Proteomic Analysis Research Articles

Impact of different food-grade protein extraction methods on the proteomic profile and potential allergenicity of Spirulina (Arthrospira platensis)

Various optimized methods for cell disintegration and protein extraction of algae have been reported, but there is a lack of information regarding the proteomic characterization of the extracted proteins; thus, systematic verification of the protein profiles to find potentially exploitable proteins, while minimizing allergenicity risks, is profitable. The method described in this study was developed to thoroughly investigate the proteome characterization of A. platensis following aqueous protein extraction by high-shear homogenization and pH shift. Liquid chromatography-tandem mass spectrometry was applied to assess the proteome obtained from four protein extraction methods using data-dependent proteome analysis. Overall, 699 proteins were identified; however, each extraction method identified unique proteins. The maximum number of exclusive proteins was observed using a combination of high-shear homogenization and acidic pH. The evaluation of protein abundance revealed a clear distinction between proteins isolated from pH 2 treatment compared to those obtained via neutral or basic pH treatment. The applied extraction methods affected the in silico computed physicochemical properties of the proteins. Using the AllerCatPro database, 12 putative allergenic proteins were detected, the most predominant of which were related to the C-phycocyanin beta subunit (P72508). This study demonstrated that extraction methods affect the detection, physicochemical properties, and potential allergenicity of the obtained proteins. Hence, the extraction methods used to obtain novel proteins must consider these aspects before using them as functional foods.

Identification of potential hub genes associated with recurrent miscarriage through combined transcriptomic and proteomic analysis

Recurrent miscarriage (RM) is currently difficult to prevent and treat due to a lack of comprehensive understanding of its molecular mechanisms. The aim of this study was to identify genes potentially involved in the pathogenesis of RM and to observe their expression in the decidual tissues of RM patients. A total of 1823 differentially expressed genes (DEGs) and 148 differentially expressed proteins (DEPs) in decidual tissues between RM and control groups were identified. Subsequently, DCN, DPT, LUM, MFAP4, and ISG15 were identified from the DEGs/DEPs as RM-related hub genes through systematic bioinformatics analysis. Bioinformatics analysis of the single-cell dataset GSE214607 revealed that the expression of these five hub genes in the decidual stromal cells of RM patients appeared to be upregulated, while the RT-qPCR assay showed that their decidual expression levels were significantly increased in RM patients. Uterine Isg15expression was significantly increased, whereas the uterine expression of Dcn, Dpt, Lum, and Mfap4 was decreased in LPS-induced early pregnancy loss mice. MiR-16-5p, -21-3p, -27a-3p, and -941 were identified as potentially involved in the regulation of these five hub genes, and their decidual expression levels were significantly decreased in RM patients. The abnormally increased ISG15 expression in the decidual tissues of RM patients and uterine tissues of LPS-induced mice was validated by WB analysis. ISG15 expression was significantly reduced during the in vitro decidualization of human endometrial stromal cells (hESCs). Collectively, DCN, DPT, LUM, MFAP4, and ISG15 were identified as RM-related hub genes, and their expression in the decidual tissues of RM patients was significantly increased. The decidualization of hESCs was accompanied by reduced ISG15 expression, suggesting that increased decidual ISG15 expression might lead to early pregnancy loss by disrupting the decidualization process.

Comprehensive proteomic analysis of buffalo milk extracellular vesicles

Extracellular vesicles are secretory vesicles involved in cell-to-cell communication via their encapsulated cargo of proteins, lipids, and nucleic acids. Bovine milk provides a rich source of extracellular vesicles (mEVs) that have been studied as therapeutics and drug delivery systems. Therefore, insight into the mEV cargo, such as its proteome, may help in understanding the molecular mechanism underlying the potential health benefits attributed to the mEVs. Hence, mEVs were isolated from healthy buffalo milk after screening the milk somatic cell count. The total proteins of mEVs were analyzed using LC-MS, and 331 proteins were found commonly present among three buffalo milk samples. These proteins were primarily derived from extracellular regions and lysosomes. The major biological roles associated with the proteins were immune response, metabolism, and cell cycle regulation. The molecular functions of the proteins were transporter activity, catalytic activity, and GTPase activity. Further, comparative analysis with the previously available bovine mEVs proteome data showed 114 proteins to be newly identified in the buffalo mEVs. The biological pathways associated with these proteins may play a major role in muscle development. These findings shed a light on the potential health benefits of buffalo mEVs as therapeutics as well as drug delivery vehicles.

Mechanism of the cardioprotective effect of empagliflozin on diabetic nephropathy mice based on the basis of proteomics

Diabetic nephropathy affects a significant proportion of individuals with diabetes, and its progression often leads to cardiovascular disease and infections before the need for renal replacement therapy arises. Empagliflozin has been shown to have various protective effects in cardiovascular disease studies, such as improving diabetic myocardial structure and function, and reducing myocardial oxidative stress. However, the impact of empagliflozin on cardiac protein expression and signaling pathways has not been comprehensively analyzed. To address this gap, we conducted proteome analysis to identify specific protein markers in cardiac tissue from the diabetes model group, including Myh7, Wdr37, Eif3k, Acot1, Acot2, Cat, and Scp2, in cardiac tissue from the diabetes model group. In our drug model, empagliflozin primarily modulates the fat-related metabolic signaling pathway within the heart. Empagliflozin downregulated the protein expression levels of ACOX1, ACADVL and CPT1A in the model group. Overall, our findings demonstrate that empagliflozin provides cardiac protection by targeting metabolic signaling pathways, particularly those related to fat metabolism. Moreover, the identification of cardiac biomarkers in a mouse model of diabetic nephropathy lays the foundation for further exploration of disease biomarkers in cardiac tissue.

Circulating RAC1 contributed to steroid-sensitive nephrotic syndrome: Mendelian randomization, single-cell RNA-sequencing, proteomic, and experimental evidence

Objectives The small GTPase Rac1 (RAC1) has been linked to podocyte disorders and steroid-sensitive nephrotic syndrome (SSNS). The aim of this study was to explore and validate the potential causal association between circulating RAC1 and SSNS. Methods The association between circulating RAC1 and SSNS at both gene expression and proteomic levels was investigated using Mendelian randomization analysis, and further validated by single-cell RNA-sequencing, proteomic analysis, and experimental studies. The genetic instruments comprised cis-expression quantitative trait loci (cis-eQTLs) associated with RAC1 gene expression and protein QTLs correlated with plasma RAC1 protein levels. Causal associations were estimated utilizing the inverse variance weighted and MR-PRESSO methods. Validation of RAC1 expression was conducted through single-cell RNA-sequencing of peripheral blood mononuclear cells from patients with SSNS and healthy controls. Proteomic analysis was performed among patients with minimal change nephrotic syndrome. Experimental validation was conducted using a puromycin aminonucleoside (PAN)-induced nephrosis model. Results Increased expression of RAC1 was associated with a higher risk of SSNS (gene expression level: odds ratio [OR], 1.53; 95% confidence interval [CI], 1.02–2.28; protein level: OR, 1.82; 95% CI, 1.05–3.17). The results of MR-PRESSO were consistent (gene expression level: OR, 1.49; 95% CI, 1.17–1.92; protein level: OR, 1.81; 95% CI, 1.16–2.85). Single-cell RNA sequencing and proteomic analysis confirmed elevated RAC1 expression in patients with SSNS compared to healthy controls. Experimental data further supported increased RAC1 expression in PAN-induced nephropathy. Conclusions Increased expression of RAC1 might be causally associated with SSNS, suggesting that targeting RAC1 might represent a potential therapeutic strategy for SSNS.

Unveiling new protein biomarkers and therapeutic targets for acne through integrated analysis of human plasma proteomics and genomics

BackgroundThe current landscape of acne therapeutics is notably lacking in targeted treatments, highlighting a critical need for the discovery of new drug targets to improve treatment outcomes.ObjectivesThis study aims to investigate the connections between proteomics and genetics in relation to acne across extensive population cohorts, aspiring to identify innovative preventive and therapeutic approaches.MethodsEmploying a longitudinal cohort of 54,306 participants from the UK Biobank Pharmacological Proteomics Project (UKB-PPP), we performed an exhaustive evaluation of the associations between 2,923 serum proteins and acne risk. Initial multivariate Cox regression analyses assessed the relationship between protein expression levels and acne onset, followed by two-sample Mendelian Randomization (TSMR), Summary-data-based Mendelian Randomization (SMR), and colocalization to identify genetic correlations with potential protein targets.ResultsWithin the UKB cohort, we identified 19 proteins significantly associated with the risk of acne. Subsequent analysis using Two-Sample Mendelian Randomization (TSMR) refined this to two specific proteins: FSTL1 and ANXA5. Each one-standard deviation increase in the expression levels of FSTL1 and ANXA5 was associated with a 24% and 32% increase in acne incidence, respectively. These results were further validated by additional Summary-data-based Mendelian Randomization (SMR) and differential expression analyses.ConclusionsOur comprehensive analysis of proteomic and genetic data from a European adult cohort provides compelling causal evidence that several proteins are promising targets for novel acne treatments.

Transcriptomics and proteomics analyses reveal the molecular mechanisms of yeast cells regulated by Phe-Cys against ethanol-oxidation cross-stress

Antioxidant dipeptide Phe-Cys (FC) could dramatically improve yeast cells resistance to ethanol-oxidation cross-stress, but the regulatory mechanisms remain unclear. Therefore, transcriptomic and proteomic analyses were conducted to investigate the effects of FC treatment on yeast under ethanol-oxidation cross-stress. Following FC supplementation, 875 differential expressed genes (DEGs) and 1296 differential expressed proteins (DEPs) were identified. Integrated analysis revealed a substantial enrichment of DEGs and DEPs in the KEGG pathways of carbon metabolism, amino acid biosynthesis, cofactor biosynthesis, and glycolysis/gluconeogenesis. Furthermore, FC improved yeast cell membrane integrity by promoting fatty acids and steroids biosynthesis, and implemented a high-energy strategy by upregulating glycolysis and oxidative phosphorylation. Additionally, alterations in DEGs and DEPs levels associated with amino acids metabolism accelerated protein synthesis and enhanced cell viability. In conclusion, this study elucidated the response mechanisms of yeast to FC treatment under ethanol-oxidation cross-stress, providing a theoretical basis for the application of FC in high-gravity brewing.

L-Carnitine: A New Therapeutic Option for the Prevention of Atrial Fibrillation in Non-Cardiac Surgery-A Single-Group Interventional Pilot Study.

Background: L-carnitine is essential in lipid metabolism and reportedly has preventive effects for arrhythmia. Our objective was to examine the incidence of postoperative atrial fibrillation (POAF) and changes in serum biomarker levels following perioperative L-carnitine administration in patients with lung cancer. Methods: Thirteen patients undergoing a lobectomy with preoperative serum brain natriuretic peptide levels >24 pg/mL were perioperatively administered L-carnitine for 5 days (3 g/3×). Accurate 95% confidence intervals (CI) for POAF incidence were calculated. Serum biomarkers for POAF in lung cancer and target proteins for L-carnitine were evaluated by using open-source data from proteomic analysis. Results: The incidence of POAF was 38.5% (95% CI 13.9%-68.4%). Fatty acid-binding protein 4 (FABP4) was selected as a candidate biomarker from 1472, 63, and 26 proteins related to lung cancer, L-carnitine, and AF, respectively. A positive correlation was observed between the predicted POAF incidence rate and preoperative FABP4 levels (Pearson's r = 0.5183). The mean change in serum FABP4 after L-carnitine administration for 5 days was -2.9 ng/mL (95% CI -4.9 to -0.89 ng/mL). Conclusions: The incidence of POAF after a lobectomy was 38.5% after the perioperative administration of L-carnitine for patients at a high risk of POAF. The serum FABP4 level demonstrates potential as a candidate biomarker for POAF prediction.

Multidimensional analysis of matched primary and recurrent glioblastoma identifies contributors to tumor recurrence influencing time to relapse.

Glioblastoma (GBM) is a lethal brain tumor without effective treatment options. This study aimed to characterize longitudinal tumor changes in order to find potentially actionable targets to prevent GBM relapse. We extracted RNA and proteins from fresh frozen tumor samples from patient-matched IDHwt WHO grade 4 primary (pGBM) and recurrent (rGBM) tumors for transcriptomics and proteomics analysis. A tissue microarray containing paired tumor samples was processed for spatial transcriptomics analysis. Differentially expressed genes and proteins between pGBM and rGBM were involved in synapse development and myelination. By categorizing patients into short (STTR) and long (LTTR) time-to-lapse, we identified genes/proteins whose expression levels positively or negatively correlated with TTR. In rGBM, expressions of Fcγ receptors (FCGRs) and complement system genes were negatively correlated with TTR, whereas expression of genes involved in DNA methylation was positively correlated with TTR. Spatial transcriptomics of the tumor cells showed enrichment of oligodendrocytes in rGBM. Besides, we observed changes in the myeloid compartment such as a switch from quiescent to activated microglia and an enrichment in B and T cells in rGBM with STTR. Our results uncover a role for activated microglia/macrophages in GBM recurrence and suggest that interfering with these cells may hinder GBM relapse.

Vascular endothelial growth factor/connective tissue growth factor and proteomic analysis of aqueous humor after intravitreal conbercept for proliferative diabetes retinopathy.

To investigate the role of connective tissue growth factor (CTGF) and vascular endothelial growth factor (VEGF) in the protein profile of the aqueous humor in patients with proliferative diabetic retinopathy (PDR) following intravitreal injection of conbercept. This study included 72 PDR patients and 8 cataract patients as controls. PDR patients were divided into 3 groups according to the intervals of 3, 5, and 7d between intravitreal conbercept (IVC, 0.5 mg/0.05 mL) injection and pars plana vitrectomy (PPV) performed. Aqueous humor samples were collected before and after IVC and PPV for VEGF and CTGF levels detected with enzyme-linked immunosorbent assay (ELISA). The differential proteomics of 10 patients who underwent PPV surgery 5d after IVC and 8 normal controls was studied, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed on the data, and the protein interaction network of 23 differential proteins was studied. Post-IVC, VEGF levels decreased and CTGF levels increased significantly in aqueous humor, with the CTGF/VEGF ratio rising significantly at all intervals. Liquid chromatography tandem mass spectrometry (LC-MS/MS) identified differentially expressed proteins between pre- and post-IVC samples. GO and KEGG analyses revealed involvement in immune response, stress response, complement and coagulation cascades, ferroptosis, and PPAR signaling pathways. PPI analysis highlighted key proteins like APOA1, C3, and transferrin (TF). ELISA assay confirmed the differential expression of proteins such as HBA1, SERPINA1, COL1A1, and ACTB, with significant changes in the IVC groups. The study demonstrates that IVC effectively reduces VEGF levels while increasing CTGF levels, thereby modifying the CTGF/VEGF ratio, and IVC significantly alters the protein profile in the aqueous humor of patients with PDR. Proteomic analysis reveals that these changes are associated with critical biological pathways and protein interactions involved in immune response, stress response, and cellular metabolism.

Beyond hemoglobin: Critical role of 2,3-bisphosphoglycerate mutase in kidney function and injury.

2,3-bisphosphoglycerate mutase (BPGM) is traditionally recognized for its role in modulating oxygen affinity to hemoglobin in erythrocytes. Recent transcriptomic analyses, however, have indicated a significant upregulation of BPGM in acutely injured murine and human kidneys, suggesting a potential renal function for this enzyme. Here we aim to explore the physiological role of BPGM in the kidney. A tubular-specific, doxycycline-inducible Bpgm-knockout mouse model was generated. Histological, immunofluorescence, and proteomic analyses were conducted to examine the localization of BPGM expression and the impact of its knockout on kidney structure and function. Invitro studies were performed to investigate the metabolic consequences of Bpgm knockdown under osmotic stress. BPGM expression was localized to the distal nephron and was absent in proximal tubules. Inducible knockout of Bpgm resulted in rapid kidney injury within 4 days, characterized by proximal tubular damage and tubulointerstitial fibrosis. Proteomic analyses revealed involvement of BPGM in key metabolic pathways, including glycolysis, oxidative stress response, and inflammation. Invitro, Bpgm knockdown led to enhanced glycolysis, decreased reactive oxygen species elimination capacity under osmotic stress, and increased apoptosis. Furthermore, interactions between nephron segments and immune cells in the kidney suggested a mechanism for propagating stress signals from distal to proximal tubules. BPGM fulfills critical functions beyond the erythrocyte in maintaining glucose metabolism in the distal nephron. Its absence leads to metabolic imbalances, increased oxidative stress, inflammation, and ultimately kidney injury.

Study on the mechanism of Xinmailong injection against chronic heart failure based on transcriptomics and proteomics

Xinmailong (XML), a traditional Chinese medicine derived from Periplaneta americana, is commonly used in China to treat chronic heart failure (CHF). However, its pharmacological mechanism remains unclear. In our research, we employed Doxorubicin (Dox) to create a CHF animal model and administered XML treatment to investigate the pharmacological effects of XML on CHF rats by combining transcriptomic and proteomic analyses. XML improved dox-induced CHF and improved cardiac function, and a joint multi-omics analysis demonstrated that it reduced cardiomyocyte fibrosis during CHF. There is further evidence that XML may alleviate cardiomyocyte fibrosis through its effects on the cGMP-PKG signaling pathway or by reducing the expression levels of COL1A1, COL3A1, MMP9, and CXCR2. In this study, the effects of XML on rats with CHF are examined at the transcriptional and protein levels, as well as its mechanism and mode of action in treating CHF. There may be novel therapeutic targets or clinical indications for XML-based CHF therapy resulting from the study's identification of significant differential genes and signaling pathways.

Proteomic Analysis of Fibroblasts Exposed to Resin Composite Release.

To investigate the potential effects of products released by a resin composite on the proteome of human gingival fibroblasts. Fifteen resin composite cylinders of a Bis-GMA-based resin composite (Tetric EvoCeram, Ivoclar) were made and placed in a culture medium for 24h. Then, 30mL of this medium was placed for 72h in contact with human gingival fibroblasts and a second control group consisted of cells placed in culture medium only. Afterward, cells were collected, washed, and their proteins extracted. Three two-dimensional electrophoresis were performed per condition. Image analysis of the gels was carried out to highlight the differential protein spots. These spots were then analyzed by an ESI/qTOF mass spectrometer. Finally, specific databases provided protein identification, their interactions, and the pathways where they are implicated. Delta2D software allowed the detection of 21 spots of different proteins. The MASCOT identified 28 proteins. Five proteins from four spots were upregulated, 23 proteins from 17 spots were downregulated. The UniProt database showed that all these proteins were involved in cellular architecture, structural modifications and quality control of proteins, cellular homeostasis, and metabolic pathways. The STRING database revealed the interactions between the regulated proteins. The GO enrichment analysis showed that 19 pathways were affected. The products released from the resin composite tested led to changes in the fibroblast proteome. Under the conditions of this study, resin composite released products can cause early adverse effects on cells, but without complete inhibition of their cellular functions.

Ferroptosis Mediated Inflammation Promotes Pulmonary Hypertension.

Mitochondrial dysfunction, characterized by impaired lipid metabolism and heightened reactive oxygen species generation, results in lipid peroxidation and ferroptosis. Ferroptosis is an inflammatory mode of cell death that promotes complement activation and macrophage recruitment. In pulmonary arterial hypertension (PAH), pulmonary arterial endothelial cells exhibit cellular phenotypes that promote ferroptosis. Moreover, there is ectopic complement deposition and inflammatory macrophage accumulation in the pulmonary vasculature. However, the effects of ferroptosis inhibition on these pathogenic mechanisms and the cellular landscape of the pulmonary vasculature are incompletely defined. Multiomics and physiological analyses evaluated how ferroptosis inhibition-modulated preclinical PAH. The impact of adeno-associated virus 1-mediated expression of the proferroptotic protein ACSL (acyl-CoA synthetase long-chain family member) 4 on PAH was determined, and a genetic association study in humans further probed the relationship between ferroptosis and pulmonary hypertension. Ferrostatin-1, a small-molecule ferroptosis inhibitor, mitigated PAH severity in monocrotaline rats. RNA-sequencing and proteomics analyses demonstrated that ferroptosis was associated with PAH severity. RNA-sequencing, proteomics, and confocal microscopy revealed that complement activation and proinflammatory cytokines/chemokines were suppressed by ferrostatin-1. In addition, ferrostatin-1 combatted changes in endothelial, smooth muscle, and interstitial macrophage abundance and gene activation patterns as revealed by deconvolution RNA-sequencing. Ferroptotic pulmonary arterial endothelial cell damage-associated molecular patterns restructured the transcriptomic signature and mitochondrial morphology, promoted the proliferation of pulmonary artery smooth muscle cells, and created a proinflammatory phenotype in monocytes in vitro. Adeno-associated virus 1-Acsl4 induced an inflammatory PAH phenotype in rats. Finally, single-nucleotide polymorphisms in 6 ferroptosis genes identified a potential link between ferroptosis and pulmonary hypertension severity in the Vanderbilt BioVU repository. Ferroptosis promotes PAH through metabolic and inflammatory mechanisms in the pulmonary vasculature.

Comparison of sGC activator and sGC stimulator in 5/6 nephrectomized rats on high-salt-diet

IntroductionSoluble guanylate cyclase (sGC) stimulators and activators are known to enhance kidney function in various models of chronic kidney disease (CKD) by increasing cyclic guanosine monophosphate (cGMP). Their differential effects on CKD progression, particularly under conditions of oxidative stress, remain unexplored by direct comparative studies.MethodsWe conducted a side-by-side comparison using 5/6 nephrectomized rats on a high salt diet (5/6Nx+HSD) to evaluate the efficacy of the sGC stimulator BAY 41–8543 and the sGC activator BAY 60–2770 in CKD progression. BAY 41–8543 (1 mg/kg; twice daily) and BAY 60–2770 (1 mg/kg; once daily) were administered by gavage for 11 weeks.ResultsThe 5/6Nx+HSD model led to increased plasma creatinine, proteinuria, and blood pressure. Both BAY 41–8543 and BAY 60–2770 significantly reduced systolic and diastolic blood pressure to a similar extent but did not improve renal function parameters. Notably, BAY 60–2770 reduced renal fibrosis, including interstitial fibrosis and glomerulosclerosis, whereas BAY 41–8543 did not. These antifibrotic effects of BAY 60–2770 were independent of blood pressure reduction. Proteomic analysis revealed that BAY 60–2770 corrected the upregulation of 9 proteins associated with apoptosis and fibrosis, including Caspase-3, MKK6 (Mitogen-Activated Protein Kinase Kinase 6), Prdx5 (Peroxiredoxin-5), in the 5/6Nx+HSD group.DiscussionIn contrast, BAY 41–8543 had no significant impact on these proteins. sGC activators were more effective than sGC stimulators in reducing renal fibrosis in 5/6 nephrectomized rats on a high salt diet, and this effect was due to modulation of apoptosis-associated proteins beyond the control of blood pressure.

Serum proteomic changes related to residual impairment in remittent depression are associated with immune and inflammatory processes.

In patients with major depressive disorder, various functional areas are impaired, negatively impacting the quality of life. Remission can restore pre-depression functions; however, some patients may still have residual impairments. Distinguishing between near-normal recovery and residual impairment helps identify those at a high risk of relapse risk and helps tailor treatment. Accordingly, we aimed to discover and validate biomarkers that distinguish between near-normal recovery and residual impairment in remission states through serum proteome analysis. Pooled serum and individual serum samples from three groups (depression status, remission status with residual impairment, and remission status with normal recovery) were analyzed using liquid chromatography-tandem mass spectrometry. The combination of four proteins-antithrombin-III, serum amyloid A4 protein, C1q subcomponent subunit B, and serum amyloid P-component-was selected as a candidate biomarker. The trend of protein changes suggests complement C1q subcomponent subunit B and serum amyloid P-component as potential biomarkers for distinguishing remission from residual impairment. Changes in complement C1q subcomponent subunit B and serum amyloid P-component suggest that the complement system and inflammation-related immune mechanisms are associated with residual impairment in remittent major depressive disorder.

TMT-based quantitative proteomics unveils the protective mechanism of Polygonatum sibiricum polysaccharides on septic acute liver injury

Polygonatum sibiricum polysaccharides (PSP) has been shown to possess multiple pharmacological functions. Our previous study found that PSP could protect against acute liver injury during sepsis via inhibiting inflammatory response. However, the underlying molecular mechanism by which PSP alleviates septic acute liver injury (SALI) remains unknown. Herein, TMT-based quantitative proteomics was utilized to explore the essential pathways and proteins involved in the protective effects of PSP on SALI. The results revealed that 632 and 176 differentially expressed proteins (DEPs) were identified in Model_vs_Control and PSP_vs_Model, respectively. GO annotation showed similar trends, suggesting that these DEPs were primarily involved in the cellular anatomical entity in Cellular Component, the cellular processe and the biological regulation in Biological Process, the binding and the catalytic activity in Molecular Function. Meanwhile, KEGG enrichment analysis implied that four common pathways, including the NF-κB signaling pathway, the IL-17 signaling pathway, the TNF signaling pathway and the Toll-like receptor signaling pathway, were closely associated with the pathogenesis of sepsis among the top 20 remarkably enriched pathways in Model_vs_Control_up and PSP_vs_Model_down. Moreover, the levels of several common DEPs, including TLR2, IKKi, JunB and CXCL9, were validated by WB, which was in line with the results of proteomics. Therefore, the protective effects of PSP on SALI might exert via blocking the above-mentioned inflammation pathways.Significance: PSP, recognized as a key component of Polygonatum sibiricum, exhibits a range of pharmacological functions. Our previous study found that PSP could protect against SALI, yet failing to clarify the mechanism of action. To reveal the underlying molecular mechanism involved in the protective effects of PSP on SALI, a TMT-based quantitative proteomic analysis was performed to detect and analyse the DEPs in liver tissue among the control group, the model group and the PSP group in this study. The results provide theoretical references for exploring the action mechanism of drugs and facilitate the comprehensive utilization of PSP. SignificancePSP have been identified as the most crucial components of Polygonatum sibiricum with various pharmacological functions. Our previous study found that PSP could protect against SALI, but the mechanism of action remains unknown. To reveal the underlying molecular mechanism involved in the protective effects of PSP on SALI, a TMT-based quantitative proteomic analysis was performed to detect and analyse the DEPs in liver tissue among the control group, the model group and the PSP group in this study. The results provide theoretical references for exploring the action mechanism of drugs and facilitate the comprehensive utilization of PSP.

Histone deacetylase upregulation of neuropilin-1 in osteosarcoma is essential for pulmonary metastasis

The lungs represent the most common site of metastasis for osteosarcoma (OS). Despite our advances in developing targeted therapies for treating solid malignancies, broad acting chemotherapies remain the first line treatment for OS. In assaying the efficacy of approved therapeutics for non-OS malignancies, we previously identified the histone deacetylase 1 and 2 (HDAC1 and 2) inhibitor, romidepsin, as effective for the treatment of established lung metastatic OS. Yet, romidepsin has noted toxicities in humans and so here we aimed to define the primary mechanisms through which HDAC1/2 mediate OS progression to identify more selective druggable targets/pathways. Microarray and proteomics analyses of romidepsin treated OS cells revealed a significant suppression of neuropilin-1 (NRP1), a known regulator of cancer cell migration and invasion. Silencing of NRP1 significantly reduced OS proliferation, migration, invasion and adhesion in vitro. More strikingly, in vivo, reduced NRP1 expression significantly mitigated the lung metastatic potential of OS in two independent models (K7M2 and SAOS-LM7). Mechanistically, our data point to NRP1 mediating this effect via the down regulation of migration machinery, namely SRC, FAK and ROCK1 expression/activity, that is in part, related to NRP1 interaction with integrin beta 1 (ITGB1). In summary, our data indicate that romidepsin down regulation of NRP1 significantly mitigates the ability of OS cells to seed the lung and establish metastases, and that targeting NRP1 or its effectors with selective inhibitors may be a viable means with which to prevent this deadly aspect of the disease.

Proteomics and EPS Compositional Analysis Reveals Desulfovibrio bisertensis SY-1 Induced Corrosion on Q235 Steel by Biofilm Formation

Microorganisms that exist in the seawater form microbial biofilms on materials used in marine construction, especially on metal surfaces submerged in seawater, where they form biofilms and cause severe corrosion. Biofilms are mainly composed of bacteria and their secreted polymeric substances. In order to understand how biofilms promote metal corrosion, planktonic and biofilm cells of Desulfovibrio bizertensis SY-1 (D. bizertensis) from Q235 steel were collected and analyzed as to their intracellular proteome and extracellular polymeric substances (EPS). The intracellular proteome analysis showed that the cellular proteins were strongly regulated in biofilm cells compared to planktonic cells, e.g., along with flagellar proteins, signaling-related proteins were significantly increased, whereas energy production and conversion proteins and DNA replication proteins were significantly regulated. The up-and-down regulation of proteins revealed that biofilm formation by bacteria on metal surfaces is affected by flagellar and signaling proteins. A significant decrease in DNA replication proteins indicated that DNA is no longer replicated and transcribed in mature biofilms, thus reducing energy consumption. Quantitative analysis and lectin staining of the biofilm on the metal’s surface revealed that the bacteria secreted a substantial amount of EPS when they began to attach to the surface, and proteins dominated the main components of EPS. Further, the infrared analysis showed that the secondary structure of the proteins in the EPS of the biofilm was mainly dominated by β-sheet and 3-turn helix, which may help to enhance the adhesion of EPS. The functional groups of EPS analyzed using XPS showed that the C element of EPS in the biofilm mainly existed in the form of combinations with N. Furthermore, the hydroxyl structure in the EPS extracted from the biofilm had a stronger hydrogen bonding effect, which could maintain the stability of the EPS structure and biofilm. The study results revealed that D. bizertensis regulates the metabolic pathways and their secreted EPS structure to affect biofilm formation and cause metal corrosion, which has a certain reference significance for the study of the microbially influenced corrosion (MIC) mechanism.

Exploring Structural and Molecular Features of Sciatic Nerve Lesions in Diabetic Neuropathy: Unveiling Pathogenic Pathways and Targets.

Lesioned fascicles (LF) in the sciatic nerves of individuals with diabetic neuropathy (DN) correlate with clinical symptom severity. This study aimed to characterize the structural and molecular composition of these lesions to better understand DN pathogenesis. Sciatic nerves from amputees with and without type 2 diabetes (T2D) were examined using ex vivo magnetic resonance neurography, in vitro imaging, and proteomic analysis. Lesions were only found in T2D donors and exhibited significant structural abnormalities, including axonal degeneration, demyelination, and impaired blood nerve barrier (BNB). While non-lesioned fascicles from T2D donors showed activation of neuroprotective pathways, lesioned fascicles lacked this response and instead displayed increased complement activation via the classical pathway. The detection of liver-derived acute-phase proteins suggests that BNB disruption facilitates harmful inter-organ communication between the liver and nerves. These findings reveal key molecular mechanisms contributing to DN and highlight potential targets for therapeutic intervention.