Search Results (7,318)

Metastatic hormone-naïve prostate cancer (mHNPC) is a clinically aggressive form of prostate cancer characterized by early systemic dissemination and poor long-term outcomes; however, the intrinsic epithelial cell states present at diagnosis remain poorly defined. In this study, we performed single-cell transcriptomic profiling of diagnostic prostate biopsy specimens from five patients with treatment-naïve mHNPC using Fixed RNA Profiling. Integrated and case-specific analyses characterized epithelial heterogeneity and lineage-associated transcriptional programs. Across 17,825 high-quality single cells, epithelial heterogeneity was identified in all cases. In addition to luminal androgen receptor (AR)-dependent epithelial cells, reproducible basal-associated epithelial populations with reduced AR signaling and stem-like transcriptional features were observed across tumors. Epithelial–mesenchymal transition (EMT)-related transcriptional programs were detected across multiple epithelial states with inter-case variability without forming a distinct EMT cluster, whereas no transcriptionally discrete neuroendocrine epithelial cluster was identified at baseline. These findings demonstrate that treatment-naïve mHNPC harbors pre-existing basal-associated epithelial states that contribute to intrinsic tumor heterogeneity at diagnosis. The presence of AR-low and stem-like epithelial populations prior to systemic therapy suggests a potential role for lineage plasticity in the aggressive biological behavior of metastatic prostate cancer. Full article

Splicing factor 3b1 (SF3B1), a component of U2 small nuclear ribonucleoprotein (U2 snRNP), has been known for its essential roles in pre-mRNA splicing and alternative splicing. Here we show that knocking down (KD) of SF3B1 broadly induced a significant reduction in mRNA expression in the genome. One of the genes whose expression is reduced by SF3B1 KD is methyl-transferase-like 3 (METTL3), a writer of N6-methyladenosine (m⁶A). We demonstrate that expression of both METTL3 mRNA and protein is affected by SF3B1 KD, which further decreases the m⁶A RNA expression level. m⁶A-seq indicates that SF3B1 KD affects m⁶A distribution within multiple genes in the genome. In addition, a high proportion of hypo-methylation events by SF3B1 KD (~70%) are overlapped in METTL3 KD cells, and a conserved m⁶A motif is observed in the hypo-methylated regions as in SF3B1 KD cells, suggesting the m⁶A decrease by SF3B1 is a direct effect of the reduced METTL3 expression. Furthermore, RT-qPCR using unlabeled RNA and 5-Bromouridine (BrU)-labeled nascent RNA and actinomycin D treatment demonstrates that transcription of METTL3 is significantly reduced but the mRNA decay rate is not altered, suggesting that METTL3 expression is altered at the transcription level. We further show that SF3B1 interacts with RNA polymerase (Pol) II in the RNA independent manner, further indicating the involvement of SF3B1 in transcription. Lastly, we demonstrate that the transcription inactive H3K27me3 on the METTL3 promoter was significantly increased whereas transcription active H3K4me3 was not changed by SF3B1 KD. Taken together, we conclude that reduced SF3B1 expression suppresses the transcription of METTL3 and inhibits m⁶A RNA expression. Full article

Background: The oral squamous cell carcinoma (OSCC) is a very aggressive cancer that is the product of tumor cell interactions with the microenvironment. The tumor microenvironment (TME) has a severe impact on OSCC progression, metastasis, and resistance to treatment by altering gene expression via various cellular and molecular signal transductions. Aim: This review systematizes the information on gene regulation in the OSCC TME (cellular components, signaling pathways that regulate tumor progression and resistance). Methods: We used PRISMA guidelines to search PubMed, Scopus, Web of Science, and Google Scholar (up to April 2025) with OSCC studies addressing the subject of gene regulation and tumor microenvironment. The quality of human or experimental models was evaluated using the Newcastle–Ottawa Scale and the qualitative synthesis was performed because of heterogeneity. Results: The significant regulatory functions of tumor-associated macrophages, cancer-associated fibroblasts, immune cells, and non-coding RNAs were found, especially in the pathways like JAK/STAT, EGFR, Wnt/ -β catenin, and PI3K/AKT/mTOR. Conclusions: The conceptualization of gene regulatory networks in the OSCC TME identifies the emerging biomarkers and targets of therapy. Merging multimodal omics and single-cell studies can further contribute to the precision strategies to enhance the outcomes of OSCC. Full article

The primary route of SARS-CoV-2 entry is via respiratory epithelium. However, many COVID-19 patients developed dermatological lesions, and SARS-CoV-2 RNA has been detected in the patients’ skin. Inflammatory skin diseases, psoriasis and atopic dermatitis (AD), significantly increased the risk of COVID-19. To evaluate the potential role of skin in SARS-CoV-2 host interactions, we utilized 3D human skin organoids (HSO) generated from human epidermal keratinocytes, as well as neonatal skin explants. HSO were treated with cytokines involved in acute and chronic skin inflammation and cytokine storm in severe COVID-19 disease: TNF-α, IL-6, IL-1β, and IFN-γ, individually and in combination. HSO were also treated with Th1 (TNF-α + IL-17) and Th2 (IL-4 + IL-13) cocktails inducing pro-psoriasis and pro-AD HSO changes, respectively. All individual cytokines, and especially their combinations, elevated the expression of ACE2 and TMPRSS2 at mRNA/protein levels. The Th2 cocktail induced only TMPRSS2, the Th1 cocktail predominantly induced ACE2. Topically applied Spike-pseudotyped lentiviral Tomato reporter, which binds ACE2 similarly to SARS-CoV-2, successfully transduced control and cytokine-treated HSO as well as neonatal skin explants. Cytokine treatment, especially TNF-α + IL-6 + IL-1β + IFN-γ and the Th1 cocktail, significantly increased viral entry. Transcriptomic analysis further revealed partial overlap between gene expression signatures induced by Spike-mediated entry in inflamed HSO and those observed in lung tissue from COVID-19 patients, supporting the biological relevance of skin models. Together, these findings demonstrate that inflammation may transiently alter the permissiveness of human skin to SARS-CoV-2 entry, suggesting that the skin may represent a previously underappreciated, although likely limited, interface in viral- host interactions. Full article

Chagas disease, caused by Trypanosoma cruzi (T. cruzi), includes clinically relevant intestinal inflammation; however, the mechanisms associated with tissue injury remain incompletely understood. ArtinM is an immunomodulatory lectin with known effects on innate and adaptive immunity, although its intestinal role during acute T. cruzi infection remains unclear. This study investigated whether ArtinM modulates the intestinal inflammatory response during acute experimental T. cruzi infection. In vivo, BALB/c mice were allocated to Saline control, T. cruzi + Saline, and T. cruzi + ArtinM groups. Intestinal inflammatory infiltrate and tissue concentrations of TNF-α, IFN-γ, IL-12p40, and IL-10 were quantified. Acute infection markedly increased TNF-α, IFN-γ, IL-12p40, and inflammatory infiltrate, whereas ArtinM significantly attenuated these responses. TNF-α, IFN-γ, and IL-12p40 remained associated with group after adjustment for infiltrate, whereas IL-10 reached statistical significance only in the adjusted model and was therefore interpreted cautiously. In parallel, an exploratory analysis of a public murine intestinal scRNA-seq dataset (GSE319934; GSM9529706 and GSM9529707), derived from a chronic infection setting, was performed to provide pathway-level context for inflammatory mediators assessed in vivo. This transcriptomic analysis indicated that related inflammatory, innate immune, chemotactic, and adhesion-associated genes were detectable in intestinal single-cell data from T. cruzi infection. However, because this dataset was not temporally matched to the acute model, it was not interpreted as a phase-matched comparator, mechanistic validation, or temporal extension of the experimental findings. Together, the results support that ArtinM treatment is associated with attenuation of acute intestinal inflammatory outcomes in experimental T. cruzi infection. Because local intestinal parasite burden was not measured, these findings should be interpreted as evidence of inflammatory modulation rather than as direct evidence of local antiparasitic activity. The public scRNA-seq analysis provides only exploratory contextual information for related inflammatory pathways. Full article

Background: Diabetic retinopathy (DR) is one of the major complications of diabetes mellitus. EJPs (Erjing Pills) are believed in Traditional Chinese Medicine to have the effects of a nourishing essence and a brightening of the eyes, but the specific effect on DR remains unclear. This study aims to investigate the therapeutic effects and underlying mechanisms of EJPs on DR. Methods: The chemical profile of EJPs was characterized by UHPLC-MS. Network pharmacology and molecular docking were employed to predict its active ingredients and potential targets. A DR rat model was induced by streptozotocin. Retinal morphology and function were assessed by OCT, FFA, and H&E staining. The expressions of proteins and mRNAs related to the AGE-RAGE pathway, oxidative stress, inflammation, and tight junctions were detected by Western blot, qPCR, and ELISA. Results: LC-MS and network pharmacology analysis identified 638 common targets between EJPs and DR, with core targets including SRC, AKT1, and MAPK1, primarily enriched in the AGE-RAGE signaling pathway. Molecular docking confirmed strong binding (binding energy < −5.0 kcal/mol) between key EJP constituents and core targets. In vivo, EJP treatment significantly alleviated retinal vascular leakage, improved retinal thickness, and alleviated histopathological damage. In addition, EJPs downregulated the AGEs-RAGE/NF-κB axis and pro-inflammatory cytokines while enhancing antioxidant defenses and tight junction proteins in the retinas of DR rats. Conclusions: EJPs ameliorate DR by protecting the blood–retinal barrier and modulating the AGE-RAGE/oxidative stress/inflammation network, demonstrating a multi-component, multi-target, and multi-pathway mechanism. This study provides a mechanistic basis for the potential application of EJPs in DR management. Full article

Background: Salinity, which hampers wheat growth and development, is one of the major abiotic stresses. Plant-derived smoke (PDS) solution alleviates salt stress and promotes wheat growth and development; however, the underlying molecular mechanisms have not been completely clarified. Methods: In this study, nuclear proteomics was employed to reveal the promotive effect of PDS solution on salt-stressed wheat. Nuclear fractions were isolated from wheat roots, and their purity was confirmed via enrichment of histone H3 and reduction of cytosolic ascorbate peroxidase. Using this nuclear purification technique, label-free nano LC–MS/MS-based nuclear proteomics was performed to identify differentially abundant nuclear proteins in salt-stressed wheat with or without PDS solution treatment. Results: Salt stress decreased histone H2A and DNA polymerase levels, whereas PDS solution treatment of salt-stressed wheat increased levels of histone variants (H2A, H2B, H3, and H4), DNA polymerase, and DNA topoisomerase II. In addition, the PDS solution increased the levels of pre-mRNA cleavage factor Im 25 kDa subunit and RNA helicase in salt-stressed wheat. Immunoblot analysis further validated the increase in histone deacetylase levels triggered by the PDS solution treatment in the salt-stressed wheat. Conclusions: These results suggest that PDS solution alters nuclear proteins in a way that contributes to chromatin remodeling and transcription during salt stress. Full article

Glioblastoma (GBM) is an extremely invasive and incurable tumor. We previously reported predominant ALDH1A3 expression at the invasive front of GBM tumors, which was associated with shorter patient survival, and further showed that ALDH1A3 promoted tumor angiogenesis involving plasminogen activator inhibitor-1 (PAI-1). Here, we investigated whether ALDH1A3 drives cell invasion through retinoic acid (RA) and PAI-1 signaling. Analysis of the TCGA-GBM dataset revealed a positive association between ALDH1A3 and PAI-1 (SERPINE1) expression. Overexpression of ALDH1A3 in GBM cells markedly increased PAI-1 mRNA and protein levels, with cellular colocalization of both proteins, accompanied by robust migration and invasion. These effects were reversed by treatment with a pan-RA receptor (RAR) antagonist AGN193109 (AGN), with a specific PAI-1 inhibitor tiplaxtinin (Tip) or by CRISPR/Cas9-mediated knockout of PAI-1. In a chick chorioallantoic membrane (CAM) model, ALDH1A3-overexpressing cells showed increased invasion, which was reduced by tiplaxtinin (Tip) treatment or PAI-1 knockout. Mechanistically, ChIP-qPCR demonstrated that RA treatment or ALDH1A3 overexpression increased RARα occupancy at the PAI-1 regulatory region, accompanied by increased PAI-1 expression, both of which were diminished by AGN. Collectively, the present study defines an ALDH1A3-RA-PAI-1 signaling axis that contributes to GBM cell motility and invasion. Full article

Azole resistance in Candida albicans is an increasing clinical challenge. Upc2 is a key transcription factor regulating ergosterol biosynthesis, but its additional roles in azole tolerance remain unclear. This study investigated whether Upc2 contributes to azole resistance through pathways beyond ergosterol synthesis. Chemical sensitivity screening, RNA sequencing, flow cytometry, and molecular assays were performed to compare wild-type C. albicans and the upc2Δ/upc2Δ mutant under fluconazole (FLC) treatment. The UPC2 gene deletion affected physiological processes that are dependent on the calcineurin signaling pathway and led to an overall negative enrichment trend in the unfolded protein response (UPR) pathway gene set. Mechanistically, the UPC2 gene deletion impaired unconventional splicing of HAC1 mRNA, leading to accumulation of unfolded proteins and phenotypically its deletion enhanced sensitivity of C. albicans to FLC in planktonic growth, hyphal development, and biofilm formation. Our findings reveal that Upc2 regulates proteostasis in C. albicans, and its absence enhances FLC efficacy by disrupting the UPR pathway. Targeting Upc2-mediated UPR signaling may represent a promising strategy to combat azole resistance. Full article

Hydrogen-rich water (HRW) is an aqueous solution containing dissolved molecular hydrogen. This study evaluated its effects on juvenile largemouth bass (Micropterus salmoides) under acute low-temperature stress. A total of 480 juveniles (2.4 ± 0.5 g) were randomly assigned to four groups: the control group was reared in standard water; the treatment groups were exposed to different hydrogen concentrations, specifically H1 (0.3 mg/L), H2 (0.5 mg/L), and H3 (0.9 mg/L). The fry were reared at 26 ± 0.5 °C for 30 days, followed by acute low-temperature stress (11 ± 0.5 °C) for 48 h. Samples were collected at 0, 8, 24, and 48 h. Results showed that after 30 days of HRW rearing, the final body weight (FBW), specific growth rate (SGR), and condition factor (CF) of the H1 group were significantly increased, while the H3 group only increased CF. No significant differences were observed in hepatopancreas somatic index (HSI) and survival rate (SR) among groups. Acute low-temperature stress induced liver and intestinal damage, which were alleviated in the H1 group. The H1 group exhibited significantly increased SOD, CAT, and GSH-Px activities in the liver, as well as CAT and SOD in the intestine and gills, while reducing MDA levels, thereby enhancing the antioxidant capacity. The H1 group significantly upregulated the antioxidant genes expression (sod, cat, and gsh-px mRNA levels) in the liver and gills but downregulated them in the intestine. 16S rDNA analysis revealed that HRW increased intestinal microbiota and the relative abundance of Bacillota. In conclusion, the H1 group significantly improved growth performance, mitigated acute low-temperature damage, enhanced antioxidant capacity, and increased the relative abundance of Bacillota in the intestines. This provides an innovative, safe, and effective solution for aquaculture industries confronting low-temperature challenges. Full article

Background: Progesterone (P4) is used as an antiseizure medication (ASM) to treat catamenial epilepsy, refractory to first-line drugs. P4 and other neurosteroids (NSs) are important regulators of multiple nervous system functions, including neuronal excitability and synaptic plasticity. In addition to their antiseizure properties, P4 and other NSs are also anti-inflammatory agents. Neuroinflammation is an important pathophysiological mechanism of epilepsy refractory to ASMs. Accordingly, we evaluated the ability of P4 to modulate neuroinflammation, using human microglia activated by lipopolysaccharide (LPS). Methods: Human microglia (HMC3) were stimulated for 3 h with LPS in the absence or presence of various concentrations of P4. Thereafter, levels of (i) toll-like receptor 4 (TLR4), (ii) the NLRP3 inflammasome, and (iii) pro-inflammatory cytokines were quantitated by real-time PCR and Western blot analyses. Phagocytic activity was also assessed using a phagocytosis assay employing fluorescent beads. Results: P4 treatment significantly reduced the microglial inflammatory state induced by LPS, which was mediated by upregulation of the TLR4- and NLRP3-axes. The protective effects of P4 were mediated by inhibition of Nuclear Factor kappa-light-chain-enhancer of activated B cells (NFκB) phosphorylation and reduced activation of Mitogen-Activated Protein Kinases (MAPK). The effects of P4 included a significant reduction in mRNA levels of the main pro-inflammatory cytokines and a reduction in phagocytic activity of HMC3. Conclusions: P4 is endowed with significant anti-inflammatory properties, which may be involved in the beneficial effects reported for drug-resistant catamenial epilepsy. Further research is required to clarify P4 post-receptor mechanisms of action and to explore the roles of other P4-derived NSs. Full article

HER2DX is a 27-gene genomic assay generating three complementary scores: a pCR score predicting the likelihood of achieving pathological complete response (pCR, defined as absence of residual invasive disease after neoadjuvant therapy), a Risk score estimating long-term recurrence risk, and an ERBB2 mRNA score quantifying HER2 transcriptional activation. Together, these scores may guide treatment escalation or de-escalation strategies in routine practice. We performed a single-center observational study at 12 de Octubre University Hospital (Madrid, Spain), including patients with early-stage HER2-positive breast cancer who underwent HER2DX testing (2023–2025), and analyzed clinicopathologic features, treatment decisions, and pathological outcomes. Forty-five patients were included (median age 57 years). Stage II accounted for 71.1% of cases; 66.7% were hormone receptor-positive, and 31.3% were node-positive. HER2DX modified clinical management in 51.1% of patients. The pCR score changed the initial strategy (neoadjuvant therapy versus upfront surgery) in 17.8% of cases and, independently, favored de-escalation to taxane plus dual HER2 blockade, with 90% of high-score tumors achieving a pathological complete response. The Risk score informed chemotherapy backbone selection within stage II disease. The ERBB2 score correlated with HER2 immunohistochemical intensity. In this exploratory real-world cohort, HER2DX provided biologically distinct information beyond traditional immunohistochemistry and was associated with modifications in multidisciplinary treatment decision-making in early-stage HER2-positive breast cancer, warranting prospective validation in larger cohorts. Full article

In this study, we assessed the impact of repeated valproate administration on its anticonvulsant effects and side effects in mice. We measured the plasma and brain concentrations of valproate and examined changes in the expression of selected genes in the mouse hippocampus after both acute and chronic treatments. Electroconvulsions were induced using an alternating current (50 Hz, 25 mA, 0.2 s) through ear clip electrodes. Motor impairment and long-term memory deficits were assessed with the chimney test and passive avoidance task. Valproate concentrations in the brain and plasma were measured by a fluorescence polarization immunoassay. mRNA was isolated using a modified Chomczyński and Sacchi method, and RQ-PCR was performed with an Applied Biosystems 7900 using SDS and RQ Study software. The 50% effective dose (ED₅₀) of valproate in the 14 × 2 protocol was significantly lower than the control. Despite no observed memory deficits in chronic protocols, the 50% toxic dose (TD₅₀) for motor impairment was also significantly lower. Chronic valproate treatment did not alter the plasma and brain concentrations. However, the expression levels of three genes (CACNA1G, GAD1, SCN1A) were significantly higher in the chronic protocols with the higher dose of valproate compared to single protocols, suggesting a dose-dependent effect. The repeated administration of valproate resulted in both enhanced efficacy and increased toxicity in terms of motor impairment. The observed effect may be associated with transcriptional adaptations potentially mediated by epigenetic mechanisms rather than with pharmacokinetic events. To enhance the reliability of the results obtained in animal epilepsy models, antiepileptic drugs should be administered chronically. Full article

Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide, characterized by a multi-step carcinogenesis process involving genetic mutations and epigenetic alterations. Despite advances in screening and therapy, challenges such as treatment resistance, recurrence, and metastasis persist. Emerging evidence highlights the critical role of epigenetic modifications, particularly N7-methylguanosine (m7G), in post-transcriptional regulation. This ubiquitous RNA modification participates extensively in tumor biological behaviors by regulating RNA stability, processing, and translation. Studies have shown that dysregulation of m7G modification is closely associated with adverse clinical outcomes in CRC. This review systematically summarizes the biological functions of m7G modification and its key regulatory proteins (such as METTL1/WDR4, eIF4E, etc.), with a focus on their roles in the pathogenesis, progression, prognosis, and diagnosis of, as well as therapy for, colorectal cancer. m7G modification and related molecules hold potential as novel biomarkers and therapeutic targets, thereby providing new strategies for the precision diagnosis and treatment of colorectal cancer. Full article

The senescence-associated secretory phenotype (SASP) contributes to various age-related pathologies. Methyl caffeate exhibits strong SASP-inhibitory activity; however, its molecular targets and the precise mechanisms underlying its effects remain unclear. Therefore, in this study, we performed affinity chromatography using methyl caffeate-immobilized beads to identify its intracellular binding proteins. The functional roles of the identified target were validated via knockdown experiments, assessment of SASP factor (interleukin [IL]-6 and IL-8) expression at the mRNA and secretion levels, and analysis of nuclear factor-κB and p38 mitogen-activated protein kinase signaling pathways. IQ motif-containing GTPase-activating protein 1 (IQGAP1) was identified as a methyl caffeate-binding partner. IQGAP1 knockdown significantly reduced IL-6 and IL-8 expression levels, mimicking the effects of methyl caffeate treatment. Furthermore, IQGAP1 depletion suppressed nuclear factor-κB activation and p38 phosphorylation. Overall, this study identified IQGAP1 as a critical scaffold protein essential for SASP induction and a target of methyl caffeate. Our findings provide key insights into SASP regulation, facilitating the development of SASP-modulating therapeutics targeting specific IQGAP1 domains. Full article