Objective To investigate the gene expression and regulatory mechanisms of mouse embryonic fibroblasts (MEFs) under inflammatory conditions, aiming to elucidate the role of MEFs in inflammatory responses and provide a foundation for discovering anti-inflammatory drugs that act by modulating MEF function. Methods MEFs cultured in vitro were divided into the following groups: lipopolysaccharides (LPS)-treated group, inflammatory conditioned medium (CM)-treated group, and control group, which were treated with LPS, CM, and equal volume solvent, respectively. Transcriptome sequencing was used to analyze the effects of two stimuli on gene expression profile of MEFs. Real time fluorescence quantitative PCR (RT-qPCR) was employed to verify the transcription levels of highly expressed genes of MEFs induced by CM. ELISA was performed to determine the concentrations of cytokines in cell supernatants. Finally, the regulatory effects of CM on the activation of signaling pathways in MEFs were analyzed by immunoblotting. Results Transcriptome analysis showed that both LPS and CM induced the transcription of a large number of genes in MEFs. Compared with LPS, CM potentiated the mRNA transcription of some acute phase proteins, inflammatory cytokines, chemokines, matrix metalloproteinases (MMP), prostaglandin synthetases, and colony-stimulating factors. The transcriptome analysis was verified by RT-qPCR. The results of ELISA showed that CM treatment significantly increased the secretion of interleukin 6 (IL-6), C-C motif chemokine ligand (CCL2), and C-X-C motif chemokine ligand (CXCL1) by MEFs compared with LPS. Mechanism study showed that both LPS and CM induced the phosphorylation of nuclear factor-κB p65 (NF-κB p65), p38 mitogen-activated protein kinase (p38 MAPK), extracellular regulated protein kinases 1/2 (ERK1/2), and TANK-binding kinase (TBK) in MEFs, and CM strongly stimulated the phosphorylation of signal transducer and activator of transcription 3 (STAT3) in MEFs. Conclusion Both LPS and CM can induce transcription and protein secretion of various inflammation-related genes in MEFs. CM can partly enhance LPS-induced activation of MEFs, and the mechanism may be related to the enhancement effect of CM on the activation STAT3 signaling pathway.

Puerarin is the major bioactive ingredient extracted from Pueraria lobata. Puerarin has an antitumor effect on many kinds of cancer. Accordingly, the aim of this study was to investigate the effect and mechanism of puerarin on thyroid cancer (TC) proliferation and apoptosis.

Arctigenin, a natural lignan from Arctium lappa L., exhibits potent antifibrotic activity, yet its molecular mechanisms remain unclear. Endoplasmic reticulum (ER) stress is known to promote hepatic stellate cell (HSC) activation and liver fibrosis. This study investigates the therapeutic potential of arctigenin in HSC activation through ER stress modulation. Primary rat HSCs were activated (3-7 days) and treated with tunicamycin (ER stress inducer) or 4-PBA (ER stress inhibitor). Arctigenin attenuated ER stress markers (e.g., GRP78) and suppressed the expression of fibrotic marker α-SMA in ER stress-challenged activating (day 3) and activated (day 7) HSCs. Arctigenin restored lipid homeostasis by modulation of both lipogenesis (via Dgat2 and Ppar-γ upregulation) and lipolysis (suppression via ATGL inhibition). ER stress activated ER-associated degradation (ERAD), triggering the formation of small lipid droplets (LD). Arctigenin normalized the ERAD activity, thereby rescuing LD integrity and suppressing HSC activation. Our findings demonstrate that arctigenin mitigates HSC activation by suppressing ER stress and restoring lipid homeostasis via modulating ERAD-mediated lipid dysregulation. As a dietary and medicinal compound, arctigenin emerges as a promising therapeutic candidate for liver fibrosis.

Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide, necessitating the development of novel therapeutic strategies. We explore the expression characteristics of SLC39A6 in CRC by combining multiple cohorts and multi-omics. The therapeutic effect and potential mechanism of BRY812 on CRC were explored through in vitro experiments. Our research results show that the expression of SLC39A6 in CRC tissues is higher than that in normal tissues, and it is closely related to tumor pathways, making it a good therapeutic target. BRY812 has an inhibitory effect on the growth, migration and stemness of CRC cells, and may exert its killing effect by downregulating the AKT pathway. This study has identified SLC39A6 as a potential therapeutic target in CRC. BRY812 is expected to become a highly promising therapeutic drug, bringing new hope to patients with CRC.

Osimertinib, a third-generation EGFR tyrosine kinase inhibitor (EGFR-TKI), has dramatically transformed the treatment landscape for patients with EGFR-mutant NSCLC. However, the long-term success of this therapy is often compromised by the onset of acquired resistance, with non-genetic mechanisms increasingly recognized as pivotal contributors. Here, we exploit a multi-omics approach to profile genome-wide chromatin accessibility and transcriptional landscapes between drug sensitive and resistant EGFR-mutant cells. Our findings reveal a robust concordance between epigenetic regulome and transcriptomic changes that characterize the osimertinib resistant state. Through CRISPR-based functional genomics screen targeting epigenetic regulators and transcription factors, we uncover a critical regulatory network featuring key members of the NuRD and PRC2 complexes that mediate resistance. Most critically, our screen identifies FOSL1 and JUN, two subunits of the AP-1 transcription factor within this network, as the most significant hits. Mechanistically, we demonstrate that cis-regulatory elements exhibiting altered chromatin accessibility in the resistant state are enriched for cognate AP-1 binding motifs, enabling AP-1 to orchestrate a gene expression program that underpins the druggable MEK/ERK signaling axis, potentially enhancing cell viability and fitness of resistant cells. Importantly, genetic depletion or pharmacological inhibition of AP-1 reinstates cellular and molecular sensitivity, and reverts resistance-associated phenotypes, such as epithelial-to-mesenchymal transition, upon anti-EGFR rechallenge by repressing AKT and ERK signaling. These findings provide novel insights into the epigenetic and transcriptional control of osimertinib resistance in EGFR-mutant NSCLC, highlighting AP-1 as a targetable vulnerability of resistance-related hallmarks and offering a promising avenue for developing resistance reversal strategies.

Soybean (Glycine max L. Merrill), a vital source of edible oil and protein, ranks seventh in global agricultural production, yet its productivity is significantly hindered by potential toxic metal/liods (PTM) stress. Arsenic (As), a highly toxic soil contaminant, poses substantial risks to both plants and humans, even at trace concentrations, particularly in China.

Cetuximab resistance severely restricts its effectiveness in the treatment of patients with metastatic colorectal cancer (CRC). Previous studies have predominantly focused on the genetic level, with scant attention to the nongenetic aspects. This study aimed to identify the crucial microRNA (miRNA) that is responsible for cetuximab resistance.

Fusobacterium nucleatum (Fn) has been implicated in various diseases, including colorectal cancer (CRC). This study elucidates Fn's contribution to cholesterol synthesis and the underlying link with CRC, as well as butyrate's counteracting effects in this process. Cells and mouse models were treated with Fn followed/accompanied by butyrate treatments to investigate the interplay between butyrate and Fn's oncogenic properties. Transcriptomics analysis pinpointed Fn's profound impact on cholesterol biosynthesis genes and pathways. Fn treatment upregulated the expression of genes involved in cholesterol synthesis (FDPS, FDFT1, and SQLE) and increased SREBF2 activity in cells and mouse intestines, elevating cholesterol levels in cells, intestines, and sera. Fn upregulated miR-130a-3p, identified through transcriptomics and target prediction, through nuclear factor-κB activation. miR-130a-3p subsequently downregulated AMPKα/β1 expression to activate SREBF2 and upregulate cholesterol biosynthesis genes. These effects were predominantly mitigated by butyrate. Notably, analysis of TCGA data revealed that fusobacterial abundance correlated significantly with the expression of FDPS, FDFT1, SQLE, and AMPKα/β1 in CRC. Fn abundance and miRNA expression in human stools were quantified using qPCR and RT-qPCR. Fecal miR-130a-3p levels increased progressively from normal subjects through adenoma patients to CRC patients, correlating significantly with fecal Fn abundance. Additionally, heightened fecal Fn abundance was associated with an increased incidence of hypercholesterolemia in CRC patients. Fn promotes cholesterol biosynthesis by upregulating miR-130a-3p, which downregulates AMPK proteins and activates SREBF2. This study highlights the influence of gut bacteria on host cholesterol synthesis. Targeted modulation of gut microbiota to reduce cholesterol may represent a promising preventive strategy for CRC.

The Wnt/β-catenin signaling pathway regulates key cellular processes, including proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT). Dysregulation of this pathway has been implicated in various human cancers, including colorectal cancer (CRC), where it plays a critical role in promoting EMT and metastatic progression. In a recent study, triazole derivatives were shown to possess anti-EMT activity in cancer cells. Building on this finding, we synthesized a triazolyl-quinoxaline-based small molecule, SRN-18, and evaluated its impact on EMT in CRC cells. Specifically, we investigated the effect of SRN-18 on the mRNA and protein expression levels of CXCR4 and CXCR7, as well as its influence on the expression of MMP-2, MMP-9, and key EMT-associated proteins. As CXCL12 is a known ligand for both CXCR4 and CXCR7, we also examined the effects of CXCL12 stimulation on cell migration and invasion. Western blot analyses were conducted to determine whether SRN-18 modulates the expression of CXCR4/7, MMP-2/9, and EMT markers in the presence or absence of CXCL12 stimulation. Additionally, our findings revealed that the Wnt/β-catenin signaling pathway is involved in SRN-18-mediated EMT suppression. Since inhibition of the Wnt/β-catenin pathway has been shown to reduce the expression of CXCR4 and CXCR7, SRN-18-mediated suppression of this pathway led to the downregulation of CXCR4- and CXCR7-associated signaling proteins, including NF-κB and JNK. In summary, SRN-18 exerted its anti-EMT effects in colorectal cancer cells by targeting the Wnt/β-catenin signaling axis and its downstream signaling cascades.

The aim of this study was to determine the freezability of ram semen with extenders containing mitoquinone or caffeic acid. Collected ram semen samples were pooled and divided into seven equal aliquots. Each aliquot was diluted with Tris-based extender according to control and antioxidant groups (Control, Mitoquinone (MitoQ) 100 nM, 150 nM, 200 nM; Caffeic Acid (CA) 50 µM, 100 µM, 150 µM). The post-thaw spermatological, antioxidant parameters and OGG1/ROMO1 gene expression and methylation were evaluated. It was determined that the CASA post-thaw motility of MitoQ200, CA100 and CA150 antioxidant groups were statistically higher than the control group (P < 0.05). The post-thaw plasma membrane integrity of MitoQ groups was compared with CA groups, CA100 group, which had the lowest plasma membrane integrity among the antioxidant groups. The post-thaw acrosome membrane damage of all the antioxidant groups were statistically lower than control group, except CA50 and CA100 groups (P < 0.05). For the post-thaw mitochondrial membrane potential, all groups except the CA50 group were determined to be superior to the control group (P < 0.05). No statistical difference was observed among all groups including control group in terms of post-thaw DNA fragmentation, MDA and TAC values. MitoQ significantly altered the expression of the OGG1 genes, an effect mediated through DNA methylation (P < 0.05). Furthermore, caffeic acid altered the ROMO1 gene expression (P < 0.05). Based on the spermatological parameters and gene expression and methylation levels obtained in the current study, it was determined that mitoquinone 200 nM and caffeic acid 150 µM doses had a positive effect on the freezability of ram semen.

Dengue virus (DENV) infection remains a major global health threat. Its incidence is increasing, with frequent outbreaks affecting millions of people each year. Although vaccines are available, their limited effectiveness and the absence of targeted antiviral therapies highlight the critical need for alternative treatment approaches. In this study, we investigated the antiviral activity of bidebiline A and heteropsine, two dimeric aporphine alkaloids isolated from Trivalvaria costata, against DENV-infected Huh7 liver cells. Our findings reveal that heteropsine inhibits DENV production and infection in Huh7 cells more effectively than bidebiline A. Heteropsine also exerts antiviral activity in endothelial and lung cell lines. Mechanistic studies, including time-of-addition assays and molecular docking, elucidate that heteropsine targets early steps during cellular infection, possibly by binding to domain III of the dengue virus envelope protein (EDIII). Viral binding and internalization assays confirmed that heteropsine disrupts viral entry. Furthermore, heteropsine suppresses DENV-induced immunopathogenesis by downregulating the expression of cytokine/chemokine genes (TNF-α, IL-6, RANTES, and IP-10) and attenuating nuclear translocation of the p65 subunit of the nuclear factor-kappaB (NF-κB) transcription factor. These findings highlight the importance of heteropsine as a promising antiviral candidate with the potential for further development to address the urgent need for effective dengue therapeutics.

Small cell lung cancer (SCLC) is a highly aggressive form of cancer, commonly treated with DNA-damaging therapies such as chemotherapy and radiotherapy. Unfortunately, relapse occurs early and frequently, suggesting that epigenetic mechanisms may play a role in this aggressive behavior. Targeting these mechanisms during initial treatment could potentially enhance anti-cancer effects. This study investigated the combination of DNA-damaging treatments with a panel of Epigenetic Chemical Probes (EpiProbes). Among these, MS023, a PRMT inhibitor, showed the greatest synergy with cisplatin and etoposide across various SCLC cell lines. The cytotoxicity of MS023 was correlated with PRMT1 gene expression and protein levels. BioID analysis revealed that many PRMT1 interactors are involved in mRNA splicing. Mechanistic validation demonstrated that MS023 impaired RNA splicing, increased DNA:RNA hybrids, and caused DNA double-strand breaks (DSBs). When combined with ionizing radiation (IR), MS023 significantly increased DSBs, as indicated by γH2AX foci. Additionally, MS023 enhanced the effects of IR and the PARP inhibitor talazoparib, both in vitro and in vivo. Therefore, targeting PRMT1 in combination with DNA-damaging therapies presents a promising strategy to improve treatment outcomes for SCLC.

Melatonin (MT), a neurohormone synthesized and secreted primarily by the pineal gland, is of vital function to animal reproduction. However, the effects of gene expression and metabolism exerted by MT on porcine immature Sertoli cells (iSCs) remain unclear. Here, MT treatment (10 nM, 36h) elevated mitochondrial function and reduced oxidative stress, to promote proliferation and inhibit apoptosis of porcine iSCs. Transcriptome profiling identified 39 differentially expressed genes (DEGs) (33 known and 6 novel) (MT vs. Control), mainly involved in the steroid and glutamine metabolic processes, oxidoreductase activity and G protein coupled receptor binding (GO terms), and steroid biogenesis, pyruvate metabolism and AMPK signal pathways, etc (KEGG pathways). RT-qPCR validated 6 DEGs (Phgdh, Scd, Hmgcs1, Cytb, Pck2 and Sqle), with similar expression pattern to RNA-seq. Metabolomics further showed that 14 metabolites were significantly altered. The HMGCS1 protein abundance and the estradiol level were confirmed to be significantly decreased by MT (10 nM, 36h) treatment, and direct inhibition of HMGCS1 could also significantly reduce the estradiol level. However, levels of cholesterol and lactate were unchanged. Collectively, through integrated transcriptomics and metabolomics analysis, MT is demonstrated to inhibit the HMGCS1-estradiol pathway, to enhance the function of porcine iSCs.

The prevalence of nonalcoholic fatty liver disease (NAFLD) is rising at an alarming rate, making it a major global public health problem. The main pathophysiology of NAFLD is elevated de novo lipogenesis (DNL) in hepatocytes which leads to lipid accumulation. Because of their function in controlling DNL, sirtuin 1 (SIRT1) and AMP-activated protein kinase (AMPK) have been considered viable therapy targets for reduce lipid accumulation.

In recent years, metabolic reprogramming has emerged as a significant breakthrough in elucidating the onset and progression of gastrointestinal (GI) malignancies. As central regulatory hubs for lipid metabolism, sterol regulatory element binding proteins (SREBPs) integrate dietary metabolic signals and carcinogenic stimuli through subtype-specific mechanisms, thereby promoting malignant tumour phenotypes. In this review, we first present the molecular background, structural characteristics, and posttranscriptional regulatory networks associated with SREBPs. We subsequently describe a systematic analysis of the distinct activation patterns of SREBPs in liver, gastric, colorectal, and other gastrointestinal cancers. Furthermore, we explore targeted intervention strategies for different SREBP subtypes, including small molecule inhibitors (such as fatostatin, which inhibits SREBP cleavage), natural compounds (such as berberine, which modulates the AMPK/mTOR pathway), and statin-mediated inhibition of the mevalonic acid pathway. These strategies may enhance tumour cell sensitivity to chemotherapeutic agents (such as 5-FU, gezil, and tabine) and improve the response to synergistic chemoradiotherapy by reversing adaptive metabolic resistance driven by the tumour microenvironment. Through this review, we hope to provide new insights into precise interventions targeting various subtypes of the SREBP molecule.

Chronic non-healing foot ulcers are a major complication in diabetic patients, contributing to significant morbidity and mortality. Microorganisms in these wounds form biofilms, conferring greater virulence and enhanced protection from antibiotics. Hence, we examined naringenin, and other natural compounds like chlorofuranone, 4-nitropyridine N-oxide, and quercetin as a positive control against the major pathogenic organism that forms biofilm in foot ulcers. Here, we focused on Pseudomonas aeruginosa, which produces high levels of biofilm in diabetic foot ulcers. Naringenin (47.10 µg/ml for PA21; 124.7 µg/ml for PA333) and other natural compounds were tested for their ability to inhibit biofilm formation and virulence in vitro, and their effect on biofilm-associated gene expression was studied. The biofilm inhibitory mechanism of naringenin was elucidated using in silico analysis and in vitro reporter gene assay. In vitro biofilm assays, confocal and scanning electron microscopy showed that natural compounds effectively inhibited biofilm, without causing cell death. Treatment with these compounds significantly altered the expression of genes associated with quorum sensing in P. aeruginosa, such as lasR, pslA, algA, gacS, and pelA. Naringenin decreased the production of major virulence factors in P. aeruginosa. Molecular docking showed that naringenin exhibited the strongest binding affinity to LasR, and the same was validated by reporter gene assay using plasmid pSB1142 indicating its role as a competitive inhibitor in the las quorum sensing system in P. aeruginosa. The findings of this study could be extrapolated to in vivo diabetic wound infection models to help optimize the use of naringenin in effective biofilm control for better wound management in diabetic patients.

The incidence of prostate cancer (PCa) is high among elderly men. Cepharanthine hydrochloride (CH) is recognized for its important role in the prevention and treatment of various diseases. However, its effects and mechanisms of action in the context of PCa remain unclear. Our study aims to examine the therapeutic role and mechanisms of action of CH in PCa. Targets of CH and PCa-related genes were identified using different databases, and the biological processes through which CH might exert its therapeutic effects were predicted via protein-protein interaction (PPI) network and enrichment analyses. Subsequently, the PCa cell lines PC-3 and DU145 were used to assess the concentration- and time-dependent effects of CH on cell viability, proliferation, and migration. Transcriptomic sequencing and differential expression analysis were used to identify the key target protein of CH and the key signaling pathways involved in its therapeutic effects against PCa. Molecular docking was used to analyze the binding between CH and its target protein. Additionally, quantitative reverse transcription polymerase chain reaction (qRT-PCR), western blotting, gene knockout, pharmacological intervention, and tumor formation experiments were performed to validate the therapeutic effects and mechanisms of action of CH against PCa in vitro and in vivo. Network pharmacology showed that CH, a Chinese herbal medication, might prevent PCa by regulating protein phosphorylation-related biological processes. In vitro experiments showed that CH inhibited the proliferation and migration of PCa cells in a concentration-dependent manner. In addition, integration of transcriptomic sequencing, differential expression analysis, and GO enrichment analysis suggested that the ERK protein played a crucial role in the anti-tumor activity of CH. Molecular docking and molecular dynamics simulations revealed strong binding affinities between CH and ERK1/2. Further experimental verification, involving qRT-PCR, western blotting, gene knockout, pharmacological intervention, and tumor formation experiments, demonstrated that CH upregulated dual-specificity phosphatase (DUSP) 1 and suppressed the phosphorylation of ERK, thereby inhibiting the development and progression of PCa in vivo and in vitro. In conclusion, the findings of this study suggest that CH suppresses the ERK signaling pathway by enhancing the expression of DUSP1, thereby exerting anti-tumor effects against PCa in vitro and in vivo. Therefore, CH may serve as a novel therapeutic agent for PCa, showing remarkable potential for clinical application.

Compound 5, a cinnamanilide derivative, upregulates brain derivated neurotrophic factor (BDNF) expression but with low soluablity. In this study, PX5-9, a N-oxide derivative of 5, demonstrated significant protective effects in the HT22 glutamate-induced toxicity model and showed no significant toxicity at 30 μM. Western blot analysis confirmed that PX5-9 increased BDNF levels similar to 5. Solubility tests revealed a significant improvement in PX5-9 (37.10 ± 0.33 μg/mL) compared to 5 (< 15 ng/mL). Pharmacokinetic studies of PX5-9 revealed favorable properties, fast absorption and also can be transformated into parent compound 5, suggesting it is a potential candidate for these diseases involving with BDNF. The N-oxide modification might be a good prodrug design to enhance solubility while preserving biological activity.

Anti-angiogenic therapies (AATs) exhibit limited efficacy, as most patients with cancer inevitably develop resistance to them. In this study, data generated using a nasopharyngeal carcinoma orthotopic mouse model, combined with clinical data, reveal compensatory vasculogenic mimicry (VM) formation during AAT treatment and the association of VM with poor prognosis in nasopharyngeal carcinoma. Additionally, data-independent acquisition mass spectrometry-based proteomics shows that upregulation of a disintegrin And metalloprotease 10 (ADAM10) contributes to VM. Mechanistically, epigenetic and high-resolution chromatin interaction landscape analyses demonstrate that although ADAM10 does not interact with either the proximal or distal enhancers, DEAD-box helicase 5 (DDX5), a transcription factor of ADAM10, is regulated by long-range looping enhancer-promoter interactions. Further analyses identify transcription factors binding to critical constituents of the DDX5 super-enhancer. Ingenol mebutate, which docks excellently with DDX5, reverses ADAM10-mediated gene expression changes, thereby effectively suppressing compensatory VM formation and metastasis and improving prognosis. Collectively, these findings provide insights into the clinical application of AATs.

Pancreatic cancer is a highly aggressive gastrointestinal tumor with limited treatment options, such as surgery and chemotherapy. Thus, further research into its pathogenesis and new treatments is necessary.