Label-free Liquid Chromatography-tandem Mass Spectrometry Research Articles

Proteomic analysis of rat colonic mucosa following acupuncture treatment for irritable bowel syndrome with diarrhea

To investigate the molecular pathological mechanisms of irritable bowel syndrome with diarrhea (IBS-D) and elucidate the effects of acupuncture on IBS-D colonic mucosa protein abundance in rats, a label-free high-throughput liquid chromatography-tandem mass spectrometry (LC-MS)-based proteomics analysis was used to survey the global changes of colonic mucosa proteins between different groups. Sixteen Sprague-Dawley (SD) male rats were randomly divided into four groups: the control group (C); the IBS-D model group (M); the syndrome differentiation acupuncture group (SD) and the traditional acupuncture group (T). IBS-D model rats were obtained using the CAS (chronic acute combining stress model) method. Comparative bioinformatics analysis of the proteomic data was analyzed using MaxQuant software, Perseus software, online tools DAVID, VENNY and STRING. Functional enrichment and network analyses revealed a close relationship between IBS-D and several biological processes including energy metabolism, muscular excitation/contraction, and both traditional acupuncture and syndrome differentiation acupuncture can reverse the impairments of normal energy metabolism. Moreover, the syndrome differentiation acupuncture can regulate the protein cluster relating inflammation, wound repair and cell protection against oxidative stress which is associated with acupuncture analgesic effect. Differentially expressed proteins Atp5a1 and Bpnt1 were selected as representative proteins and subjected to western blotting. In conclusion, our study provides further insight into the pathological and molecular mechanisms of IBS-D and acupuncture treatments, and serves as an experimental basis for clinical applications.

Proteomic and immunoproteomic insights into the exoproteome of Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia

Porcine pleuropneumonia caused by Actinobacillus pleuropneumoniae affects pig health status and the swine industry worldwide. Despite the extensive number of studies focused on A. pleuropneumoniae infection and vaccine development, a thorough analysis of the A. pleuropneumoniae exoproteome is still missing. Using a complementary approach of quantitative proteomics and immunoproteomics we gained an in-depth insight into the A. pleuropneumoniae serotype 2 exoproteome, which provides the basis for future functional studies. Label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed 593 exoproteins, of which 104 were predicted to be virulence factors. The RTX toxins ApxIIA and ApxIIIA -were found to be the most abundant proteins in the A. pleuropneumoniae serotype 2 exoproteome. Furthermore, the ApxIVA toxin was one of the proteins showing the highest abundance, although ApxIVA is commonly assumed to be expressed exclusively in vivo. Our study revealed several antigens, including proteins with moonlight functions, such as the elongation factor (EF)-Tu, and proteins linked to specific metabolic traits, such as the maltodextrin-binding protein MalE, that warrant future functional characterization and might present potential targets for novel therapeutics and vaccines. Our Ig-classes specific serological proteome analysis (SERPA) approach allowed us to explore the development of the host humoral immune response over the course of the infection. These SERPAs pinpointed proteins that might play a key role in virulence and persistence and showed that the immune response to the different Apx toxins is distinct. For instance, our results indicate that the ApxIIIA toxin has properties of a thymus-independent antigen, which should be studied in more detail.

Identification of N-Glycoproteins of Knee Cartilage from Adult Osteoarthritis and Kashin-Beck Disease Based on Quantitative Glycoproteomics, Compared with Normal Control Cartilage.

Glycoproteins are involved in the development of many diseases, while the type and content of N-glycoproteins in the cartilage of osteoarthritis (OA) and Kashin–Beck disease (KBD) are still unclear. This research aims to identify N-glycoproteins in knee cartilage patients with OA and KBD compared with normal control (N) adults. The cartilage samples were collected from gender- and age-matched OA (n = 9), KBD (n = 9) patients, and N (n = 9) adults. Glycoproteomics and label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) obtained N-glycoproteins of KBD and OA. A total of 594 N-glycoproteins and 1146 N-glycosylation peptides were identified. The identified data were further compared and analyzed with Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Protein–Protein Interactions (PPI). Pairwise comparison of the glycoproteins detected in the three groups showed that integrin beta-1 (ITGB1), collagen alpha-1 (II) chain (COL2A1), collagen alpha-1 (VII) chain (COL7A1), carbohydrate sulfotransferase 3 (CHST-3), carbohydrate sulfotransferase 4 (CHST-4), thrombospondin 2 (THBS2), bone morphogenetic protein 8A (BMP8A), tenascin-C (TNC), lysosome-associated membrane protein (LAMP2), and beta-glucuronidase (GUSB) were significantly differentially expressed. GO results suggested N-glycoproteins mainly belonged to protein metabolic process, single-multicellular and multicellular organism process, cell adhesion, biological adhesion, and multicellular organism development. KEGG and PPI results revealed that key N-glycoproteins were closely related to pathways for OA and KBD, such as phagosome, ECM-receptor interaction, lysosome, focal adhesion, protein digestion, and absorption. These results reflected glycoprotein expression for OA and KBD in the process of ECM degradation, material transport, cell–cell or cell–ECM interaction, and information transduction. These key significantly differentially expressed N-glycoproteins and pathways lead to the degeneration and degradation of the cartilage of OA and KBD mainly by disrupting the synthesis and catabolism of basic components of ECM and chondrocytes and interfering with the transfer of material or information. The key N-glycoproteins or pathways in this research are potential targets for pathological mechanisms and therapies of OA and KBD.

Effect of Selenium Treatment on Central Insulin Sensitivity: A Proteomic Analysis in β-Amyloid Precursor Protein/Presenilin-1 Transgenic Mice

Prior studies have demonstrated a close association between brain insulin resistance and Alzheimer’s disease (AD), while selenium supplementation was shown to improve insulin homeostasis in AD patients and to exert neuroprotective effects in a mouse model of AD. However, the mechanisms underlying the neuroprotective actions of selenium remain incompletely understood. In this study, we performed a label-free liquid chromatography-tandem mass spectrometry (LC–MS/MS) quantitative proteomics approach to analyze differentially expressed proteins (DEPs) in the hippocampus and cerebral cortex of Aβ precursor protein (APP)/presenilin-1 (PS1) mice following 2 months of treatment with sodium selenate. A total of 319 DEPs (205 upregulated and 114 downregulated proteins) were detected after selenium treatment. Functional enrichment analysis revealed that the DEPs were mainly enriched in processes affecting axon development, neuron differentiation, tau protein binding, and insulin/insulin-like growth factor type 1 (IGF1)-related pathways. These results demonstrate that a number of insulin/IGF1 signaling pathway-associated proteins are differentially expressed in ways that are consistent with reduced central insulin resistance, suggesting that selenium has therapeutic value in the treatment of neurodegenerative and metabolic diseases such as AD and non-alcoholic fatty liver disease (NAFLD).

Plasma proteomic analysis to identify potential biomarkers of histologic chorioamnionitis in women with preterm premature rupture of membranes.

IntroductionTo identify potential biomarkers in the plasma that could predict histologic chorioamnionitis (HCA) in women with preterm premature rupture of membranes (PPROM), using shotgun and targeted proteomic analyses.MethodsThis retrospective cohort study included 78 singleton pregnant women with PPROM (24–34 gestational weeks) who delivered within 96 h of blood sampling. Maternal plasma samples were analyzed by label-free liquid chromatography-tandem mass spectrometry for proteome profiling in a nested case-control study design (HCA cases vs. non-HCA controls [n = 9 each]). Differential expression of 12 candidate proteins was assessed by multiple reaction monitoring-mass spectrometry (MRM-MS) analysis in individual plasma samples from cases and controls matched by gestational age at sampling (n = 40, cohort 1). A validation study was further performed in an independent study group (n = 38, cohort 2) using ELISA and turbidimetric immunoassay for three differentially expressed proteins.ResultsShotgun proteomics analyses yielded 18 proteins that were differentially expressed (P < 0.05) between HCA cases and non-HCA controls. MRM-MS analysis of 12 differentially expressed proteins further revealed that the CRP, C4A, and SAA4 levels were significantly increased in women with HCA. A multi-marker panel comprising plasma SAA4 and C4A showed enhanced potential for differentiating HCA from non-HCA women (area under the curve = 0.899). Additional validation of these findings by ELISA assays revealed that the CRP levels were significantly higher in women with HCA than in those without HCA, whereas the plasma levels of C4A and SAA4 did not significantly differ between the two groups.ConclusionsPlasma C4A, SAA4, and CRP were identified as potential biomarkers for detecting HCA in women with PPROM, based on targeted and shotgun proteomic analyses, showing good accuracy when used as a combined dual-biomarker panel (C4A and SAA4). Nevertheless, ELISA validation of these proteins, except for CRP, may not yield clinically useful markers for predicting HCA.

Proteomic and Metabolomic Analyses of Right Ventricular Failure due to Pulmonary Arterial Hypertension.

Right ventricular failure (RVF) is the independent and strongest predictor of mortality in pulmonary arterial hypertension (PAH), but, at present, there are no preventive and therapeutic strategies directly targeting the failing right ventricle (RV). The underlying mechanism of RV hypertrophy (RVH) and dysfunction needs to be explored in depth. In this study, we used myocardial proteomics combined with metabolomics to elucidate potential pathophysiological changes of RV remodeling in a monocrotaline (MCT)-induced PAH rat model. The proteins and metabolites extracted from the RV myocardium were identified using label-free liquid chromatography–tandem mass spectrometry (LC-MS/MS). The bioinformatic analysis indicated that elevated intracellular Ca2+ concentrations and inflammation may contribute to myocardial proliferation and contraction, which may be beneficial for maintaining the compensated state of the RV. In the RVF stage, ferroptosis, mitochondrial metabolic shift, and insulin resistance are significantly involved. Dysregulated iron homeostasis, glutathione metabolism, and lipid peroxidation related to ferroptosis may contribute to RV decompensation. In conclusion, we depicted a proteomic and metabolomic profile of the RV myocardium during the progression of MCT-induced PAH, and also provided the insights for potential therapeutic targets facilitating the retardation or reversal of RV dysfunction in PAH.

Tualang Honey Promotes Apoptosis of the A549 Lung Adenocarcinoma Cell Line via Modulation of PI3K/AKT Signaling Pathway-Related Proteins

The phosphatidylinositol 3-kinases (PI3Ks)/protein kinase B (AKT) signaling pathway is frequently overexpressed in lung adenocarcinoma and associated with carcinogenesis through cell proliferation, and apoptosis deactivation; and it also enhances chemotherapeutic drugs resistance. Tualang honey (TH) has proven anticancer property on lung adenocarcinoma. However, the underlying mechanisms remain unreported. Hence, this study investigates the apoptosisinducing effect of TH on A549 lung adenocarcinoma cell line using RayBio® Human Apoptosis Array and label-free quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis to elucidate the modulation of upstream and downstream proteins of PI3K/AKT signaling pathway. The apoptosis-promoting effects of TH were associated with (i) the upregulation of pro-apoptotic proteins (i.e. cytochrome c, histone H1.2, and histone H1.4) and tumor suppressor proteins (i.e. IGFBP-3 and IGFBP-5), and (ii) downregulation of XIAP, insulin-growth factor (IGF) system (i.e. IGF-1, IGF1R, IGFBP-1, IGFBP-2, and IGFBP-4), HSP90AB1, YWHAQ, endoplasmin, and ITGB1. The effects were also linked with the suppression of receptor tyrosine kinase, integrins, G proteins, CHUK, RAC1, and JAK. Thus, TH may promote apoptosis of A549 lung adenocarcinoma cell line through alteration of the PI3K/AKT signaling pathway-related proteins. However, further studies involving animal models to provide a better model of understanding would prove necessary.

Understanding Myoblast Differentiation Pathways When Cultured on Electroactive Scaffolds through Proteomic Analysis.

Electroactive materials allow the modulation of cell-materials interactions and cell fate, leading to advanced tissue regeneration strategies. Nevertheless, their effect at the cellular level is still poorly understood. In this context, the proteome analysis of C2C12 cell differentiation cultured on piezoelectric polymer films with null average surface charge (non-poled), net positive surface charge (poled +), and net negative surface charge (poled -) has been addressed. Protein/pathway alterations for skeletal muscle development were identified comparing proteomic profiles of C2C12 cells differentiated on poly(vinylidene fluoride), with similar cells differentiated on a polystyrene plate (control), using label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS). Only significantly expressed proteins (P < 0.01, analysis of variance) were used for bioinformatic analyses. A total of 37 significantly expressed proteins were detected on the C2C12 proteome with PVDF "poled -" at 24 h, whereas on the PVDF "poled +", a total of 105 significantly expressed proteins were considered. At 5 days of differentiation, the number of significantly expressed proteins decreased to 23 and 31 in cells grown on negative and positive surface charge, respectively, the influence of surface charge being more explicit in some proteins. In both cases, proteins such as Fbn1, Hspg2, Rcn3, Tgm2, Mylpf, Anxa2, and Anxa6, involved in calcium-related signaling, were highly expressed during myoblast differentiation. Furthermore, some proteins involved in muscle contraction (Acta2, Anxa2, and Anxa6) were detected in the PVDF "poled +" sample. Upregulation of several proteins that enhance skeletal muscle development was detected in the PVDF "poled -" sample, including Ckm (422%), Tmem14c (384%), Serpinb6a (460%), adh7 (199%), and Car3 (171%), while for the "poled +" samples, these proteins were also upregulated at a smaller magnitude (254, 317, 253, 123, and 72%, respectively). Other differentially expressed proteins such as Mylpf (189%), Mybph (168%), and Mbnl1 (168%) were upregulated only in PVDF "poled -" samples, while Hba-a1 levels (581%) were increased in the PVDF "poled +" sample. On the other hand, cells cultured on non-poled samples have no differences with respect to the ones cultured on the control, in contrary to the poled films, with overall surface charge, demonstrating the relevance of scaffold surface charge on cell behavior. This study demonstrates that both positive and negative overall surface charges promote the differentiation of C2C12 cells through involvement of proteins related with the contraction of the skeletal muscle cells, with a more pronounced effect with the negative charged surfaces.

The crosstalk signals of Sodium Tanshinone ⅡA Sulfonate in rats with cerebral ischemic stroke: Insights from proteomics

BackgroundStroke could cause long-term disability, even mortality around the world. Recently, Sodium tanshinone IIA sulfonate (STS), identified from Salvia miltiorrhiza Bunge and was found to have unique efficiency in clinical practice as a potential therapeutic agent for ischemic cerebral infarction. However, systematic investigation about the biological mechanism is still lacking. Herein, we utilized high-throughput proteomics approach to identify the underlying targets for the treatment of STS in stroke. MethodsWe investigated the effect of STS on stroke outcomes on rat model of the Middle Cerebral Artery Occlusion and Reperfusion (MCAO/R), assessing by Z-Longa score, infarct volume and HE staining. Pharmacoproteomic profiling of ischemic penumbra in cortical (IPC) was performed using DIA-based label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) technique. Bioinformatics analysis was processed for further investigation. The expression of core proteins was semi-quantified by DIA, and the major protein correlating with stroke was examined using parallel reaction monitoring (PRM). ResultsRats in the MCAO/R group showed neurological function deterioration, which was improved by STS. There were 423 differentially expressed proteins (DEPs) in IPC being detected and quantified in both the sham group and the MCAO/R group. Meanwhile, 285 proteins were significantly changed in the STS treated group, compared to the MCAO/R model. Protein-protein interaction (PPI) network, pathway and biological function enrichment were processed for the DEPs across each two groups, the results of which were integrated for analysis. Alb, mTOR, Dync1h1, Stxbp1, Cltc, and Sptan1 were contained as the core proteins. Altered molecules were discovered to be enriched in 18 signal pathways such as phosphatidylinositol signaling system, PI3K/AKT signal pathway and HIF-1 signal pathway. The results also showed the correlation with sleep disturbances and depression post-stroke. ConclusionsWe concluded that STS could prevent penumbra from progressively ongoing damage and improve neurological deficits in MCAO/R model rats. The intersected pathways and protein networks predicted by proteomics might provide much more detailed information for the therapeutic mechanisms of STS in the treatment of CIS.

Potential Biomarkers of Acute Ischemic Stroke Etiology Revealed by Mass Spectrometry-Based Proteomic Characterization of Formalin-Fixed Paraffin-Embedded Blood Clots.

Background and AimsBesides the crucial role in the treatment of acute ischemic stroke (AIS), mechanical thrombectomy represents a unique opportunity for researchers to study the retrieved clots, with the possibility of unveiling biological patterns linked to stroke pathophysiology and etiology. We aimed to develop a shotgun proteomic approach to study and compare the proteome of formalin-fixed paraffin-embedded (FFPE) cardioembolic and large artery atherosclerotic (LAA) clots.MethodsWe used 16 cardioembolic and 15 LAA FFPE thrombi from 31 AIS patients. The thrombus proteome was analyzed by label-free quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS). MaxQuant v1.5.2.8 and Perseus v.1.6.15.0 were used for bioinformatics analysis. Protein classes were identified using the PANTHER database and the STRING database was used to predict protein interactions.ResultsWe identified 1,581 protein groups as part of the AIS thrombus proteome. Fourteen significantly differentially abundant proteins across the two etiologies were identified. Four proteins involved in the ubiquitin-proteasome pathway, blood coagulation or plasminogen activating cascade were identified as significantly abundant in LAA clots. Ten proteins involved in the ubiquitin proteasome-pathway, cytoskeletal remodeling of platelets, platelet adhesion or blood coagulation were identified as significantly abundant in cardioembolic clots.ConclusionOur results outlined a set of 14 proteins for a proof-of-principle characterization of cardioembolic and LAA FFPE clots, advancing the proteome profile of AIS human thrombi and understanding the pathophysiology of ischemic stroke.

Label-Free LC-MS/MS Analysis Reveals Different Proteomic Profiles between Egg Yolks of Silky Fowl and Ordinary Chickens.

The proteomic profiles of Silky fowl egg yolk (SFEY) and Leghorn egg yolk (LEY) were analyzed by bottom-up label-free liquid chromatography–tandem mass spectrometry (LC-MS/MS). From a total of 186 identified proteins, 26 proteins were found significantly differentially abundant between two yolks, of which, 19 were up-regulated and 7 were down-regulated in SFEY, particularly, vitelline membrane outer layer protein 1, transthyretin and ovoinhibitor were up-regulated by 26, 25, and 16 times, respectively. In addition, there were 57 and 6 unique proteins in SFEY and LEY, respectively. Gene Ontology (GO) revealed SFEY contained relatively more abundant protease inhibitors and coagulation-related proteins. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed differentially abundant proteins in SFEY may be actively involved in the regulation of the neuroactive ligand–receptor interaction pathway. This study provides a theoretical basis for the understanding of proteomic and biological differences between these two yolks and can guide for further exploration of nutritional and biomedical use of Silky fowl egg.

Comparative Proteomics Analysis Reveals the Reversal Effect of Cryptotanshinone on Gefitinib-Resistant Cells in Epidermal Growth Factor Receptor-Mutant Lung Cancer.

Cryptotanshinone (CTS) is a lipophilic constituent of Salvia miltiorrhiza, with a broad-spectrum anticancer activity. We have observed that CTS enhances the efficacy of gefitinib in human lung cancer H1975 cells, yet little is known about its molecular mechanism. To explore how CTS enhances H1975 cell sensitivity to gefitinib, we figured out differential proteins of H1975 cells treated by gefitinib alone or in combination with CTS using label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein–protein interaction (PPI) bioinformatic analyses of the differential proteins were performed. CTS enhanced H1975 cell sensitivity to gefitinib in vitro and in vivo, with 115 and 128 differential proteins identified, respectively. GO enrichment, KEGG analysis, and PPI network comprehensively demonstrated that CTS mainly impacted the redox process and fatty acid metabolism in H1975 cells. Moreover, three differential proteins, namely, catalase (CAT), heme oxygenase 1 (HMOX1), and stearoyl-CoA desaturase (SCD) were validated by RT-qPCR and Western blot. In conclusion, we used a proteomic method to study the mechanism of CTS enhancing gefitinib sensitivity in H1975 cells. Our finding reveals the potential protein targets of CTS in overcoming gefitinib resistance, which may be therapeutical targets in lung cancer.

Discovery and confirmation of protein action site AK1 of ginsenosides in brain based on DARTS technology

This study aims to explore the targets of ginsenosides in brain based on drug affinity responsive target stability(DARTS) technology. Specifically, DARTS technology was combined with label-free liquid chromatography tandem mass spectrometry(LC-MS) to screen out the proteins in the brain that might interact with ginsenosides. Based on the screening results, adenylate kinase 1(AK1) was selected for further confirmation. First, the His-AK1 fusion protein was yielded successively through the construction of recombinant prokaryotic expression vector, expression of target protein, and purification of the fusion protein. Biolayer interferometry(BLI) was employed to detect the direct interaction of Rg_1, Re, Rb_1, Rd, Rh_2, F1, Rh_1, compound K(CK), 25-OH-PPD, protopanaxa-diol(PPD), and protopanaxatriol(PPT) with AK1, thereby screening the ginsenoside monomer or sapogenin that had strong direct interaction with the suspected target protein AK1. Then, the BLI was used to further determine the kinetic parameters for the binding of PPD(strongest interaction with AK1) to His-AK1 fusion protein. Finally, molecular docking technology was applied to analyze the binding properties between the two. With DARTS and LC-MS, multiple differential proteins were screened out, and AK1 was selected based on previous research for target verification. Fusion protein His-AK1 was obtained by prokaryotic expression, and the response(nm) of Re, Rg_1, Rd, Rb_1, Rh_1, Rh_2, F1, PPT, PPD, 25-OH-PPD, and CK with His-AK1 was respectively 0.003 1, 0.001 9, 0.042 8, 0.022 2, 0.013 4, 0.037 3, 0.013 9, 0.030 7, 0.140 2, 0.016 0, and 0.040 8. The K_(on), K_(off), and K_D values of PPD and His-AK1 were determined by the BLI as 1.22×10~2 mol~(-1)·L·s~(-1), 1.04×10~(-2) s~(-1), 8.52×10~(-5) mol·L~(-1). According to the molecular docking result, PPD bound to AK1 with the absolute value of the docking score of 3.438, and hydrogen bonds mainly formed between the two. Thus, AK1 is one of the protein action sites of ginsenosides in the brain. The direct interaction between ginsenoside metabolite PPD and AK1 is the strongest.

Proteomic analysis of japonica sorghum following microwave intermittent drying based on label-free technology

The aim of this study was to investigate the influence of microwave drying on the protein quality of japonica sorghum following an intermittent drying test. Using label-free technology and liquid chromatography-tandem mass spectrometry for proteomic analysis, the effects of microwave drying on sorghum differential protein expression, functional classification, and metabolic pathways were analyzed at the molecular level. After sorghum was dried using a microwave, 85 differential proteins were identified. Among them, 51 showed up-regulated expression while 34 had down-regulated expression. The up-regulation and down-regulation of differential protein expressions significantly changed them, and proteins with larger up-regulated and down-regulated expressions were postulated to affect biological and metabolic processes of sorghum during subsequent processing. Differential proteins were significantly (P ˂ 0.01) involved in metabolic pathways, such as carbon metabolism, glycolysis/gluconeogenesis, carbon fixation in photosynthetic organisms, biosynthesis of amino acids, amino sugar and nucleotide sugar metabolism, and the TCA cycle. For the protein interaction network, glyceraldehyde-3-phosphate dehydrogenase of the down-regulated proteins was postulated to be the key factor affecting the entire metabolic system or signal transduction pathway. Up-regulated proteins, including phosphoglycerate mutase and phosphopyruvate hydratase, as well as down-regulated proteins such as glyceraldehyde-3-phosphate dehydrogenase and fructose-bisphosphate aldolase, not only directly or indirectly affected a variety of metabolic processes, but were specifically closely related to glycolysis and glycometabolism. Overall, this study showed that among the related metabolic pathways, differential protein changes in glycometabolism pathways may have the greatest impact on metabolic processes. The research results discussed herein can provide theoretical support for the industrial application of microwave drying and deep processing of sorghum.

Agrobacterium tumefaciens Type IV and Type VI Secretion Systems Reside in Detergent-Resistant Membranes.

Cell membranes are not homogenous but compartmentalized into lateral microdomains, which are considered as biochemical reaction centers for various physiological processes in eukaryotes and prokaryotes. Due to their special lipid and protein composition, some of these microdomains are resistant to treatment with non-ionic detergents and can be purified as detergent-resistant membranes (DRMs). Here we report the proteome of DRMs from the Gram-negative phytopathogen Agrobacterium tumefaciens. Using label-free liquid chromatography-tandem mass spectrometry, we identified proteins enriched in DRMs isolated under normal and virulence-mimicking growth conditions. Prominent microdomain marker proteins such as the SPFH (stomatin/prohibitin/flotillin/HflKC) proteins HflK, HflC and Atu3772, along with the protease FtsH were highly enriched in DRMs isolated under any given condition. Moreover, proteins involved in cell envelope biogenesis, transport and secretion, as well as motility- and chemotaxis-associated proteins were overrepresented in DRMs. Most strikingly, we found virulence-associated proteins such as the VirA/VirG two-component system, and the membrane-spanning type IV and type VI secretion systems enriched in DRMs. Fluorescence microscopy of the cellular localization of both secretion systems and of marker proteins was in agreement with the results from the proteomics approach. These findings suggest that virulence traits are micro-compartmentalized into functional microdomains in A. tumefaciens.

Putative Biomarkers for Acute Pulmonary Embolism in Exhaled Breath Condensate.

Current diagnostic markers for pulmonary embolism (PE) are unspecific. We investigated the proteome of the exhaled breath condensate (EBC) in a porcine model of acute PE in order to identify putative diagnostic markers for PE. EBC was collected at baseline and after the induction of autologous intermediate-risk PE in 14 pigs, plus four negative control pigs. The protein profiles of the EBC were analyzed using label-free quantitative nano liquid chromatography–tandem mass spectrometry. A total of 897 proteins were identified in the EBCs from the pigs. Alterations were found in the levels of 145 different proteins after PE compared with the baseline and negative controls: albumin was among the most upregulated proteins, with 14-fold higher levels 2.5 h after PE (p-value: 0.02). The levels of 49 other proteins were between 1.3- and 17.1-fold higher after PE. The levels of 95 proteins were lower after PE. Neutrophil gelatinase-associated lipocalin (fold change 0.3, p-value < 0.01) was among the most reduced proteins 2.5 h after PE. A prediction model based on penalized regression identified five proteins including albumin and neutrophil gelatinase-associated lipocalin. The model was capable of discriminating baseline samples from EBC samples collected 2.5 h after PE correctly in 22 out of 27 samples. In conclusion, the EBC from pigs with acute PE contained several putative diagnostic markers of PE.

Proteomics Profiling with SWATH-MS Quantitative Analysis of Changes in the Human Brain with HIV Infection Reveals a Differential Impact on the Frontal and Temporal Lobes

The chronic irreversible regression of cognitive ability and memory function in human immunodeficiency virus (HIV)-associated dementia (HAND) is linked with late-stage HIV infection in the brain. The molecular-level signatures of neuroinflammation and neurodegeneration are linked with dysfunction in HAND patients. Protein expression changes and posttranslational modification are epigenetic cues for dementia and neurodegenerative disease. In this study quantitative proteome analysis was performed to comprehensively elucidate changes in protein profiles in HIV-positive (HIV+) human brains. Frontal and temporal lobes of normal and HIV+ brains were subjected to label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis using the data-independent acquisition method. Comprehensive proteomic identification and quantification analysis revealed that 3294 total proteins and 251 proteins were differentially expressed in HIV+ brains; specifically, HIV+ frontal and temporal lobes had 132 and 119 differentially expressed proteins, respectively. Proteomic and bioinformatic analyses revealed protein alterations predominantly in the HIV+ frontal lobe region. The expression of GOLPH3, IMPDH2, DYNLL1, RPL11, and GPNMB proteins was significantly altered in HIV+ frontal lobes compared to that in normal brains. These proteins are associated with metabolic pathways, neurodegenerative disorders, and dementia. These proteomic-level changes may be potential biological markers and therapeutic targets to relieve the dementia-associated symptoms in individuals with HAND.

Psycho-cardiology therapeutic effects of Shuangxinfang in rats with depression-behavior post acute myocardial infarction: Focus on protein S100A9 from proteomics

BackgroundDepressive disorders induced by acute myocardial infarction (AMI) play a pivotal role in the deterioration of cardiac function, and Shuangxinfang (Psycho-cardiology Formula, PCF) was reported to alleviate heart function damage and improve depression-like behavior, but the complex mechanism in such process has not been clarified. MethodsAMI models were established and PCF was administered in rats. Subjects were then assessed in open field test (OFT) and forced swimming test (FST) recapitulating symptoms of depressive disorder. Afterward, pharmacoproteomic profiling of the hippocampus and peri-infarct border zone (BZ) was performed using a label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) technique, to identify contributing proteins and pathways responsible for myocardial ischemia and behavioral allostasis. Bioinformatics analysis was processed for further investigation, while western blotting was employed for testing dominating proteins to validate proteomic results. ResultsRats in the AMI group showed depression-like behavior in OFT and FST, which was improved by PCF. There were 131 differentially expressed proteins (DEPs) in BZ and 64 proteins in the hippocampus being detected and quantified shared by the sham group, the AMI group, and the PCF group. Subsequently, pertinent pathways and molecular functions were further identified. Altered molecules were discovered to be enriched in the apoptotic process, innate immune response, and NF-κB transcription factor activity in BZ, as well as chemical synaptic transmission, axon, collagen binding, cell adhesion, response to carbohydrate, laminin binding, and cellular response to nitric oxide in the hippocampus. Groups of signal transducers were also able to select multiple pathways, including innate immunity and arginine biosynthesis in the heart, also integrin signaling in the brain. DEPs were intersected from the myocardium and hippocampus to screen out the protein S100A9, which was up-regulated in the AMI group compared with the sham, and showed a down-regulation trend after treatment with PCF. ConclusionTaken together, we present a comprehensive proteomics analysis of rat models with depression post-AMI. Reviewing the literatures concerned, it’s hypothesized that macrophage/microglia inflammation mediated by S100A9 might be the pivotal pathogenic process of psycho-cardiology disease, as well as potential mechanisms for the treatment of PCF.

Vitamin C Differentially Impacts the Serum Proteome Profile in Female and Male Mice.

A suboptimal blood vitamin C (ascorbate) level increases the risk of several chronic diseases. However, the detection of hypovitaminosis C is not a simple task, as ascorbate is unstable in blood samples. In this study, we examined the serum proteome of mice lacking the gulonolactone oxidase (Gulo) required for the ascorbate biosynthesis. Gulo-/- mice were supplemented with different concentrations of ascorbate in drinking water, and serum was collected to identify proteins correlating with serum ascorbate levels using an unbiased label-free liquid chromatography-tandem mass spectrometry global quantitative proteomic approach. Parallel reaction monitoring was performed to validate the correlations. We uncovered that the serum proteome profiles differ significantly between male and female mice. Also, unlike Gulo-/- males, a four-week ascorbate treatment did not entirely re-establish the serum proteome profile of ascorbate-deficient Gulo-/- females to the optimal profile exhibited by Gulo-/- females that never experienced an ascorbate deficiency. Finally, the serum proteins involved in retinoid metabolism, cholesterol, and lipid transport were similarly affected by ascorbate levels in males and females. In contrast, the proteins regulating serum peptidases and the protein of the acute phase response were different between males and females. These proteins are potential biomarkers correlating with blood ascorbate levels and require further study in standard clinical settings. The complete proteomics data set generated in this study has been deposited to the public repository ProteomeXchange with the data set identifier: PXD027019.

Label-free quantitative proteomic and phosphoproteomic analyses of renal biopsy tissues in membranous nephropathy.

Membranous nephropathy (MN) is a common cause of nephrotic syndrome in adults. However, the underlying mechanisms of its occurrence and development are not completely clear. Thus, it is essential to explore the mechanisms. Here, we employed label-free quantification and liquid chromatography-tandem mass spectrometry analysis techniques to investigate the proteomic and phosphoproteomic alterations in renal biopsy tissues of MN patients. Samples were collected from 16 MN patients and 10 controls. Immunohistochemistry (IHC) was performed to validate the hub phosphoprotein. We focused on the changes in the phosphoproteome in MN group versus control group (CG). Totally, 1704 phosphoproteins containing 3241 phosphosites were identified and quantified. The phosphorylation levels of 216 phosphoproteins containing 297 phosphosites were differentially regulated in stage II MN group versus CG, and 333 phosphoproteins containing 461 phosphosites were differentially phosphorylated in stage III MN group versus CG. In each comparison, several differential phosphoproteins were factors, kinases and receptors involved in cellular processes, biological regulation and other biological processes. The subcellular location of most of the differential phosphoproteins was the nucleus. Protein-protein interaction analysis showed that the connections among the differential phosphoproteins were extremely complex, and several signalling pathways probably associated with MN were identified. The hub phosphoprotein was validated by IHC. This investigation can provide direct insight into the global phosphorylation events in MN group versus CG and may help to shed light on the potential pathogenic mechanisms of MN.