Molecular omics最新文献

YAP and TAZ are transcriptional co-activators that are inhibited by sequestration in the cytoplasm. Cellular signalling pathways integrate soluble, mechanical (cytoskeleton, adhesion), and geometric (cell size, morphology) cues to regulate the translocation of YAP/TAZ to the nucleus. In triple-negative breast cancer (TNBC) cells, both signalling and morphogenesis are frequently rewired, leading to increased YAP/TAZ translocation, which drives proliferation, invasion, and drug resistance. However, whether this increased YAP/TAZ translocation is due to alterations in upstream signalling events or changes in cell morphology remains unclear. To gain insight into YAP/TAZ regulation in TNBC cells, we performed multiplexed quantitative genetic screens for YAP/TAZ localisation and cell shape, enabling us to determine whether changes in YAP/TAZ localisation following gene knockdown could be explained by alterations in cell morphology. These screens revealed that the focal adhesion (FA)-associated RhoGEF DOCK5 is essential for YAP/TAZ nuclear localisation in TNBC cells. DOCK5-defective cells exhibit defects in FA morphogenesis and fail to generate a stable, polarised leading edge, which we propose contributes to impaired YAP/TAZ translocation. Mechanistically, we implicate DOCK5's ability to act as a RacGEF and as a scaffold for NCK/AKT as key to its role in FA morphogenesis. Importantly, DOCK5 is essential for promoting the resistance of LM2 cells to the clinically used MEK inhibitor Binimetinib. Taken together, our findings suggest that DOCK5's role in TNBC cell shape determination drives YAP/TAZ upregulation and drug resistance.

Cow's milk protein allergy (CMA) is one of the most common food allergies in children worldwide. However, it is still not well understood why certain children outgrow their CMA and others do not. While there is increasing evidence for a link of CMA with the gut microbiome, it is still unclear how the gut microbiome and metabolome interact with the immune system. Integrating data from different omics platforms and clinical data can help to unravel these interactions. In this study, we integrate clinical, microbial, (meta)proteomics, immune and metabolomics data into machine learning (ML) classification, using multi-view learning by late integration. The aim is to group infants into those that outgrew their CMA and those that did not. The results show that integration of microbiome data with clinical, immune, (meta)proteomics and metabolomics data could considerably improve classification of infants on outgrowth of CMA, compared to only considering one type of data. Moreover, pathways previously linked to development of CMA could also be related to outgrowth of this allergy.

In this study, we analyzed the combination of affinity purification mass spectrometry (AP-MS) with high-field asymmetric waveform ion mobility spectrometry (FAIMS), integrated between nanoLC-MS and an Orbitrap Ascend tribrid mass spectrometer. Our primary objective was to evaluate the application of the FAIMS interface for detecting affinity purified SAP25 protein complexes with enhanced sensitivity and robustness. As a result, we observed that nanoLC-FAIMS-MS (with FAIMS) significantly improved the sensitivity and detection limits at the protein level, peptide level and significantly reduced chemical contaminants compared to nanoLC-MS alone without FAIMS (No FAIMS). This FAIMS configuration resulted in 42% and 92% increases for the total proteins and unique proteins, respectively, and 44% and 88% increases for total peptides and unique peptides compared to the No FAIMS configuration. Our in-depth comparison of FAIMS and No FAIMS shows that FAIMS outperforms by significantly reducing the missing value by <15% in datasets and plays a significant role in filtering chemical contaminants. Lastly, we searched the datasets for multiple post-translational modifications important in chromatin remodeling and found several arginine methylation sites on the bait protein SAP25. Our findings highlight the potential of FAIMS with Orbitrap Ascend tribrid mass spectrometer to enhance the depth of AP-MS analysis. The data were deposited with the MASSIVE repository with the identifier MSV000096548.

Candida albicans, an opportunistic and systemic infection causing fungus, causes skin, nail, and mucosal layer lesions in healthy individuals and hospital borne catheter-related and nosocomial infections. This particular fungus exists in two distinct stages in its life cycle: yeast and hyphae. In this study, 20 signaling pathways associated with 177 proteins from C. albicans were identified to construct a PPI network. The core part of the network consisted of 165 proteins. Network topology analyses revealed that the formed PPI network is biologically robust and scale-free, with significant interactions between proteins through 19 252 shortest pathways. In this network, the top 10 hub proteins (RAS1, CDC42, HOG1, CPH1, STE11, EFG1, CEK1, HSP90, TEC1 and CST20) were identified using network analysis, which seem to be the most important proteins involved in different pathways for the development of pathogenesis and virulence. Modular analysis of the network resulted in top six sub-networks, three of which shared eight hub proteins. Ontology and functional enrichment analyses revealed that the majority of the proteins were associated with regulation of transcription by RNA polymerase II, plasma membrane and nucleic acid binding in biological processes, and cellular components and molecular functions, respectively. Enrichment analysis indicated that the proteins were mostly involved in oxidative phosphorylation and purine metabolism signaling pathways. We determined the complex web of signaling pathway involving proteins via PPI network analysis to unravel and decipher protein interactions within C. albicans to understand the complex pathogenesis processes for targeted therapeutic interferences using novel bioinformatics strategies.

The progressive illness known as chronic kidney disease (CKD) can often be challenging to diagnose in its early stages with conventional diagnostic approaches such as serum creatinine and albumin assessment. Early-stage CKD (stages G1–G3) is defined by a GFR of ≥30 mL min⁻¹/1.73 m², which indicates normal to moderately reduced kidney function with or without symptoms of impaired kidney function. Identifying possible biomarkers for early detection and personalised treatment, as well as physiological changes linked to early CKD—an area that has not been fully investigated before—is the goal of the study to address this gap. We performed a metabolomic analysis using ¹H NMR on 115 human serum samples (24 healthy controls and 91 patients with early-stage CKD). MetaboAnalyst 6.0 was used for data pre-processing and statistical analyses (PCA, PLS-DA, OPLS-DA, ANOVA, and Wilcoxon Mann–Whitney test). Strong differentiation between CKD stages was achieved by random forest modelling. The KEGG database was used to perform pathway enrichment, and ROC analysis was used to evaluate the diagnostic value of important metabolites. Across CKD stages, significant changes were observed in ten different metabolites: myo-Inositol, glycerol, pyruvate, carnitine, phenylalanine, tyrosine, histidine, TMAO, 2-hydroxyisobutyrate, and 3-hydroxyisobutyrate (p < 0.05, VIP > 1). AUC values > 0.7 from ROC curves demonstrated its potential for diagnosis. Pathway analysis revealed significant dysregulation in the metabolism of inositol phosphate, tyrosine, histidine, and pyruvate, and biosynthesis of phenylalanine, tryptophan and tyrosine. This comprehensive metabolomics investigation identified potential early-stage CKD biomarkers in addition to significant metabolic abnormalities. These findings could help provide individualized care for early CKD management.

Vibrio alginolyticus is an opportunistic infectious pathogen, and its pathogenicity is related to various virulence factors, with the type III secretion system (T3SS) being one of the important systems for secreting virulence factors. vopR is one of the effector genes of V. alginolyticus T3SS1. To investigate its pathogenicity, this study constructed an overexpression vector to express vopR in host cells, using the empty plasmid as a control, and analyzed its impact on the mRNA and protein expression levels of host cells. Transcriptomic analysis revealed that overexpression of vopR led to the upregulation of 410 genes and the downregulation of 207 genes. Proteomic analysis showed that 126 proteins were upregulated, and 518 proteins were downregulated. GO enrichment analysis indicated that the differential genes were significantly enriched in various biological processes such as cellular processes, metabolic processes, and biological regulation, as well as in cellular components like cell parts and membranes, and molecular functions such as binding and catalytic activity. KEGG enrichment analysis demonstrated that the differential genes were mainly enriched in metabolic pathways, cancer-related pathways, and the MAPK signaling pathway. The combined analysis of the transcriptome and proteome screened out 144 overlapping differentially expressed genes, with 60 being upregulated and 54 being downregulated. These results suggest that vopR has a significant impact on the cytoskeleton, metabolism, and immune regulation of host cells during the pathogenic process of V. alginolyticus. This study provides a theoretical basis for a deeper understanding of the pathogenic mechanism of V. alginolyticus.

Non-small cell lung cancer (NSCLC) is the most common subtype of lung cancer, and 4% of NSCLC patients are reported to harbor mutations in BRAF, which encodes a serine/threonine kinase capable of activating the mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) pathway. However, the role and effects of BRAF mutation in NSCLC or lung lineage cells are not fully understood. To mimic the naturally occurring BRAF V600E mutation in lung cancer, a BRAF V600E knock-in BEAS-2B cell model was established using CRISPR/Cas9. Although the BRAF V600E mutation alone was not sufficient to drive lung carcinogenesis, it induced remarkable changes in cellular migration capacity and tumorigenic potential. Proteomics analysis revealed significant changes in the proteins involved in the biological processes including epithelial–mesenchymal transition (EMT), extracellular matrix (ECM)–receptor interaction, cell adhesion, focal adhesion, and cell metabolism upon the BRAF V600E mutation. Untargeted metabolomics experiments revealed that amino acid metabolism, especially glycine, serine and threonine metabolism, was significantly modulated in BRAF V600E knock-in cells. In summary, this study provides a new isogenic cell model that allows us to systematically dissect the underlying molecular events involved in the transition of cellular states upon the introduction of the BRAF V600E mutation.

Retraction of ‘Tetracycline-controllable artificial microRNA-HOTAIR + EZH2 suppressed the progression of bladder cancer cells’ by Yincong Chen et al., Mol. BioSyst., 2017, 13, 1597–1607, https://doi.org/10.1039/C7MB00202E.

The increasing exposure to nanoparticles raises a concern over their toxicity. Incidentally, reactive oxygen species (ROS) are produced as a result of the nanoparticle's physicochemical characteristics and interactions with intracellular elements, primarily enzymes, leading to oxidative stress. In this context, the extent of oxidative stress resulting from the toxicity of titanium dioxide nanoparticles (TiO₂-NPs) on the cardiovascular system has not yet been thoroughly investigated. Initially, the gel/label-free proteomics (nLC-HRMS/MS) method was used to examine human serum protein interaction and corona composition. Furthermore, different oxidative stress assays (superoxide, total ROS, mitochondrial ROS, and lipid peroxidation) and cell stress assays (apoptosis, ER stress, mitochondrial dysfunction, autophagy, and hypertrophy) were performed in conjunction with endothelial (rat aortic cells) and cardiomyoblast (H9c2) cell cultures. In addition, expression studies (RT-qPCR and immunofluorescence), kinase signalling, and siRNA-mediated gene knockout (NOX2 and XO) studies were conducted. Alongside, in ovo effects on the heart's antioxidant enzymes (SOD and CAT) and metabolomic pathways (1H NMR) confirmed the involvement of oxidative stress in cardiotoxicity. The present results demonstrate a dose-dependent increase in cytotoxicity via the activation of caspase 3 and 9. The dose-dependent increase and its synergistic relationship with cardiovascular stress signalling (ET-1 and Ang-II) highlight the significant role of oxidative stress in nanoparticle toxicity. In summary, this study expands our understanding of the precise health risks associated with human exposure by establishing a connection between the role of the redox system and molecular stress pathways in TiO₂-NPs-induced cardiotoxicity.

The incidence of chronic kidney disease (CKD) is increasing globally; however, effective preventive and therapeutic strategies are currently limited. Roxadustat is being clinically used to treat renal anemia in CKD patients to reduce anemia-related complications and improve patients' life quality. Exosomes are small vesicles carrying important information that contribute to cell-to-cell communication and are present in various body fluids. However, little is known about the role of serum exosomes and their association with CKD after roxadustat treatment. Next-generation sequencing approaches have revealed that exosomes are enriched in noncoding RNAs and thus exhibit great potential as sensitive nucleic acid biomarkers in various human diseases. In this study, we aimed to identify the changed mRNAs–lncRNAs after roxadustat treatment as novel biomarkers for assessing the efficiency of the treatment. Through our study using RNA-seq data, we identified 957 mRNAs (626 upregulated and 331 downregulated after roxadustat treatment) and 914 lncRNAs (444 upregulated and 470 downregulated) derived from exosomes that were significantly changed, which was highly correlated to lipid metabolism. Our analysis through whole transcriptome profiling of exosome RNAs encompasses an identified differentially expressed mRNA–lncRNA regulatory axis in a larger patient cohort for the validation of suitable biomarkers for assessing CKD after roxadustat treatment.