For steady transgenic expression, lentiviral vector-mediated gene delivery is a commonly used technique. One question that needs to be explored is how external lentiviral vectors and overexpressed genes perturb cellular homeostasis, potentially altering transcriptional networks. In this study, two Human Embryonic Kidney 293T (HEK293T)-derived cell lines were established via lentiviral transduction, one overexpressing green fluorescent protein (GFP) and the other co-overexpressing GFP and ADORA3 following puromycin selection to ensure stable genomic integration. Genes with differentially transcript utilization (gDTUs) and differentially expressed genes (DEGs) across cell lines were identified after short-read and long-read RNA-seq. Only 31 genes were discovered to have changed in expression when GFP was expressed, although hundreds of genes showed variations in transcript use. In contrast, even when co-overexpression of GFP and ADORA3 alters the expression of more than 1000 genes, there are still less than 1000 gDTUs. Moreover, DEGs linked to ADORA3 overexpression play a major role in RNA splicing, whereas gDTUs are highly linked to a number of malignancies and the molecular mechanisms that underlie them. For the analysis of gene expression data from stable cell lines derived from HEK293T, our findings provide important insights into changes in gene expression and alternative splicing.

Phenotypic modifications and their effects on cellular functions through the up-regulation of target gene expression have frequently been observed in genetic studies, but the unique roles of cell lines and their introduced plasmids in influencing these functions have not been fully revealed. In this research, we developed two distinct cell lines derived from the A549 cell line: one that stably overexpresses GFP and another that is a polyclonal stable line overexpressing both GFP and P2RY12. We then utilized transcriptome sequencing (RNA-seq) technology to screen out differentially expressed genes (DEGs) and genes with differential transcript usage (gDTUs) after GFP overexpression (GFP-OE) and P2RY12 overexpression (P2RY12-OE). We found that, compared with A549, there were more than 1700 differentially expressed genes (DEGs) in both GFP-OE and P2RY12-OE cells, while only 866 DEGs were identified in GFP-OE and P2RY12-OE cells. Notably, the differences in transcript usage were relatively minor, with only over 400 genes exhibiting changes across all three groups. The functional analysis of DEGs and gDTUs showed that they were both highly enriched in the pathways associated with cell proliferation and migration. In summary, we performed an extensive analysis of the transcriptome profile of gene expression and alternative splicing with GFP-OE and P2RY12-OE, enhancing our comprehension of how genes function within cells and the processes that control gene expression.

Severe respiratory inflammation or viral infections can lead to acute lung injury (ALI), a disease characterized by diffuse inflammatory injury of the pulmonary epithelium and endothelium. Cepharanthine (CEP) is reported as a promising drug candidate due to its antiviral properties. However, CEP exhibits poor solubility and low bioavailability. Therefore, we developed a novel liposome, named CEP@LP-M^CCR2, which integrates the advantages of cell membranes and lipid materials, to achieve effective accumulation of CEP in inflamed lungs. It exhibits a 1.73-fold increase in lung accumulation at 24 h in vivo, a 4.56-fold increase in cellular uptake in MLE-12 cells. CEP@LP-M^CCR2 is equipped with a CCR2-overexpressed surface, enabling it to selectively neutralize elevated levels of CCL2, which is related to ALI, thereby reducing macrophage infiltration, thereby reducing the spread of inflammation, such as a reduction in levels of key pro-inflammatory cytokines (TNF-α, IL-1β, and IL-6). CEP@LP-M^CCR2 could suppress M1 macrophage polarization, which led to a marked decrease in iNOS and an increase in Arg1. It upregulated the expression of junctional proteins E-cadherin and Occludin, indicating potential recovery of the pulmonary epithelial barrier. RNA sequencing analysis implied the potential of CEP@LP-M^CCR2 to inactivate the TNF/NF-κB signaling axis.

Medicinal plants are valuable resources globally and are used worldwide to maintain health and treat disease; however, the presence of adulteration obstructs their development. DNA barcoding, a technique for species identification by standard DNA regions, facilitates prompt and accurate identification of traditional medicinal plants. The process of DNA barcoding entails six basic steps: 1) processing the medicinal plants, 2) extracting high-quality total DNA from the medicinal plants using centrifugal column method, 3) amplifying target DNA region internal transcribed spacer 2 (ITS2) with universal primers of plants and performing Sanger sequencing, 4) splicing and aligning sequence to obtain the target sequence, 5) matching the barcode sequence against the barcode library for identification, 6) aligning sequence, comparing intraspecific and interspecific variation, constructing phylogenetic neighbor-joining tree. As shown in the results, the universal primer can amplify the target region. Basic Local Alignment Search Tool (BLAST) demonstrates the percentage identified was 100%, and the neighbor-joining tree demonstrates that the splicing sequences were clustered with the A. sinensis OR879715.1 clade, and the clade support value is 100. This protocol provides a reference for applying DNA barcoding technology as an effective method to identify medicinal plants and adulterants.

Rhizoma coptidis (RC), known as Huang Lian, is widely used for treating diabetes in Traditional Chinese Medicine. G protein-coupled bile acid receptor 1 (TGR5) is a potential therapeutic target for glucose-lipid metabolic disorders due to its capacity to stimulate glucagon-like peptide-1 (GLP-1) secretion. However, whether RC contains ingredients targeting TGR5 remains unclear. In this study, we screened 330 secondary metabolites of RC via molecular docking and identified obacunone as a top candidate. We confirmed binding using Cell Membrane Chromatography (CMC) and quantified affinity via Surface Plasmon Resonance (SPR), determining a KD of 101 μM. cAMP assays identified obacunone as an activator of TGR5. Subsequently, concentration-dependent cAMP assays characterized it as a partial agonist with an EC50 of 9.6 μM. Finally, transcriptomic profiling revealed a stress adaptation response, identifying Heme Oxygenase 1 (HMOX1) as the most significantly upregulated gene (padj = 9.99 × 10⁻⁷², log₂FoldChange = 1.65). These findings contribute to understanding the pharmacological profile of RC and provide a screening example for identifying components with GPCR activity in RC.

Benzylisoquinoline alkaloids (BIAs) exhibit diverse biological activities, such as neuroprotective effects. The delta-opioid receptor (DOR) has emerged as a promising therapeutic target due to its potential role in enhancing neuroprotection and regeneration. However, reports on the binding of BIAs to the DOR remain scarce. Here, neferine, a BIA from Nelumbo nucifera, as a potential DOR agonist. Molecular docking ranked neferine among the top of 15 BIAs. Initial binding was detected by cellular membrane chromatography and quantitatively confirmed by bio-layer interferometry, with a K_D value of 37.4 μM. ONE vector G protein Optical biosensor revealed that G_i2, G_i3 and G_Z signaling could be activated by neferine through DOR modulation. Consistent with the G_i/z activation, neferine dose-dependently inhibited cAMP accumulation with an EC₅₀ of 0.25 µM. Transcriptomic analysis in DOR-overexpressing HEK293T cells indicated that neferine stimulation predominantly regulates gene networks governing cell cycle and stress adaptation. However, direct transcriptional signature for neuroprotection was not predominant in our system, suggesting that DOR signaling may exhibit context-dependent effects. In conclusion, we identified the neferine as a natural DOR agonist through in silico and in vitro approach, providing a reference for further investigation into its pharmacological potential.