Label-free Quantification Proteomics Research Articles

Proteomics analysis of coronary atherosclerotic heart disease with different Traditional Chinese Medicine syndrome types before and after percutaneous coronary intervention.

To investigate the underlying protein molecular mechanisms of "Qi stagnation and blood stasis syndrome" (QS) and "Qi deficiency and blood stasis syndrome" (QD), as two subtypes of coronary artery disease (CAD) in Traditional Chinese Medicine (TCM), following percutaneous coronary intervention (PCI). In this study, a total of 227 CAD patients with QS and 211 CAD patients with QD were enrolled; all participants underwent PCI. Label-free quantification proteomics were employed to analyze the changes in serum in two subtypes of CAD patients before and 6 months after PCI, aiming to elucidate the intervention mechanism of PCI in treating CAD characterized by two different TCM syndromes. Biochemical analysis revealed significant changes in tumor necrosis factor-α, high density lipoprotein cholesterol, blood stasis clinical symptoms observation, and Gensini levels in both patient groups post-PCI; Proteomic analysis identified 79 and 95 differentially expressed proteins in the QS and QD patient groups, respectively, compared to their control groups. complement C8 alpha chain, complement factor H, apolipoprotein H, apolipoprotein B, plasminogen, carbonic anhydrase 2, and complement factor I were altered in both comparison groups. Furthermore, enrichment analysis demonstrated that cell adhesion and connectivity-related processes underwent changes in QS patients post-PCI, whereas lipid metabolism-related pathways, including the peroxisome proliferator-activated receptor signaling pathway and extracellular matrix receptor interaction, underwent changes in the QD group. The protein-protein interaction network analysis further enriched 52 node proteins, including apolipoprotein B, lipoprotein (a), complement C5, apolipoprotein A4, complement C8 alpha chain, complement C8 beta chain, complement C8 gamma chain, apolipoprotein H, apolipoprotein A-Ⅱ, albumin, complement C4-B, apolipoprotein C3, among others. The functional network of these proteins is posited to contribute to the pathophysiology of CAD characterized by TCM syndromes. The current quantitative proteomic study has preliminarily identified biomarkers of CAD in different TCM subtypes treated with PCI, potentially laying the groundwork for understanding the protein profiles associated with the treatment of various TCM subtypes of CAD.

Targeting USP7 to induce ubiquitination degradation of oncogenic ATAD2 and effects on cholangiocarcinoma growth.

e16215 Background: Cholangiocarcinoma (CCA) is a highly fatal disease due to limited therapeutic targets. Deubiquitinase USP7 is an oncogene and has been suggested to be deeply involved in regulating tumor initiation and progression, but its abundance and role in CCA still remain unclear. Methods: USP7 mRNA expression was performed using TCGA and GEO database. Survival analysis in CCA patients with high- and low-USP7 mRNA expression was performed using NODE database. CCK8, colony formation, flow cytometry and shRNA interference assay were used to evaluate the biological function of USP7-ATAD2 axis on CCA cancer cells in vitro. 4D label-free quantification proteomics was used to analyze the targets and networks regulated by USP7. The molecular mechanism of USP7 and ATAD2 in CCA was determined by conducting Western blot, co-immunoprecipitation, IHC and quantitative real-time PCR (qPCR) analyses. The CCA PDX model was used to evaluate the efficacy of targeting USP7 in the treatment of cholangiocarcinoma. Results: Here, we found USP7 is highly expressed in CAA, and is associated with poor outcomes of CCA patients. We show that USP7 depletion induces S phase arrest, and suppresses CCA tumor cells proliferation. Next, we provide a comprehensive understanding of targets and networks affected by USP7 depletion by performing a 4D label-free quantification proteomics analysis. We show that ATAD2 is a USP7 target, and USP7 interacts with and deubiquitinates ATAD2 to stabilize ATAD2 protein level. Ectopic expression of ATAD2 in USP7-depleted cells rescues the cell proliferation phenotype. Further, pharmacological blocking the activity of USP7 by P5091 inhibits tumor growth in CCA patient-derived xenograft (PDX) mouse model. Conclusions: This study uncovers the role of USP7-ATAD2 axis in regulating tumor growth, and targeting USP7 may provide a novel therapeutic strategy for CCA.

Targeting USP7 to induce ubiquitination degradation of oncogenic ATAD2 and effects on cholangiocarcinoma growth.

e16215 Background: Cholangiocarcinoma (CCA) is a highly fatal disease due to limited therapeutic targets. Deubiquitinase USP7 is an oncogene and has been suggested to be deeply involved in regulating tumor initiation and progression, but its abundance and role in CCA still remain unclear. Methods: USP7 mRNA expression was performed using TCGA and GEO database. Survival analysis in CCA patients with high- and low-USP7 mRNA expression was performed using NODE database. CCK8, colony formation, flow cytometry and shRNA interference assay were used to evaluate the biological function of USP7-ATAD2 axis on CCA cancer cells in vitro. 4D label-free quantification proteomics was used to analyze the targets and networks regulated by USP7. The molecular mechanism of USP7 and ATAD2 in CCA was determined by conducting Western blot, co-immunoprecipitation, IHC and quantitative real-time PCR (qPCR) analyses. The CCA PDX model was used to evaluate the efficacy of targeting USP7 in the treatment of cholangiocarcinoma. Results: Here, we found USP7 is highly expressed in CAA, and is associated with poor outcomes of CCA patients. We show that USP7 depletion induces S phase arrest, and suppresses CCA tumor cells proliferation. Next, we provide a comprehensive understanding of targets and networks affected by USP7 depletion by performing a 4D label-free quantification proteomics analysis. We show that ATAD2 is a USP7 target, and USP7 interacts with and deubiquitinates ATAD2 to stabilize ATAD2 protein level. Ectopic expression of ATAD2 in USP7-depleted cells rescues the cell proliferation phenotype. Further, pharmacological blocking the activity of USP7 by P5091 inhibits tumor growth in CCA patient-derived xenograft (PDX) mouse model. Conclusions: This study uncovers the role of USP7-ATAD2 axis in regulating tumor growth, and targeting USP7 may provide a novel therapeutic strategy for CCA.

The cuticle proteome of a planktonic crustacean.

The cuticles of arthropods provide an interface between the organism and its environment. Thus, the cuticle's structure influences how the organism responds to and interacts with its surroundings. Here, we used label-free quantification proteomics to provide a proteome of the moulted cuticle of the aquatic crustacean Daphnia magna, which has long been a prominent subject of studies on ecology, evolution, and developmental biology. We detected a total of 278 high-confidence proteins. Using protein sequence domain and functional enrichment analyses, we identified chitin-binding structural proteins and chitin-modifying enzymes as the most abundant protein groups in the cuticle proteome. Structural cuticular protein families showed a similar distribution to those found in other arthropods and indicated proteins responsible for the soft and flexible structure of the Daphnia cuticle. Finally, cuticle protein genes were also clustered as tandem gene arrays in the D. magna genome. The cuticle proteome presented here will be a valuable resource to the Daphnia research community, informing genome annotations and investigations on diverse topics such as the genetic basis of interactions with predators and parasites.

Tissue-derived exosome proteomics identifies promising diagnostic biomarkers for esophageal cancer.

Esophageal cancer (EC) is a fatal digestive disease with a poor prognosis and frequent lymphatic metastases. Nevertheless, reliable biomarkers for EC diagnosis are currently unavailable. Accordingly, we have performed a comparative proteomics analysis on cancer and paracancer tissue-derived exosomes from eight pairs of EC patients using label-free quantification proteomics profiling and have analyzed the differentially expressed proteins through bioinformatics. Furthermore, nano-flow cytometry (NanoFCM) was used to validate the candidate proteins from plasma-derived exosomes in 122 EC patients. Of the 803 differentially expressed proteins discovered in cancer and paracancer tissue-derived exosomes, 686 were up-regulated and 117 were down-regulated. Intercellular adhesion molecule-1 (CD54) was identified as an up-regulated candidate for further investigation, and its high expression in cancer tissues of EC patients was validated using immunohistochemistry, real-time quantitative PCR (RT-qPCR), and western blot analyses. In addition, plasma-derived exosome NanoFCM data from 122 EC patients concurred with our proteomic analysis. The receiver operating characteristic (ROC) analysis demonstrated that the AUC, sensitivity, and specificity values for CD54 were 0.702, 66.13%, and 71.31%, respectively, for EC diagnosis. Small interference (si)RNA was employed to silence the CD54 gene in EC cells. A series of assays, including cell counting kit-8, adhesion, wound healing, and Matrigel invasion, were performed to investigate EC viability, adhesive, migratory, and invasive abilities, respectively. The results showed that CD54 promoted EC proliferation, migration, and invasion. Collectively, tissue-derived exosomal proteomics strongly demonstrates that CD54 is a promising biomarker for EC diagnosis and a key molecule for EC development.

Congenital cataracts affect the retinal visual cycle and mitochondrial function: A multi-omics study of GJA8 knockout rabbits

Congenital cataracts are a threat to visual development in children, and the visual impairment persists after surgical treatment; however, the mechanisms involved remain unclear. Previous clinical studies have identified the effect of congenital cataracts on retinal morphology and function. To further understand the molecular mechanisms by which congenital cataracts affect retinal development, we analyzed retina samples from 7-week-old GJA8-knockout rabbits with congenital cataracts and controls by four-dimensional label-free quantification proteomics and untargeted metabolomics. Bioinformatics analysis of proteomic data showed that retinol metabolism, oxidative phosphorylation, and fatty acid degradation pathways were downregulated in the retinas of rabbits with congenital cataracts, indicating that their visual cycle and mitochondrial function were affected. Additional validation of differentially abundant proteins related to the visual cycle and mitochondrial function was performed using Parallel reaction monitoring and western blot experiments. Untargeted metabolome analysis showed significant upregulation of the antioxidant glutathione and ascorbic acid in the retinas of rabbits with congenital cataracts, indicating that their oxidative stress balance was not dysregulated. SignificanceCongenital cataracts in children can alter retinal structure and function, yet the mechanisms are uncertain. Here is the first study to use proteomics and metabolomics approaches to investigate the effects of congenital cataracts on retinal development in the early postnatal period. Our findings suggest that congenital cataracts have an impact on the retinal visual cycle and mitochondrial function. These findings give insight on the molecular pathways behind congenital cataract-induced visual function impairment in the early postnatal period.

Inter-Regional Proteomic Profiling of the Human Brain Using an Optimized Protein Extraction Method from Formalin-Fixed Tissue to Identify Signaling Pathways.

Proteomics offers vast potential for studying the molecular regulation of the human brain. Formalin fixation is a common method for preserving human tissue; however, it presents challenges for proteomic analysis. In this study, we compared the efficiency of two different protein-extraction buffers on three post-mortem, formalin-fixed human brains. Equal amounts of extracted proteins were subjected to in-gel tryptic digestion and LC-MS/MS. Protein, peptide sequence, and peptide group identifications; protein abundance; and gene ontology pathways were analyzed. Protein extraction was superior using lysis buffer containing tris(hydroxymethyl)aminomethane hydrochloride, sodium dodecyl sulfate, sodium deoxycholate, and Triton X-100 (TrisHCl, SDS, SDC, Triton X-100), which was then used for inter-regional analysis. Pre-frontal, motor, temporal, and occipital cortex tissues were analyzed by label free quantification (LFQ) proteomics, Ingenuity Pathway Analysis and PANTHERdb. Inter-regional analysis revealed differential enrichment of proteins. We found similarly activated cellular signaling pathways in different brain regions, suggesting commonalities in the molecular regulation of neuroanatomically-linked brain functions. Overall, we developed an optimized, robust, and efficient method for protein extraction from formalin-fixed human brain tissue for in-depth LFQ proteomics. We also demonstrate herein that this method is suitable for rapid and routine analysis to uncover molecular signaling pathways in the human brain.

Effect of different drying techniques on rose (Rosa rugosa cv. Plena) proteome based on label-free quantitative proteomics

To explore the molecular mechanisms of different processing technologies on rose tea (Rosa rugosa cv. Plena), we investigated the rose tea proteome (fresh rose tea [CS], vacuum freeze-drying rose tea [FD], and vacuum microwave rose tea [VD]) using label-free quantification proteomics (LFQ). A total of 2187 proteins were identified, with 1864, 1905, and 1660 proteins identified in CS, FD, and VD, respectively. Of those, 1500 proteins were quantified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation and enrichment analysis of differential expression proteins (DEPs) in VD vs. CS, FD vs. CS, and FD vs. VD showed that these pathways were associated with energy metabolism, the metabolic breakdown of energy substances and protein biosynthesis, such as oxidative phosphorylation, citrate cycle, carbon metabolism pathways, and ribosome and protein processing in endoplasmic reticulum. FD could ensure the synthesis of protein translation and energy metabolism, thereby maintaining the high quality of rose tea.

Promor: a comprehensive R package for label-free proteomics data analysis and predictive modeling.

We present promor, a comprehensive, user-friendly R package that streamlines label-free quantification proteomics data analysis and building machine learning-based predictive models with top protein candidates. promor is freely available as an open source R package on the Comprehensive R Archive Network (CRAN) (https://CRAN.R-project.org/package=promor) and distributed under the Lesser General Public License (version 2.1 or later). Development version of promor is maintained on GitHub (https://github.com/caranathunge/promor) and additional documentation and tutorials are provided on the package website (https://caranathunge.github.io/promor/). Supplementary data are available at Bioinformatics Advances online.

A bottom-up proteomics workflow for a system containing multiple organisms.

Discovery proteomics has been popularized to be essential in the investigator's biological toolbox. Many biological problems involve the interplay of multiple organisms. Herein, a bottom-up proteomics workflow was developed to study a system containing multiple organisms to promote a thorough understanding of how each interacts with the others. A label-free quantification proteomics workflow was developed with nanoscale liquid chromatography coupled to tandem mass spectrometry (nanoLC-MS/MS). This protocol describes a bottom-up proteomics workflow used to study differential protein expression in the context of fleas (Ctenocephalides felis felis) experimentally infected by the bacterium Bartonella henselae, the etiological agent of Cat Scratch Disease (CSD). Step-by-step instructions are provided for protein extraction, protein cleanup, total protein measurement, nanoLC-MS/MS data acquisition, and data analysis using Proteome Discoverer software. Comprehensive and exhaustive details are included to promote the adoption of this proteomics workflow in other laboratories. A proteomics protocol is detailed for a system containing multiple proteomes from different taxonomic lineages using CSD (cats bitten by fleas infected with Bartonella henselae) as a model. The operating protocol can be readily applied to other label-free proteomics work involving multiple proteomes from taxonomically distinct organisms.

Coexpression modules constructed identifies regulation pathways of winter jujube (Ziziphus jujuba Mill. 'Dongzao') following postharvest treatment with ozone

Winter jujube (Ziziphus jujuba Mill. 'Dongzao') is a member of the Rhamnaceae family known for its favorable nutritional and flavor profile. It has been considered a unique and excellent cultivar in China. Nevertheless, fresh winter jujube fruit is sensitive to diseases because of microbial decay and mechanical damage. Ozone treatment (OT) is reported to prevent fruit decay in many fruit during postharvest storage. In the present study, we first found that postharvest winter jujube fruit treated with 2.14 mg m −3 ozone concentration exhibited decreased accumulation of superoxide anion O2− generation rate, H2O2 content and MDA content and increased activities of aseorbate peroxidase (APX), catalase(CAT), peroxidase (POD), superoxide dismutase (SOD) and GSH content in the antioxidant bioactive compounds or enzymes, which was beneficial to the enhancement of antioxidant capacity over the entire storage period compared with the other three groups. Then, label-free quantification proteomics and weighted gene coexpression network analysis (WGCNA) of winter jujube fruit revealed black module (containing 94 differentially expressed proteins with increased and decreased levels of abundance respectively) was of greatest importance to study mechanisms of ozone preservation on winter jujube. Gene Ontology (GO) and KEGG annotation and enrichment analysis showed that the black module included ribosomal and glutathione metabolism pathways, suggesting the involvement of these pathways in ozone-mediated antisenescence. There are 26 hub proteins in the black module, and 6 intersecting proteins through protein–protein interaction (PPI) network analysis and KEGG annotation and enrichment analysis, a 60 S acidic ribosomal protein P2B, a 60 S ribosomal protein L12, a 40 S ribosomal protein S19–3, and a phospholipid hydroperoxide glutathione peroxidase, and others. Our qRT-PCR results were consistent with the RNA sequencing results, confirming our findings. We propose a link between protein profiles and physiological traits important for preservation, which identified the WGCNA modules, the hub proteins, and the important pathways, and provided new insights into the molecular mechanisms of OT as the method of storage and preservation of fresh fruit at the proteomic level.

To explore the regulatory role of Wnt/P53/Caspase3 signal in mouse ovarian development based on LFQ proteomics

Early ovarian follicular development is regulated by multiple proteins and signaling pathways, including the Wnt gene. To explore the regulatory mechanism of Wnt signaling on early ovarian follicular development, ovaries from 17.5 days post coitum (17.5 dpc) mice were collected and cultured in vitro for four days in the presence of IWP2 as a Wnt activity inhibitor and KN93 as a CaMKII inhibitor. LFQ proteomics technique was then used to analyze the significant differentially abundant (P-SDA) 93 and 262 proteins in the IWP2 and KN93 groups, respectively. Of these, 63 up-regulated proteins and 30 down-regulated proteins were identified for IWP2, along with 3 significant KEGG pathways (P < 0.05). For the KN93 group, 168 up-regulated proteins and 94 down-regulated ones were P-SDA, with 9 significant KEGG pathways also noted (P < 0.05). In both IWP2 and KN93 groups, key pathways (Wnt signaling pathway, Notch signaling pathway, P53 signaling pathway, TGF-β signaling pathway, ovarian steroid production) and metabolic regulation (energy metabolism, metal ion metabolism) were found to be related to early ovarian follicular development. Finally, western blotting demonstrated the regulatory role of Wnt/P53/Caspase3 signaling pathway in mouse ovarian development. These results contribute new knowledge to the understanding of regulatory factors of early ovarian follicular development. SignificanceIn this study, label-free quantification (LFQ) was used in combination with liquid chromatography-mass spectrometer (LC-MS/MS) to study potential changes in the proteomic profiles of embryonic mice subjected to Wnt inhibitor IWP2 and CaMKIIinhibitor KN93. In addition, bioinformatics and comparative analyses were performed using publicly available proteomics databases to further explore the underlying mechanisms associated with early mouse ovarian growth and development.

Regulation of piglet T-cell immune responses by thioredoxin peroxidase from Cysticercus cellulosae excretory-secretory antigens.

Taenia solium (T. solium) cysticercosis is a serious threat to human health and animal husbandry. During parasitization, Cysticercus cellulosae (C. cellulosae) can excrete and secrete antigens that modulate the host's T-cell immune responses. However, the composition of C. cellulosae excretory-secretory antigens (ESAs) is complex. This study sought to identify the key molecules in C. cellulosae ESAs involved in regulating T-cell immune responses. Thus, we screened for thioredoxin peroxidase (TPx), with the highest differential expression, as the key target by label-free quantification proteomics of C. cellulosae and its ESAs. In addition, we verified whether TPx protein mainly exists in C. cellulosae ESAs. The TPx recombinant protein was prepared by eukaryotic expression, and ESAs were used as the experimental group to further investigate the effect of TPx protein on the immune response of piglet T cells in vitro. TPx protein induced an increase in CD4+ T cells in piglet peripheral blood mononuclear cells (PBMCs), while CD8+ T cells did not change significantly. This resulted in an imbalance in the CD4+/CD8+ T-cell ratio and an increase in CD4+CD25+Foxp3+ Treg cells in the PBMCs. In addition, TPx protein initiated T helper 2 (Th2)-type immune responses by secreting IL-4 and IL-10 and suppressed Th1/Th17-type immune responses. The results showed that ESAs were involved in regulating piglet T-cell immune responses cells. This suggests that TPx protein found in ESAs plays an essential role to help the parasite evade host immune attack. Moreover, this lays a foundation for the subsequent exploration of the mechanism through which TPx protein regulates signaling molecules to influence T-cell differentiation.

Anthocyanin improves kidney function in diabetic kidney disease by regulating amino acid metabolism

BackgroundDiabetic kidney disease (DKD) is among the most important causes for chronic kidney disease. Anthocyanins (ANT) are polyphenolic compounds present in various food and play an important role in ameliorating hyperglycemia and insulin sensitivity. However, the effects of ANT in DKD are still poorly understood. This study aimed to investigate the effect of ANT (cyanidin-3-O-glucoside [C3G]) on the renal function of DKD, and whether the anti-DKD effect of ANT is related to metabolic pathways.MethodsTo explore the role of ANT in DKD, we performed the examination of blood glucose, renal function, and histopathology. As for the mechanism, we designed the label-free quantification proteomics and nontargeted metabolomics analysis for kidney and serum. Subsequently, we revealed the anti-DKD effect of ANT through the bioinformatic analysis.ResultsWe showed that the fasting blood glucose level (− 6.1 mmol/L, P = 0.037), perimeter of glomerular lesions (− 24.1 μm, P = 0.030), fibrosis score of glomerular (− 8.8%, P = 0.002), and kidney function (Cystatin C: − 701.4 pg/mL, P = 0.043; urine creatinine: − 701.4 mmol/L, P = 0.032) were significantly alleviated in DKD mice after ANT treatment compared to untreated in the 20th week. Further, proteins and metabolites in the kidneys of DKD mice were observed to be dramatically altered due to changes in amino acid metabolism with ANT treatment; mainly, taurine and hypotaurine metabolism pathway was upregulated (P = 0.0001, t value = 5.97). Furthermore, upregulated tryptophan metabolism (P < 0.0001, t value = 5.94) and tyrosine metabolism (P = 0.0037, t value = 2.91) pathways had effects on serum of DKD mice as responsed ANT regulating.ConclusionsOur results suggested that prevention of the progression of DKD by ANT could be related to the regulation of amino acid metabolism. The use of dietary ANT may be one of the dietary strategies to prevent and treat DKD.

Extracellular Vesicle Subproteome Differences among Filifactor alocis Clinical Isolates

Filifactor alocis is a Gram-positive asaccharolytic, obligate anaerobic rod of the Firmicutes phylum, which has recently been implicated in oral infections. Extracellular vesicles (EVs) are crucial conveyors of microbial virulence in bacteria and archaea. Previously, in highly purified EVs from the F. alocis reference strain ATCC 35896 (CCUG 47790), 28 proteins were identified. The present study aimed to use label-free quantification proteomics in order to chart these EV proteins, in the reference strain, and in nine less-well-characterized clinical F. alocis isolates. In total, 25 of the EV proteins were identified and 24 were quantified. Sixteen of those were differentially expressed between the ten strains and the novel FtxA RTX toxin and one lipoprotein were among them. Consistent expression was observed among ribosomal proteins and proteins involved in L-arginine biosynthesis and type IV pilin, demonstrating a degree of EV protein expression preservation among strains. In terms of protein–protein interaction analysis, 21 functional associations were revealed between 19 EV proteins. Interestingly, FtxA did not display predicted interactions with any other EV protein. In conclusion, the present study charted 25 EV proteins in ten F. alocis strains. While most EV proteins were consistently identified among the strains, several of them were also differentially expressed, which justifies that there may be potential variations in the virulence potential among EVs of different F. alocis strains.

Label-free quantification proteomics reveals potential proteins associated with the freshness status of crayfish (Procambarus clarkii) as affected by cooking

In order to characterize the freshness status of raw material of cooked crayfish products, protein and physicochemical changes were investigated in raw and cooked crayfish from fresh-live state to the early postmortem using Label-free quantification proteomics, total volatile basic nitrogen (TVB-N) and biogenic amines (BAs) analysis. Results showed that the TVB-N and BAs contents in both raw and cooked crayfish remained low levels and no obvious changes were observed within 24 h of postmortem storage at 4 °C. Altogether, six differentially expressed proteins (DEPs) were detected in both C6/C0 and C24/C0 groups by proteomics. Furthermore, five among the six DEPs were verified both in cooked and raw crayfish samples by parallel reaction monitoring. Among the six DEPs, “Unigene990_S_0_Gene.8754” changed most significantly with the increasing of postmortem time and not obviously influenced by heating, indicating that “Unigene990_S_0_Gene.8754” may be highly associated to the freshness status of crayfish.

Label-free quantification proteomics analysis reveals acute hyper-osmotic responsive proteins in the gills of Chinese mitten crab (Eriocheir sinensis)

Chinese mitten crab (Eriocheir sinensis) is a typical euryhaline crustacean to study osmotic regulation of crustaceans. Osmotic-regulation of Chinese mitten crab is a complex process. In order to study the osmotic-regulation related proteins of Chinese mitten crab, we domesticated Chinese mitten crab for 144 h with 25 salinity sea water (SW) and 0 salinity fresh water (FW) respectively, and then analyzed the proteome of its posterior gills. A total of 1453 proteins were identified by label free proteomics. Under the threshold of 2 fold change (FC), 242 differentially expressed proteins (DEPs) were screened, including 122 up-regulated DEPs and 120 down-regulated DEPs. GO database and KEGG database were used to annotate and enrich DEPs. It was found that DEPs were significantly enriched in energy metabolism, signal transduction, ion transport, actin cytoskeleton, immunity, lipid metabolism, amino acid metabolism and other biological functions. After 144 h of high salinity stress, the energy metabolism of Chinese mitten crab decreased and the expression of actin and cytoskeleton protein increased. In order to cope with oxidative damage caused by high salinity, Chinese mitten crab improved its immunity and antioxidant capacity.

Proteomic Characterization of the Oral Pathogen Filifactor alocis Reveals Key Inter-Protein Interactions of Its RTX Toxin: FtxA

Filifactor alocis is a Gram-positive asaccharolytic, obligate anaerobic rod that has been isolated from a variety of oral infections including periodontitis, peri-implantitis, and odontogenic abscesses. As a newly emerging pathogen, its type strain has been investigated for pathogenic properties, yet little is known about its virulence variations among strains. We previously screened the whole genome of nine clinical oral isolates and a reference strain of F. alocis, and they expressed a novel RTX toxin, FtxA. In the present study, we aimed to use label-free quantification proteomics to characterize the full proteome of those ten F. alocis strains. A total of 872 proteins were quantified, and 97 among them were differentially expressed in FtxA-positive strains compared with the negative strains. In addition, 44 of these differentially expressed proteins formed 66 pairs of associations based on their predicted functions, which included clusters of proteins with DNA repair/mediated transformation and catalytic activity-related function, indicating different biosynthetic activities among strains. FtxA displayed specific interactions with another six intracellular proteins, forming a functional cluster that could discriminate between FtxA-producing and non-producing strains. Among them were FtxB and FtxD, predicted to be encoded by the same operon as FtxA. While revealing the broader qualitative and quantitative proteomic landscape of F. alocis, this study also sheds light on the deeper functional inter-relationships of FtxA, thus placing this RTX family member into context as a major virulence factor of this species.

Insights into the hippocampus proteome and phosphorylation modification alterations in C57BL/6 revealed the memory improvement mechanisms of a walnut-derived peptide

This work aimed to explore the underlying mechanisms of memory improvement effects of a walnut derived peptide WNP-10. The morris water maze test, combined with ultrastructural observation, hematoxylin and eosin and Nissl staining showed that WNP–10 significantly improved the learning and memory capability of the scopolamine–injured mice. The four–dimensional label-free quantification proteomics analysis identified 88 differentially expressed proteins in the WNP–10-treated group compared with scopolamine-induced impairment group. Pathway enrichment analysis and western blotting demonstrated that the WNP-10 can regulate the phosphatidylinositol-3-phosphate 5-kinase, cathepsin L, N-acetylgalactosamine 6-sulfate sulfatase and AP-3 complex subunit mu-1 expression to affect inositol phosphate metabolism, thereby maintaining lysosome homeostasis in scopolamine–injured mice. Notably, the results of phosphoproteomics demonstrated that WNP–10 administration resulted in the increased phosphorylation of phosphatidylinositol-3-phosphate 5-kinase. These findings provide novel insights into the underlying mechanism of memory improvement of walnut peptides.

Potential Clinical Value of Biomarker-Guided Emergency Triage for Thoracic Aortic Dissection.

Aim: Thoracic aortic dissection (TAD) is a high-risk vascular disease. The mortality rate of untreated TADs in 24 h was as high as 50%. Thus, rapid diagnosis of TAD in the emergency department would get patients to the right treatments to save their lives.Methods: We profiled the proteome of aortic tissues from TAD patients using a label-free quantification proteomics method. The differentially expressed proteins were screened and subjected to bioinformatics analysis. Candidate biomarkers were selected and validated in independent serum samples using enzyme-linked immunosorbent assays (ELISAs). The diagnostic values were further predicted via receiver operating characteristic (ROC) curve analysis.Results: A total of 1,141 differentially expressed proteins were identified in aortic tissues from 17 TAD patients and eight myocardial infarction (MI) patients. Six proteins were selected as candidate biomarkers for ELISAs in an independent training set of 20 serum samples (TAD = 10, MI = 10). Of these proteins, four with a P-value < 0.01 were further validated in another independent set of 64 serum samples (TAD = 32, MI = 32) via ELISAs. ITGA2, COL2A1, and MIF had P-values < 0.0001, and their areas under the curve (AUCs) were 0.801 (95% CI: 0.691–0.911), 0.773 (95% CI: 0.660–0.887), and 0.701 (95% CI: 0.574–0.828), respectively.Conclusion: ITGA2, COL2A1, and MIF were identified as promising biomarkers for discriminating TAD from emergency patients with severe chest pain. Biomarker-guided emergency triage could further shorten the time for patients to get more effective treatments.