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
The wild Lepista sordida is a kind of precious and rare edible fungus.An excellent strain of it by artificial domestication was obtained,which was high-yield and high in iron content.In this study,high-throughput comp...The wild Lepista sordida is a kind of precious and rare edible fungus.An excellent strain of it by artificial domestication was obtained,which was high-yield and high in iron content.In this study,high-throughput comparative proteomics was used to reveal the regulatory mechanism of its primordium differentiation in the early fruiting body formation.The mycelium before the primordium differentiation mainly expressed high levels of mitochondrial functional proteins and carbon dioxide concentration regulatory proteins.In young mushrooms,the highly expressed proteins were mainly involved in cell component generation,cell proliferation,nitrogen compound metabolism,nucleotide metabolism,glutathione metabolism,and purine metabolism.The differential regulation patterns of pileus and stipe growth to maturity were also revealed.The highly expressed proteins related to transcription,RNA splicing,the production of various organelles,DNA conformational change,nucleosome organization,protein processing,maturation and transport,and cell detoxification regulated the pileus development and maturity.The proteins related to carbohydrate and energy metabolism,large amounts of obsolete cytoplasmic parts,nutrient deprivation,and external stimuli regulated the stipe development and maturity.Multiple CAZymes regulated nutrient absorption,morphogenesis,spore production,stress response,and other life activities at different growth and development stages.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
White Hypsizygus marmoreus is a popular edible mushroom.Its mycelium is easy to be contaminated by Penicillium,which leads to a decrease in its quality and yield.Penicillium could compete for limited space and nutrien...White Hypsizygus marmoreus is a popular edible mushroom.Its mycelium is easy to be contaminated by Penicillium,which leads to a decrease in its quality and yield.Penicillium could compete for limited space and nutrients through rapid growth and produce a variety of harmful gases,such as benzene,aldehydes,phenols,etc.,to inhibit the growth of H.marmoreus mycelium.A series of changes occurred in H.marmoreus proteome after contamination when detected by the label-free tandem mass spectrometry(MS/MS)technique.Some proteins with up-regulated expression worked together to participate in some processes,such as the non-toxic transformation of harmful gases,glutathione metabolism,histone modification,nucleotide excision repair,clearing misfolded proteins,and synthesizing glutamine,which were mainly used in response to biological stress.The proteins with down-regulated expression are mainly related to the processes of ribosome function,protein processing,spliceosome,carbon metabolism,glycolysis,and gluconeogenesis.The reduction in the function of these proteins affected the production of the cell components,which might be an adjustment to adapt to growth retardation.This study further enhanced the understanding of the biological stress response and the growth restriction adaptation mechanisms in edible fungi.It also provided a theoretical basis for protein function exploration and edible mushroom food safety research.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
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
Proteomics is a powerful tool that can be used to elucidate the underlying mechanisms of diseases and identify new biomarkers.Therefore,it may also be helpful for understanding the detailed pathological mechanism of t...Proteomics is a powerful tool that can be used to elucidate the underlying mechanisms of diseases and identify new biomarkers.Therefore,it may also be helpful for understanding the detailed pathological mechanism of traumatic brain injury(TBI).In this study,we performed Tandem Mass Tag-based quantitative analysis of cortical proteome profiles in a mouse model of TBI.Our results showed that there were 302 differentially expressed proteins in TBI mice compared with normal mice 7 days after injury.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that these differentially expressed proteins were predominantly involved in inflammatory responses,including complement and coagulation cascades,as well as chemokine signaling pathways.Subsequent transcription factor analysis revealed that the inflammation-related transcription factors NF-κB1,RelA,IRF1,STAT1,and Spi1 play pivotal roles in the secondary injury that occurs after TBI,which further corroborates the functional enrichment for inflammatory factors.Our results suggest that inflammation-related proteins and inflammatory responses are promising targets for the treatment of TBI.展开更多
Single-cell or low-input multi-omics techniques have revolutionized the study of pre-implantation embryo development.However,the single-cell or low-input proteomic research in this field is relatively underdeveloped b...Single-cell or low-input multi-omics techniques have revolutionized the study of pre-implantation embryo development.However,the single-cell or low-input proteomic research in this field is relatively underdeveloped because of the higher threshold of the starting material for mammalian embryo samples and the lack of hypersensitive proteome technology.In this study,a comprehensive solution of ultrasensitive proteome technology(CS-UPT)was developed for single-cell or low-input mouse oocyte/embryo samples.The deep coverage and high-throughput routes significantly reduced the starting material and were selected by investigators based on their demands.Using the deep coverage route,we provided the first large-scale snapshot of the very early stage of mouse maternal-to-zygotic transition,including almost 5,500 protein groups from 20 mouse oocytes or zygotes for each sample.Moreover,significant protein regulatory networks centered on transcription factors and kinases between the MII oocyte and 1-cell embryo provided rich insights into minor zygotic genome activation.展开更多
The sensorimotor and histological aspects of peripheral neuropathies were already studied by our team in two rat models:the sciatic nerve crush and the Charcot-Marie-Tooth-1A disease.In this study,we sought to highlig...The sensorimotor and histological aspects of peripheral neuropathies were already studied by our team in two rat models:the sciatic nerve crush and the Charcot-Marie-Tooth-1A disease.In this study,we sought to highlight and compare the protein signature of these two pathological situations.Indeed,the identification of protein profiles in diseases can play an important role in the development of pharmacological targets.In fact,Charcot-Marie-Tooth-1A rats develop motor impairments that are more severe in the hind limbs.Therefore,for the first time,protein expression in sciatic nerve of Charcot-Marie-Tooth-1A rats was examined.First,distal sciatic nerves were collected from Charcot-Marie-Tooth-1A and uninjured wild-type rats aged 3 months.After protein extraction,sequential window acquisition of all theoretical fragment ion spectra liquid chromatography and mass spectrometry was employed.445 proteins mapped to Swiss-Prot or trEMBL Uniprot databases were identified and quantified.Of these,153 proteins showed statistically significant differences between Charcot-Marie-Tooth-1A and wild-type groups.The majority of these proteins were overexpressed in Charcot-Marie-Tooth-1A.Hierarchical clustering and functional enrichment using Gene Ontology were used to group these proteins based on their biological effects concerning Charcot-Marie-Tooth-1A pathophysiology.Second,proteomic characterization of wild-type rats subjected to sciatic nerve crush was performed sequential window acquisition of all theoretical fragment ion spectra liquid chromatography and mass spectrometry.One month after injury,distal sciatic nerves were collected and analyzed as described above.Out of 459 identified proteins,92 showed significant differences between sciatic nerve crush and the uninjured wild-type rats used in the first study.The results suggest that young adult Charcot-Marie-Tooth-1A rats(3 months old)develop compensatory mechanisms at the level of redox balance,protein folding,myelination,and axonogenesis.These mechanisms seem insufficient to hurdle the progress of the disease.Notably,response to oxidative stress appears to be a significant feature of Charcot-Marie-Tooth-1A,potentially playing a role in the pathological process.In contrast to the first experiment,the majority of the proteins that differed from wild-type were downregulated in the sciatic nerve crush group.Functional enrichment suggested that neurogenesis,response to axon injury,and oxidative stress were important biological processes.Protein analysis revealed an imperfect repair at this time point after injury and identified several distinguishable proteins.In conclusion,we suggest that peripheral neuropathies,whether of a genetic or traumatic cause,share some common pathological pathways.This study may provide directions for better characterization of these models and/or identifying new specific therapeutic targets.展开更多
This study aimed to analyze and compare the differentially expressed whey proteins(DEWPs)of donkey and bovine colostrum using high-performance liquid chromatography with tandem mass spectrometry-based proteomics.A tot...This study aimed to analyze and compare the differentially expressed whey proteins(DEWPs)of donkey and bovine colostrum using high-performance liquid chromatography with tandem mass spectrometry-based proteomics.A total of 620 and 696 whey proteins were characterized in the donkey and bovine colostrum,respectively,including 383 common whey proteins.Among these common proteins,80 were identified as DEWPs,including 21 upregulated and 59 downregulated DEWPs in donkey colostrum compared to bovine colostrum.Gene Ontology analysis revealed that these DEWPs were mainly related to cellular components,such as extracellular exosome,plasma membrane,and mitochondrion;biological processes,such as oxidation-reduction process,cell-cell adhesion,and small guanosine triphosphate(GTP)ase-mediated signal transduction;and molecular functions,such as GTP binding,GTPase activity,and soluble N-ethylmaleimide-sensitive factor(NSF)attachment protein receptor activity.Metabolic pathway analysis suggested that the majority of the DEWPs were associated with soluble NSF factor attachment protein receptor interactions in vesicular transport,fatty acid biosynthesis,and estrogen signaling pathways.Our results provide a vital insight into the differences between donkey and bovine colostrum,along with important information on the significant components as nutritional and functional factors to be included in infant formula based on multiple milk sources.展开更多
Background:The underlying mechanism of sciatic nerve injury(SNI)is a common motor functional disorder,necessitates further research.Methods:A rat model of SNI was established,with the injury group subjected to compres...Background:The underlying mechanism of sciatic nerve injury(SNI)is a common motor functional disorder,necessitates further research.Methods:A rat model of SNI was established,with the injury group subjected to compressive injury of the right sciatic nerve exposed at the midpoint of the thigh and the sham surgery group undergoing the same surgical procedure.An oxygen-glucose deprivation model was employed to simulate in vitro SNI in PC12 cells.Following data acquisition and quality control,differentially expressed proteins(DEPs)in each model were identified through differential analysis,and enrichment analysis was used to explore the potential functions and pathways of the DEPs.Venn diagrams were drawn,and DEPs from both in vivo and in vitro SNI models were imported into the STRING database to construct a protein-protein interaction network and screen for hub proteins.Results:After the peptide segments obtained from rat nerve blockade and PC12 cells met quality requirements,258 DEPs were identified in rat nerve samples,and 119 DEPs were screened in PC12 cells.Enrichment analysis revealed that DEPs in the rat model were predominantly concentrated in biological functions such as myogenic cell proliferation and signaling related to lipid and energy metabolism.DEPs in the in vitro model were mainly enriched in biological processes such as phagocytosis and were associated with lipid transport and metabolism.Two hub proteins,amyloid precursor protein(APP)and fibronectin 1(FN1),were identified through MCC,MCODE,and Degree scoring.Both PC12 cells and external validation sets showed relatively higher expression of APP and FN1 in injured samples.Results of gene set enrichment analysis indicated that these two proteins were associated with metabolic pathways,such as biosynthesis of glycosaminoglycan chondroitin sulfate and biosynthesis of unsaturated fatty acids.Conclusion:APP and FN1 are potential key molecules involved in SNI and are associated with various metabolic pathways in nerve repair.These findings provide a theoretical basis for the development of therapeutic targets for SNI.展开更多
[目的]探讨加味丹栀逍遥散对慢性不可预知性温和应激(CUMS)抑郁小鼠模型的干预作用及可能机制.[方法]C57BL/6N小鼠分为正常组、模型组、加味丹栀逍遥散组和氟西汀组.采用CUMS复制抑郁模型,模型成功后灌胃给药4周.末次给药后进行行为学测...[目的]探讨加味丹栀逍遥散对慢性不可预知性温和应激(CUMS)抑郁小鼠模型的干预作用及可能机制.[方法]C57BL/6N小鼠分为正常组、模型组、加味丹栀逍遥散组和氟西汀组.采用CUMS复制抑郁模型,模型成功后灌胃给药4周.末次给药后进行行为学测试,采用串联质谱标签法(TMT)蛋白质组学分析小鼠肝脏差异蛋白的表达谱,通过Kyoto encyclopedia of genes and genomes(KEGG)通路富集加味丹栀逍遥散抗抑郁的相关通路和蛋白;血液生化检测总胆固醇及总胆汁酸含量.[结果]与正常组相比,模型组小鼠糖水偏好率下降,自主活动次数减少,加味丹栀逍遥散给药后上调小鼠糖水偏好率及自主活动次数.蛋白组学结果显示模型组与加味丹栀逍遥散给药组之间肝脏差异表达蛋白20个,其中上调11个,下调9个.KEGG通路富集分析发现差异表达蛋白主要参与了胆固醇代谢、初级胆汁酸的合成等.生化检测发现,与正常组相比,模型组总胆固醇含量下降而胆汁酸含量升高,加味丹栀逍遥散给药能显著增加总胆固醇含量而减少总胆汁酸含量.[结论]加味丹栀逍遥散具有良好的抗抑郁效应,其机制可能与调节肝脏胆固醇异常代谢、降低血液总胆汁酸有关.展开更多
目的分析单核细胞增生李斯特氏菌(简称单增李斯特菌)感染人绒毛膜滋养层细胞HTR-8/Svneo过程中引起的细胞蛋白质组变化。从宿主细胞分子水平对单增李斯特菌感染胎盘的机制进行研究。方法运用TMT(Tandem Mass Tags)蛋白质组学技术对HTR-8...目的分析单核细胞增生李斯特氏菌(简称单增李斯特菌)感染人绒毛膜滋养层细胞HTR-8/Svneo过程中引起的细胞蛋白质组变化。从宿主细胞分子水平对单增李斯特菌感染胎盘的机制进行研究。方法运用TMT(Tandem Mass Tags)蛋白质组学技术对HTR-8/Svneo感染组和非感染组蛋白质组进行定量分析,运用GO(Gene Ontology)、KEGG(Kyoto Encyclopedia of Genes and Genomes)数据库对差异表达蛋白进行分子功能、生物过程及代谢途径富集分析。结果共鉴定肽段76285个,可定量蛋白6979个。HTR-8/Svneo感染过程中356个蛋白发生了显著性差异表达。153个表达量上调,203个表达量下调。差异表达量倍数最高的蛋白为微管马达蛋白(B4DYE2),最低为翻译起始因子1(Q6IAV3)。GO功能富集和KEGG代谢途径富集结果表明,上调蛋白参与的生物过程和代谢途径集中在微管、微丝运动,细胞自噬等方面,下调蛋白集中在碳代谢、氮代谢、氨基酸生物合成、核酸代谢等初级代谢途径和泛素介导的蛋白质水解等方面。结论单增李斯特菌侵袭HTR-8/Svneo过程中,宿主细胞的基础代谢可能发生了显著降低,并处于较高的自噬水平。细胞迁移诱导透明质酸酶CEMIP(Q8WUJ3)的显著上调说明该蛋白可能在调节滋养层细胞迁移、侵袭能力进而造成不良妊娠方面具有重要作用,为单增李斯特菌感染胎盘分子机制研究提供新的思路。展开更多
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funded by the Shandong Edible Fungus Agricultural Technology System(SDAIT-07-02)the National Natural Science Foundation of China(Grant No.32000041 and 32272789)+2 种基金the Shandong Provincial Natural Science Foundation,China(ZR2020QC005)the Qingdao Agricultural University Scientific Research Foundation(6631120076)horizontal project:Breeding and property protection of new varieties of factory produced Hypsizygus marmoreus(20183702012614).
文摘The wild Lepista sordida is a kind of precious and rare edible fungus.An excellent strain of it by artificial domestication was obtained,which was high-yield and high in iron content.In this study,high-throughput comparative proteomics was used to reveal the regulatory mechanism of its primordium differentiation in the early fruiting body formation.The mycelium before the primordium differentiation mainly expressed high levels of mitochondrial functional proteins and carbon dioxide concentration regulatory proteins.In young mushrooms,the highly expressed proteins were mainly involved in cell component generation,cell proliferation,nitrogen compound metabolism,nucleotide metabolism,glutathione metabolism,and purine metabolism.The differential regulation patterns of pileus and stipe growth to maturity were also revealed.The highly expressed proteins related to transcription,RNA splicing,the production of various organelles,DNA conformational change,nucleosome organization,protein processing,maturation and transport,and cell detoxification regulated the pileus development and maturity.The proteins related to carbohydrate and energy metabolism,large amounts of obsolete cytoplasmic parts,nutrient deprivation,and external stimuli regulated the stipe development and maturity.Multiple CAZymes regulated nutrient absorption,morphogenesis,spore production,stress response,and other life activities at different growth and development stages.
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funded by the Shandong Provincial Natural Science Foundation,China (ZR2020QC005)the National Natural Science Foundation of China (32272789)+3 种基金the National Natural Science Foundation of China (32000041)the Shandong Edible Fungus Agricultural Technology System (SDAIT-07-02)the Shandong Provincial Key Research and Development Plan (2021ZDSYS28)the Qingdao Agricultural University Scientific Research Foundation (6631120076)。
文摘White Hypsizygus marmoreus is a popular edible mushroom.Its mycelium is easy to be contaminated by Penicillium,which leads to a decrease in its quality and yield.Penicillium could compete for limited space and nutrients through rapid growth and produce a variety of harmful gases,such as benzene,aldehydes,phenols,etc.,to inhibit the growth of H.marmoreus mycelium.A series of changes occurred in H.marmoreus proteome after contamination when detected by the label-free tandem mass spectrometry(MS/MS)technique.Some proteins with up-regulated expression worked together to participate in some processes,such as the non-toxic transformation of harmful gases,glutathione metabolism,histone modification,nucleotide excision repair,clearing misfolded proteins,and synthesizing glutamine,which were mainly used in response to biological stress.The proteins with down-regulated expression are mainly related to the processes of ribosome function,protein processing,spliceosome,carbon metabolism,glycolysis,and gluconeogenesis.The reduction in the function of these proteins affected the production of the cell components,which might be an adjustment to adapt to growth retardation.This study further enhanced the understanding of the biological stress response and the growth restriction adaptation mechanisms in edible fungi.It also provided a theoretical basis for protein function exploration and edible mushroom food safety research.
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.
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,No. 81771327a grant for the Platform Construction of Basic Research and Clinical Translation of Nervous System Injury,China,No. PXM2020_026280_000002 (both to BYL)
文摘Proteomics is a powerful tool that can be used to elucidate the underlying mechanisms of diseases and identify new biomarkers.Therefore,it may also be helpful for understanding the detailed pathological mechanism of traumatic brain injury(TBI).In this study,we performed Tandem Mass Tag-based quantitative analysis of cortical proteome profiles in a mouse model of TBI.Our results showed that there were 302 differentially expressed proteins in TBI mice compared with normal mice 7 days after injury.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that these differentially expressed proteins were predominantly involved in inflammatory responses,including complement and coagulation cascades,as well as chemokine signaling pathways.Subsequent transcription factor analysis revealed that the inflammation-related transcription factors NF-κB1,RelA,IRF1,STAT1,and Spi1 play pivotal roles in the secondary injury that occurs after TBI,which further corroborates the functional enrichment for inflammatory factors.Our results suggest that inflammation-related proteins and inflammatory responses are promising targets for the treatment of TBI.
基金supported by the National Natural Science Foundation of China(NSFC)(Grant Nos.:82030099,30700397 Detail)the National Key R&D Program of China(Grant No.:2022YFD2101500)+5 种基金the Science and Technology Commission of Shanghai Municipality,China(Grant No.:22DZ2303000)the Shanghai Municipal Science and Technology Commission“Science and Technology Innovation Action Plan”Technical Standard Project,China(Grant No.:21DZ2201700)the Shanghai Municipal Science and Technology Commission“Science and Technology Innovation Action Plan”Natural Science Foundation Project,China(Grant No.:23ZR1435800)the Strategic Priority Research Program of the Chinese Academy of Sciences,China(Grant No.:XDB32060000)the Basic Frontier Scientific Research Program of Chinese Academy of Sciences(Grant No.:ZDBS-LY-SM019)the Yangfan Project of Shanghai Science and Technology Commission,China(Grant No.:22YF1454100),and the Innovative Research Team of High-level Local Universities in Shanghai,China.
文摘Single-cell or low-input multi-omics techniques have revolutionized the study of pre-implantation embryo development.However,the single-cell or low-input proteomic research in this field is relatively underdeveloped because of the higher threshold of the starting material for mammalian embryo samples and the lack of hypersensitive proteome technology.In this study,a comprehensive solution of ultrasensitive proteome technology(CS-UPT)was developed for single-cell or low-input mouse oocyte/embryo samples.The deep coverage and high-throughput routes significantly reduced the starting material and were selected by investigators based on their demands.Using the deep coverage route,we provided the first large-scale snapshot of the very early stage of mouse maternal-to-zygotic transition,including almost 5,500 protein groups from 20 mouse oocytes or zygotes for each sample.Moreover,significant protein regulatory networks centered on transcription factors and kinases between the MII oocyte and 1-cell embryo provided rich insights into minor zygotic genome activation.
基金supported by a doctoral fellowship from the European Union(European Regional Development Fund).
文摘The sensorimotor and histological aspects of peripheral neuropathies were already studied by our team in two rat models:the sciatic nerve crush and the Charcot-Marie-Tooth-1A disease.In this study,we sought to highlight and compare the protein signature of these two pathological situations.Indeed,the identification of protein profiles in diseases can play an important role in the development of pharmacological targets.In fact,Charcot-Marie-Tooth-1A rats develop motor impairments that are more severe in the hind limbs.Therefore,for the first time,protein expression in sciatic nerve of Charcot-Marie-Tooth-1A rats was examined.First,distal sciatic nerves were collected from Charcot-Marie-Tooth-1A and uninjured wild-type rats aged 3 months.After protein extraction,sequential window acquisition of all theoretical fragment ion spectra liquid chromatography and mass spectrometry was employed.445 proteins mapped to Swiss-Prot or trEMBL Uniprot databases were identified and quantified.Of these,153 proteins showed statistically significant differences between Charcot-Marie-Tooth-1A and wild-type groups.The majority of these proteins were overexpressed in Charcot-Marie-Tooth-1A.Hierarchical clustering and functional enrichment using Gene Ontology were used to group these proteins based on their biological effects concerning Charcot-Marie-Tooth-1A pathophysiology.Second,proteomic characterization of wild-type rats subjected to sciatic nerve crush was performed sequential window acquisition of all theoretical fragment ion spectra liquid chromatography and mass spectrometry.One month after injury,distal sciatic nerves were collected and analyzed as described above.Out of 459 identified proteins,92 showed significant differences between sciatic nerve crush and the uninjured wild-type rats used in the first study.The results suggest that young adult Charcot-Marie-Tooth-1A rats(3 months old)develop compensatory mechanisms at the level of redox balance,protein folding,myelination,and axonogenesis.These mechanisms seem insufficient to hurdle the progress of the disease.Notably,response to oxidative stress appears to be a significant feature of Charcot-Marie-Tooth-1A,potentially playing a role in the pathological process.In contrast to the first experiment,the majority of the proteins that differed from wild-type were downregulated in the sciatic nerve crush group.Functional enrichment suggested that neurogenesis,response to axon injury,and oxidative stress were important biological processes.Protein analysis revealed an imperfect repair at this time point after injury and identified several distinguishable proteins.In conclusion,we suggest that peripheral neuropathies,whether of a genetic or traumatic cause,share some common pathological pathways.This study may provide directions for better characterization of these models and/or identifying new specific therapeutic targets.
基金supported by the by National Key R&D Program of China(2018YFC1604302)“Twelfth Five Year”National Science and Technology Plan Project(2013BAD18B03)+2 种基金Chinese Scholarship Council(202008210391)Shenyang Technological Innovation Project(Y17-0-028)LiaoNing Revitalization Talents Project(XLYC1902083).
文摘This study aimed to analyze and compare the differentially expressed whey proteins(DEWPs)of donkey and bovine colostrum using high-performance liquid chromatography with tandem mass spectrometry-based proteomics.A total of 620 and 696 whey proteins were characterized in the donkey and bovine colostrum,respectively,including 383 common whey proteins.Among these common proteins,80 were identified as DEWPs,including 21 upregulated and 59 downregulated DEWPs in donkey colostrum compared to bovine colostrum.Gene Ontology analysis revealed that these DEWPs were mainly related to cellular components,such as extracellular exosome,plasma membrane,and mitochondrion;biological processes,such as oxidation-reduction process,cell-cell adhesion,and small guanosine triphosphate(GTP)ase-mediated signal transduction;and molecular functions,such as GTP binding,GTPase activity,and soluble N-ethylmaleimide-sensitive factor(NSF)attachment protein receptor activity.Metabolic pathway analysis suggested that the majority of the DEWPs were associated with soluble NSF factor attachment protein receptor interactions in vesicular transport,fatty acid biosynthesis,and estrogen signaling pathways.Our results provide a vital insight into the differences between donkey and bovine colostrum,along with important information on the significant components as nutritional and functional factors to be included in infant formula based on multiple milk sources.
基金funded by the Project of 2022 Health Commission Technology Plan of Zhejiang Province(Project Number:2022KY1169)the 2022 Ningbo Natural Science Foundation Young Doctoral Project(Project Number:2022J027).
文摘Background:The underlying mechanism of sciatic nerve injury(SNI)is a common motor functional disorder,necessitates further research.Methods:A rat model of SNI was established,with the injury group subjected to compressive injury of the right sciatic nerve exposed at the midpoint of the thigh and the sham surgery group undergoing the same surgical procedure.An oxygen-glucose deprivation model was employed to simulate in vitro SNI in PC12 cells.Following data acquisition and quality control,differentially expressed proteins(DEPs)in each model were identified through differential analysis,and enrichment analysis was used to explore the potential functions and pathways of the DEPs.Venn diagrams were drawn,and DEPs from both in vivo and in vitro SNI models were imported into the STRING database to construct a protein-protein interaction network and screen for hub proteins.Results:After the peptide segments obtained from rat nerve blockade and PC12 cells met quality requirements,258 DEPs were identified in rat nerve samples,and 119 DEPs were screened in PC12 cells.Enrichment analysis revealed that DEPs in the rat model were predominantly concentrated in biological functions such as myogenic cell proliferation and signaling related to lipid and energy metabolism.DEPs in the in vitro model were mainly enriched in biological processes such as phagocytosis and were associated with lipid transport and metabolism.Two hub proteins,amyloid precursor protein(APP)and fibronectin 1(FN1),were identified through MCC,MCODE,and Degree scoring.Both PC12 cells and external validation sets showed relatively higher expression of APP and FN1 in injured samples.Results of gene set enrichment analysis indicated that these two proteins were associated with metabolic pathways,such as biosynthesis of glycosaminoglycan chondroitin sulfate and biosynthesis of unsaturated fatty acids.Conclusion:APP and FN1 are potential key molecules involved in SNI and are associated with various metabolic pathways in nerve repair.These findings provide a theoretical basis for the development of therapeutic targets for SNI.
文摘[目的]探讨加味丹栀逍遥散对慢性不可预知性温和应激(CUMS)抑郁小鼠模型的干预作用及可能机制.[方法]C57BL/6N小鼠分为正常组、模型组、加味丹栀逍遥散组和氟西汀组.采用CUMS复制抑郁模型,模型成功后灌胃给药4周.末次给药后进行行为学测试,采用串联质谱标签法(TMT)蛋白质组学分析小鼠肝脏差异蛋白的表达谱,通过Kyoto encyclopedia of genes and genomes(KEGG)通路富集加味丹栀逍遥散抗抑郁的相关通路和蛋白;血液生化检测总胆固醇及总胆汁酸含量.[结果]与正常组相比,模型组小鼠糖水偏好率下降,自主活动次数减少,加味丹栀逍遥散给药后上调小鼠糖水偏好率及自主活动次数.蛋白组学结果显示模型组与加味丹栀逍遥散给药组之间肝脏差异表达蛋白20个,其中上调11个,下调9个.KEGG通路富集分析发现差异表达蛋白主要参与了胆固醇代谢、初级胆汁酸的合成等.生化检测发现,与正常组相比,模型组总胆固醇含量下降而胆汁酸含量升高,加味丹栀逍遥散给药能显著增加总胆固醇含量而减少总胆汁酸含量.[结论]加味丹栀逍遥散具有良好的抗抑郁效应,其机制可能与调节肝脏胆固醇异常代谢、降低血液总胆汁酸有关.
文摘目的分析单核细胞增生李斯特氏菌(简称单增李斯特菌)感染人绒毛膜滋养层细胞HTR-8/Svneo过程中引起的细胞蛋白质组变化。从宿主细胞分子水平对单增李斯特菌感染胎盘的机制进行研究。方法运用TMT(Tandem Mass Tags)蛋白质组学技术对HTR-8/Svneo感染组和非感染组蛋白质组进行定量分析,运用GO(Gene Ontology)、KEGG(Kyoto Encyclopedia of Genes and Genomes)数据库对差异表达蛋白进行分子功能、生物过程及代谢途径富集分析。结果共鉴定肽段76285个,可定量蛋白6979个。HTR-8/Svneo感染过程中356个蛋白发生了显著性差异表达。153个表达量上调,203个表达量下调。差异表达量倍数最高的蛋白为微管马达蛋白(B4DYE2),最低为翻译起始因子1(Q6IAV3)。GO功能富集和KEGG代谢途径富集结果表明,上调蛋白参与的生物过程和代谢途径集中在微管、微丝运动,细胞自噬等方面,下调蛋白集中在碳代谢、氮代谢、氨基酸生物合成、核酸代谢等初级代谢途径和泛素介导的蛋白质水解等方面。结论单增李斯特菌侵袭HTR-8/Svneo过程中,宿主细胞的基础代谢可能发生了显著降低,并处于较高的自噬水平。细胞迁移诱导透明质酸酶CEMIP(Q8WUJ3)的显著上调说明该蛋白可能在调节滋养层细胞迁移、侵袭能力进而造成不良妊娠方面具有重要作用,为单增李斯特菌感染胎盘分子机制研究提供新的思路。
