early screening of AA and CRC.METHODS We collected 43 serum samples from 8 normal controls(NCs),19 AA patients and 16 CRC patients at China-Japan Friendship Hospital.Quantitative proteomic analysis was performed using liquid chromatography–mass spectrometry/mass spectrometry and data independent acquisition,and differentially expressed proteins(DEPs)with P-values<0.05 and absolute fold changes>1.5 were screened out,followed by bioinformatics analysis.Prognosis was further analyzed based on public databases,and proteins expression in tissues were validated by immunohistochemistry.RESULTS A total of 2132 proteins and 17365 peptides were identified in the serum samples.There were 459 upregulated proteins and 118 downregulated proteins in the NC vs AA group,289 and 180 in the NC vs CRC group,and 52 and 248 in the AA vs CRC group,respectively.Bioinformatic analysis revealed that these DEPs had different functions and participated in extensive signaling pathways.We also identified DIAPH1,VASP,RAB11B,LBP,SAR1A,TUBGCP5,and DOK3 as important proteins for the progression of AA and CRC.Furthermore,VASP(P<0.01),LBP(P=0.01),TUBGCP5(P<0.01),and DOK3(P<0.01)were associated with a poor prognosis.In addition,we propose that LBP and VASP may be more promising protein biomarkers for the early screening of colorectal tumors.CONCLUSION Our study elucidated the serum proteomic profiles of AA and CRC patients,and the identified proteins,such as LBP and VASP,may contribute to the early detection of AA and CRC.展开更多
基金supported by the National Natural Science Foundation of China(32372223)the National Key Research and Development Program of China(2022YFD2301404)+1 种基金the College Students'Innovationand Entrepreneurship Training Program of Anhui Province,China(S202210364136)the Natural Science Research Project of Anhui Educational Committee,China(2023AH040133).
文摘Low temperature(LT)in spring has become one of the principal abiotic stresses that restrict the growth and development of wheat.Diverse analyses were performed to investigate the mechanism underlying the response of wheat grain development to LT stress during booting.These included morphological observation,measurements of starch synthase activity,and determination of amylose and amylopectin content of wheat grain after exposure to treatment with LT during booting.Additionally,proteomic analysis was performed using tandem mass tags(TMT).Results showed that the plumpness of wheat grains decreased after LT stress.Moreover,the activities of sucrose synthase(SuS,EC 2.4.1.13)and ADP-glucose pyrophosphorylase(AGPase,EC 2.7.7.27)exhibited a significant reduction,leading to a significant reduction in the contents of amylose and amylopectin.A total of 509 differentially expressed proteins(DEPs)were identified by proteomics analysis.The Gene Ontology(GO)enrichment analysis showed that the protein difference multiple in the nutritional repository activity was the largest among the molecular functions,and the up-regulated seed storage protein(ssP)played an active role in the response of grains to LT stress and subsequent damage.The Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis showed that LT stress reduced the expression of DEPs such as sucrose phosphate synthase(SPS),glucose-1-phosphate adenylyltransferase(glgC),andβ-fructofuranosidase(FFase)in sucrose and starch metabolic pathways,thus affecting the synthesis of grain starch.In addition,many heat shock proteins(HsPs)were found in the protein processing in endoplasmic reticulum pathways,which can resist some damage caused by LT stress.These findings provide a new theoretical foundation for elucidating the underlying mechanism governing wheat yield developmentafterexposuretoLTstress inspring.
文摘BACKGROUND Despite the developments in the field of kidney transplantation,the already existing diagnostic techniques for patient monitoring are considered insufficient.Protein biomarkers that can be derived from modern approaches of proteomic analysis of liquid biopsies(serum,urine)represent a promising innovation in the monitoring of kidney transplant recipients.AIM To investigate the diagnostic utility of protein biomarkers derived from proteomics approaches in renal allograft assessment.METHODS A systematic review was conducted in accordance with PRISMA guidelines,based on research results from the PubMed and Scopus databases.The primary focus was on evaluating the role of biomarkers in the non-invasive diagnosis of transplant-related com-plications.Eligibility criteria included protein biomarkers and urine and blood samples,while exclusion criteria were language other than English and the use of low resolution and sensitivity methods.The selected research articles,were categorized based on the biological sample,condition and methodology and the significantly and reproducibly differentiated proteins were manually selected and extracted.Functional and network analysis of the selected proteins was performed.RESULTS In 17 included studies,58 proteins were studied,with the cytokine CXCL10 being the most investigated.Biological pathways related to immune response and fibrosis have shown to be enriched.Applications of biomarkers for the assessment of renal damage as well as the prediction of short-term and long-term function of the graft were reported.Overall,all studies have shown satisfactory diagnostic accuracy of proteins alone or in combination with conventional methods,as far as renal graft assessment is concerned.CONCLUSION Our review suggests that protein biomarkers,evaluated in specific biological fluids,can make a significant contribution to the timely,valid and non-invasive assessment of kidney graft.
基金National Natural Science Foundation of China projects:Research on the Mechanism of Moxibustion Activating Calcium/Calmodulin-dependent Protein KinaseⅡPhosphorylation Mediating Long-term Potentiation to Regulate Synaptic Plasticity in the Treatment of Chronic Fatigue Syndrome Cognitive Impairment(No.82305394)Research on the Mechanism of Electroacupuncture Regulating Murine Double Minute 2 Ubiquitination Postsynaptic Density Protein 95 Levels to Reshape the Synaptic Structure of Hippocampal Neurons and Improve Chronic Fatigue Syndrome Cognitive Impairment(No.82074539)+7 种基金Outstanding Youth Project of Heilongjiang Provincial Natural Science Foundation:the Mechanism of Moxibustion in Improving Chronic Fatigue Syndrome Cognitive Impairment by Regulating Calcium/Calmodulin-dependent Protein Kinase II-mediated Long-Term Potentiation(No.YQ2023H019)Youth Talent Support Project of the Chinese Association of Traditional Chinese Medicine:Research on the Molecular Pathways of Moxibustion at the Zusanli(ST36)Point in Regulating Synaptic Plasticity to Improve Chronic Fatigue Syndrome Cognitive Impairment(No.2023-QNRC2-A04)China Postdoctoral Science Foundation:Research on the Mechanism of Moxibustion in Regulating Mitochondrial Autophagy Mediating Microglial Polarization to Promote Synaptic Remodeling in Chronic Fatigue Syndrome Cognitive Impairment(No.2024MD763980)Post-doctoral Program of Heilongjiang Province:based on the Calcium/Calmodulin-dependent Protein Kinase II/Parkin/NLR Family Pyrin Domain Containing 3 Signaling Axis to Explore the Mechanism of Moxibustion in Mitochondrial Autophagy Mediating Microglial Polarization to Promote Synaptic Remodeling in Chronic Fatigue Syndrome Cognitive Impairment(No.LBH-TZ2420)Study on the Mechanism of Moxibustion at the Zusanli(ST36)Regulating Long-Term Potentiation to Promote Synaptic Remodeling and Improve Cognitive Impairment in Chronic Fatigue Syndrome(No.LBH-Z23281)Chunhui Plan of the Ministry of Education:Study on the Mechanism of the Tongdu Yu Pi Tiaoshen Acupuncture in Improving Hippocampal Synaptic Plasticity of Chronic Fatigue Syndrome Cognitive Impairment(No.HZKY20220308-202201357)Youth Talent Support Project of the Heilongjiang Provincial Association of Traditional Chinese Medicine:Study on the Effect and Mechanism of Tongdu Yupi Tiaoshen Acupuncture on Improving Hippocampal Synaptic Plasticity in Chronic Fatigue Syndrome Cognitive Impairment(No.2022-QNRC1-05)Research Project of Traditional Chinese Medicine in Heilongjiang Province:Study on the Mechanism of Acupuncture in Improving Hippocampal Synaptic Plasticity of Chronic Fatigue Syndrome Cognitive Impairment(No.ZHY2022-136)。
文摘OBJECTIVE:To observe the effects of moxibustion at Zusanli(ST36)on rats with chronic fatigue syndrome(CFS)and to analyze the mechanisms of moxibustion through hippocampal Proteomics.METHODS:Male Sprague-Dawley(SD)rats were randomly divided into three groups:control group(CON),model group(MOD),and moxibustion group(MOX),with 12 rats in each group.The MOD and MOX groups underwent chronic multi-factor stress stimulation for 35 d to establish the CFS model.After modeling,the rats in the MOX group received mild moxibustion at Zusanli(ST36)(bilateral)for 10 minutes daily for 28 d.During the treatment period,rats in both the MOD and MOX groups continued modeling,while the CON group was kept under normal breeding conditions.The general condition of the rats was monitored,and behaviors were assessed using the Open Field Test(OFT),Exhaustion Treadmill Test,and Morris Water Maze(MWM).Hematoxylin and eosin(HE)staining and transmission electron microscopy(TEM)were employed to observe morphological changes in the hippocampus.Label-free Proteomics were utilized to identify differentially expressed proteins(DEPs)in the hippocampus,followed by bioinformatics analysis.The reliability of the Proteomics results was verified using Parallel Reaction Monitoring.RESULTS:A:Moxibustion at Zusanli(ST36)significantly reduced the general condition score of CFS rats,improved their behavioral performance in OFT,treadmill and MWM,and repaired the pathological and synaptic structural damage in the hippocampus.B:We identified DEPs by applying a fold change threshold of 1.2 and a significance level of P<0.05.In the comparison between the CON and the MOD,we identified a total of 72 DEPs(31 up-regulated and 41 down-regulated)associated with the development of CFS.In the comparison between the MOX and the MOD group,we identified a total of 103 DEPs(40 up-regulated and 63 down-regulated)related to the therapeutic effects of moxibustion.Gene Ontology(GO)enrichment analysis showed that CFS and moxibustion treatment were related to multiple biological processes,molecular functions,and cellular components.Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis revealed that CFS pathogenesis was linked to base excision repair,steroid biosynthesis,and systemic lupus erythematosus,Furthermore,the treatment of CFS with moxibustion was relevant to terpenoid skeleton biosynthesis.C:Compared with the two comparison groups,we identified 16 potential biomarkers,noting that moxibustion reversed the upregulation of 14 DEPs and the down-regulation of 2 DEPs in CFS.These proteins are mainly associated with synaptic plasticity,ribosomal function,neurotransmitter secretion,glycine metabolism,and mitochondrial function.CONCLUSION:Moxibustion at Zusanli(ST36)is effective in treating CFS,the potential biomarkers identified by Proteomics confirm that the mechanisms of moxibustion involve multiple targets and pathways,which may be key to regulating the structural and functional damage in the hippocampus associated with CFS,highlighting their significant value for future research.
基金supported in part by the Science and Technology Development Fund,Macao SAR(0098/2021/A2 and 0048/2023/AFJ)the Chinese Medicine Guangdong Laboratory(HQCML-C-2024006).
文摘Natural products(NPs)have long been recognized for their therapeutic potential,especially in cancer treatment,due to an ability to interact with multiple cellular pathways.The identification of molecular targets for NPs is a critical step in understanding anticancer mechanisms,with chemical proteomics emerging as a powerful approach.Both label-based and-free proteomic techniques have been utilized to identify these targets,each with their own advantages and limitations.While label-based methods provide high specificity through chemical tagging,the requirement for labeling can be a limitation,potentially altering NP natural properties.Conversely,label-free techniques allow for the detection of NP-protein interactions without structural modification but may struggle with transient interactions or low-abundance targets.Recent advances in artificial intelligence(AI)have further enhanced the field by improving target prediction and streamlining data analysis.AI-driven models,especially machine learning algorithms,have proven effective in processing complex proteomic data and predicting potential NP-protein interactions.The integration of AI with chemical proteomics accelerates target identification and deepens our understanding of the molecular mechanisms underlying the anticancer effects of NPs.This review explores the application of chemical proteomics and AI in the identification of cancer-related targets for NPs,highlighting current challenges and future directions for clinical translation.
基金National Natural Science Foundation of China (General Program, 81874510)Natural Science Foundation of Hunan Province (2022JJ40301)Scientific Research Project of the Hunan Provincial Department of Education (21B0369)。
文摘Objectives To elucidate the potential mechanisms of electroacupuncture(EA)in restoring detrusor-bladder neck dyssynergia(DBND)following suprasacral spinal cord injury(SSCI).Methods A total of 52 specific pathogen-free(SPF)grade famale Sprague-Dawley(SD)rats(10-12 weeks,250-280 g)were randomly assigned to either a sham group(n=12)or a spinal cord injury model group(n=40).In the model group,DBND was induced through Hassan Shaker spinal cord transection at T10 level,with 24 rats meeting inclusion criteria and subse-quently randomized into DBND group(n=12)and EA intervention group(DBND+EA group,n=12).After spinal shock recovery(day 19 after modeling),DBND+EA group received EA treatment at Ciliao(BL32),Zhongji(RN3),and Sanyinjiao(SP6)acupoints for 20 min per ses-sion at 10/50 Hz frequencies,once daily for 10 d.Sham and DBND groups received anesthe-sia only without EA intervention.On day 29 post-modeling,all rats underwent urodynamic assessments,followed by hematoxylin and eosin(HE)staining,tandem mass tag(TMT)pro-teomics,and Western blot(WB)analysis of detrusor and bladder neck tissues.Differentially expressed proteins(DEPs)were defined as proteins with P<0.05,unique peptides≥2,and fold change>1.2 or<0.83.Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway anal-ysis was performed using KOBAS 3.0(P<0.01),and protein-protein interaction(PPI)net-works were analyzed using Search Tool for the Retrieval of Interacting Genes/Proteins(STRING)11.5 and Cytoscape 3.9.1.Results Compared with sham group,DBND group showed significantly elevated leak point pressure(LPP)and maximum cystometric capacity(MCC)(both P<0.01).EA treatment sig-nificantly reduced both LPP and MCC compared with DBND group(P<0.01 and P<0.05,re-spectively).HE staining revealed that EA reduced detrusor fibrosis and improved bladder neck inflammation.TMT proteomics identified 30 overlapping DEPs in detrusor and 59 over-lapping DEPs in bladder neck when comparing DBND+EA/DBND groups with sham group.In detrusor tissue,KEGG analysis revealed 10 significantly enriched pathways(P<0.01),in-cluding mitogen-activated protein kinase(MAPK)signaling pathway.PPI analysis showed 22 of 30 DEPs were interconnected.In bladder neck tissue,14 pathways were significantly en-riched(P<0.01),including relaxin signaling pathway,with 51 of 59 DEPs showing intercon-nections.Both TMT and WB validations demonstrated that compared with sham controls,DBND rats exhibited upregulated collagen type IV alpha 2 chain(Col4a2)and downregulated guanine nucleotide-binding protein G(z)subunit alpha(Gnaz)in detrusor tissue,while EA treatment normalized both proteins(both P<0.05).In bladder neck tissue,DBND rats showed decreased expression of smoothelin(Smtn)and calcium-activated potassium chan-nel subunit beta-1(Kcnmb1)compared with sham controls(both P<0.01),which were both upregulated following EA treatment(P<0.01 and P<0.05,respectively).Conclusion EA restores detrusor-bladder neck coordination in DBND through dual-target mechanisms.In detrusor tissue,EA modulates contraction via extracellular matrix remodel-ing,cyclic adenosine monophosphate(cAMP)signaling pathway regulation,and enhanced adenosine triphosphate(ATP)biosynthesis mediated by neurotransmitters.In bladder neck tissue,EA promotes relaxation by maintaining contractile phenotypes,reducing fibrosis,sup-pressing smooth muscle excitation,and regulating presynaptic neurotransmitter release.These findings provide mechanistic insights into EA's therapeutic role in managing DBND.
基金supported by grants from the National Natural Science Foundation of China(81773838).
文摘Objective:To explore the impact of exogenous chitosan on the growth and metabolism of Glycyrrhiza uralensis Fisch.(G.uralensis)and to improve the quality of cultivated G.uralensis for both medicine and food and aid in the increase in the content of effective components in G.uralensis.Methods:In this study,whole G.uralensis plants were treated with exogenous chitosan,and compre-hensive analyses of secondary metabolites and proteins were conducted using liquid chromatography with tandem mass spectrometry and isobaric tag for relative and absolute quantitation,respectively.Effects of chitosan induction on endogenous hormones of G.uralensis were analyzed using an enzyme-linked immunosorbent assay.Gene ontology function annotation and Kyoto Encyclopedia of Genes and Genomes pathway annotation were conducted to study the effect of chitosan induction on the proteome.Results:Chitosan induction significantly increased the levels of flavonoids in G.uralensis;however,the variation in triterpenoids was not substantial.Biological processes,including photosynthesis,secondary metabolism,and abiotic stress responses,were significantly enriched.Additionally,the photosynthetic pathway,photosynthesis-antenna protein pathway,and plant hormone signal transduction pathway were significantly enriched.In the flavonoid biosynthesis pathway,the upstream-related enzyme phenylalanine ammonia-lyase(PAL)and the downstream-related enzymes chalcone synthase(CHS),polyketide reductase(PKR),chalcone isomerase(CHI),and vestitone reductase(VR)were significantly upregulated.Conclusions:Our findings suggest that chitosan induction may promote the tricarboxylic acid(TCA)cycle,and the TCA cycle enhancement significantly upregulated PAL,CHS,PKR,CHI,and VR,the five key enzymes involved in flavonoid synthesis of G.uralensis,indicating that chitosan induction activated the entire metabolic pathway associated with flavonoids in G.uralensis.Our findings provide a reference for improving the quality of cultivated G.uralensis from the perspective of pharmacodynamic components.
基金supported by the National Key Research and Development Program of China(2021YFC2501800,2023YFC0872500 and 2024YFC3044600)the National Natural Science Foundation of China(82072214,82272198,82202373)+1 种基金the Science and Technology of Shanghai Committee(21MC1930400,22Y11900100 and 23Y31900100)the Shanghai Municipal Health Commission(2023ZDFC0101)。
文摘BACKGROUND:Community-acquired pneumonia(CAP)represents a significant public health concern due to its widespread prevalence and substantial healthcare costs.This study was to utilize an integrated proteomic and metabolomic approach to explore the mechanisms involved in severe CAP.METHODS:We integrated proteomics and metabolomics data to identify potential biomarkers for early diagnosis of severe CAP.Plasma samples were collected from 46 CAP patients(including27 with severe CAP and 19 with non-severe CAP)and 19 healthy controls upon admission.A comprehensive analysis of the combined proteomics and metabolomics data was then performed to elucidate the key pathological features associated with CAP severity.RESULTS:The proteomic and metabolic signature was markedly dif ferent between CAPs and healthy controls.Pathway analysis of changes revealed complement and coagulation cascades,ribosome,tumor necrosis factor(TNF)signaling pathway and lipid metabolic process as contributors to CAP.Furthermore,alterations in lipid metabolism,including sphingolipids and phosphatidylcholines(PCs),and dysregulation of cadherin binding were observed,potentially contributing to the development of severe CAP.Specifi cally,within the severe CAP group,sphingosine-1-phosphate(S1P)and apolipoproteins(APOC1 and APOA2)levels were downregulated,while S100P level was signifi cantly upregulated.CONCLUSION:The combined proteomic and metabolomic analysis may elucidate the complexity of CAP severity and inform the development of improved diagnostic tools.
基金Supported by the National Natural Science Foundation of China(No.82000919)Science and Technology Project of Education Department of Jilin Province(No.JJKH20201089KJ).
文摘AIM:To employ proteome-wide Mendelian randomization(MR)to explore novel protein and drug targets for retinal neurodegenerative diseases(RND)in individuals of European ancestry.METHODS:This study used summary data-based MR to analyze the correlation between plasma protein levels and three RND,with protein data derived from two independent large-scale proteomics datasets.Potential drug targets were identified using Bayesian colocalization,followed by MR analysis,sensitivity testing,and external validation.Drug prediction and molecular docking were conducted to evaluate the druggability of the target proteins.RESULTS:The study identified six promising protein targets,each successfully replicated at least twice.The results included three proteins related to diabetic retinopathy(ICAM1,GCKR,WARS),two proteins related to age-related macular degeneration(WARS,BRD2),and two proteins related to glaucoma(SVEP1,NPTXR).Additionally,drug prediction and molecular docking indicated that five drugs(fenofibrate,trofinetide,ticagrelor,lifitegrast,acetaminophen)effectively bound to the target proteins.CONCLUSION:This study identified six potential protein targets for RND and five existing drugs with therapeutic potential.By integrating plasma proteomics with genetic data,it provides a cost-effective framework for drug discovery.
基金National Natural Science Foundation of China(82104532 and 82173913)Joint Program(Applied Basic Research Project)of Liaoning Provincial Science and Technology Program(2023JH2/101700074)+1 种基金High-level Talent Innovation Support Program of Dalian(2021RD10)Fundamental Research Funds for the Central Universities(2023-SWGC-0101)。
文摘Background:Fufang Muji Granules is a traditional Chinese medicine of the Manchu ethnic group and is thought to treat hepatitis and liver injury by inhibiting the elevation of alpha-fetoprotein.Methods:In this investigation,tandem mass tag(TMT)-based quantitative proteomics was performed to figure out the therapeutic mechanisms of Fufang Muji Granules on liver injury caused by carbon tetrachloride(CCl_(4))in rats.Results:Biochemical analyses(alanine aminotransferase;glutamate aminotransferase;aspartate aminotransferase)and histologic analyses(hematoxylin-eosin)demonstrated that FMG was effective in ameliorating liver injury.A sum of 6,208 proteins were identified and 2,475 proteins were determined as differential abundance proteins(DAPs)in rat liver treated with Fufang Muji Granules which compared to the model group.Bioinformatics analysis indicated that the DAPs are primarily enriched in multiple pathways such as rno00280(valine,leucine,and isoleucine degradation),rno00640(Propanoate metabolism),and rno00380(Tryptophan metabolism).Western blot was employed to validate the findings from the proteomic analysis.Conclusion:This study not only provides useful information on the mechanism of Fufang Muji Granules in the treatment of liver injury but also serves as a basis for further study of Fufang Muji Granules in vivo.
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.
文摘Neonatal hypoxic-ischemic encephalopathy(HIE)refers to neonatal brain damage caused by various factors during the perinatal period that lead to hypoxia and reduced cerebral blood flow[1].Globally,0.2%to 2.26%of newborns develop HIE,with approximately 20%resulting in neonatal death and about 25%of survivors suffering from neurological impairment[2].Currently,there is a lack of highly sensitive and specific diagnostic tools for HIE,posing significant challenges to reducing HIE mortality and neurological abnormalities[3].The development of high-throughput proteomics technology based on mass spectrometry(MS)has significantly enhanced the potential to discover biomarkers in biological fluids such as plasma,cerebrospinal fluid,saliva,and urine[4].Proteomics technology has become an engine for exploring novel markers of HIE[5].This article systematically reviews the progress of proteomics technology in the study of biomarkers for the early diagnosis of HIE,elucidating its potential application value.
基金supported by the National Key Research and Development Project of China(Grant No.2021YFF1201300 and 2021YFF1201302)the Shanghai Committee of Science and Technology(Grant No.24DX2800100)the Institutional Projects of SIBPT(Grant No.YZ2024-07)。
文摘Objective:While immunotherapy holds great potential for triple-negative breast cancer(TNBC),the lack of non-invasive biomarkers to identify beneficiaries limits the application.Methods:Paired baseline,on-treatment,and post-treatment plasma samples were collected from 195 TNBC patients receiving anti-PD-1 immunotherapy in this retrospective study conducted at the Fudan University Shanghai Cancer Center(FUSCC)for sequential high-precision proteomic profiling.Results:ARG1,NOS3,and CD28 were identified as plasma proteins significantly associated with the response to immunotherapy in neoadjuvant settings or in advanced stages of TNBC.Matched single-cell RNA sequencing data were incorporated to correlate peripheral plasma with the tumor microenvironment.Furthermore,the Plasma Immuno Prediction Score was developed to demonstrate significant predictive power for evaluating the efficacy and prognosis of patients undergoing neoadjuvant immunotherapy.Conclusions:The results underscore the importance of systemic immunity in the immunotherapy response and support the use of plasma protein profiles as a feasible tool for enhancing personalized management of immunotherapy in breast cancer.
基金supported by funding from the Bluesand Foundation,Alzheimer's Association(AARG-21-852072 and Bias Frangione Early Career Achievement Award)to EDan Australian Government Research Training Program scholarship and the University of Sydney's Brain and Mind Centre fellowship to AH。
文摘Tauopathies,diseases characterized by neuropathological aggregates of tau including Alzheimer's disease and subtypes of fro ntotemporal dementia,make up the vast majority of dementia cases.Although there have been recent developments in tauopathy biomarkers and disease-modifying treatments,ongoing progress is required to ensure these are effective,economical,and accessible for the globally ageing population.As such,continued identification of new potential drug targets and biomarkers is critical."Big data"studies,such as proteomics,can generate information on thousands of possible new targets for dementia diagnostics and therapeutics,but currently remain underutilized due to the lack of a clear process by which targets are selected for future drug development.In this review,we discuss current tauopathy biomarkers and therapeutics,and highlight areas in need of improvement,particularly when addressing the needs of frail,comorbid and cognitively impaired populations.We highlight biomarkers which have been developed from proteomic data,and outline possible future directions in this field.We propose new criteria by which potential targets in proteomics studies can be objectively ranked as favorable for drug development,and demonstrate its application to our group's recent tau interactome dataset as an example.
基金This study was reviewed and approved by the Maternal and child health hospital of Hubei Province(Approval No.20201025).
文摘BACKGROUND As a well-known fact to the public,gestational diabetes mellitus(GDM)could bring serious risks for both pregnant women and infants.During this important investigation into the linkage between GDM patients and their altered expression in the serum,proteomics techniques were deployed to detect the differentially expressed proteins(DEPs)of in the serum of GDM patients to further explore its pathogenesis,and find out possible biomarkers to forecast GDM occurrence.METHODS Subjects were divided into GDM and normal control groups according to the IADPSG diagnostic criteria.Serum samples were randomly selected from four cases in each group at 24-28 wk of gestation,and the blood samples were identified by applying iTRAQ technology combined with liquid chromatography-tandem mass spectrometry.Key proteins and signaling pathways associated with GDM were identified by bioinformatics analysis,and the expression of key proteins in serum from 12 wk to 16 wk of gestation was further verified using enzyme-linked immunosorbent assay (ELISA).RESULTS Forty-seven proteins were significantly differentially expressed by analyzing the serum samples between the GDMgravidas as well as the healthy ones. Among them, 31 proteins were found to be upregulated notably and the rest16 proteins were downregulated remarkably. Bioinformatic data report revealed abnormal expression of proteinsassociated with lipid metabolism, coagulation cascade activation, complement system and inflammatory responsein the GDM group. ELISA results showed that the contents of RBP4, as well as ANGPTL8, increased in the serumof GDM gravidas compared with the healthy ones, and this change was found to initiate from 12 wk to 16 wk ofgestation.CONCLUSION GDM symptoms may involve abnormalities in lipid metabolism, coagulation cascade activation, complementsystem and inflammatory response. RBP4 and ANGPTL8 are expected to be early predictors of GDM.
基金National Natural Science Foundation of China:Biological Mechanism of Platelet System in the Occurrence and Evolution of Blood Stasis Syndrome (No. 82030124)。
文摘OBJECTIVE: To investigate the underlying protein molecular mechanisms of "Qi stagnation and blood stasis syndrome"(QS) and "Qi deficiency and blood stasis syndrome"(QD), as two subtypes of coronary artery disease(CAD) in Traditional Chinese Medicine(TCM),following percutaneous coronary intervention(PCI).METHODS: In this study, a total of 227 CAD patients with QS and 211 CAD patients with QD were enrolled;all participants underwent PCI. Label-free quantification proteomics were employed to analyze the changes in serum in two subtypes of CAD patients before and 6 months after PCI, aiming to elucidate the intervention mechanism of PCI in treating CAD characterized by two different TCM syndromes.RESULTS: Biochemical analysis revealed significant changes in tumor necrosis factor-α, high density lipoprotein cholesterol, blood stasis clinical symptoms observation, and Gensini levels in both patient groups post-PCI;Proteomic analysis identified 79 and 95 differentially expressed proteins in the QS and QD patient groups, respectively, compared to their control groups.complement C8 alpha chain, complement factor H,apolipoprotein H, apolipoprotein B, plasminogen,carbonic anhydrase 2, and complement factor Ⅰ were altered in both comparison groups. Furthermore,enrichment analysis demonstrated that cell adhesion and connectivity-related processes underwent changes in QS patients post-PCI, whereas lipid metabolism-related pathways, including the peroxisome proliferator-activated receptor signaling pathway and extracellular matrix receptor interaction, underwent changes in the QD group.The protein-protein interaction network analysis further enriched 52 node proteins, including apolipoprotein B,lipoprotein(a), complement C5, apolipoprotein A4,complement C8 alpha chain, complement C8 beta chain,complement C8 gamma chain, apolipoprotein H,apolipoprotein A-Ⅱ, albumin, complement C4-B,apolipoprotein C3, among others. The functional network of these proteins is posited to contribute to the pathophysiology of CAD characterized by TCM syndromes.CONCLUSION: The current quantitative proteomic study has preliminarily identified biomarkers of CAD in different TCM subtypes treated with PCI, potentially laying the groundwork for understanding the protein profiles associated with the treatment of various TCM subtypes of CAD.
文摘In this editorial,we comment on the article by Cao et al.Through applying isobaric tags for relative and absolute quantification technology coupled with liquid chromatography-tandem mass spectrometry,the researchers observed significant differential expression of 47 proteins when comparing serum samples from pregnant women with gestational diabetes mellitus(GDM)to the healthy ones.GDM symptoms may involve abnormalities in inflammatory response,complement system,coagulation cascade activation,and lipid metabolism.Retinol binding protein 4 and angiopoietin like 8 are potential early indicators of GDM.GDM stands out as one of the most prevalent metabolic complications during pregnancy and is linked to severe maternal and fetal outcomes like pre-eclampsia and stillbirth.Nevertheless,none of the biomarkers discovered so far have demonstrated effectiveness in predicting GDM.Our topic was designed to foster insights into advances in the application of proteomics for early prenatal screening of GDM.
基金supported by the National Natural Science Foundation of China[Project No.81573192].
文摘Objective Hydroquinone(HQ),one of the phenolic metabolites of benzene,is widely recognized as an important participant in benzene-induced hematotoxicity.However,there are few relevant proteomics in HQ-induced hematotoxicity and the mechanism hasn’t been fully understood yet.Methods In this study,we treated K562 cells with 40μmol/L HQ for 72 h,examined and validated protein expression changes by Label-free proteomic analysis and Parallel reaction monitoring(PRM),and performed bioinformatics analysis to identify interaction networks.Results One hundred and eighty-seven upregulated differentially expressed proteins(DEPs)and 279 downregulated DEPs were identified in HQ-exposed K562 cells,which were involved in neutrophilmediated immunity,blood microparticle,and other GO terms,as well as the lysosome,metabolic,cell cycle,and cellular senescence-related pathways.Focusing on the 23 DEGs and 5 DEPs in erythroid differentiation-related pathways,we constructed the network of protein interactions and determined 6 DEPs(STAT1,STAT3,CASP3,KIT,STAT5B,and VEGFA)as main hub proteins with the most interactions,among which STATs made a central impact and may be potential biomarkers of HQ-induced hematotoxicity.Conclusion Our work reinforced the use of proteomics and bioinformatic approaches to advance knowledge on molecular mechanisms of HQ-induced hematotoxicity at the protein level and provide a valuable basis for further clarification.
基金Supported by the National Natural Science Foundation of China,No.81500505the Construction of Predominant Disciplines of Zhongnan Hospital of Wuhan University,No.XKJS202017+1 种基金the Medical Science and Technology Innovation Platform of Joint Foundation of Health Commission of Hubei Province,Zhongnan Hospital of Wuhan University,No.PTXM2021025the Hubei Provincial Natural Science Foundation,No.2023AFC013.
文摘BACKGROUND Obstructed defecation syndrome(ODS)represents the most prevalent form of chronic constipation,affecting a diverse patient population,leading to numerous complications,and imposing a significant burden on healthcare resources.Most ODS patients have insufficient rectal propulsion,but the exact mechanism underlying the pathogenesis of ODS remains unclear.AIM To explore the molecular mechanism underlying the pathogenesis of ODS.METHODS A total of 30 pairs of rectal samples were collected from patients with ODS(ODS group)or grade IV prolapsed hemorrhoids without constipation(control group)for quantitative proteomic and bioinformatic analysis.Subsequently,50 pairs of paraffin-embedded rectal specimens were selected for immunohistochemistry and immunofluorescence studies to validate the analysis results.Human intestinal smooth cell contractile function experiments and electrophysiological experiments were conducted to verify the physiological functions of target proteins.Cellular ultrastructure was detected using transmission electron microscopy.RESULTS In comparison to the control group,the expression level of dystrophin(DMD)in rectal specimens from ODS patients was markedly reduced.This finding was corroborated using immunohistochemistry and immunofluorescence techniques.The diminished expression of DMD compromised the contractile function of intestinal smooth muscle cells.At the molecular level,nucleoporin protein 153 and L-type voltage-gated calcium channel were found to be overexpressed in intestinal smooth muscle cells exhibiting downregulated DMD expression.Electrophysiological experiments confirmed an excessive influx of calcium ions into these cells.Moreover,vacuolar-like structures which may be associated with excessive calcium influx were observed in the cells by transmission electron microscopy.CONCLUSION Decreased DMD expression in intestinal smooth muscle may upregulate L-type voltage-gated calcium channel expression,leading to excessive calcium influx which may cause a decrease in rectal propulsion,thereby contributing to the pathogenesis of ODS.
基金supported by the National Natural Science Foundation of China(81874421)the Innovation Team and Talents Cultivation Program of the National Administration of Traditional Chinese Medicine(ZYYCXTD-C-202006).
文摘Objective:To uncover the underlying mechanisms of action of the Yinlai decoction on high-calorie dietinduced pneumonia through proteomics analysis.Methods:Based on the Gene Expression Omnibus(GEO)database,lung tissue samples from normal and high-fat diet(HFD)fed mice in the GSE16377 dataset were selected as test cohorts to identify differentially expressed genes and conduct bioinformatics analyses.In the animal experiments,mice were randomly divided into the control(N),high-calorie diet pneumonia(M),and Yinlai decoction treatment(Y)groups.Mice in the M group received high-calorie feed and a 0.5 mg/mL lipopolysaccharide solution spray for 30 min for 3 d.The mice in the Y group were intragastrically administered 2 mL/10 g Yinlai decoction twice daily for 3 d.Pathological evaluation of the lung tissue was performed.Differentially expressed proteins(DEPs)in the lung tissue were identified using quantitative proteomics and bioinformatics analyses.The drug-target relationships between Yinlai decoction and core DEPs in the lung tissue were verified using AutoDock Vina and Molecular Graphics Laboratory(MGL)Tools.DEPs were verified by western blot.Results:GEO data mining showed that an HFD altered oxidative phosphorylation in mouse lung tissue.The Yinlai decoction alleviated pathological damage to lung tissue and pneumonia in mice that were fed a high-calorie diet.A total of 47 DEPs were identified between the Y and M groups.Enrichment analysis revealed their association with energy metabolism pathways such as the tricarboxylic acid cycle(TCA)and oxidative phosphorylation.The protein-protein interaction network revealed that Atp5a1,Pdha1,and Sdha were the target proteins mediating the therapeutic effects of Yinlai decoction.Molecular docking results suggested that the mechanism of the therapeutic effect of Yinlai decoction involves the binding of brassinolide,praeruptorin B,chrysoeriol,and other components in Yinlai decoction to Atp5a1.Conclusion:The Yinlai decoction alleviated lung tissue damage and pneumonia in mice that were fed a high-calorie diet by regulating the TCA and oxidative phosphorylation.Our study highlights the importance of a healthy diet for patients with pneumonia and provides a scientific basis for the prevention and treatment of pneumonia through dietary adjustments.
基金Supported by National Key Development Plan for Precision Medicine Research,No.2017YFC0910002.
文摘BACKGROUND The majority of colorectal cancer(CRC)cases develop from precursor advanced adenoma(AA).With the development of proteomics technologies,blood protein biomarkers have potential applications in the early screening of AA and CRC in the general population.AIM To identify serum protein biomarkers for the early screening of AA and CRC.METHODS We collected 43 serum samples from 8 normal controls(NCs),19 AA patients and 16 CRC patients at China-Japan Friendship Hospital.Quantitative proteomic analysis was performed using liquid chromatography–mass spectrometry/mass spectrometry and data independent acquisition,and differentially expressed proteins(DEPs)with P-values<0.05 and absolute fold changes>1.5 were screened out,followed by bioinformatics analysis.Prognosis was further analyzed based on public databases,and proteins expression in tissues were validated by immunohistochemistry.RESULTS A total of 2132 proteins and 17365 peptides were identified in the serum samples.There were 459 upregulated proteins and 118 downregulated proteins in the NC vs AA group,289 and 180 in the NC vs CRC group,and 52 and 248 in the AA vs CRC group,respectively.Bioinformatic analysis revealed that these DEPs had different functions and participated in extensive signaling pathways.We also identified DIAPH1,VASP,RAB11B,LBP,SAR1A,TUBGCP5,and DOK3 as important proteins for the progression of AA and CRC.Furthermore,VASP(P<0.01),LBP(P=0.01),TUBGCP5(P<0.01),and DOK3(P<0.01)were associated with a poor prognosis.In addition,we propose that LBP and VASP may be more promising protein biomarkers for the early screening of colorectal tumors.CONCLUSION Our study elucidated the serum proteomic profiles of AA and CRC patients,and the identified proteins,such as LBP and VASP,may contribute to the early detection of AA and CRC.
