Metastatic gastric cancer (GC) has a poor prognosis. Recent research demonstrated the aberrant expression of nuclear receptor HNF4α and the regulatory roles of its isoforms during the processes of tumorigenesis and development. However, the expression patterns of HNF4α and its potential as a therapeutic target in metastatic GC remain elusive. In this study, we unveiled that P2 promoter-driven HNF4α (P2-HNF4α) was highly expressed in distant metastasis of GC, playing a pivotal role in fostering the migration and metastasis of GC cells both in vitro and in vivo. The transactivational activity was essential for HNF4α to promote GC cell migration. An integrative analysis of transcriptome and metabolome implied the involvement of the glycolytic pathway in the promotion of GC cell migration by P2-HNF4α. We further found that P2-HNF4α directly bound to the enhancer of the HKDC1 gene and upregulated its expression, thereby orchestrating a metabolic rewiring conducive to promoting GC migration and metastasis. Mycophenolic acid, an active metabolite of the FDA-approved drug mycophenolate mofetil, demonstrated the ability to suppress HKDC1 expression and GC migration and metastasis in vitro and in vivo through antagonizing HNF4α. Therefore, this study sheds light on the HNF4α-HKDC1 axis as a key player in GC metastasis, providing a promising targeted therapeutic strategy for metastatic GC.

Hexanoic acid (Hx) is a naturally occurring fatty acid with antimicrobial properties and potential to induce plant defense responses. This study evaluated the in vitro effect of Hx on Xanthomonas vesicatoria and Xanthomonas euvesicatoria, focusing on bacterial growth and biofilm formation, key factors for pathogen survival and virulence. The obtained results indicate that Hx did not exert a direct lethal effect at low concentrations on bacterial cells, but higher doses (≥ 12 mM) displayed a bactericidal effect against both species, with X. euvesicatoria showing higher sensitivity than X. vesicatoria. Scanning electron microscopy (SEM) revealed cell wall damage and absence of biofilm at ≥ 10 mM Hx, consistent with the quorum sensing (QS) inhibition observed at this concentration. Moreover, exposure to 5 mM Hx triggered a significant increase in reactive oxygen species (ROS), indicating the inability of both bacteria to overcome the toxic environment generated by this compound. In addition, gene expression analysis demonstrated that Hx significantly impaired early biofilm establishment by downregulating motility- and virulence-related genes, particularly evident in X. euvesicatoria from lower concentrations. Although responses differed between the two species in survival strategies and sensitivities to Hx, both converged in a compromised biofilm formation and stress response capacity. Overall, this study provides mechanistic insights into Xanthomonas sensitivity to Hx and highlights biofilm disruption as a central mechanism underlying its antimicrobial activity under in vitro conditions.

Vascular occlusions are a major cause of cardiovascular disease and require interventions including graft bypass surgery; yet, the development of synthetic vascular grafts remains a challenge due to the inability of synthetic biomaterials to support an anti-immunogenic endothelium. Topographical micropatterning of biophysical cues offers a promising strategy to enhance graft endothelialization. As the interface between the biomaterial and blood, endothelial cells provide a bioactive interface which regulates inflammation. We utilized topographical micropatterning of polyurethane biomaterial to induce endothelial cell elongation and alignment and measured the resultant transcriptional changes using bulk RNA-sequencing. Cell phenotype was characterized by gene and protein expression as well as chemokine secretion. The biomaterial micropatterning-modulated elongated and aligned morphology promoted an anti-inflammatory transcriptome, reduced pro-inflammatory chemokine secretion, and induced the transcription coregulator yes-associated protein (YAP) phosphorylation, supporting the anti-immunogenic properties of endothelial cells. Cytoskeletal regulation of this anti-immunogenic phenotype was quantified through measurement of intermediate filament vimentin regulation of YAP localization and endothelial pro-immunogenic gene expression. Aggregation of vimentin was positively correlated with YAP dephosphorylation and suppressed proinflammatory gene expression, indicating that endothelial elongation and alignment influence gene regulation and cellular function independent of vimentin-mediated mechanisms. The ability of micropatterned endothelial cells to maintain their anti-immunogenic functions under pro-inflammatory conditions was demonstrated by the increased phosphorylation of YAP and decrease in pro-inflammatory IL-8 release. Our study highlights the potential of biomaterial cues to regulate endothelial cell behavior for vascular graft design. STATEMENT OF SIGNIFICANCE: We used topographical micropatterning to separate the role of endothelial monolayer morphology from unidirectional blood flow and test how architecture alone regulates gene programs. Micropatterned substrates produced a reproducibly elongated, aligned endothelium with coordinated modeling of the vimentin intermediate filament network. Bulk transcriptomics revealed a distinct morphology-associated expression state, including reduced inflammatory signaling and altered secretory profiles, alongside shifts in mechanosensitive regulatory programs and downstream transcriptional signatures. Together, these findings link cytoskeletal organization to endothelial mechanotransduction and highlight biomaterial topography as a design lever to tune endothelial function for preclinical and clinical applications.

Cellular stresses regulate transcriptional readthrough, whereby RNA polymerase II elongates past a gene's polyadenylation cleavage site without RNA cleavage. Readthrough has been reported in several cancer types. Here, we use long-read sequencing of nascent RNA to quantify transcriptional readthrough in chronic myeloid leukemia (CML) cells and characterize early responses to the targeted therapeutic, imatinib. We show that the amount, length, and gene specificity of readthrough increase within 1 hour, before gene expression and alternative splicing alterations emerge. Notably, imatinib-dependent messenger RNA (mRNA) isoform changes involved "readthrough chimeras," in which exons from an upstream gene are alternatively spliced to exons in a downstream gene. Altered mRNA isoforms and chimera levels were detected in imatinib-resistant K562 cells as well as cells of patients with CML. Thus, imatinib can provoke a cascade of early changes to transcription and splicing fidelity that may lead to longer-term adjustments in gene expression, cancer cell differentiation, and the development of therapy resistance.

Preoperative systemic chemotherapy plays a crucial role in enhancing the outcomes of patients with locally advanced esophageal squamous cell carcinoma (ESCC). Andrographis (major bioactive diterpenoid lactone isolated from Andrographis paniculata; PubChem ID: 5318517), a safe and cost‑effective dietary compound, has demonstrated antitumor effects against various gastrointestinal adenocarcinomas. However, its impact on squamous cell carcinoma remains unclear. The present study explored the antitumor effects of Andrographis and its potential to augment the antitumor efficacy of 5‑fluorouracil (5‑FU). A series of in vitro experiments was conducted, including cell proliferation, colony formation and apoptosis assays, using the ESCC cell lines KYSE410 and TE1. Compared with the controls, Andrographis significantly inhibited cell proliferation (P<0.05), suppressed colony formation (P<0.05), induced apoptosis (P<0.05), and upregulated the expression of ferroptosis‑related genes and proteins, such as HMOX1 (P<0.01), GCLC (P<0.05) and GCLM (P<0.001). Notably, even at a sub‑IC50 dose of 5‑FU, its combination with Andrographis resulted in additive antitumor effects (P<0.05) and further upregulation of ferroptosis‑related gene expression, particularly HMOX1 (P<0.05), compared with either mono‑treatment. The findings of the present study indicate that Andrographis exerts antitumor effects and enhances the efficacy of 5‑FU in ESCC by activating both apoptosis and ferroptosis, suggesting its potential as an adjunctive therapy for ESCC to improve efficacy and reduce 5‑FU dosage and toxicity.

Exposure to waste anesthetic gases (WAGs) is an underestimated occupational hazard in veterinary operating rooms (VORs), where insufficient ventilation and the absence of scavenging systems remain common worldwide. Veterinarians occupationally exposed to WAGs have been poorly investigated to date. Addressing this critical gap, we present the first integrative study evaluating circulating microRNAs (miRNAs), global DNA methylation, and urinary anesthetic quantification in veterinarians occupationally exposed to WAGs isoflurane and sevoflurane. In a case-control design, plasma profiling revealed 11 dysregulated miRNAs in the exposed group (n = 29) compared to the control group (n = 28) based on nominal p-values (p < 0.05), as part of an exploratory screening approach, including seven upregulated miRNAs meeting a predefined fold-change criterion (FC≥1.5). Among these, hsa-miR-1252-5p and hsa-miR-520f-3p showed robust discriminatory performance based on Receiver Operating Characteristic (ROC) curve analysis (AUC≥0.70). Functional enrichment analysis highlighted epigenetic regulators as major network hubs. For hsa-miR-1252-5p, hubs included EP300, TP53, CREBBP, HDAC1 and SIRT1, linking miRNAs modulation to histone acetylation/deacetylation, DNA damage response, apoptosis, and stress regulation. For hsa-miR-520f-3p, included MAPK1, TNRC6B, MECP2 and KMT2A, associated with cell signaling pathways, proliferation and epigenetic regulation. Global DNA methylation levels did not differ significantly between groups, suggesting that exposure under the evaluated conditions may not trigger genome-wide alterations. Occupational exposure was confirmed by urinary quantification of isoflurane and sevoflurane, indicating highly polluted workplaces. In conclusion, although global DNA methylation remained unchanged, WAG exposure was associated with modulation of circulating miRNAs, and our findings suggest that hsa-miR-1252-5p and hsa-miR-520f-3p emerge as potential biomarkers of effect associated to WAG occupational exposure in veterinarians who work in inadequately equipped VORs.

Evidence suggests that environmental exposures induce epigenetic modifications that can have long-lasting effects on multiple health outcomes, and an in-depth review of the epidemiological evidence is urgent. We aimed to comprehensively assess the associations between long-term exposure to air pollution and epigenetic changes in adults.

SUMOylation regulates chromatin states and transcriptional programs that preserve cellular identity, yet how perturbation of the SUMOylation pathway impacts adipocyte plasticity remains unclear. Here, we show that brief pharmacologic inhibition of SUMOylation in human pre-adipocytes using TAK-981 primes stable de novo beige differentiation in the presence of the PPARG agonist rosiglitazone. Transient TAK-981 exposure produces changes in the transcriptome and metabolism of mature adipocytes, including robust induction of canonical beiging markers like UCP1 and increased mitochondrial respiration. Mechanistically, ATAC-seq and RNA-sequencing revealed immediate chromatin remodeling and early mobilization of CEBP family members, followed by stable activation of CEBPA and PPARG regulatory networks. ChIP experiments demonstrated loss of H3K27me3 and gain of H3K27ac at PPAR response elements at thermogenic enhancers, and increased PPARG occupancy across the UCP1 regulatory unit. This mechanism is enforced by enhanced cAMP-PKA-p38 signaling and stabilization of beiging transcription activators. We propose that transient relief of SUMO-mediated repression unlocks dominant regulatory units, notably the UCP1 enhancer cluster, producing a monomorphic reprogramming toward adaptive thermogenesis. These findings identify SUMOylation as a reversible epigenetic barrier to adipocyte beiging and suggest that temporally controlled SUMO pathway inhibition combined with PPARG activation could be exploited to modulate adipose tissue thermogenic capacity.

The oomycete Phytophthora capsici causes Phytophthora blight, a major constraint on global pepper production. Our previous observations indicated that pretreating plants with thiamethoxam (TMX) and imidacloprid (IMI) could reduce the incidence of pepper blight, but the underlying mechanisms remained unclear. Here, we investigated how TMX and IMI induced resistance in pepper (Capsicum frutescens) against P. capsici. Both in vitro and in vivo assays demonstrated that TMX and IMI suppressed disease, not by directly impairing pathogen virulence but by inducing systemic resistance in susceptible (Cusheng L09) and resistant (Cusheng 356) pepper cultivars. Split-plant systemic resistance assays showed that TMX/IMI-primed plants developed smaller lesions in both treated and untreated leaves following P. capsici infection. Foliar application of TMX and IMI effectively alleviated disease severity, with IMI showing superior efficacy in attenuating reactive oxygen species (ROS) accumulation, and TMX/IMI priming concomitantly altering the activities of ROS-scavenging enzymes under pathogen challenge. Reverse transcription-quantitative PCR analysis revealed time-dependent changes in defence gene expression, and whole-genome transcriptome profiling highlighted temporal reprogramming of pathogenesis-related genes. Further functional validation identified CaNEN4 as a susceptibility factor. Collectively, our findings reveal that IMI/TMX primes pepper plants with systemic resistance by modulating ROS homeostasis, defence gene expression, and susceptibility gene function, offering novel insights into chemical-induced plant immunity and genetic targets for durable blight resistance in crops.

EGFR, one of the most successful therapeutic targets, has recently been found to exert a novel function for regulating homologous recombination (HR). Activation of HR is the critical event of treatment failure of PARPi in BRCA1/2 wild-type ovarian cancer (OC). Besides, the antitumor effects of biguanides have also been a focus of attention. Here, we discovered that the new biguanide 4C inhibited HR and sensitized BRCA1/2 wild-type OC cells to PARPi by targeting EGFR. Mechanistically, EGFR promoted nuclear accumulation of both BRCA2 and Rad51, and HR activation by competitively inhibiting the binding of BRCA2 and Rad51 to E3 ubiquitin ligase c-Cbl, thereby reducing cancer cell sensitivity to PARPi following ATM-mediated DNA damage signal transmission from the nucleus to the cytoplasm. Interestingly, EGFR was downregulated by 4C, which in turn enhanced the interaction of BRCA2 and Rad51 with c-Cbl. Consequently, BRCA2 and Rad51 were then ubiquitinated and degraded to inhibit HR and increase the sensitivity of OC to PARPi. Thus, these findings reveal that the combination of 4C with PARPi leading to "synthetic lethality" is an effective strategy for treating BRCA1/2 wild-type OC.

Children with favorable-histology Wilms tumor (FHWT) who relapse or whose tumors show blastemal predominance post-chemotherapy often face poor outcomes. The purpose of this study is to identify mechanisms of chemotherapy resistance in FHWT. We induce a patient-derived xenograft model (KT-47) to develop blastemal predominance after chemotherapy and to become resistant to vincristine, actinomycin-D, and doxorubicin (VAD). Multi-omics analyses reveal chromatin and transcriptional changes, including increased H3K4me3 and decreased H3K27me3 at stem cell and nephrogenesis gene loci. LIN28B is the most upregulated resistance-associated gene, linked to MYCN copy gain/upregulation and chromatin remodeling. ABCB1 expression correlates with interchromosomal enhancer interactions and functions as the mediator of chemotherapy resistance in vitro. These findings are validated in additional Wilms tumor models. Overall, resistance is associated with de-differentiation to a stem-like state and is driven by ABCB1 upregulation, suggesting that therapeutic strategies targeting chromatin regulation and drug efflux may be relevant in therapy-resistant Wilms tumor.

Eradicating leukemia stem cells (LSCs) and overcoming tyrosine kinase inhibitor (TKI) resistance is urgent for chronic myeloid leukemia (CML) treatment. We find that F-box protein 3 (FBXO3) is highly upregulated in CD34+ CML stem cells from TKI-resistant patients and identify it as an innovative CML-LSC marker via single-cell RNA sequencing (scRNA-seq). FBXO3 deficiency induces apoptosis and reduces proliferation of CML cell lines and LSCs in vitro and in vivo, with minimal effects on normal CD34+ hematopoietic stem cells (HSCs). Mechanistically, FBXO3 interacts with DUSP9 to promote its ubiquitination and activate the MAPK pathway, critical for CML cell activity. DUSP9 knockdown partially reverses FBXO3-deficiency-mediated LSC elimination. Furthermore, FBXO3 inhibitor monotherapy or combination with imatinib effectively eradicates CML-LSCs, overcomes TKI resistance, and spares normal hematopoiesis. Collectively, our findings highlight FBXO3's role in CML progression and support combining FBXO3 inhibitors with TKIs for durable LSC elimination.

Antimicrobial resistance (AMR) poses a serious threat to global public health. To tackle this challenge, identifying novel effective antibacterial targets and antibiotics is crucial. The serine kinase HPrK, widely present in gram-positive bacteria and mycoplasmas, primarily regulates carbon metabolism and virulence factor expression. In a previous study, we failed to knockout the hprK gene using the conventional homologous recombination method in the zoonotic Streptococcus suis. Here, we employed an anhydrotetracycline (ATc)-inducible promoter (AiP) and hprK fusion to replace its original expression cassette in the S. suis genome. However, in the absence of ATc, mutations in the AiP elements resulted in ATc-independent expression of HPrK, suggesting that HPrK is essential for S. suis and a potential antimicrobial target. Accordingly, a high-throughput inhibitor screening assay based on the kinase activity of HPrK was designed, and an inhibitor compound CDK9-IN-2 was identified. Molecular docking and bio-layer interferometry revealed that CDK9-IN-2 targets highly conserved residues D242, D249, and N281 on HPrK protein in several species of gram-positive bacteria. CDK9-IN-2 exhibited significant antibacterial effects against multidrug-resistant S. suis clinical isolates and various species of gram-positives and mycoplasmas with a minimum inhibitory concentration (MIC) of 16 to 32 μg/mL. Its therapeutic effect on S. suis infection was further proved in a Galleria mellonella larval infection model. Collectively, HPrK is a conserved kinase in gram-positives and mycoplasmas, and its essentiality is confirmed in S. suis. Based on this conserved target HPrK, an inhibitor with a broad antibacterial activity has been identified, suggesting HPrK is a promising antimicrobial target for antibacterial drug innovation.

Glioblastoma (GBM) is a fast-growing primary brain tumor with high mortality and recurrence rates. Dysregulation of the cell cycle is a hallmark of GBM, and cyclin B1 (CCNB1) is a key regulator of the cell cycle. However, the role of CCNB1 in GBM remains unclear. In this study, we found that CCNB1 mRNA and protein expression levels were significantly higher in GBM tissues than normal tissues. High CCNB1 mRNA expression was associated with poorer prognosis in GBM patients. Single-cell and spatial transcriptomics data revealed that CCNB1+ cells represent a proliferative subcluster in GBM, annotated as proliferative cells, and characterized by the upregulation of cell cycle-related pathways. CCNB1 inhibition decreased the proliferation of GBM cells and impaired cell cycle progression from S phase to G2/M. Additionally, resveratrol could inhibit the expression of CCNB1 and its interacting gene polo-like kinase 1 (PLK1). Importantly, through in vitro and in vivo experiments, we found that resveratrol suppressed GBM cell growth with low toxicity. CCNB1 silencing combined with resveratrol treatment further inhibited the proliferation of GBM cells. Collectively, these data suggest that CCNB1 is highly expressed in GBM and may promote GBM progression. Inhibition of CCNB1 may represent a potential therapeutic strategy for GBM.

Natural products are a rich sources for developing anti-cancer drugs with low toxicity and high efficiency. Limonin has anti-cancer activity; however, its effect on cervical squamous cell carcinoma remains unreported. The aim of this study was to explore how Limonin affects ferroptosis in cervical squamous cell carcinoma (CESC) and its underlying mechanism. Based on differential gene analysis of the Gene Expression Omnibus database and drug target prediction of the Comparative Toxicogenomics Database, combined with molecular docking technology, potential anti-cancer targets of Limonin were identified. In vitro experiments were conducted to create epoxide hydrolase 2 (EPHX2) knockdown and overexpression cell lines. Relevant phenotypic experiments were conducted to verify how Limonin targeting EPHX2 affects cell proliferation and ferroptosis. Integrated bioinformatic analysis revealed EPHX2 as a key target of Limonin. Functional experiments showed that EPHX2 overexpression inhibited the proliferation of CESC and induced ferroptosis, while Limonin treatment could enhance EPHX2 expression in a concentration-dependent manner. Furthermore, EPHX2 knockdown could reverse the inhibitory effect of Limonin on CESC proliferation and alterations in ferroptosis-related indicators. This study results reveals a new mechanism by which Limonin induces ferroptosis in CESC by activating EPHX2, providing a new strategy for natural compound-based ferroptosis-targeted therapy.

Artificial control of gene expression in bacteria offers interesting prospects for influencing bacterial pathogenicity and antibiotic resistance. We show that the methyl-transferase cofactor, AdoHcy azide, can silence gene expression in modified plasmids in some strains of Escherichia coli, where ampicillin and kanamycin resistance as well as eGFP genes were selectively and independently disabled. The disabling of transcription is likely due to steric inhibition during transcription initiation, which is supported by Sanger and nanopore sequencing results. Both sequencing methods showed that 3-6 nucleotides were absent from around the modification site. Postgrowth, extracted AmpR/eGFP plasmid shows evidence of restriction, with sections of the plasmid, including the modification site, missing for the AdoHcy azide modified plasmids. Notably, the AdoHcy azide modification on the DNA appears to be resistant against demethylation in the BL21 strain of E. coli.

Chemotherapy-induced neutropenia (CIN) remains a major dose-limiting toxicity associated with myelosuppressive chemotherapy regimens. The development of therapeutic strategies capable of effectively restoring neutrophil production and function could address a critical unmet clinical issue. ZGSII, a bioactive compound derived from Sanguisorba officinalis, has shown potential in ameliorating leukopenia. To further evaluate its therapeutic applicability for CIN, a comprehensive understanding of its underlying mechanisms is essential. This study aims to assess the efficacy of ZGSII in mitigating cyclophosphamide-induced neutropenia and myelosuppression and to elucidate the underlying mechanism involved through transcriptome sequencing, protein-protein interaction network construction, and functional validation assays.

Bortezomib, a first-in-class proteasome inhibitor, is widely used to treat multiple myeloma and other hematological malignancies. Despite its therapeutic efficacy, bortezomib causes peripheral neuropathy (PN) in approximately 20-30% of patients, often leading to dose reduction or discontinuation. Preventive or therapeutic approaches to bortezomib-induced PN are currently unavailable, as its precise mechanism remains unclear. In this study, we compared the effects of bortezomib and the second-generation proteasome inhibitor carfilzomib on peripheral nerve cells to identify candidate molecules involved in PN development. Transcriptome profiling of differentiated F11 cells, a hybridoma of a rat embryonic dorsal root ganglion and mouse neuroblastoma cell line N18TG2, revealed that bortezomib selectively upregulated α/β-hydrolase containing domain 4 (Abhd4), whereas carfilzomib did not. This finding was confirmed by quantitative RT-PCR and immunoblotting, which demonstrated consistent increases in Abhd4 mRNA and protein levels following bortezomib treatment. Functional analysis further revealed that Abhd4 overexpression promoted early apoptosis, suggesting a mechanistic link between bortezomib-induced Abhd4 elevation and neuronal vulnerability. Therefore, these results suggest that Abhd4 represents a candidate molecular signature associated with bortezomib-induced PN. Although further in vivo validation is needed, these findings warrant further investigation of Abhd4 as a potential contributor to bortezomib-induced PN.

Coffee silverskin (CSS), the major by-product of coffee roasting, is reported to contain bioactive compounds, including xanthines and polyphenols, showing promising potential for food and nutraceutical applications. This study investigated the beneficial effects of CSS hydroalcoholic extracts, which were chemically characterized by Attenuated Total Reflectance-Fourier-Transform Infrared Spectroscopy and ElectroSpray Ionization tandem Mass Spectrometry, on Caenorhabditis elegans physiology. CSS supplementation improved healthspan-related parameters and delayed aging-associated functional decline, without significantly extending lifespan in wild-type nematodes. Treated worms exhibited a 57% reduction in reactive oxygen species (ROS) levels and upregulation of antioxidant genes (gst-4 and sod-3), suggesting that CSS mitigates oxidative stress through the DAF-2/DAF-16 pathway. Under high-glucose diet conditions, CSS reduced lipid droplet accumulation and modulated the expression of metabolic genes, including upregulation of nhr-49 which is a key regulator of fatty acid oxidation. CSS restored lipid homeostasis and rescued the shortened lifespan of obese nhr-49 mutant worms, suggesting enhanced β-oxidation. Moreover, CSS modulated serotonergic signaling by increasing tph-1 and ser-6 expression, linking its effects to serotonin-mediated regulation of fat metabolism. Finally, CSS promoted the growth of probiotic strains, suggesting potential prebiotic properties. Overall, these findings identify CSS as a metabolic modulator capable of alleviating oxidative and metabolic stress, supporting its sustainable application in the development of functional foods and nutraceuticals.

Bromodomain (BRD)-containing proteins are gaining attention as key targets in epigenetic drug development. BRDs bind to acetylated lysine residues on histones and other proteins, significantly impacting transcriptional regulation and chromatin remodeling. As our grasp of bromodomain structures and biochemistry deepens, the momentum behind developing small-molecule inhibitors for these BRD domains is triggered and potent inhibitors targeting different family members of BRDs are proposed. In addition, computational simulations have also played a significant role in advancing inhibitor design for the BRD family. This review delves into recent breakthroughs in small-molecule BRD receptor inhibitors and computational studies, spotlighting their biological impact and therapeutic potential, and outlining the research road ahead. This review is expected to provide guidance for future drug design of BRD inhibitors.