Search Results (1,794)

Kansui Radix, the root of Euphorbia kansui, was first described in Shen Nong Ben Cao Jing as a traditional Chinese medicine, known for its effects of expelling water, reducing edema, and dissipating masses. It is traditionally indicated for conditions such as “watery accumulation” and “abdominal masses (zheng-jia)”, which share certain similarities with the clinical manifestations of renal cell carcinoma (RCC), including renal masses, edema, and body cavity effusion. Despite the recognized antitumor effects of Kansui Radix, the pharmacological basis and specific molecular mechanisms underlying its inhibition of RCC progression remain unclear. The goal of this study was therefore to evaluate the antitumor efficacy of Kansui-DCM in RCC and to explore its potential mechanism. To this end, the chemical composition of the dichloromethane fraction of Kansui Radix (Kansui-DCM) was characterized by UPLC-MS. The antiproliferative effects of Kansui-DCM on 786-O and RENCA cells were evaluated using the CCK-8 assay. Apoptotic morphology, apoptosis rate, cell migration and invasion abilities were assessed. An RCC mouse model was established, and tumor growth and histopathological staining were evaluated after drug administration. Immunohistochemistry, transcriptomic analysis, WGCNA (weighted gene co-expression network analysis), network pharmacology, and immunofluorescence were employed to investigate the molecular pathway. Protein and gene expression were analyzed by Western blot and qRT-PCR, respectively. Finally, the interactions between the active components and key targets were substantiated through molecular docking and molecular dynamics simulations. A total of 1397 compounds were detected in Kansui-DCM by UPLC-MS. In vitro experiments demonstrated that Kansui-DCM inhibited the proliferation of 786-O and RENCA cells in a dose-dependent manner, induced apoptosis, and suppressed cell invasion and migration in RENCA cells. Treatment with Kansui-DCM markedly suppressed tumor growth in vivo, as reflected by a reduction in tumor volume. Immunohistochemical analysis indicated that the expression levels of CD31, COX-2, and Ki67 were markedly decreased, while the expression level of CD8 was significantly increased. Integrated analysis using WGCNA and network pharmacology predicted that Kansui-DCM may exert its effects through the regulation of the HIF/VEGF signaling pathway, which was further validated by immunofluorescence, Western blot, and qRT-PCR assays. Molecular docking and molecular dynamics simulations demonstrated stable interactions between multiple active components of Kansui-DCM and key targets such as VEGFR2 and HIF-2α. In conclusion, these findings suggested that Kansui-DCM exerts anti-RCC effects associated with regulation of the HIF/VEGF pathway. Full article

Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract and are usually driven by activating mutations in KIT or PDGFRA. Although these alterations define the core molecular biology of GISTs and guide targeted therapy, they do not fully explain the variability observed in tumor behavior, recurrence risk, or response to tyrosine kinase inhibitors. Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), have been increasingly studied as regulators of gene expression in GISTs. Recent evidence suggests that these molecules may influence KIT-centered signaling, autophagy, apoptosis, invasion, angiogenesis, and drug resistance. However, the strength of evidence differs considerably across individual ncRNAs, ranging from bioinformatic associations to functional validation in cell lines and in vivo models. This review summarizes current knowledge on ncRNA-mediated regulation in GIST biology, with emphasis on tumor progression, therapeutic resistance, and possible clinical relevance. Rather than treating ncRNAs as isolated biomarkers, they function as part of broader regulatory networks that interact with oncogenic signaling and epigenetic mechanisms. Although several ncRNAs appear promising as prognostic or predictive candidates, further validation in independent clinical cohorts is required before their integration into routine risk stratification or treatment decision-making. Full article

Background/Objective: Cinnamaldehyde (CA) is a naturally occurring bioactive compound derived from the leaves, bark, roots, and flowers of the Chinese medicinal plant Cinnamomum cassia. It exhibits a broad spectrum of pharmacological properties, encompassing antioxidant, antibacterial, anti-diabetic, antifungal, and anticancer activities. Notably, it has shown potential therapeutic benefits in the management of type 2 diabetes mellitus (T2DM) and non-alcoholic fatty liver disease (NAFLD). Ochratoxin A (OTA), a common contaminant found in foods such as cereals, coffee, and raisins, is also present in traditional Chinese medicinal materials, including Astragalus and liquorice. T2DM and NAFLD share intertwined pathophysiological pathways, including insulin resistance, dyslipidaemia, chronic low-grade inflammation and oxidative stress, with insulin resistance serving as the common pathological hub for both conditions. Consequently, they frequently co-occur and exacerbate each other. OTA exerts dual-targeted toxicity to the pancreas and liver, which may synergistically drive the development of the comorbidity of T2DM and NAFLD. These two processes are mutually causal and together constitute the pathological basis of metabolic comorbidity. Methods: Network toxicology employs toxicological data, gene expression, and protein–protein interaction (PPI) networks to predict the targets of toxins, while network pharmacology, based on systems biology principles, reveals how drugs exert regulatory effects through multiple targets and pathways. In this study, we employed an integrated network toxicology and network pharmacology approach to jointly decipher the potential mechanisms by which CA intervenes in OTA-induced comorbid T2DM-NAFLD. First, a network toxicology approach was employed to preliminarily screen for core toxicological targets responsible for OTA’s pathogenicity. Subsequently, network pharmacology was used to identify potential targets of CA-mediated intervention in the disease. Finally, the common overlap among the CA intervention targets, OTA toxicity targets, and disease targets was defined as the final set of potential targets for CA-mediated intervention in OTA-induced T2DM-NAFLD comorbidity. A PPI network was constructed using the STRING database, and topological analysis was performed with Cytoscape. Core targets were selected using the median values of six parameters—betweenness centrality, closeness centrality, degree centrality, eigenvector centrality, LAC (local average connectivity) score, and network centrality—as cut-off thresholds, and the top 10 key genes were further identified using the cytoHubba plugin. Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted via the DAVID database, and the results were visualized on the CNSknowall platform. Lastly, molecular docking of the core targets was performed using the CB-DOCK2 platform to validate binding affinity. Results: Based on an integrated analysis of network toxicology, network pharmacology, and molecular docking, 10 key targets were systematically identified. These may serve as potential mediators of cinnamaldehyde in the treatment of OTA-induced T2DM-NAFLD comorbidity. Among these, six targets—albumin (ALB), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), interleukin-6 (IL-6), tumor necrosis factor (TNF), actin beta (ACTB), and estrogen receptor 1 (ESR1)—possess crystal structures amenable to molecular docking. KEGG enrichment analysis revealed that CA and OTA jointly participate in key pathological processes such as the cancer pathway, the lipid and atherosclerosis pathway, the advanced glycation end-products–receptor for advanced glycation end-products (AGE-RAGE) signaling pathway, the phosphatidylinositol 3-kinase–protein kinase B (PI3K-Akt) signaling pathway, the TNF signaling pathway, and the interleukin-17 (IL-17) signaling pathway. OTA exacerbates inflammatory responses, impairs insulin signaling, promotes hepatic steatosis, and disrupts systemic metabolic homeostasis, ultimately contributing to T2DM-NAFLD comorbidity. Conversely, cinnamaldehyde counteracts these pathological processes through multiple mechanisms, including antioxidant and anti-inflammatory effects as well as regulation of glucose and lipid metabolism, thereby restoring metabolic homeostasis. Conclusions: This study has preliminarily identified the toxicological targets of OTA and the potential intervention targets of CA, offering new avenues for preventing and intervening in OTA-induced metabolic toxicity. Furthermore, it provides a theoretical basis for CA as a potential multi-target therapeutic agent and presents novel insights worthy of further investigation into the prevention of T2DM-NAFLD comorbidity. Full article

Background: Ankylosing Spondylitis (AS) and inflammatory bowel disease (IBD) exhibit substantial pathophysiological overlap, including dysregulated innate immunity, barrier dysfunction, and Th17-mediated inflammation. However, whether Na⁺ overload-related genes (NRGs) exhibit shared transcriptional alterations in IBD and AS remains unclear. This study aimed to characterize the expression patterns of NRGs across IBD and AS and to identify candidate genes associated with both diseases. Methods: Differential expression analysis was performed to identify differentially expressed NRGs (DE-NRGs) in diseased tissues relative to normal tissues. Shared DE-NRGs between IBD and AS were screened and defined as common differentially expressed NRGs (Co-DE-NRGs). We then analyzed the correlations of these Co-DE-NRGs and explored their relationships with immune cell infiltration in target tissues. Four machine learning algorithms were applied to screen key NRGs associated with both IBD and AS. Potential therapeutic agents targeting these core biomarkers were predicted using drug–gene interaction databases, and molecular docking was conducted for further validation. Results: A total of 32 shared Co-DE-NRGs were identified for IBD and AS, with nine key regulatory NRGs recognized: CALR, CD63, CYBA, DYSF, HYOU1, IL1B, JAK1, MMP9, and STAT3. Exploratory MR analysis identified disease-specific associations between genetically predicted expression of NRGs and CD, UC, and AS. Genetically predicted STAT3 expression showed positive associations with CD and UC but an inverse association with AS and therefore did not represent a consistent risk factor across the three diseases. Furthermore, transcriptome-based drug-response analysis identified four candidate agents shared between AS and at least one IBD dataset: ciclosporin, BCL-LZH-4, BRD-K79669418, and CID-5951923. Exploratory molecular docking generated STAT3 binding poses for BCL-LZH-4 and CID-5951923, with DOCK Grid Scores of −35.321896 and −28.361128, respectively. CID-5951923 was selected for representative visualization of its predicted interaction with STAT3. Single-cell RNA-sequencing analysis identified tissue- and cell-type-specific STAT3 mRNA expression patterns in the analyzed IBD colonic and AS peripheral-blood datasets, with monocytes representing a major cell population exhibiting detected STAT3 expression in the AS dataset. Conclusions: These findings identify shared NRG-related transcriptional alterations in IBD and AS, with STAT3 emerging as a candidate gene associated with both diseases. Further experimental studies are required to determine whether these alterations reflect the involvement of NECSO and to evaluate their potential diagnostic or therapeutic relevance. Full article

Background/Objectives: Zoonotic tuberculosis (TB) remains a persistent public health challenge worldwide. It is particularly common in settings with close human–livestock–environment interactions. In Tanzania, progress toward TB control is increasingly threatened by multidrug-resistant tuberculosis (MDR-TB), yet genomic data from regions characterized by pastoralist and mining activities remain scarce. This study employed whole-genome sequencing (WGS) to characterize M. tuberculosis complex (MTBC) strains circulating among human and cattle populations in the Manyara region of northern Tanzania, with a focus on resistance-associated mutations and phylogenetic relationships. Methods: This cross-sectional study was conducted between September 2024 and February 2025. A total of 178 presumptive human TB cases provided sputum samples. From cattle, 161 samples were collected (110 milk samples and 51 lymph node aspirates), with each animal contributing only one type of sample. Specimen were analyzed using GeneXpert MTB/RIF, Lowenstein–Jensen culture, and WGS. Phylogenetic reconstruction was performed using SNP-based methods and IQ-TREE2 version 2.2.0. Results: Among human participants, 14 (7.8%) sputum samples were GeneXpert positive and were confirmed as members of MTBC by LJ culture. In cattle, one (0.62%) lymph node aspirate was positive for MTBC. Significant predictors of MTBC positivity included previous TB history, weight loss, and occupation involving mining and cattle keeping. WGS of five human isolates identified Lineages 1, 3, and 4. One isolate (Sample 98) harbored mutations associated with XDR-TB. Conclusions: WGS revealed M. tuberculosis Lineages 1, 3 and 4 circulating in the Manyara region, with diverse genetic mutations conferring with resistance to first- and second-line anti-TB drugs. These findings highlight the importance of integrated genomic surveillance to monitor drug resistance patterns in Tanzania and similar settings across human and animal populations. Full article

Endophytic bacteria from medicinal plants are increasingly recognised as sources of antimicrobial metabolites. However, the endophytic bacterial community of Mitrephora heyneana remains poorly explored. In the present study, endophytic bacteria were isolated from the leaves of M. heyneana, collected from the Western Ghats of Tamil Nadu, India. Among seven isolates, the plant endophyte strain from leaf 6th strain (PEL6) was identified as Paenibacillus lactis through 16S rRNA gene sequencing. The ethyl acetate extract of PEL6 (EAE-PEL6) was subjected to gas chromatography–mass spectrometry (GC-MS) analysis, which putatively identified 32 metabolites based on GC-MS library matching, including pyrrolo [1,2-a] pyrazine-1,4-dione derivatives and triazole compounds as major constituents. The EAE-PEL6 demonstrated significant in vitro antibacterial activity against Staphylococcus aureus. In silico ADMET (absorption, distribution, metabolism, excretion, and toxicity), profiling predicted drug-likeness and pharmacokinetic properties of selected candidate compounds. Molecular docking suggested favourable binding of selected metabolites to S. aureus target proteins; however, these interactions require experimental validation. Density Functional Theory calculations indicated that CID 70504 had the lowest Highest Occupied Molecular Orbital (HOMO)–Lowest Unoccupied Molecular Orbital (LUMO) energy gap, reflecting higher electronic reactivity. Molecular electrostatic potential mapping further supported its enhanced binding propensity. Molecular dynamics simulations suggested structural stability, with Root Mean Square Deviation, Solvent Accessible Surface Area, radius of gyration, and hydrogen-bond analyses indicating stable interactions throughout the 100 ns trajectory. Overall, this study identifies P. lactis PEL6 as a promising endophytic source of anti-S. aureus metabolites and provides candidates for future purification, structural confirmation, and biological validation. Full article

Triple negative breast cancer (TNBC) continues to have a poor prognosis relative to other forms of this disease. Previous studies have shown that the HOX family of transcription factors generally show increased expression in breast cancer and may have a primarily pro-oncogenic role. In this study, we assessed the sensitivity of a range of TNBC-derived cell lines to an inhibitor of HOX protein function, HTL-001, which blocks the interaction between HOX proteins and the Pre-B-cell Leukaemia Homeobox (PBX) cofactor. The sensitivity of cell lines was measured by MTS viability assays, and gene expression by RT-qPCR. Combination studies were performed with epigenetic modifiers (5-azacytidine (5-aza), Trichostatin A (TSA)) and standard-of-care chemotherapeutic drugs including Paclitaxel. A mouse tumour flank model of MDA-MB-231 cells was used to assess response to HTL-001, paclitaxel, or combination therapy. All the cell lines exhibited high levels of HOX dysregulation compared to an immortalised line derived from normal breast cells, and greater sensitivity to HTL-001-induced apoptosis. Epigenetic changes have previously been shown to be key modulators of HOX expression and, correspondingly, we show that reversing epigenetic changes in these cell lines significantly alters HOX expression and generally reduces sensitivity to HTL-001. In addition, HTL-001 shows synergistic interactions with several established chemotherapeutic agents in vitro. We further demonstrate that HTL-001 can significantly reduce tumour growth in a mouse model of TNBC. Our findings indicate that HOX/PBX dimers are a potential therapeutic target in this cancer. Full article

Ethanol (EtOH)-induced gastric ulcer (GU) is a common model used to investigate mechanisms of mucosal injury and repair. Omeprazole (OMP) is a conventional anti-ulcer drug that effectively suppresses gastric acid secretion, but its efficacy may be enhanced by combining it with bioactive phytochemicals derived from a Glycyrrhiza glabra L. (licorice; LIQ) extract that possess potent antioxidant and anti-inflammatory properties. The aim of the present study was to evaluate the gastroprotective effects of OMP, LIQ extract, and their combined treatment against EtOH-induced GU in rats, focusing on modulation of TLR4/NF-κB/NLRP3 signaling and PI3K/AKT/mTOR gene expression. The ethanolic extract of LIQ was chemically characterized by LC-ESI-QTOF-MS/MS, and molecular docking was performed to evaluate the potential binding interactions of its major constituents with H⁺/K⁺-ATPase and COX-2. Thirty male Wistar rats were randomly allocated into control, ulcer (ULC), OMP-treated, LIQ-treated, and combined treatment groups. GU was induced by absolute EtOH. Subsequently, gastric pH, stomach coefficient, oxidative stress, inflammatory mediators, and PI3K, AKT, and mTOR gene expression were assessed. Histopathological and immunohistochemical analyses of mucosal architecture and the expression of TNF-α, caspase-3, and PCNA were performed. Coadministration of OMP and LIQ demonstrated the greatest gastroprotective activity, marked by a significant increase in gastric pH, restoration of antioxidant status, and substantial reduction in ROS, TLR4, NF-κB, and NLRP3 levels. The combined therapy significantly upregulated the expression of PI3K, AKT, and mTOR genes in comparison to ULC. Histopathological and immunohistochemical findings further demonstrated preservation of gastric mucosal integrity, reduced inflammatory cell infiltration, and decreased TNF-α, caspase-3, and PCNA immunoreactivity, indicating attenuation of mucosal injury. In conclusion, LIQ extract enhanced the gastroprotective effect of OMP against EtOH-induced GU, supporting its potential as an adjunct to OMP. Further studies are warranted to confirm the underlying molecular mechanisms. Full article

Triple-negative breast cancer (TNBC) remains a highly aggressive malignancy with limited therapeutic options and frequent resistance to platinum-based chemotherapy. Rosmarinic acid (RA), a naturally occurring polyphenol, has attracted considerable interest as a potential chemosensitising agent. This study investigated the anticancer activity and the underlying mechanisms of RA combined with cisplatin (CDDP) in 4T1 breast cancer cells while assessing the cytotoxic responses of non-cancerous HaCaT keratinocytes as a preliminary indicator of differential treatment sensitivity. Cytotoxicity was assessed using the MTT assay, followed by calculation of the Combination Index (CI), Drug Reduction Index (DRI), and Selectivity Index (SI). The generation of intracellular reactive oxygen species (ROS) was evaluated by DCFH-DA fluorescence imaging, and the functional contribution of oxidative stress was examined using N-acetyl-L-cysteine (NAC) rescue experiments. Apoptosis was analysed by Annexin V/PI flow cytometry, NucBlue nuclear staining, and Calcein-AM/propidium iodide (PI) Live/Dead fluorescence imaging. Three-dimensional (3D) tumour spheroids were used to assess treatment-induced alterations in spheroid morphology, morphometric parameters, viability based on adenosine triphosphate (ATP), and Live/Dead staining. The expression of genes related to apoptosis was determined by RT-qPCR, and potential molecular mechanisms were explored using the construction of protein–protein interaction (PPI) networks together with Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses. The combination of RA + CDDP exhibited strong synergistic cytotoxicity in 4T1 cells while demonstrating comparatively lower toxicity toward HaCaT keratinocytes. Combination treatment markedly increased intracellular ROS generation, whereas NAC significantly reduced ROS accumulation and partially restored cell viability, indicating that oxidative stress is a major but not exclusive mediator of cytotoxicity. Combined treatment significantly enhanced apoptotic cell death, increased chromatin condensation and membrane damage, upregulated the expression of Bax, Casp9, Cycs, and Trp53, and downregulated Bcl2, consistent with transcriptional regulation of intrinsic apoptotic signalling. In 3D tumour spheroids, the combination markedly reduced spheroid size, disrupted structural integrity, decreased ATP-based viability, and substantially increased tumour cell death compared to monotherapy. Bioinformatic analyses identified central genes related to apoptosis and cell survival and predicted significant enrichment of PI3K/Akt, p53, MAPK, and apoptosis signalling pathways. RA significantly potentiates the antitumor efficacy of CDDP through synergistic induction of ROS-associated apoptotic signalling while showing a more favourable cytotoxic response in 4T1 breast cancer cells than in non-cancerous HaCaT keratinocytes. The integrated findings from two-dimensional (2D) and 3D models, NAC rescue experiments, molecular analyses, and bioinformatics collectively support the potential of RA as a promising chemosensitising adjuvant for CDDP-based breast cancer therapy and warrant further validation in preclinical in vivo models. Full article

Hepatocellular carcinoma (HCC) is an aggressive liver cancer requiring reliable biomarkers, while current approaches are limited by high-dimensional data and complex nonlinear gene interactions. In this study, differentially expressed genes were identified and fed to a deep autoencoder to reduce dimensionality, capture nonlinear interactions, and extract informative latent features. Predictive gene features were selected through mutual information (MI) ranking and LASSO regression and subsequently evaluated using logistic regression (LR), random forest (RF), and support vector machine (SVM) classifiers with 5-fold cross-validation (CV). The top 50 genes underwent enrichment analyses. Protein–protein interaction (PPI) networks were constructed to identify hub genes, followed by gene–drug interaction, transcription factor analysis, and survival validation. Enrichment analysis highlighted critical pathways involved in metabolic, signaling, and cell-cycle, and viral carcinogenesis. CV showed stable and high performance across classifiers (accuracy = 0.969, F1 ≈ 0.97), with RF and SVM achieving the highest AUC values (~0.983 and ~0.982). Independent tests showed excellent performance, with RF achieving perfect performance (1.0) across all evaluation metrics, confirming high feature discriminative power. Survival analysis showed that hub genes, including HSP90AB1, TUBA1B, PKM, H2AZ1, YWHAZ, ACLY, RAN, ILF2, KPNA2, and TXNRD1, were significantly associated with poor prognosis (HR > 1.5, p < 0.05), correlating with reduced overall, relapse-free, and disease-specific survival in HCC. The integrative novel framework effectively identifies biologically relevant biomarkers, providing insights into HCC mechanisms and potential targets for precision therapy. Full article

Background: Pharmacogenetic (PGx) testing could identify actionable drug–gene interactions, reducing the risks of inappropriate prescribing of certain medications in some patients. An area of growing public health concern is rising global rates of depression and antidepressant use over the last two decades. Prior research has elucidated perspectives of healthcare providers who prescribe antidepressants regarding the clinical utility of genetic information, including PGx testing, but there is a gap in understanding how individual perspectives and systemic contextual factors may combine to influence PGx testing adoption. Objective: The objective of this study was to elucidate combinations of individual and contextual conditions associated with willingness to adopt PGx testing for Cytochrome P450 Subfamily IID, Polypeptide 6 (CYP2D6) and Subfamily IIC, Polypeptide 19 (CYP2C19) among antidepressant prescribers. Methods: We conducted a cross-sectional, mixed-methods study using structured questionnaires and semi-structured interviews with healthcare providers who prescribe antidepressants within their scope of practice across four healthcare systems in the United States. We collected data on implementation science concepts from the Theoretical Domains Framework, the Consolidated Framework for Implementation Research (CFIR), and the Implementation Outcomes Framework. Coincidence analysis (CNA), a case-based, Boolean logic-based method that identifies minimally sufficient combinations of conditions that lead to a particular outcome, was used to identify combinations of conditions for PGx test adoption among antidepressant prescribers. Interviews were also conducted with 10 patients who received pharmacogenetic testing within these healthcare systems to contextualize findings with patient perspectives. Results: Prescribers adopted PGx testing when they believed it would be beneficial to patients and were not deterred by cost-related concerns; the combination of these conditions led to PGx adoption in the most highly supported CNA model. Patient perspectives were also consistent with the selected model, with data suggesting they may have greater willingness to tolerate costs when they perceived or experienced benefits from testing. Conclusions: Insights from this study may be used by health system administrators and public health policymakers to inform future PGx implementation strategies that enhance uptake and awareness of existing evidence for clinical benefits of PGx testing and mitigate cost-related barriers to adoption. Full article

Endoplasmic reticulum (ER) stress represents a critical pathophysiological condition that plays a central role in the development of various human diseases, including protein misfolding diseases. While the small molecule Vx-445 (Elexacaftor) exhibits robust cellular bioactivity, its cryptic intracellular targets and off-label mechanisms of action remain poorly defined. This study investigates the cytoprotective efficacy and molecular targets of Vx-445 in Thapsigargin-induced ER stress in a neuronal cell model. Integrating biochemical assays, gene expression proteomics, and label-free functional proteomics, we demonstrate that Vx-445 significantly mitigates oxidative stress by reducing intracellular levels of reactive oxygen species, restores calcium homeostasis to baseline levels, and prevents apoptosis by inhibiting cytochrome c release. These phenotypic modifications correlated with changes in proteomic expression and were validated by Drug Affinity Responsive Target Stability (DARTS) analysis to map restored cellular pathways and identify potential protein interaction partners. Together, these findings uncover alternative molecular targets for Vx-445, providing a mechanistic basis for drug repurposing strategies in endoplasmic reticulum stress-related diseases. Full article

Background: HER2 is a key oncogenic gene in breast cancer, involved in tumor progression, metastasis, and therapeutic resistance. This study aimed to find new HER2 inhibitors using a hybrid of machine learning (ML) and structure-based virtual screening (VS), combined with molecular dynamics (MD) simulations on various scaffolds. Methods: Four supervised molecular fingerprint classification models were trained on a dataset of 10,000 validated compounds from ChEMBL. Random Forest was the top model for screening a large compound library. Selected compounds underwent molecular docking in the HER2 ATP binding site, ADMET, drug likeness, toxicity analysis, and 200 ns MD simulations. Methods like PCA, FEL, hydrogen-bond analysis, DCCM, RDF, salt-bridge analysis, and MM/PBSA were used to assess binding stability. Results: Virtual screening identified three compounds, CHMEBL193865 (Lead-1), CHMEBL46740 (Lead-2), and CHMEBL151318 (Lead-3)—with better binding affinity and interaction profiles than the reference inhibitor. MD simulations showed stable protein–ligand complexes with RMSD values of 2.32–2.76 Å. Among these, Lead-2 was the most structurally stable, and Lead-1 had the most favorable binding free energy. All three compounds showed good drug likeness, ADMET properties, and low predicted toxicity. Conclusions: These findings support further in vitro and in vivo testing for developing new therapeutics against HER2-overexpressing breast cancer, highlighting two scaffolds with promising lead optimization potential. Full article

Increasing evidence shows that epistasis, defined as interactive effects between genetic loci, may contribute to the missing heritability of cancer. However, systematic genome-wide epistasis identification in cancer remains challenging. Here, by leveraging genotype and clinical data from 380,983 samples in the UK Biobank, we identified 202,032 candidate epistatic single nucleotide polymorphism (epiSNP) pairs associated with cancer risk across 16 cancer types. Notably, multivariable Cox regression identified 123 epiSNP pairs with significant interaction effects on overall survival, suggesting that interaction-level genetic signals can provide prognostic information beyond individual SNP effects. Through functional analysis of the 202,032 candidate epiSNP pairs, we identified 7152 pairs supported by gene co-expression data and 12,326 pairs with protein–protein interaction (PPI) evidence. By mapping epiSNP pairs to corresponding gene pairs and then linking these gene pairs to drug–target databases, we identified 1040 epistatic gene pairs with FDA-approved drug–target records. Additionally, through KM survival analysis of the candidate epiSNP pairs, we detected 7068 pairs significantly associated with patient overall survival. Finally, we constructed an open-access database, EpiSNPdb, to facilitate cancer epistasis research. Full article

Background: Drug resistance and treatment-associated toxicity remain major limitations of conventional chemotherapy for triple-negative breast cancer (TNBC). Thymoquinone (TQ), a bioactive phytochemical derived from Nigella sativa, has demonstrated anticancer properties and may enhance the therapeutic efficacy of docetaxel (DTX) through complementary molecular mechanisms. Objective: To investigate whether TQ potentiates the antitumor activity of DTX in MDA-MB-231 TNBC cells by affecting apoptosis, oxidative stress, wound closure, and PI3K/AKT pathway-related gene expression. Methods: MDA-MB-231 TNBC cells and HaCaT keratinocytes were treated with TQ, DTX, or their combination. Cell viability was determined using the MTT assay, and drug interactions were evaluated by the Chou–Talalay combination index (CI) method. Apoptosis, intracellular reactive oxygen species (ROS) production, ROS rescue experiments using N-acetyl-L-cysteine (NAC), caspase-9 expression, wound closure, and gene-expression changes were assessed using Annexin V/PI flow cytometry, DCFH-DA-based flow cytometric and fluorescence analyses, immunocytochemistry, wound-healing assay, and quantitative real-time PCR (qRT-PCR), respectively. Bioinformatic analyses were performed to identify signaling pathways associated with the observed molecular alterations. Results: The TQ + DTX combination demonstrated synergistic cytotoxicity and significantly increased apoptotic cell death compared with either monotherapy. Combination treatment markedly enhanced intracellular ROS accumulation, whereas NAC pretreatment significantly attenuated ROS generation and partially reversed the cytotoxic and pro-apoptotic effects, suggesting the involvement of ROS in the observed antitumor effects. Caspase-9 immunoreactivity was markedly increased following combination treatment, suggesting the involvement of the intrinsic apoptotic pathway. Furthermore, the combination significantly suppressed wound closure and downregulated BCL2, PIK3CA, and AKT1 while upregulating BAX, CASP9, and PTEN. Bioinformatic analyses identified apoptosis, p53, PI3K/AKT, mTOR, and MAPK signaling as the principal pathways potentially associated with the observed gene expression changes. Conclusions: TQ potentiates the antitumor activity of DTX, with the involvement of oxidative stress, apoptotic signaling, suppression of wound closure, and regulation of PI3K/AKT pathway-related gene expression in TNBC cells. These findings provide evidence supporting further preclinical investigation of the TQ + DTX combination as a promising therapeutic strategy for triple-negative breast cancer. Full article