scholarly journals Comparative proteome analysis of the spinal dural arteriovenous fistula arterial draining vein with label-free quantitative proteomics

2020 ◽  
Author(s):  
Peixi Liu ◽  
Yuan Shi ◽  
Sichen Li ◽  
Yingjun Liu ◽  
Yingjie Zhou ◽  
...  
Keyword(s):  
Quantitative Proteomics ◽  
Dural Arteriovenous Fistula ◽  
Kegg Pathway ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Spinal Dural Arteriovenous Fistula ◽  
Differentially Expressed Protein ◽  
Kegg Pathway Analysis ◽  
Go Terms

Abstract Background: Spinal dural arteriovenous fistula (SDAVF) is the most common spinal vascular shunt lesion. Although pathological changes in the SDAVF draining vein (SDAVF-DV) have been elucidated, protein changes remain enigmatic. We investigated protein changes in the SDAVF-DV.Methods: Three SDAVF-DV samples were collected, and superficial temporal artery (STA) and superficial temporal vein (STV) samples were used as controls. After quantification and enzymolysis of the proteins, label-free quantitative proteomics was performed, and the peptide mixture was fractionated and analysed by liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify the differentially expressed proteins. Bioinformatics analysis of the differentially expressed proteins was also performed using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein-protein interaction (PPI) network analyses.Results: Compared with the STA, the SDAVF-DV had 195 upregulated proteins and 303 downregulated proteins. GO analysis showed that the most differential GO terms in each category were the adenylate cyclase-modulating G protein-coupled receptor signalling pathway, U6 snRNP and SH3 domain binding. KEGG pathway analysis showed that the most differentially expressed protein pathway was focal adhesion. Compared with the STV, the SDAVF-DV had 158 upregulated proteins and 362 downregulated proteins. GO analysis showed that the most differential GO terms in each category were lamellipodium assembly, U6 snRNP, and SH3 domain binding. KEGG pathway analysis showed that the most differentially expressed protein pathway was dilated cardiomyopathy. The PPI analysis revealed PPIs among the top 300 proteins.Conclusions: We demonstrated that the SDAVF-DV showed specific protein expression changes under long-period venous hypertension. The results of the present study will provide insights into the pathogenesis of SDAVF formation at the protein level. The proteomic results provide a scientific foundation for further study to explore the pathophysiological mechanism of SDAVF.

scholarly journals Pathology and Protein Changes of the Spinal Dural Arteriovenous Fistula Arterial Draining Vein Under Sustained High Vascular Pressure

2021 ◽  
Vol 12 ◽  
Author(s):  
Peixi Liu ◽  
Yuan Shi ◽  
Sichen Li ◽  
Yingjun Liu ◽  
Yingjie Zhou ◽  
...  
Keyword(s):  
Arteriovenous Fistula ◽  
Dural Arteriovenous Fistula ◽  
Sh3 Domain ◽  
Differentially Expressed ◽  
Pathophysiological Mechanism ◽  
Differentially Expressed Proteins ◽  
Spinal Dural Arteriovenous Fistula ◽  
Ppi Networks ◽  
Go Terms ◽  
Masson Staining

Object: Spinal dural arteriovenous fistula (SDAVF) is the most common spinal vascular shunt lesion. Although pathological changes in the SDAVF draining vein (SDAVF-DV) have been elucidated, protein changes remain enigmatic. We investigated the pathology and protein changes in the SDAVF-DV under sustained high vascular pressure.Methods: Three SDAVF-DV samples were compared with superficial temporal artery (STA) and superficial temporal vein (STV) samples as controls. Vascular structure was revealed by hematoxylin and eosin (H&E) and Masson staining; and cell distribution, extracellular matrix, and inflammation infiltration were observed by immunohistochemistry. Label-free quantitative proteomics was performed, and the peptide mixture was fractionated and analyzed by liquid chromatography–tandem mass spectrometry (LC-MS/MS) to identify differentially expressed proteins. Bioinformatics analysis of the differentially expressed proteins was performed using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein–protein interaction (PPI) networks.Results: H&E and Masson staining showed an artery-like structure of the SDAVF-DV. Immunostaining showed that vWF+ cells were not continuous in the SDAVF-DV. Although α-SMA+ and AT1+ cells were more abundant in the STV than in the SDAVF-DV, piezo-1 expression was lower in the SDAVF-DV. The SDAVF-DV showed different distributions of elastin, COL I, and COL III. COL IV and COL VI were decreased in the SDAVF-DV, while CD45+ cells and COX-1 were increased compared with those in the controls. No differences in CD68 expression and COX-2 staining were observed between the SDAVF-DV and controls. Compared with the STA, 95 proteins were upregulated and 303 proteins were downregulated in the SDAVF-DV. The most differential GO terms in each category were the adenylate cyclase-modulating G protein-coupled receptor signaling pathway, U6 snRNP, and SH3 domain binding. The most differentially expressed KEGG protein pathway was focal adhesion. Compared with the STV, the SDAVF-DV had 158 upregulated proteins and 362 downregulated proteins. The most differential GO terms in each category were lamellipodium assembly, U6 snRNP, and SH3 domain binding; and the most differentially expressed KEGG protein pathway was dilated cardiomyopathy. PPI analysis revealed PPIs among the top 300 proteins.Conclusions: The SDAVF-DV exhibits specific pathology and protein expression changes under sustained high vascular pressure. The results of the present study provide insights into the pathogenesis of SDAVF formation at the protein level as well as a scientific foundation for further exploration of the pathophysiological mechanism of the SDAVF.

scholarly journals Label-Free Proteomic Analysis of Flavohemoglobin Deleted Strain of Saccharomyces cerevisiae

2016 ◽  
Vol 2016 ◽  
pp. 1-12
Author(s):  
Chiranjit Panja ◽  
Rakesh K.S. Setty ◽  
Gopal Vaidyanathan ◽  
Sanjay Ghosh
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Stress Responses ◽  
Nitrosative Stress ◽  
Nitrogen Compound ◽  
Nuclear Gene ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Differential Proteomics ◽  
Go Terms

Yeast flavohemoglobin, YHb, encoded by the nuclear gene YHB1, has been implicated in the nitrosative stress responses in Saccharomyces cerevisiae. It is still unclear how S. cerevisiae can withstand this NO level in the absence of flavohemoglobin. To better understand the physiological function of flavohemoglobin in yeast, in the present study a label-free differential proteomics study has been carried out in wild-type and YHB1 deleted strains of S. cerevisiae grown under fermentative conditions. From the analysis, 417 proteins in Y190 and 392 proteins in ΔYHB1 were identified with high confidence. Interestingly, among the differentially expressed identified proteins, 40 proteins were found to be downregulated whereas 41 were found to be upregulated in ΔYHB1 strain of S. cerevisiae (p value < 0.05). The differentially expressed proteins were also classified according to gene ontology (GO) terms. The most enriched and significant GO terms included nitrogen compound biosynthesis, amino acid biosynthesis, translational regulation, and protein folding. Interactions of differentially expressed proteins were generated using Search Tool for the Retrieval of Interacting Genes (STRING) database. This is the first report which offers a more complete view of the proteome changes in S. cerevisiae in the absence of flavohemoglobin.

scholarly journals Label-free quantitative proteomic analysis of the inhibition effect of Lactobacillus rhamnosus GG on Escherich coli biofilm formation in coculture

2020 ◽  
Author(s):  
Huiyi Song ◽  
Ni Lou ◽  
Jianjun Liu ◽  
Hong Xiang ◽  
Dong Shang
Keyword(s):  
Proteomic Analysis ◽  
Biofilm Formation ◽  
Quantitative Proteomics ◽  
Lactobacillus Rhamnosus ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Proteomics Analysis ◽  
Biofilm Inhibition ◽  
Sterile Culture

Abstract Background: Escherich coli (E.coli) is the principal pathogen that causes biofilm formation; the latter is associated with infectious diseases and antibiotic resistance. In our previous work, we demonstrated that probiotic microcapsules have superior biofilm inhibition capacity compared to probiotic sterile culture supernatant. Herein, the mechanism of the inhibition effects was investigated using label-free quantitative proteomics analysis. Results: The proteomic analysis characterized a total of 1655 proteins in E.coli K12MG1655 and 1431 proteins in Lactobacillus rhamnosus GG (LGG). Among them, after coculture treatment, there were 262 and differentially expressed proteins that were specific for E.coli and 291 for LGG. The differentially expressed proteins after coculture were related to cellular metabolism, the stress response, transcription, and the cell membrane. In addition, we identified five strain-specific genes in E.coli and LGG, respectively, which were consistent with the proteomics results. Conclusions: These findings indicate that LGG microcapsules may inhibit E.coli biofilm inhibition by disrupting metabolic processes, particularly in relation to energy metabolism and stimulus responses, both of which are critical for the growth of LGG. Together, these findings increase our understanding of the interactions between bacteria under coculture conditions.

Label-free Quantitative Proteomics Combined With Transcriptomics Revealed the Importance of Cardiac Development in Producing the High Metabolic Capacity of Yellowfin Tuna (Thunnus Albacares)

2022 ◽  
Author(s):  
Lulu Yan ◽  
Jieyun Guo ◽  
Chao Zhao ◽  
Yong Liu ◽  
Pengfei Wang ◽  
...  
Keyword(s):  
Body Weight ◽  
Cardiac Function ◽  
Quantitative Proteomics ◽  
Heart Function ◽  
Yellowfin Tuna ◽  
Differentially Expressed ◽  
Thunnus Albacares ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Gene And Protein Expression

Abstract Tuna are commercially important fish throughout the world, and they are renowned for their endothermy, which allows them to maintain elevated temperatures in the oxidative locomotor muscles, viscera, brain, and eyes while occupying cold, productive, high-latitude waters. The endothermic mechanism is supported by a high heart rate and cardiac output, but the genes and proteins that participate in this cardiac function are poorly known. In this study, we combined label-free quantitative proteomics and transcriptomics to investigate the changes in the heart of yellowfin tuna (Thunnus albacares) before and after they developed endothermy. We identified 515,428 transcripts and 3355 protein groups in the hearts of two development stages of yellowfin tuna. Twenty-eight differentially expressed proteins were correlated with differentially expressed genes. The proteins that accelerate energy production were more highly expressed in the hearts of the large yellowfin tuna compared with the small specimens. Moreover, the proteins in the Z-disk, which protect against mechanical damage, were only detected in the hearts of large fish. These results indicate that as yellowfin tuna grow, the heart develops a self-protection strategy to cope with high metabolic rates and high mechanical forces. The differentially expressed proteins related to cardiac function, which are closely associated with striated muscle differentiation, glycosylation, and cardiac myocytes motility, were highly expressed in the larger (endothermic) tuna than that in the smaller (poikilothermic) tuna. Therefore, we suggest that the heart function of yellowfin tuna changes and improves during the transition from poikilothermic tuna (small size, 126 mm < fork length (FL) < 152 mm, 30 g < body weight < 46 g) to endothermic tuna (large size, 207 mm < FL < 235 mm, 170 g < body weight < 200 g). This is the first report of how gene and protein expression levels explain the strong heart function of yellowfin tuna.

scholarly journals The Quantitative Proteomics Analysis in Glioblastoma After HULC Silencing

2020 ◽  
Author(s):  
Shan Ye ◽  
Yiran Wang ◽  
Tiantian Yin ◽  
Yuchen Hu ◽  
Jie He
Keyword(s):  
Quantitative Proteomics ◽  
Kegg Pathway ◽  
Transfection Efficiency ◽  
Negative Control ◽  
Arachidonic Acid Metabolism ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Differentially Expressed Proteins ◽  
Pathway Enrichment ◽  
Qrt Pcr

Abstract Background: Glioblastoma multiforme (GBM) is a malignant intracranial tumor threatening patients' survival. The study aimed to find the menchanisms of lncRNA highly up-regulated in liver cancer (HULC) affecting GBM or involved signaling pathways, which may providing theoretical support for targeted therapy.Methods: Two cell lines were constructed: HULC-small interfering RNA (siRNA) and negative control. Then qRT-PCR was operated to detect the transfection efficiency and quantitative proteomics based on mass spectrometry (MS) were conducted. Finally, the differentially expressed proteins were analyzed in gene ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment.Results: The relative expression level of HULC in HULC-siRNA was significantly lower than that in NC detected by qRT-PCR. A total of 136 differentially expressed proteins were identified, including 24 down-regulated and 112 up-regulated. GO classification results illustrated that they were centralized in cellular or single-organism process and biological regulation in biological process, cell and organelle in cellular component, binding and catalytic activity in molecular function. KEGG pathway enrichment analysis indicated that some were sinificantly enriched, including tight junction, metabolic pathways and arachidonic acid metabolism. It was further discovered that PLA2G4A was down regulated obviously after HULC silencing.Conclusion: HULC changed the proteomics characteristics of GBM, including regulating the expression of PLA2G4A. This study provided a new perspective on the menchanisms and potential drug targets of GBM.

Transcriptional identification of differentially expressed genes during the prepupal–pupal transition in the oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae)

2021 ◽  
pp. 1-14
Author(s):  
Peirong Li ◽  
Xinru Li ◽  
Wei Wang ◽  
Xiaoling Tan ◽  
Xiaoqi Wang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Developmental Stages ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Mythimna Separata ◽  
Kegg Pathway Analysis ◽  
Oriental Armyworm ◽  
Lepidoptera Noctuidae

Abstract The oriental armyworm, Mythimna separata (Walker) is a serious pest of agriculture that does particular damage to Gramineae crops in Asia, Europe, and Oceania. Metamorphosis is a key developmental stage in insects, although the genes underlying the metamorphic transition in M. separata remain largely unknown. Here, we sequenced the transcriptomes of five stages; mature larvae (ML), wandering (W), and pupation (1, 5, and 10 days after pupation, designated P1, P5, and P10) to identify transition-associated genes. Four libraries were generated, with 22,884, 23,534, 26,643, and 33,238 differentially expressed genes (DEGs) for the ML-vs-W, W-vs-P1, P1-vs-P5, and P5-vs-P10, respectively. Gene ontology enrichment analysis of DEGs showed that genes regulating the biosynthesis of the membrane and integral components of the membrane, which includes the cuticular protein (CP), 20-hydroxyecdysone (20E), and juvenile hormone (JH) biosynthesis, were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that DEGs were enriched in the metabolic pathways. Of these DEGs, thirty CP, seventeen 20E, and seven JH genes were differentially expressed across the developmental stages. For transcriptome validation, ten CP, 20E, and JH-related genes were selected and verified by real-time PCR quantitative. Collectively, our results provided a basis for further studies of the molecular mechanism of metamorphosis in M. separata.

scholarly journals Label-free quantitative proteomic analysis of the inhibition effect of Lactobacillus rhamnosus GG on Escherichia coli biofilm formation in co-culture

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Huiyi Song ◽  
Ni Lou ◽  
Jianjun Liu ◽  
Hong Xiang ◽  
Dong Shang
Keyword(s):  
Escherichia Coli ◽  
Proteomic Analysis ◽  
Biofilm Formation ◽  
Lactobacillus Rhamnosus ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Quantitative Proteomic Analysis ◽  
E Coli ◽  
Protein Ubiquitination

Abstract Background Escherichia coli (E. coli) is the principal pathogen that causes biofilm formation. Biofilms are associated with infectious diseases and antibiotic resistance. This study employed proteomic analysis to identify differentially expressed proteins after coculture of E. coli with Lactobacillus rhamnosus GG (LGG) microcapsules. Methods To explore the relevant protein abundance changes after E. coli and LGG coculture, label-free quantitative proteomic analysis and qRT-PCR were applied to E. coli and LGG microcapsule groups before and after coculture, respectively. Results The proteomic analysis characterised a total of 1655 proteins in E. coli K12MG1655 and 1431 proteins in the LGG. After coculture treatment, there were 262 differentially expressed proteins in E. coli and 291 in LGG. Gene ontology analysis showed that the differentially expressed proteins were mainly related to cellular metabolism, the stress response, transcription and the cell membrane. A protein interaction network and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated that the differentiated proteins were mainly involved in the protein ubiquitination pathway and mitochondrial dysfunction. Conclusions These findings indicated that LGG microcapsules may inhibit E. coli biofilm formation by disrupting metabolic processes, particularly in relation to energy metabolism and stimulus responses, both of which are critical for the growth of LGG. Together, these findings increase our understanding of the interactions between bacteria under coculture conditions.

scholarly journals Label-Free Comparative Proteomics of Differentially Expressed Mycobacterium tuberculosis Protein in Rifampicin-Related Drug-Resistant Strains

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 607
Author(s):  
Nadeem Ullah ◽  
Ling Hao ◽  
Jo-Lewis Banga Ndzouboukou ◽  
Shiyun Chen ◽  
Yaqi Wu ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Drug Targets ◽  
Control Strategies ◽  
Multidrug Resistant ◽  
Differentially Expressed ◽  
Effective Control ◽  
Drug Resistant ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Candidate Target

Rifampicin (RIF) is one of the most important first-line anti-tuberculosis (TB) drugs, and more than 90% of RIF-resistant (RR) Mycobacterium tuberculosis clinical isolates belong to multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. In order to identify specific candidate target proteins as diagnostic markers or drug targets, differential protein expression between drug-sensitive (DS) and drug-resistant (DR) strains remains to be investigated. In the present study, a label-free, quantitative proteomics technique was performed to compare the proteome of DS, RR, MDR, and XDR clinical strains. We found iniC, Rv2141c, folB, and Rv2561 were up-regulated in both RR and MDR strains, while fadE9, espB, espL, esxK, and Rv3175 were down-regulated in the three DR strains when compared to the DS strain. In addition, lprF, mce2R, mce2B, and Rv2627c were specifically expressed in the three DR strains, and 41 proteins were not detected in the DS strain. Functional category showed that these differentially expressed proteins were mainly involved in the cell wall and cell processes. When compared to the RR strain, Rv2272, smtB, lpqB, icd1, and folK were up-regulated, while esxK, PPE19, Rv1534, rpmI, ureA, tpx, mpt64, frr, Rv3678c, esxB, esxA, and espL were down-regulated in both MDR and XDR strains. Additionally, nrp, PPE3, mntH, Rv1188, Rv1473, nadB, PPE36, and sseA were specifically expressed in both MDR and XDR strains, whereas 292 proteins were not identified when compared to the RR strain. When compared between MDR and XDR strains, 52 proteins were up-regulated, while 45 proteins were down-regulated in the XDR strain. 316 proteins were especially expressed in the XDR strain, while 92 proteins were especially detected in the MDR strain. Protein interaction networks further revealed the mechanism of their involvement in virulence and drug resistance. Therefore, these differentially expressed proteins are of great significance for exploring effective control strategies of DR-TB.

scholarly journals POS0399 TMT-BASED QUANTITATIVE PROTEOMICS ANALYSIS OF SYNOVIAL FLUID-DERIVED EXOSOMES IN RHEUMATOID ARTHRITIS, AXIAL SPONDYLOARTHRITIS, GOUT AND OSTEOARTHRITIS

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 428.3-429
Author(s):  
Y. Liu ◽  
Y. Huang ◽  
Q. Huang ◽  
Z. Huang ◽  
Z. Li ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Cluster Analysis ◽  
Synovial Fluid ◽  
Pathway Analysis ◽  
Quantitative Proteomics ◽  
Axial Spondyloarthritis ◽  
Kegg Pathway ◽  
Hierarchical Cluster ◽  
Kegg Pathway Analysis ◽  
Differential Proteins

Background:The pathogeneses of the joint diseases rheumatoid arthritis (RA), axial spondyloarthritis (axSpA), gout, and osteoarthritis (OA) are still not fully elucidated. Exosomes in synovial fluid (SF) has a critical role in the pathogenesis of arthritis. None of study has compared the proteomics of SF-derived exosomes in RA, axSpA, gout and OA.Objectives:To compare the proteomics of SF-derived exosomes in RA, axSpA, gout and OA based on tandem mass tags (TMT) labeled quantitative proteomics technique.Methods:SF-derived exosomes was isolated from RA, axSpA, gout and OA patients by the Exoquick kit combined ultracentrifugation method. TMT labeled quantitative proteomics technique was used to compare the proteomics of SF-derived exosomes. Volcano plot, hierarchical cluster, Gene Ontologies (GO), Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted.Results:A total of 1678 credible proteins were detected. With the cut off criteria of |log2 (fold-change)| ≥1.2 and p-value <0.05, 267 (140 up-regulated and 127 down-regulated)differential proteins were found in OA vs gout, 291 (179 and 112) in axSpA vs OA, 515 (109 and 406) in RA vs axSpA, 298 (191 and 107) in axSpA vs gout, 462 (160 and 302) in RA vs gout, 536 (170 and 366) in RA vs OA. GO analysis showed that the biological progress of differential proteins were mainly enriched in the “immune response”. Regarding the molecular function, the differential proteins mainly mediated “antigen binding”. GO analysis of the cellular components indicated that most proteins were annotated as “extracellular exosomes”. KEGG pathway analysis demonstrated differential proteins were significantly enriched in “complement and coagulation cascades”. The hierarchical cluster analysis of the differential proteins in the four groups showed that Lysozyme C and Keratin were more abundant in gout, Hemoglobin and Actin-related protein 2/3 complex subunit 3 in OA, Sodium/potassium-transporting ATPase subunit alpha-1 and Immunoglobulin heavy constant delta in axSpA, Pregnancy zone protein and Stromelysin-1 in RA.Conclusion:The protein profiles of SF-derived exosomes in RA, axSpA, gout and OA patients were different. The differential proteins were the potential biomarkers of RA, axSpA, gout and OA.References:[1]Cretu D, Diamandis E P, Chandran V. Delineating the synovial fluid proteome: recent advancements and ongoing challenges in biomarker research.[J]. Critical reviews in clinical laboratory sciences, 2013,50(2):51-63.[2]McArdle A J, Menikou S. What is proteomics?[J]. Archives of disease in childhood. Education and practice edition, 2020.Figure 1.The hierarchical cluster analysis of differential proteins in axSpA, OA, Gout and RA.Disclosure of Interests:None declared

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