Differential Protein Expression Research Articles

A Proteomic Analysis of Nasopharyngeal Carcinoma in a Moroccan Subpopulation.

Nasopharyngeal carcinoma (NPC) is a distinct cancer of the head and neck that is highly prevalent in Southeast Asia and North Africa. Though an extensive analysis of environmental and genetic contributors has been performed, very little is known about the proteome of this disease. A proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tissues can provide valuable information on protein expression and molecular patterns for both increasing our understanding of the disease and for biomarker discovery. To date, very few NPC proteomic studies have been performed, and none focused on patients from Morocco and North Africa. Label-free Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) was used to perform a proteomic analysis of FFPE tissue samples from a cohort of 41 NPC tumor samples of Morocco and North Africa origins. The LC-MS/MS data from this cohort were analyzed alongside 21 healthy controls using MaxQuant 2.4.2.0. A differential expression analysis was performed using the MSstats package in R. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotations were carried out using the DAVID bioinformatic tool. 3341 proteins were identified across our NPC cases, revealing three main clusters and five DEPs with prognostic significance. The sex disparity of NPC was investigated from a proteomic perspective in which 59 DEPs were found between males and females, with significantly enriched terms associated with the immune response and gene expression. Furthermore, 26 DEPs were observed between patients with early and advanced stages of NPC with a significant cluster related to the immune response, implicating up-regulated DEPs such as IGHA, IGKC, and VAT1. Across both datasets, 6532 proteins were quantified between NPC patients and healthy controls. Among them, 1507 differentially expressed proteins (DEPs) were observed. GO and KEGG pathway analyses showed enriched terms of DEPs related to increased cellular activity, cell proliferation, and survival. PI3K and MAPK proteins as well as RAC1 BCL2 and PPIA were found to be overexpressed between cancer tissues and healthy controls. EBV infection was also one of the enriched pathways implicating its latent genes like LMP1 and LMP2 that activate several proteins and signaling pathways including NF-Kappa B, MAPK, and JAK-STAT pathways. Our findings unveil the proteomic landscape of NPC for the first time in the Moroccan population. These studies additionally may provide a foundation for identifying potential biomarkers. Further research is still needed to help develop tools for the early diagnosis and treatment of NPC in Moroccan and North African populations.

TMT-proteomics reveals the therapeutic effects of Lianling decoction against atopic dermatitis through Staphylococcus aureus infection

BackgroundLianling Tang (LLT), a traditional Chinese herbal decoction, is utilized for managing inflammatory skin conditions in China. This study explores the therapeutic effects and molecular mechanisms of LLT on atopic dermatitis (AD) in a mouse model, employing proteomics techniques. MethodsWe evaluated the therapeutic efficacy of LLT on AD in mice by assessing skin inflammation scores, conducting histopathological examinations, and measuring serum levels of IgE, IL-4, and IL-6. Using Tandem Mass Tag (TMT) technology, we performed proteomics analysis of skin samples from Control, Model, LLT-treated, and positive control drug-treated mice, and identified differentially expressed proteins (DEPs). These proteins were then analyzed via GO and KEGG pathways to elucidate LLT's mechanisms in treating AD. ResultsLLT markedly reduced skin inflammation scores, epidermal thickening, and mast cell infiltration, and decreased serum IgE, IL-4, and IL-6 levels in AD model mice, highlighting its therapeutic potential. Proteomics analysis identified Staphylococcus aureus infection as a pivotal AD pathogenesis mechanism and revealed critical proteins such as C1QA, C4B, C5, and FCGR3. LLT's mechanisms, such as modulating the complement activation, and influencing phagocytosis, effectively reduce inflammation and alleviate symptoms caused by Staphylococcus aureus in AD. ConclusionLLT shows potential in AD treatment by modulating pathways associated with Staphylococcus aureus infection, effectively alleviating symptoms.

Peripherally-restricted recurrent infection by engineered E. coli strain modulates hippocampal proteome promoting memory impairments in a rat model

Commensal bacteria that breach endothelial barrier has been reported to induce low grade chronic inflammation producing disease symptoms in major peripheral tissues. In this study, we investigated the role of genetically modified cellular invasive form of commensal E. coli K12 (SK3842) in cognitive impairment. Low-grade systemic infection model was developed using recurring peripheral inoculation of live bacteria in Wistar rats. To examine memory parameters, Novel object recognition test and Radial arm maze test were performed. Differential protein expression profiling of rat hippocampus was carried out using LC-MS/MS and subsequently quantified using SWATH. HBA1/2, NEFH, PFN1 and ATP5d were chosen for validation using quantitative RT-PCR. Results showed drastic decline in Recognition memory of the SK3842 infected rats. Reference and Working Memory of the infected group were also significantly reduced in comparison to control group. Proteome analysis using LC-MS/MS coupled with SWATH revealed differential expression of key proteins that are crucial for the maintenance of various neurological functions. Moreover, expression of NEFH and PFN1transcripts were found to be in line with the proteomics data. Protein interaction network of these validated proteins generated by STRING database converged to RhoA protein. Thus, the present study establishes an association between peripheral infection of a hippocampal protein network dysregulation and overall memory decline.

Network Medicine Approach Unravels Endophenotype Signature in Alzheimer's Disease through Large-Scale Comparative Proteomics Analysis: Vascular Dysfunction as a Prime Example.

Alzheimer's disease (AD) is the most common neurodegenerative disease burdening public health. We proposed a network-based infrastructure to identify protein signatures for five AD pathological endophenotypes: amyloidosis, tauopathy, vascular dysfunction, lysosomal dysfunction, and neuroinflammation. We analyzed 23 proteomic data sets from AD patients and transgenic mouse models, using network proximity to measure associations between endophenotype modules and differentially expressed proteins (DEPs) in the integrated AD proteome. We focused on the vascular dysfunction signature with 21 DEPs by integrating RNA-seq, single-cell transcriptomics, GWAS, and literature. Experiments on APP/PS1 and MCAO models highlighted three proteins (SEPT5, SNAP25, STXBP1) as novel AD biomarker candidates. This study demonstrates a network medicine framework for deciphering endophenotype signatures in AD.

TMT-based proteomics reveals methylprotodioscin alleviates oxidative stress and inflammation via COX6C in myocardial infraction

The effect of methylprotodioscin (MPD), a steroidal saponin obtained from medicinal plants, on myocardial infarction (MI) remains elusive. In this study, HL-1 and AC16 cells were subjected to injury induced by hypoxic environment, and a mouse model of MI was established by ligating the left anterior descending. MPD significantly increased viabilities and proliferations, improved the stability of MMP, reduced ROS and inflammatory factor levels in hypoxia cardiomyocytes. Moreover, MPD significantly improved cardiac functions, increased the ventricular ejection fraction and short axis shortening rate of mice with MI, reduced the infarction area, alleviated oxidative stress and increased ATPase activities. Then, differentially expressed proteins (DEPs) were discovered and evaluated using tandem mass tag (TMT)-based proteomics and bioinformatics approaches. Compared with sham group, there were 420 DEPs in the cardiac tissue of MI group, likewise, 163 DEPs in MPD group were identified compared to MI group. By validating, the expression of COX6C was elevated in MI group and declined in MPD groups, consistent with the TMT-based proteomics results. Correspondingly, p-NF-κB expression was downregulated, while Nrf2 and SOD expressions were upregulated by MPD. Moreover, si-COX6C transfection blocked the regulatory effects of MPD on COX6C-mediated inflammation and oxidative stress in MI. Our findings indicate that MPD, a naturally occurring active ingredient, could effectively improve cardiac function. Its ability may result from regulating COX6C to reduce oxidative stress and suppress inflammation, suggesting that MPD is very attractive for the treatment of MI.

Dysregulated plasma autoantibodies are associated with B cell dysfunction in young Arab children with autism spectrum disorder in Qatar.

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impaired social interaction and communication, as well as the occurrence of stereotyped and repetitive behaviors. Previous studies have provided solid evidence of dysregulated immune system in ASD; however, limited studies have investigated autoantibody profiles in individuals with ASD. This study aims to screen plasma autoantibodies in a well-defined cohort of young children with ASD (n = 100) and their matched controls (n = 60) utilizing a high-throughput KoRectly Expressed (KREX) i-Ome protein-array technology. We identified differential protein expression of 16 autoantibodies in ASD, which were correlated with differential gene expression of these markers in independent ASD cohorts. Meanwhile, we identified a distinct list of 33 autoantibodies associated with ASD severity; several of which were correlated with maternal age and birth weight in ASD. In addition, we found dysregulated numbers of circulating B cells and activated HLADR+ B cells in ASD, which were correlated with altered levels of several autoantibodies. Further in-depth analysis of B cell subpopulations revealed an increased frequency of activated naïve B cells in ASD, as well as an association of resting naïve B cells and transitional B cells with ASD severity. Pathway enrichment analysis revealed disrupted MAPK signaling in ASD, suggesting a potential relevance of this pathway to altered autoantibodies and B cell dysfunction in ASD. Finally, we found that a combination of eight autoantibodies associated with ASD severity showed an area under the curve (ROC-AUC) of 0.937 (95% CI = 0.890, 0.983; p < 0.001), which demonstrated the diagnostic accuracy of the eight-marker signature in the severity classification of ASD cases. Overall, this study determined dysregulated autoantibody profiles and B cell dysfunction in children with ASD and identified an eight-autoantibody panel for ASD severity classification.

Remifentanil-induced inflammation in microglial cells: Activation of the PAK4-mediated NF-κB/NLRP3 pathway and onset of hyperalgesia

BackgroundThe perioperative use of remifentanil is associated with postoperative hyperalgesia, which can impair recovery and extend hospitalization. Recent studies have revealed that microglia-mediated activation of the NLRP3 inflammasome plays a critical role in opioid-induced hyperalgesia, with NF-κB acting as a pivotal activation point for NLRP3. Despite these findings, the specific molecular mechanisms underlying remifentanil-induced postoperative hyperalgesia remain unclear. This study aims to develop a model of remifentanil-induced hyperalgesia and investigate the molecular mechanisms, focusing on the NF-κB/NLRP3 pathway, using both in vitro and in vivo approaches. MethodWe established a remifentanil-induced hyperalgesia model and performed proteomic analysis to identify differential protein expression in the spinal cord tissue of rats. NLRP3 or PAK4 antagonists were administered intrathecally in vivo, and mechanical pain thresholds in the hind paws were measured using Von Frey testing. In vitro, we applied NLRP3 or PAK4 inhibitors or used lentivirus infection to silence PAK4, NF-κB, and NLRP3 genes. Protein expression was assessed through immunohistochemistry, immunofluorescence, and Western blotting. Additionally, ELISA was performed to measure IL-1β and IL-18 levels, and RT-qPCR was conducted to evaluate the transcription of target genes. ResultsProteomic analysis revealed that remifentanil upregulates PAK4 protein in spinal cord tissue two hours after the surgery. In addition, remifentanil induces morphological changes in the spinal cord dorsal horn, characterized by increased expression of PAK4, p-p65, NLRP3 and Iba-1 proteins, which in turn leads to elevated IL-1β and IL-18 levels and an inflammatory response. Intrathecal injection of NLRP3 or PAK4 inhibitors mitigates remifentanil-induced hyperalgesia and associated changes. In vitro, downregulation of PAK4 inhibits the increase in PAK4, p-p65, NLRP3 and Caspase-1 induced by LPS. Conversely, the downregulation of NLRP3 does not impact the levels of PAK4 and p-p65 proteins, aligning with the in vivo results and suggesting that PAK4 acts as an upstream signaling molecule of NLRP3. ConclusionRemifentanil can increase PAK4 expression in spinal cord dorsal horn cells by activating the NF-κB/NLRP3 pathway and mediating microglial activation, thereby contributing to postoperative hyperalgesia.

Research on the mechanism of Bacillus velezensis A-27 in enhancing the resistance of red kidney beans to soybean cyst nematode based on TMT proteomics analysis.

Soybean cyst nematode (SCN) poses a significant challenge to red kidney beans cultivation, resulting in yield losses and quality deterioration. This study investigates the molecular mechanisms using Tandem Mass Tag (TMT) based proteomics technology to explore how the plant growth-promoting rhizobacterium (PGPR) Bacillus velezensis A-27 enhances the resistance of red kidney beans against SCN. The results revealed that out of 1,374 differentially expressed proteins (DEPs) in the red kidney beans roots, 734 DEPs were upregulated and 640 DEPs were downregulated in the A-27 + J2 vs J2 treatment group. KEGG analysis revealed that 14 DEPs were involved in the α-LeA metabolic pathway, crucial for the biosynthesis of jasmonic acid (JA) in plants. Quantitative real-time PCR (qRT-PCR) confirmed the upregulation of 4 key genes (PLA1, AOS, AOC, ACX) in the JA biosynthesis pathway, while enzyme-linked immunosorbent assay (ELISA) demonstrated a significant increase in JA content in the roots. The study demonstrates that B. velezensis A-27 stimulates induced systemic resistance (ISR) in red kidney beans, and induce JA biosynthesis by regulating the expression of key enzymes in the α-LeA metabolic pathway. This enhances the plant's defense against SCN, providing a theoretical foundation for the potential use of B. velezensis A-27 as a biocontrol agent for managing SCN in leguminous crops.

Proteomic Profiling in Pediococcus pentosaceus SF11 Exposed to Condensed Tannins from Sainfoin.

The antibacterial mechanism of condensed tannins (CTs) obtained from tea has been elucidated, but the mechanism of legume-derived CTs remains unclear. The mechanisms of legume- and tea-derived CTs probably differ due to the diverse compositions of CTs. Previous research found that sainfoin CTs directly inhibited the growth of Pediococcus. The present study investigated the inhibition mechanism of CTs against Pediococcus pentosaceus SF11 (SF11) through proteomic analysis. The results showed that the minimum inhibitory concentration (MIC) of CTs against SF11 was 1500 mg/L and that CTs increased cell membrane permeability in a dose-dependent manner. In total, 418 differentially expressed proteins (DEPs) were identified between the CT treatment and the control, among which 341 were down-regulated and 77 were up-regulated in the CT treatment. The protein interaction network showed that the expression of only two DEPs was highly different between CT treated and control (|log2FC|> 2); the atpD protein was up-regulated in the CT-treated group, which was involved in ATP synthesis; down-regulated DEPs were most involved in lipoteichoic acid synthesis, peptidoglycan synthesis, and glycine metabolism. Twenty-seven proteins were not detected after CT treatment, which were involved in functions including fatty acid synthesis, RNA synthesis and translation, drug resistance, and cell membrane permeability in SF11. Therefore, the findings suggest that the inhibition mechanism of CTs may be related to cell membrane damage and inhibition of cell reproduction.

Targeted proteomics profiling reveals valuable biomarkers in the diagnosis of primary immune thrombocytopaenia.

The lack of biomarkers for accurate diagnosis and prognosis is a major clinical challenge of primary immune thrombocytopaenia (ITP). Using an Olink proteomics platform with a 92 immune response-related human protein panel, we analysed plasma samples from ITP patients (ITP, n = 40), patients with thrombocytopaenia secondary to other causes (Non-ITP, n = 19) and healthy controls (NC, n = 18), of a discovery cohort as well as a validation cohort (ITP, n = 36; NC, n = 20). A total of 10 differentially expressed proteins (DEPs) were identified in the ITP group compared with the non-ITP and NC groups of the discovery cohort. These include CXCL11, GZMH, ARG1, TGF-β1, ANGPT1, CXCL12, CD40-L, PDGF subunit B, IL4 and TNFSF14. Furthermore, least absolute shrinkage and selection operator regression analysis showed some of these DEPs, such as CXCL11, TGF-β1, ARG1 and GZMH to be significant in differentiating between patients with ITP and healthy controls (validation area under the curve = 0.87). The analysis demonstrated that the ITP group has a specific proteomic profile relative to non-ITP and NC groups. In summary, we report for the first time that Olink precision proteomics can specifically detect up-regulated inflammatory proteins as potential diagnostic biomarkers for ITP.

Combining Transcriptomics and Proteomics to Screen Candidate Genes Related to Bovine Birth Weight.

We established transcriptome and proteome databases for low-birth-weight (LB) and high-birth-weight (HB) calf placentae, identifying key genes and proteins associated with birth weight through bioinformatics analyses that included functional enrichment and protein-protein interactions (PPIs). Both mRNA and protein levels were validated. A total of 1494 differentially expressed genes (DEGs) and 294 differentially expressed proteins (DEPs) were identified when comparing the LB group to the HB group. Furthermore, we identified 53 genes and proteins exhibiting significant co-expression across both transcriptomic and proteomic datasets; among these, 40 were co-upregulated, 8 co-downregulated, while 5 displayed upregulation at the protein level despite downregulation at the mRNA level. Functional enrichment analyses (GO and KEGG) and protein-protein interaction (PPI) analysis indicate that, at the transcriptional level, the primary factor contributing to differences in calf birth weight is that the placenta of the high-birth-weight (HB) group provides more nutrients to the fetus, characterized by enhanced nutrient transport (SLC2A1 and SLC2A11), energy metabolism (ACSL1, MICALL2, PAG2, COL14A1, and ELOVL5), and lipid synthesis (ELOVL5 and ELOVL7). In contrast, the placenta of the low-birth-weight (LB) group prioritizes cell proliferation (PAK1 and ITGA3) and angiogenesis. At the protein level, while the placentae from the HB group exhibit efficient energy production and lipid synthesis, they also demonstrate reduced immunity to various diseases such as systemic lupus erythematosus and bacterial dysentery. Conversely, the LB group placentae excel in regulating critical biological processes, including cell migration, proliferation, differentiation, apoptosis, and signal transduction; they also display higher disease immunity markers (COL6A1, TNC CD36, CD81, Igh-1a, and IGHG) compared to those of the HB group placentae. Co-expression analysis further suggests that increases in calf birth weight can be attributed to both high-efficiency energy production and lipid synthesis within the HB group placentae (ELOVL5, ELOVL7, and ACSL1), alongside cholesterol biosynthesis and metabolic pathways involving CYP11A1 and CYP17A1. We propose that ELOVL5, ELOVL7, ACSL1, CYP11A1, and CYP17A1 serve as potential protein biomarkers for regulating calf birth weight through the modulation of the fatty acid metabolism, lipid synthesis, and cholesterol levels.

Expression, potential biological behaviour and clinical significance of MCM3 in pancreatic adenocarcinoma: a comprehensive study integrating high throughput sequencing, CRISPR screening and in-house immunohistochemistry

Background Minichromosome maintenance complex component 3 (MCM3) plays a key role in various tumours. However, it remains largely unknown what the specific role and clinical significance of MCM3 in pancreatic adenocarcinoma (PAAD) are. Materials and Methods We integrated high-throughput data from PAAD worldwide to analyse the expression level of MCM3 mRNA. We used immunohistochemistry to analyse MCM3 protein expression levels in 145 cases in the PAAD group and 29 cases in the non-PAAD group. We also mainly analysed the necessity of MCM3 for PAAD growth based on CRISPR screen data. In addition, we used enrichment analysis and protein–protein interaction networks to explore the molecular mechanism of MCM3 in PAAD. We also analysed the correlation between MCM3 expression, components of the immune microenvironment in PAAD tissue and clinical prognosis. Results In PAAD, we observed for the first time that MCM3 was significantly highly expressed at both the mRNA (SMD = 0.67, 95% CI: 0.38 ∼ 0.96) and the protein level (p < 0.05). The mRNA (AUC = 0.78, 95% CI: 0.74 ∼ 0.81; sensitivity = 0.66, 95% CI: 0.55 ∼ 0.76; specificity = 0.76, 95% CI: 0.67 ∼ 0.84) and protein (AUC = 0.929) expression levels of MCM3 had a good ability to distinguish between PAAD and non-PAAD tissue. There was heterogeneity reflected by the differential expression of MCM3 protein in PAAD cells. MCM3 played an essential role in PAAD growth, through abnormal DNA replication, p53 signalling and cell cycle checkpoints. PAAD with high MCM3 expression was sensitive to c-75, brivanib, flavopiridol and VNLG/124 drugs, with stable molecular docking models. Conclusion MCM3 is likely to be a critical element in promoting the initiation and growth of PAAD. Flavopiridol may exert its anti-PAAD effect through the interaction between MCM3, classic CDK1 targets in the cell cycle checkpoint and p53 pathway as well as related molecules in other pathways.

Rps3 Attenuates Gastric Precancerous Lesions by Promoting Dendritic Cells Maturation via AKT/β-Catenin Pathway.

This study aimed to investigate the dysregulated proteins and the underlying mechanisms of gastric precancerous lesions. Proteomic and phosphoproteomic methods were used to characterize the proteome and phosphoproteome profiles of N-methyl-N-nitro-N-nitrosoguanidine (MNNG)-induced gastric precancerous lesions. The hub differentially expressed proteins (DEPs) and phosphoproteins (DEPPs) were identified by using differential expression and protein-protein interaction network analyses. Western blot assay, quantitative reverse transcription (qRT)-PCR, and CCK-8 assays detected the expression of Rps3, N-cadherin, E-cadherin, AKT, p-AKT, and β-catenin and verified the roles of Rps3 on the MNNG-induced human gastric epithelial cell line (GES-1) cells. Hub DEPs and phosphoproteins Rps3, Akt1, and Ctnnb1 were significantly correlated with five dendritic cells (DCs) pathways, and Akt1 and Ctnnb1 were significantly negatively correlated with Rps3. MNNG administration markedly reduced the Rps3 mRNA and protein expression levels (all P < 0.05). Overexpression of Rps3 significantly inhibited tumorigenesis of MNNG-induced GES-1 cells (all P < 0.01) and changed the protein levels of N-cadherin, E-cadherin, AKT, p-AKT, and β-catenin. Similarly, SC79 treatment substantially increased the expression of interleukin (IL)-6, IL-10, and vascular endothelial growth factor (all P < 0.05). Rps3 was poorly expressed in precancerous gastric lesions. Correspondingly, overexpression of Rps3 promoted DC maturation via the AKT/β-catenin pathway, inhibiting the progression of gastric precancerous lesions.

Physiological and differential protein expression analyses of the calcium stress response in the Drynaria roosii rhizome

High concentration Ca2+ in karst soil is harmful to agriculture. Some dominant plants can adapt well to karst soil, but how Ca2+ affect plant is unknown. Drynaria roosii is a Ca2+-tolerant fern and its dry rhizome is a common Chinese medicine of Miao nationality in Guizhou, China. This study analyzed the physiological and proteomic characteristics of the rhizome of D. roosii under calcium stress. Physiological results indicated that calcium stress may lead to osmotic stress. Proteomic results showed that 147 differentially expressed proteins (96 increased, 51decreased) were identified under calcium stress, and these proteins mainly involved in signal transduction, protein translation, material transport, antioxidant defense and secondary metabolism. This study will lay a foundation for studying the calcium adaptation mechanism of D. roosii at the molecular level.

Proteomic analysis illustrates the potential involvement of motor proteins in cleft palate development

Cleft palate (CP) is a congenital condition characterized by a complex etiology and limited diagnostic and therapeutic options. In this study, we delved into the molecular mechanisms associated with retinoic acid (RA)-induced CP in Kun Ming mice. Proteomic analysis of control and RA-induced CP samples at embryonic day 15.5 revealed 25 upregulated and 19 downregulated proteins. Further analysis identified these differentially expressed proteins (DEPs) as being involved in extracellular matrix organization, actin cytoskeleton, and myosin complex. Moreover, these DEPs were found to be enriched in pathways related to motor protein activity and extracellular matrix-receptor interaction. Protein-protein interaction network analysis identified 10 hub proteins, including motor proteins and ECM-related proteins, which exhibited higher expression levels in CP compared to control tissues. These findings provide insights into the molecular mechanisms underlying CP and highlight potential targets for diagnostic and therapeutic purposes.

Label-free and TMT-labeled Proteomics Methods to Compare Differences on Normal and Attached Livers of Glyptosternum maculatum

Background: The aim of this study is to compare the molecular differences between the normal liver (NG) and attached liver (WG) of Glyptosternum maculatum (G. maculatum) based on label-free and TMT-labeled proteomics data. It provides a theoretical basis for the adaptation of G. maculatum in the plateau area with low temperature and low oxygen Methods: The differentially expressed proteins (DEPs) of label-free and TMT-labeled proteomics data were analyzed by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein structural domain (PSD) enrichment, and protein network interactions were constructed to reveal protein characteristics. Results: detected a total of 643 and 107 DEPs; 7 common DEPs (co-DEPs) were selected through PPI network information. Higher expression of evm.model.chr5.73, evm.model.chr18.610, evm.model.chr10.1201, and HIF-1 signaling pathway were associated with a hypoxic environment. evm.model.chr15.573, evm.model .chr5.320, evm.- model.chr6.360, and evm.model.chr18.610 were associated with WG production. Significant expression of Ubiquitin-like protein 4A and Heat shock 70 kDa protein protects liver cells from injury in a hypothermic and hypoxic environment. Conclusion: In terms of the number of DEPs, the labelling-free method is superior to the TMT-labeled method. The TMT-labeled method is better in terms of repeatability and accuracy. The myosin11 not only responds to low temperature and low oxygen but may also lead to WG production through Tight junctions. The NG may be more sensitive than WG in stress response to cancer and viral infections.

Endometrial Cell-Type Specific Regulation of the Endocannabinoids System and the Impact of Menstrual Cycle and Endometriosis.

Introduction: Anandamide (AEA) and 2-arachidonoylglycerol are endogenous agonists of the cannabinoid receptors and regulate and control many cellular functions. Their activities are governed by enzymes and proteins that regulate their synthesis, receptor binding, transport, and degradation, which are known as the endocannabinoid system (ECS). The aim of this study was to investigate the regulation of endocannabinoid activity in the endometrium by studying the RNA and protein expression of the ECS within endometrial cell types and during different menstrual cycle stages and the impact of endometriosis. Materials and Methods: The RNA expression of 70 ECS genes was assessed using RNA sequencing of isolated endometrial epithelial and stromal cells. Subsequent immunofluorescence-stained endometrial samples on ECS components of interest were objectively analyzed via an agnostic and automated image analysis pipeline to extract quantitative information. Differential gene and protein expression was investigated between the two cell types, menstrual cycle phases, and endometriosis cases and controls. Results: Sufficient RNA expression was detected for 45 genes, and 17 (38%) genes were significantly different between epithelial and stromal cells. FAAH RNA was significantly higher in epithelial cells compared with stromal cells. Protein expression analysis of the main synthesizing (NAPE-PLD) and catabolizing (FAAH and NAAA) enzymes of AEA revealed a significantly stronger epithelial expression compared to stromal cells. The RNA and protein expression of CB1 receptors was very low with no significant difference between epithelial and stromal cells. Eleven ECS genes were regulated across the menstrual cycle, and there was no gene with significant difference between endometriosis cases and controls in epithelial cells. Discussion: Differential expression of ECS genes supports a cell type-specific endocannabinoid activity in the endometrium. As endocannabinoids are short-lived signaling molecules, higher RNA and protein expression of FAAH in the epithelial cells suggests an active regulation of endocannabinoid activity in epithelial cells within the endometrium.

Proteomic Analysis Reveals Differential Protein Expression in Placental Tissues of Early-Onset Preeclampsia Patients.

Preeclampsia, a significant cause of maternal and perinatal morbidity and mortality, remains poorly understood, in terms of its pathogenesis. This study aims to uncover novel and effective biomarkers for preeclampsia by conducting a comparative analysis of differential proteins in placentas from early onset preeclampsia (EOPE) and normal pregnancies. Utilizing tandem mass tag (TMT)-based quantitative proteomics, we identified differentially expressed proteins in placental tissues from 15 EOPE patients and 15 normal pregnant women. These proteins were subsequently validated by using parallel reaction monitoring (PRM). Our analysis revealed a total of 59 differentially expressed proteins, with 25 up-regulated and 34 down-regulated proteins in EOPE placental tissues compared to those from normal pregnancies. Validation through PRM confirmed the differential expression of 6 proteins. Our findings suggest these 6 proteins could play crucial roles in the pathogenesis of EOPE, highlighting the potential involvement of the estrogen signaling pathway and dilated cardiomyopathy (DCM) pathway in the development of preeclampsia. The data were deposited with the ProteomeXchange Consortium via the iProX partner repository with the identifier PXD055025.

Matrix stiffness regulates the protein profile of extracellular vesicles of pancreatic cancer cell lines.

The fibrotic stroma characterizing pancreatic ductal adenocarcinoma (PDAC) derives from a progressive tissue rigidification, which induces epithelial mesenchymal transition and metastatic dissemination. The aim of this study was to investigate the influence of matrix stiffness on PDAC progression by analyzing the proteome of PDAC-derived extracellular vesicles (EVs). PDAC cell lines (mPDAC and KPC) were grown on synthetic supports with a stiffness close to non-tumor (NT) or tumor tissue (T), and the protein expression levels in cell-derived EVs were analyzed by a quantitative MSE label-free mass spectrometry approach. Our analysis figured out 15 differentially expressed proteins (DEPs) in mPDAC-EVs and 20 DEPs in KPC-EVs in response to matrix rigidification. Up-regulated proteins participate to the processes of metabolism, matrix remodeling, and immune response, altogether hallmarks of PDAC progression. A multimodal network analysis revealed that the majority of DEPs are strongly related to pancreatic cancer. Interestingly, among DEPs, 11 related genes (ACTB/ANXA7/C3/IGSF8/LAMC1/LGALS3/PCD6IP/SFN/TPM3/VARS/YWHAZ) for mPDAC-EVs and 9 (ACTB/ALDH2/GAPDH/HNRNPA2B/ITGA2/NEXN/PKM/RPN1/S100A6) for KPC-EVs were significantly overexpressed in tumor tissues according to gene expression profiling interaction analysis (GEPIA). Concerning the potential clinical relevance of these data, the cluster of ACTB, ITGA2, GAPDH and PKM genes displayed an adverse effect (p<0.05) on the overall survival of PDAC patients.

MME and PTPRC: key renal biomarkers in lupus nephritis

Background Lupus nephritis (LN) is an autoimmune-related kidney disease with a poor prognosis, however the potential pathogenic mechanism remains unclear and there is a lack of precise biomarkers. Therefore, a thorough screening and identification of renal markers in LN are immensely beneficial to the research on its pathogenic mechanisms and treatment strategies. Methods We utilized bioinformatics to analyze the differentially expressed genes (DEGs) at the transcriptome level of three clusters: total renal, glomeruli, and renal tubulointerstitium in the GEO database to discover potential renal biomarkers of LN. We utilized NephroSeq datasets and measured mRNA and protein levels in the kidneys of MRL/lpr mice to confirm the expression of key DEGs. Results Seven significantly differential genes (EGR1, MME, PTPRC, RORC, MX1, ZBTB16, FKBP5) were revealed from the transcriptome database of GSE200306, which were mostly enriched in the pathway of the hematopoietic cell lineage and T cell differentiation respectively by KEGG and GO analysis. The seven hot differential genes were verified to have consistent change trends using three datasets from NephroSeq database. The receiver operating characteristic (ROC) curve indicated that five DEGs (PTPRC, MX1, EGR1, MME and RORC) exhibited a higher diagnostic ROC value in both the glomerulus and tubulointerstitium group. Validation of core genes using MRL/lpr mice showed that MME and PTPRC exhibit significantly differential mRNA and protein expression patterns in mouse kidneys like the datasets. Conclusions This study identified seven key renal biomarkers through bioinformatics analysis using the GEO and NephroSeq databases. It was identified that MME and PTPRC may have a high predictive value as renal biomarkers in the pathogenesis of LN, as confirmed by animal validation.