proteomics

摘要： 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.

摘要： 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.

摘要： Multi-omics is a biological analysis approach in which the data sets are multiple"omics",such as genomics,transcriptomics,proteomics,metabolomics.Multiomics can be used in the detection,diagnosis,treatment,and prognosis of diseases as a kind of potential biomarker.Blood stasis syndrome(BSS)is a common syndrome in traditional Chinese medicine(TCM).Multi-omics can reflect the change of BSS as a whole.Thus,the purpose of this manuscript was to fully review the clinical multi-omics research and related problems of BSS.We found that the multi-omics of BSS reflected many pathophysiological processes through regulating vascular endothelial cells,vasodilation and contraction,oxidative stress,thrombosis,angiogenesis,platelet aggregation,lipid metabolism,inflammatory response,immune and coagulation function,energy balance,amino acid metabolism,and so forth.Many potential biomarkers of BSS were found in multi-omics and some promoting blood circulation Chinese medicines(PBCCMs)could well regulate the abnormal biomarkers and make them return to the normal level.

摘要： Sequence tag index in the field of computational proteomics can be used to facilitate faster open-search-based identification of modified peptides and in-depth analysis of mass spectrometry data. In protein-identification search engines, sequence tag index are playing a prominent role in recent ten years due to fast searching speed. However, in pursuit of less index space consumption, some protein search engines design excessively concise index schemes which lead to higher computational burden. We proposed a new tag index scheme named TIIP with a better balance between space and time complexity. TIIP has a unique two-level hierarchical index structure which allows rapid retrieval of all peptide sequences and their corresponding masses. Theoretically, the index space consumption of TIIP is not much higher compared to the typical tag index schemes, but the time complexity of sequence retrieval can be reduced to O(1), and practically, TIIP has about one million fold improvement in searching speed compared with brute force approach.

摘要： Cholangiocarcinoma(CCA)arises from the ductular epithelium of the biliary tree,either within the liver(intrahepatic CCA)or more commonly from the extrahepatic bile ducts(extrahepatic CCA).This disease has a poor prognosis and a growing worldwide prevalence.The poor outcomes of CCA are partially explained by the fact that a final diagnosis is challenging,especially the differential diagnosis between hepatocellular carcinoma and intrahepatic CCA,or distal CCA and pancreatic head adenocarcinoma.Most patients present with an advanced disease,unresectable disease,and there is a lack in non-surgical therapeutic modalities.Not least,there is an acute lack of prognostic biomarkers which further complicates disease management.Therefore,there is a dire need to find alternative diagnostic and follow-up pathways that can lead to an accurate result,either singlehandedly or combined with other methods.In the"-omics"era,this goal can be attained by various means,as it has been successfully demonstrated in other primary tumors.Numerous variants can reach a biomarker status ranging from circulating nucleic acids to proteins,metabolites,extracellular vesicles,and ultimately circulating tumor cells.However,given the relatively heterogeneous data,extracting clinical meaning from the inconsequential noise might become a tall task.The current review aims to navigate the nascent waters of the non-invasive approach to CCA and provide an evidence-based input to aid clinical decisions and provide grounds for future research.

摘要： BACKGROUND Colorectal cancer(CRC)is a highly malignant cancer with a high incidence and mortality in China.It is urgent to find a diagnostic marker with higher sensitivity and specificity than the traditional approaches for CRC diagnosis.AIM To provide new ideas for the diagnosis of CRC based on serum proteomics.METHODS Specimens from 83 healthy people,62 colon polyp(CRP)patients,and 101 CRC patients were analyzed by matrix-assisted laser desorption/ionization time-offlight mass spectrometry.The diagnostic value of the profiles of differentially expressed proteins was then analyzed.RESULTS Compared with the healthy control group,CRC patients had elevated expression of 5 proteins and reduced expression of 14 proteins.The area under the curve(AUC)for a differentially expressed protein with a mass-to-charge ratio of 2022.34 was the largest;the AUC was 0.843,which was higher than the AUC of 0.717 observed with carcinoembryonic antigen(CEA),and the sensitivity and specificity of this identified marker were 75.3%and 79.5%,respectively.After cross-validation,the accuracy of diagnosis using levels of this differentially expressed protein was 82.37%.Compared with the CRP group,the expression of 3 proteins in the serum of CRC patients was elevated and 11 proteins were expressed at reduced levels.Proteins possessing mass-to-charge ratio values of 2899.38 and 877.3 were selected to establish a classification tree model.The results showed that the accuracy of CRC diagnosis was 89.5%,the accuracy of CRP diagnosis was 81.6%,and the overall accuracy of this approach was 86.3%.The overall sensitivity and specificity of diagnosis using the proteomics approach were 81.8%and 66.75%,respectively.The sensitivities and specificities of diagnoses based on CEA and carbohydrate antigen 19-9 expression were 55.6%and 91.3%and 65.4%and 65.2%,respectively.CONCLUSION We demonstrated that serum proteomics may be helpful for the detection of CRC,and it may assist clinical practice for CRC diagnosis.

摘要： BACKGROUND Ulcerative colitis(UC)is a chronic,nonspecific intestinal inflammatory disease.Acupuncture and moxibustion is proved effective in treating UC,but the mechanism has not been clarified.Proteomic technology has revealed a variety of biological markers related to immunity and inflammation in UC,which provide new insights and directions for the study of mechanism of acupuncture and moxibustion treatment of UC.AIM To investigate the mechanism of electroacupuncture(EA)and herb-partitioned moxibustion(HM)on UC rats by using proteomics technology.METHODS Male Sprague-Dawley rats were randomly divided into the normal(N)group,the dextran sulfate sodium(DSS)-induced UC model(M)group,the HM group,and the EA group.UC rat model was prepared with 3%DSS,and HM and EA interventions at the bilateral Tianshu and Qihai acupoints were performed in HM or EA group.Haematoxylin and eosin staining was used for morphological evaluation of colon tissues.Isotope-labeled relative and absolute quantification(iTRAQ)and liquid chromatography-tandem mass spectrometry were performed for proteome analysis of the colon tissues,followed by bioinformatics analysis and protein-protein interaction networks establishment of differentially expressed proteins(DEPs)between groups.Then western blot was used for verification of selected DEPs.RESULTS The macroscopic colon injury scores and histopathology scores in the HM and EA groups were significantly decreased compared to the rats in the M group(P<0.01).Compared with the N group,a total of 202 DEPs were identified in the M group,including 111 up-regulated proteins and 91 down-regulated proteins,of which 25 and 15 proteins were reversed after HM and EA interventions,respectively.The DEPs were involved in various biological processes such as biological regulation,immune system progression and in multiple pathways including natural killer cell mediated cytotoxicity,intestinal immune network for immunoglobulin A(IgA)production,and FcγR-mediated phagocytosis.The Kyoto Encyclopedia of Genes and Genomes pathways of DEPs between HM and M groups,EA and M groups both included immuneassociated and oxidative phosphorylation.Network analysis revealed that multiple pathways for the DEPs of each group were involved in protein-protein interactions,and the expression of oxidative phosphorylation pathway-related proteins,including ATP synthase subunit g(ATP5L),ATP synthase beta subunit precursor(Atp5f),cytochrome c oxidase subunit 4 isoform 1(Cox4i1)were down-regulated after HM and EA interventions.Subsequent verification of selected DEPs(Synaptic vesicle glycoprotein 2A;nuclear cap binding protein subunit 1;carbamoyl phosphate synthetase 1;Cox4i1;ATP synthase subunit b,Atp5f1;doublecortin like kinase 3)by western blot confirmed the reliability of the iTRAQ data,HM and EA interventions can significantly downregulate the expression of oxidative phosphorylation-associated proteins(Cox4i1,Atp5f1)(P<0.01).CONCLUSION EA and HM could regulate the expression of ATP5L,Atp5f1,Cox4i1 that associated with oxidative phosphorylation,then might regulate immune-related pathways of intestinal immune network for IgA production,FcγR-mediated phagocytosis,thereby alleviating colonic inflammation of DSSinduced UC rats.

摘要： Fruit ripening has been reported to be related to calcium(Ca),but the underlying mechanisms by which Ca regulates this process remain largely unknown.In order to study the changes of proteins and enriched phosphopeptides,we conducted TMT labeling,bio-material-based PTM enrichment based on mass spectrometry in Ca-treated‘Golden Delicious’(GD)apple fruit(Malus×domestica).This dataset presents a comprehensive overview of the critical pathways involved in fruit ripening.A total of 47 proteins and 124 phosphoproteins significantly changed in Ca-treated fruit,which are crucial for regulating the cell wall and cytoskeleton,Ca-mediated signaling and transport,ethylene production,protein fate,especially ubiquitination-based protein degradation,and primary and secondary metabolisms.Our results indicated that Ca inhibited the abundance of polygalacturonase(PG)activity and increased the phosphorylation level of CSLD3.PG and phosphorylation were involved in cell wall degradation,thereby delaying fruit softening.As a secondary messenger,Ca-mediated signaling subsequently triggered downstream mitogen-activated protein kinases(MAPK)cascades and activated the membrane,transport,and ROS signaling.Moreover,MdEIN2,a key enzyme involved in the ubiquitin of protein modification,increased at Ser753 and Ser758 in Ca-treated fruit.Furthermore,diverse primary and secondary metabolisms including glycolysis,fatty acid metabolism,and oxidation respiratory chain were modulated to prevent fruit softening.These results provide basic information from protein and phosphorylation levels for apple fruit ripening during storage,which may be helpful for apple fruit storage control.

摘要： Attention-deficit hyperactivity disorder(ADHD) is a neurodevelopmental disorder prevalent in schoolage children. At present, however, its etiologies and risk factors are unknown. Transmembrane α-amino-3-hydroxy-5-methyl-4-isoxazolepropionicacid(AMPA) receptor regulatory protein γ-8(TARP γ-8,also known as calcium voltage-gated channel auxiliary subunit gamma 8(CACNG8)) is an auxiliary AMPA receptor(AMPAR) subunit. Here, we report an association between TARP γ-8 and ADHD,whereby adolescent TARP γ-8 knockout(KO) mice exhibitedADHD-likebehaviors,including hyperactivity, impulsivity, anxiety, impaired cognition,and memory deficits. Human single-nucleotide polymorphism(SNP) analysis also revealed strong associations between intronic alleles in CACNG8genes and ADHD susceptibility. In addition,synaptosomalproteomicanalysisrevealed dysfunction of the AMPA glutamate receptor complex in the hippocampi of TARP γ-8 KO mice.Proteomic analysis also revealed dysregulation of dopaminergic and glutamatergic transmissions in the prefrontal cortices of TARP γ-8 KO mice.Methylphenidate(MPH), which is commonly used to treat ADHD, significantly rescued the major behavioral deficits and abnormal synaptosomal proteins in TARP γ-8 KO mice. Notably, MPH significantly reversed the up-regulation of Grik2 and Slc6a3 in the prefrontal cortex. MPH also significantly improved synaptic AMPAR complex function by up-regulating other AMPAR auxiliary proteins in hippocampal synaptosomes. Taken together, our results suggest that TARP γ-8 is involved in the development of ADHD in humans.This study provides a useful alternative animal model with ADHD-like phenotypes related to TARP γ-8deficiency, which has great potential for the development of new therapies.

摘要： The Polian vesicle is the main accessory structure in the water vascular system of sea cucumbers.It can function to hold water vascular fluid under slight pressure and act as a hematopoiesis,excretory,and inflammatory response organ.Being the only organ to remain after evisceration,the Polian vesicle may function in the survival and regeneration of sea cucumber.We performed Tandem Mass Tag(TMT)-based proteomics to identify how proteins in the Polian vesicle of Apostichopus japonicus respond to evisceration.Among the 8453 proteins identified from vesicle samples before evisceration(PVOh)and at 6-h post-evisceration(PV6h)and 3-d post-evisceration(PV3d),we detected 222 differentially abundant proteins(DAPs).Most of the annotated DAPs were associated with cell growth and proliferation,immune response and wound healing,substance transport and metabolism,cytoskeleton/cilia/flagella,extracellular matrix,energy production and conversion,protein synthesis and modification,and signal recognition and transduction.Compared with PVOh,fewer DAPs were identified at PV6h,and more DAPs were found at PV3d,and these DAPs were widely distributed among multiple biological processes.Our results indicate that a wide range of biological processes was induced in Polian vesicles in response to evisceration.In particular,Polian vesicles may play important roles in the re storation of coelomocyte s,immune defense,and wound healing in sea cucumber.We propose that the Polian vesicle may be involved in visceral regeneration through nutrition and energy supply and by promoting dedifferentiation and migration.Together,these results provided new insights into the function of the Polian vesicle in A.japonicus post-evisceration.