The MET exon 14 skipping mutation (named METex14Del) described in lung cancer leads to prolonged activation of signaling pathways and aberrant cell responses, but the link between HGF signaling and cell responses remains unclear. A putative lung cancer regulatory network of influential transcription factors was constructed from the transcriptomes of lung cancer cell lines. Transcriptomic data from METex14Del-expressing cells, stimulated or not by HGF, were mapped onto this lung cancer reference network and revealed activation of a major regulatory node composed mainly by the highly influential transcription factors ETS1, FOSL1 and SMAD3. HGF activation of METex14Del receptor induced the expression and phosphorylation of these three master regulators and the expression of their predicted target genes involved in migration and invasion. All these molecular and biological effects were inhibited by trametinib, a MEK inhibitor, which was potentiated by combination with capmatinib, a MET inhibitor. New mapping with transcriptomic data from trametinib-treated METex14Del cells validated the key role of the RAS-ERK pathway signaling in the activation of ETS1, FOSL1 and SMAD3 regulators and the induction of their target genes in HGF-activated METex14Del receptor. Thus, we report an original and powerful strategy to uncover key regulators, including transcription factors that have not been widely described in METex14Del signaling, such as SMAD3. These factors are activated by specific signaling pathways and could provide a novel therapeutic strategy involving a combination of receptor and signaling inhibitors.

Chemoresistance in breast cancer therapy, especially for triple negative breast cancer (TNBC) remains a significant challenge. Recent studies showed that overexpression of lipolysis-stimulated lipoprotein receptor (LSR), known as a tricellular tight-junction protein, was detected in TNBC and MDR1 was among LSR upregulated genes in a screening assay but its functional impact has not been studied. This study aimed to characterize LSR overexpression-induced regulation of MDR1 in TNBC cells focusing on chemoresistance. LSR was overexpressed in MDA-MB-231 cells and knocked-out via CRISPR/Cas9 in MDA-MB-468 cells for functional studies. Chemoresistance of individual cell lines was evaluated with doxorubicin treatment, followed by cell proliferation, invasion, colony formation and apoptosis assays. Modulated protein and mRNA levels of specific genes were assessed with Western blotting and RT-qPCR. MDR1 inhibitor verapamil and MDR1-targeted siRNA were used to evaluate the functional impact of LSR-induced MDR1. Overexpression of LSR not only promotes cell proliferation and invasion in MDA-MB-231 cells, but also renders the cells resistant to doxorubicin. LSR induces MDR1 expression at both mRNA and protein levels. Moreover, inhibition of MDR1 with specific inhibitor verapamil or MDR1 knockdown reversed cellular resistance to doxorubicin in LSR-overexpressing MDA-MB-231 cells. In contrast, knockout of LSR expression in MDA-MB-468 cells, which express higher levels of LSR, significantly sensitized the cells to doxorubicin-induced growth inhibition and apoptosis. Our data demonstrated that LSR overexpression promotes TNBC cell proliferation and invasion, and upregulation of MDR1 in these cells renders them resistant to doxorubicin, suggesting that targeting LSR could be a useful strategy to overcome chemoresistance in TNBC.

The crucial necessity to cope with oxidative stress caused not only by external factors but also by the cellular intermediary metabolism has driven the selection of diverse protection mechanisms in strict anaerobic microorganisms. In this context Methanosarcina acetivorans, a marine archaeon, expresses diverse functional enzymes involved in the protection against oxidative stress induced by O2. However, enzymes involved in aldehyde metabolism/detoxification that may have an important role as part of the antioxidant machinery have not yet been evaluated. In this work, the transcriptomic regulation of 8 genes encoding putative aldehyde dehydrogenases (ALDH) and the enzymatic activity were evaluated in M. acetivorans cells grown in the presence of air as an external stressor, and compared with cells grown under anaerobic conditions. The presence of air induced significant higher content of aldehydes, however the air exposition prepared the cells for oxidative stress as judged by changes in the ROS production rate with respect to anaerobic-grown control cells. Transcript levels of 5 ALDH codifying sequences tested were up-regulated, while 3 sequences were down-regulated by the presence of air. Basal ALDH activity levels were detected in anaerobic-grown cells with NAD+ or methylviologen as electron acceptor, suggesting a role of these enzymes in the central metabolism under anaerobic conditions. However, ALDH activity was significantly incremented in cells grown in the presence of air. Incubation of cells with acetaldehyde was toxic for anaerobic cells, but it was tolerated and detoxified in cultures grown with air. Results suggested that in M. acetivorans, ALDHs play a key role metabolizing aldehydes produced as part of the central metabolism, but also in combating oxidative stress induced by air exposure episodes.

Bisphenol A (BPA) is an endocrine-disrupting chemical that may contribute to cancer development. However, its role in lung adenocarcinoma (LUAD) remains poorly understood. This study aimed to investigate how BPA affects LUAD development by examining key genes involved in tumor progression and the immune microenvironment.

Triple-negative breast cancer (TNBC) is the breast cancer subtype with the poorest prognosis. This study aimed to elucidate the molecular pathways through which isoliquiritigenin (ISL), a natural chalcone compound derived from licorice and other plant roots, targets interferon regulatory factor 5 (IRF5) in TNBC.

Disarray in microRNA (miRNA) strand selection is associated with multiple tumors. However, the mechanisms underlying miRNA strand selection-driven temozolomide (TMZ) resistance in glioblastoma (GBM) remain unexplored.

Pathogenic filamentous fungi pose a formidable threat to global food security and human health, yet current antifungal therapeutics remain constrained by the emergence of resistance mechanisms. In this study, we report engineered binuclear zinc cluster antimicrobial peptides that incorporate the AflR binuclear zinc cluster motif, achieving superior antifungal efficacy through an unprecedented multi-target mechanism. These binuclear zinc cluster peptides simultaneously disrupt membrane integrity, interfere with transcriptional regulation, and dysregulate cellular metabolism in Aspergillus flavus. Fluorescence localization studies showed that the binuclear zinc cluster peptides preferentially accumulated in the hyphal growth zone, inducing aberrant budding morphology. Transcriptome analysis found that while the original peptide primarily disrupted membrane-associated pathways, the binuclear zinc cluster peptide had extensive perturbations across DNA replication, cell cycle pathways, ribosome biogenesis, and central carbon metabolism pathways. The three-dimensional structures of the binuclear zinc cluster peptides were revealed by AlphaFold 3 structural modeling, and the key amino acids-nucleotide interaction distance were shortened compared with the native AflR protein. Although flow cytometry and biochemical analysis confirmed membrane disruption, no extensive ion leakage was observed, coinciding with severe metabolic dysfunction and oxidative stress induction. This multi-targeted strategy, integrating transcriptional interference with membrane disruption, establishes a paradigm for next-generation agents against agricultural fungal pathogens.

MYC overexpression is a well-established cancer vulnerability, yet direct therapeutic targeting of Myc remains a challenge. Here, we identify DL78 as a potent antimitotic agent with selective anticancer activity through its regulation of Myc. DL78 demonstrated broad efficacy by inhibiting growth across nine cancer types and significantly reducing tumor burden in an in vivo model of platinum-resistant high-grade serous ovarian cancer, with no overt toxicity. DL78 preferentially targets chromosomally unstable, MYC-overexpressing cancer cells, a hallmark of high-grade serous ovarian cancer. Mechanistically, DL78 exploits Myc's role in mitotic entry by disrupting its interaction with α-tubulin, leading to sustained mitotic arrest, mitotic catastrophe, and apoptosis while sparing nonmalignant cells. This study establishes a novel paradigm for Myc-targeted therapy by introducing DL78, which induces cancer-selective mitotic catastrophe by disrupting Myc's interaction with α-tubulin rather than its transcriptional activity.

Major depressive disorder (MDD) and posttraumatic stress disorder (PTSD) are debilitating psychiatric conditions associated with poor health outcomes similarly observed in non-pathological aging. Ketamine is a dissociative anesthetic and NMDA receptor antagonist with demonstrated rapid reduction in symptoms associated with Treatment Resistant Depression (TRD) and PTSD. Ketamine's effects on biological aging have not been extensively studied among patients with moderate to severe symptoms of depression and/or trauma. To address this gap, this study looked at the changes in non-epigenetic measures, DNA methylation levels, immune cell composition, and biological age based on various epigenetic biomarkers of aging, of 20 participants at baseline and after completion of a course of six ketamine 0.5 mg/kg infusions in individuals with MDD or PTSD. As expected, depression and PTSD scores decreased in participants following ketamine infusion treatments as measured by the PHQ-9 and PCL-5. We observed a reduction in epigenetic age in the OMICmAge, GrimAge V2, and PhenoAge biomarkers. In order to better understand the changes in epigenetic age, we also looked at the underlying levels of various Epigenetic Biomarker Proxies (EBPs) and surrogate protein markers and found significant changes following ketamine treatment. The results are consistent with existing literature on ketamine's effects on different biomarkers. These results underline the ability of GrimAge V2, PhenoAge, and OMICmAge in particular, to capture signals associated with key clinical biomarkers, and add to the growing body of literature on ketamine's epigenetic mechanisms and their effect on biological aging. Clinical Trial Code. NCT05294835.

Pediatric acute-myeloid-leukemia (pAML) is an aggressive malignancy and the second most common blood cancer in children. In spite of significant advances in the frontline therapeutic approaches, approximately 50% of pAML patients show poor prognosis and relapse. Though drugs show positive response against the cancer cells initially, however, it becomes resistant in the long run of treatment, requiring the use of alternative drugs. Therefore, this study aimed to discover pAML-causing druggable molecular signatures highlighting their pathogenetic processes and alternative therapeutic agents. To address these issues, at first, we performed an integrated single-cell RNA sequencing (scRNA-seq) profile analysis of two datasets with accession IDs GSE154109 and GSE235923, which revealed 6 pAML-related key cell types (Erythroid cells, GdT-cells, Naive B-cells, Naive CD4 T-cells, Non-Classical Monocytes, and T-regs) and 198 common differentially expressed genes (cDEGs) between pAML and healthy groups. The protein-protein interaction (PPI) analysis yielded top-ranked eight cDEGs (JUN, MDM2, FOS, SOD2, FBXW7, CHD3, MCL1, and MAP2K1) as common key genes (cKGs) across the key cell types. Disease-cKGs enrichment analysis further confirmed the relevance of these genes to pAML and other leukemic diseases. Regulatory network analysis identified top four transcription factors (FOXC1, GATA2, RELA, and TP53) and three microRNAs (hsa-let-7a-5p, hsa-let-7e-5p, hsa-miR-15a-5p) that regulate these cKGs. Gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis results reflected their potential roles in pAML pathogenesis. Pathway perturbation analysis through gene-set enrichment analysis (GSEA) tool identified significantly perturbed pathways, highlighting how they are altered in pAML environment and how the cKGs are linked in the process. Subsequently, three potential therapeutic candidates (IRINOTECAN HYDROCHLORIDE, IMATINIB and IBRUTINIB) were disclosed through an integrative strategy combining molecular docking, drug-likeness, ADME/T, and DFT analyses. Molecular dynamics (MD) simulation studies for the top three drug-target complexes indicated the stability of complexes. Thus, the findings potentially offer valuable insights for pAML pathogenesis and effective therapeutic candidates for pAML patients.

Short-chain carboxylic acids (SCCA) and short-chain alcohols (SCALC) are naturally occurring antimicrobials that contribute to the biopreservation of food fermentations. This study investigated the effect of structurally different SCCA/SCALC with two-carbon (acetic acid; phenylacetic acid; 2-phenylethanol), three-carbon (propionic acid; 3-phenylpropionic acid; 3-phenylpropanol), and three-carbon chain with an additional hydroxyl group (lactic acid; 3-phenyllactic acid; 1-phenylpropanol) on the fitness, metabolic activity and gene expression of the pathogen Salmonella enterica at pH 4.5. SCCA inhibited Salmonella at lower concentrations than SCALC with the exception of lactic acid, which was partly consumed. The presence of a phenyl group enhanced antimicrobial activity. SCCA but not SCALC increased the lag phase of S. enterica, and in general, acetate was formed when cell growth was reduced by 20% suggesting a negative impact on bacteria fitness. Principal component analysis and hierarchical clustering indicated distinct gene expression profiles of S. enterica in response to SCCA or SCALC. In the presence of certain SCCA/SCALC, Salmonella activated pathways related to cellular pH control, and 1,2-propanediol, propionic acid and ethanolamine metabolism that involved the formation of metabolosomes. Genes related to flagellar assembly were less expressed and mobility was lower in the presence of lactic and 3-phenyllactic acid compared to controls suggesting a compound-specific response. KEY POINTS: • Differences in response among structurally different SCCA/SCALC at acidic condition. • SCCA/SCALC stress interfered with cell growth and metabolism of acetic and propionic acid. • Lactic acid prolonged the lag phase and reduced motility of Salmonella.

NDR1 and AHA5 coordinate drought stress and immune responses via stomatal regulation, uncovering a molecular link between abiotic and biotic stress adaptation in Arabidopsis. Plant stress responses have overlapping molecular and physiological signatures. Not surprisingly, many of these are also shared with numerous other processes, including growth and development, as well as abiotic and biotic signaling. NON-RACE-SPECIFIC DISEASE RESISTANCE1 (NDR1) is a key component of plant immune signaling, required for defense against the bacterial pathogen Pseudomonas syringae. In this study, we have identified that NDR1 contributes to stomatal-based processes following exposure to biotic (flg22 (flagellin peptide) and elf26 (EF-Tu-related elicitor)) and abiotic (ABA, drought, etc.) elicitors. Interestingly, we found that NDR1 is part of a signaling cascade that confers tolerance to water loss-a required component of drought stress responses in plants, a role that couples stress signaling in an abscisic acid-dependent manner. As a definition of its broader connectivity to this response, we identified that NDR1 physically associates with the PM-localized H+-ATPases AHA1, AHA2, and AHA5, an association that is required for proper regulation of H+-ATPase activity and stomatal guard cell dynamics. Using a comprehensive whole-transcriptome analysis, we further show that NDR1 is required for multiple, genetically overlapping physiological processes, including response to water withholding. In total, we demonstrate that NDR1 functions in signaling processes associated with both biotic and abiotic stress response pathways, a function we hypothesize illustrates NDR1's role in the maintenance of cellular homeostasis during stress response activation.

CD44 serves a dual role in supporting tumor survival and promoting invasion. Claudin‑low breast cancer, characterized by a CD44+/CD24‑ phenotype and epithelial‑mesenchymal transition (EMT), displays aggressive behavior. The present study investigated the interaction between CD44 and TGF‑β signaling, and assessed the cellular effects of their combined inhibition. CD44 was knocked down in claudin‑low breast cancer cell lines (SUM159 and MDA‑MB‑231), and the TGF‑β receptor (TGFBR) inhibitor LY2109761 (LY‑61) was applied for treatment. Cell viability (MTT assay), apoptosis (annexin V assay), invasion (Transwell assay), colony formation and Smad2 phosphorylation (western blotting) were evaluated. CD44 knockdown reduced viability and increased apoptosis but did not markedly suppress invasion. Although TGF‑β stimulation enhanced Smad2 phosphorylation, CD44 knockdown alone did not increase Smad2 activation, indicating that it does not directly regulate Smad2. However, LY‑61 inhibited TGF‑β‑induced Smad2 phosphorylation, effectively counteracting pro‑invasive signaling. Notably, while CD44 knockdown alone had a negligible impact on invasion, its combination with LY‑61 markedly reduced the invasive capacity and colony formation of cells compared with the control (control cells transduced with non‑targeting short hairpin RNA without LY‑61 treatment). LY‑61 induced S phase accumulation, which was more pronounced in SUM159 cells than in MDA‑MB‑231 cells, indicating cell line‑specific effects on cell‑cycle regulation. Clinical data indicated that low CD44 expression was associated with improved survival in patients with claudin‑low breast cancer, despite its potential to enhance EMT signaling. These findings suggested that CD44 knockdown enhanced the response to TGFBR inhibition. Although CD44 depletion may increase EMT‑related signaling, invasion was primarily suppressed by TGF‑β blockade, and the combination with CD44 knockdown further enhanced the inhibition of proliferative phenotypes compared with either treatment alone. This dual‑targeting approach warrants further investigation in claudin‑low breast cancer.

Systemic lupus erythematosus (SLE) is a complex autoimmune disorder characterized by aberrant inflammation, type I IFN-stimulated gene (ISG) expression, and autoantibody production. Glucocorticoids (GCs) like dexamethasone (DEX) are standard long-term SLE treatments but cause significant side effects, highlighting the need for safer steroid-sparing options. Preclinical and clinical studies suggest that dietary supplementation with omega-3 fatty acids (O3FAs), particularly docosahexaenoic acid (DHA), suppresses inflammation and autoimmunity associated with SLE disease progression. We explored the steroid-sparing potential of DHA to influence the suppressive effects of DEX on pathogenic gene expression.

Cinchonine, an alkaloid found in the bark of various Cinchona species, possesses notable pharmacological properties, including anti-microbial, anti-parasitic, anti-inflammatory, and anti-obesity effects. Recent research highlights its potential anticancer properties, particularly against leukemia (K562) cells, as its molecular mechanisms remain underexplored. This study assessed cinchonine's antiproliferative effects on K562 cells using NRU, SRB, and MTT assays. It was further investigated for its interactions with molecular targets such as DHFR, COX-2, 5-LOX, HYAL, CATD, and ODC through cell-free and cell-based systems, docking studies, and qRT-PCR analysis. Cinchonine inhibited K562 cells growth with an IC50 of 46.55 µM (NRU assay) and significantly suppressed COX-2 activity (IC50 44.65 µM) and expression. It induced G0/G1 cell cycle arrest and increased the sub-diploid population in K562 cells. In vivo, cinchonine reduced tumor growth in EAC and S-180 models by 48.49% and 37.86%, respectively, at 50 mg/kg body weight. Toxicity predictions and ex vivo tests confirmed its safety profile. These findings suggest cinchonine as a promising chemopreventive agent for leukemia.

Triple-negative breast cancer (TNBC) is an aggressive subtype with poor prognosis and limited targeted therapies. The Hippo signaling pathway, critical in tumor progression, may harbor key genes influencing TNBC behavior. However, the specific genes and their clinical significance remain unclear.

Bladder cancer exhibits marked spatial heterogeneity in gene expression and immune infiltration. In this exploratory pilot study, we integrate multiplex fluorescence in situ hybridization (mFISH) with AI-assisted digital pathology to characterize the spatial distribution of a previously validated three-gene arsenic-responsive risk model (NKIRAS2, AKTIP, HLA-DQA1). Initially identified in arsenic-exposed individuals and associated with bladder cancer risk, this gene panel achieved 94% training and 75% validation AUC in prior genomic models (PMC8760535). We analyzed five bladder tumor specimens using whole-slide mFISH imaging and HoverNet-based nuclear segmentation to quantify gene expression at single-cell resolution. Spatial profiling revealed elevated expression scores in tumor-adjacent regions, with a strong positive correlation to tumor grade (Pearson's r = 0.83). These gene-enriched regions exhibited spatial clustering of tumor cells. Additionally, tumor-infiltrating lymphocyte (TIL) density was inversely correlated with tumor grade, suggesting immune exclusion in high-grade tumors. Our findings demonstrate the feasibility of combining spatial transcriptomics with AI-driven histopathological analysis for biomarker validation. This integrative framework provides a foundation for future population-scale studies leveraging spatial omics to evaluate arsenic-associated gene signatures and assess their relevance in bladder cancer risk stratification and disease progression.

Liver cancer is one of the deadliest cancers worldwide. There is a growing need for natural therapeutic options due to the rising global morbidity incidence of liver cancer. Due to its crucial function in angiogenesis, vascular endothelial growth factor (VEGF) signaling is considered as an ideal target for therapeutic intervention. In this in silico study, we have screened 16 microRNAs (miRNAs) that target the KDR gene, which encode VEGFR-2, and 113 natural compounds derived from Persicaria hydropiper for their anti-angiogenic properties. MicroRNA, hsa-miR-17-3p was identified with potentials of downregulating KDR gene, using several in silico tools. Two possible compounds- 6-Hydroxyluteolin and Isorhamnetin were also identified after performing ADMET profiling and molecular docking. Furthermore, 100 ns molecular dynamics simulations were run to evaluate the stability and conformational changes of protein-ligand complexes. This study identified one microRNA and two natural compounds that showed strong interaction with KDR and its encoded VEGFR-2 receptor, respectively. To validate their effectiveness as therapeutic agents against hepatocellular carcinoma, additional wet lab studies using in vitro and in vivo techniques are necessary.

Triple-negative breast cancer (TNBC) is a highly aggressive subtype of breast cancer. Although neoadjuvant chemotherapy (NACT) has some effectiveness in TNBC, a portion of patients still do not benefit from them. The critical role of DNA replication stress (DRS) in cancer therapy has been recognized, but its study in TNBC NACT remains relatively limited. Affymetrix microarray data were obtained from the GEO database for both training and test sets. These data were processed using the "affy" R package. The Boruta algorithm and SVM-RFE method were employed for key gene selection, and an integrated model based on multiple algorithms was developed to establish a risk score. Additionally, the tumor microenvironment (TME) was analyzed, and the correlation between risk score and drug sensitivity was explored, incorporating several drug databases. Through the analysis of TNBC patients' responses to NACT, we found a close correlation between DRS and TNBC treatment responses and identified eight key genes. The developed ensemble model (ENS) demonstrated high AUC values of 0.922, 0.886, and 0.858 across the three independent datasets, respectively, indicating its strong ability to accurately predict the effectiveness of NACT. The study also revealed that patients with higher risk score are more prone to recurrence and metastasis, and have a rich TME composition. Additionally, drug sensitivity analysis offers potentially effective personalized treatment options for high-risk TNBC. This study successfully constructed an ensemble model to predict TNBC patients' response to NACT. Additionally, it was discovered that the risk score held significant value in analyzing the correlation between TNBC patients' TME and drug sensitivity. These findings offer important new insights into personalized treatment strategies for TNBC.

Soil contamination by heavy metals, particularly lead (Pb), which is considered the second most toxic metal, poses serious risks to plants and humans due to its accumulation from various anthropogenic activities. Strigolactones (SLs) are a novel class of terpenoid lactones that play a vital role in regulating plant growth and development, particularly under stress conditions. This study aimed to investigate the impact of exogenous SL applications on plant growth and various physiological, biochemical, and molecular parameters in lettuce subjected to Pb stress. Pb stress harmed plant growth, whereas SL treatments improved growth parameters under both control and Pb stress conditions. While Pb stress increased the electrical conductivity (EC), malondialdehyde (MDA) and hydrogen peroxide (H2O2) content, SL applications caused a decrease in these parameters. Pb stress negatively affected chlorophyll content, whereas SL applications reduced negative effect. Pb caused an increase in superoxide dismutase (SOD), catalase (CAT), peroxidase (POD) ascorbate peroxidase (APX), glutathione reductase (GR), glutathione s-transferase (GST) activities and Glucose-6-Phosphate Dehydrogenase (G6PD), 6-Phosphogluconate Dehydrogenase (6GPD). SL treatments significantly increased the activity of antioxidant enzymes in both control and Pb stress conditions. However, Pb stressed plants had lower nitrate reductase activity (NRA) than the control plants while SL treatments increased NRA compared to the non-treatments. Pb stress significantly reduced the uptake of essential nutrients in lettuce seedlings, whereas exogenous SL applications improved nutrient accumulation, particularly under Pb-stressed conditions. Additionally, mRNA expression profiles of nine stress-related genes in different tissues of lettuce were determined. Only Pb stress significantly decreased the expression of genes, particularly LsCCD8 and LsD14, in both tissues. The combined Pb and SL treatment significantly increased the expression of LsMAX2 in both tissues. These results suggest that exogenous SL applications can be an effective strategy to mitigate Pb-induced stress in lettuce by enhancing plant tolerance at physiological, biochemical, and molecular levels.