Fluvastatin Upregulates the Expression of Tissue Factor Pathway Inhibitor in Human Umbilical Vein Endothelial Cells

Perturbation-Modulated Native Mass Spectrometry Excludes a Nonspecific Drug Target Protein Binder Based on Conformation Stability Change

Native electrospray ionization mass spectrometry (ESI-MS) is a standard technique for drug-protein screening but may be affected by nonspecific binding. To address this, a reference protein and ligand must be selected for each protein investigated. We report a versatile, informative, high-throughput screening approach to differentiate specific and nonspecific interactions based on charge state distribution (CSD) changes caused by ionization perturbations (e.g., methanol or heat) without the need for a surrogate. We show that specific binding stabilizes the protein-ligand complex against perturbations, resulting in narrower CSDs compared with the unbound protein. In contrast, no significant difference in CSDs is observed between nonspecific complexes and the free protein. To introduce ion source perturbations without affecting protein-ligand incubation, we employed a 3D-printed open port probe (OPP) that is widely compatible with different instruments and sample introduction techniques. The approach was validated with well-characterized protein-ligand pairs, confirming that cytidine phosphates, triacetylchitotriose, and fluvastatin are specific ligands for ribonuclease A, lysozyme, and beta-lactoglobulin, respectively. Further, cytidine-5'-triphosphate (CTP) was found to interact nonspecifically with lysozyme and beta-lactoglobulin. The approach was applied to screening assays of two drug target proteins, thrombin and dihydrofolate reductase, revealing that for thrombin, fluvastatin may share the same binding site as argatroban, which is supported by competition experiments and molecular docking results. These results provide new insights into the anticoagulation effect of statins and show the potential of the approach in prioritizing candidates for target proteins.

Universal concept signature analysis: genome-wide quantification of new biological and pathological functions of genes and pathways

Identifying new gene functions and pathways underlying diseases and biological processes are major challenges in genomics research. Particularly, most methods for interpreting the pathways characteristic of an experimental gene list defined by genomic data are limited by their dependence on assessing the overlapping genes or their interactome topology, which cannot account for the variety of functional relations. This is particularly problematic for pathway discovery from single-cell genomics with low gene coverage or interpreting complex pathway changes such as during change of cell states. Here, we exploited the comprehensive sets of molecular concepts that combine ontologies, pathways, interactions and domains to help inform the functional relations. We first developed a universal concept signature (uniConSig) analysis for genome-wide quantification of new gene functions underlying biological or pathological processes based on the signature molecular concepts computed from known functional gene lists. We then further developed a novel concept signature enrichment analysis (CSEA) for deep functional assessment of the pathways enriched in an experimental gene list. This method is grounded on the framework of shared concept signatures between gene sets at multiple functional levels, thus overcoming the limitations of the current methods. Through meta-analysis of transcriptomic data sets of cancer cell line models and single hematopoietic stem cells, we demonstrate the broad applications of CSEA on pathway discovery from gene expression and single-cell transcriptomic data sets for genetic perturbations and change of cell states, which complements the current modalities. The R modules for uniConSig analysis and CSEA are available through https://github.com/wangxlab/uniConSig.

TFPIα alleviated vascular endothelial cell injury by inhibiting autophagy and the class III PI3K/Beclin-1 pathway

Endothelium (EC) dysfunction plays an important role in vascular diseases, such as arteriosclerosis and hypoxia/reoxygenation (H/R) injury. Tissue factor pathway inhibitor (TFPI) is the only physiological inhibitor of the TF/FVIIa complex in vivo. This experiment aimed to determine the effect of TFPIα on H/R-induced EC injury and the possible mechanisms. The MIC101 hypoxia system was used to establish an EC H/R injury model in vitro. Our results showed that 6 h after reoxygenation, the EC injury in H/R group was higher than that in the control group, whereas after adding TFPIα, the EC injury was alleviate than that in H/R group. The level of ROS was higher in the H/R group than in the control group, while it was apparently lower in the H/R+TFPIα group than in the H/R group. After H/R, the number of autophagosomes and the autophagic flux were significantly increased, whereas TFPIα could decrease the autophagy level after H/R. The expressions of LC3-II/LC3-I, Beclin-1 and PI3K were obviously higher after H/R and lower after adding TFPIα. In conclusion, autophagy contributes to EC injury during the H/R period. TFPIα could decrease autophagy in ECs, and the mechanism might be class III PI3K/Beclin-1 pathway regulation.