Aluminum (Al) stress is typical for acidic soils and may affect cereals' yield. Al tolerance in triticale is mostly affected by the aluminum-activated malate transporter (ALMT) gene (7R) and some other QTLs (3R, 5R, and 6R). The trait is heritable in about 36% of cases, indicating that epigenetic factors may impact the phenomenon. This study demonstrates that utilizing different methods to quantify DNA methylation changes induced by Al stress results in detail differences, and the results evaluated should be compared critically. The Common and the basic General approaches are sufficient if general information is needed. The General (extended variant) approach may deliver data on methylation changes affecting symmetric sequence contexts. The markers assigned to DN-CG, DM-CG, and DN-CHG were suggested as the most important in explaining Al tolerance in triticale. Analysis of the maps constructed based on root tips and leaf tissues showed different densities of the epigenetic markers but reflected the comparable patterns of their distribution, supporting the hypothesis that Al stress could be transmitted to other plant tissues due to somatic memory. Methylation changes occur throughout the genome and are not associated with specific genes related to aluminum stress.

Molecular mechanisms responsible for the poor prognosis in patients with intrahepatic cholangiocarcinoma (CCA) are still unknown, but stem cell marker Cluster Differentiation 90 (CD90) has been reported to be associated with a more aggressive cancer phenotype. In this scenario, the TGF-β1 signaling pathway likely has a role as master gene regulator. Aim of the study is to investigate the role of CD90 in iCCA aggressiveness. The molecular profile of HuCCT1/CD90+ and HuCCT1/CD90- cells was obtained through transcriptomic analysis (NGS). Bioinformatic data were confirmed in both cell lines by qRT-PCR and Western blot. Cells were treated with Gemcitabine in monotherapy or in combination with Galunisertib, a selective inhibitor of TGF-βRI, in 2D and 3D models. HuCCT1/CD90+ cells are more proliferative, less migratory, and resistant to Gemcitabine treatment. HuCCT1/CD90+ cells also express lower levels of TGF-β1 compared to /CD90- cell lines. Finally, HuCCT1/CD90+ cells are resistant to Gemcitabine, while the combination of Gemcitabine and Galunisertib displays a synergistic effect on HuCCT1/CD90+ cell proliferation. These results underline that CD90-induced Gemcitabine resistance can be overcome by adding a TGFβ1 inhibitor such as Galunisertib, thereby moving further toward a precision medicine approach in patients with iCCA.

Ovarian cancer is a deadly gynecological malignancy often diagnosed at an advanced stage, with few treatment options available. Polyphyllin I (PPI), the primary active ingredient of Paris polyphylla, has shown excellent anti-cancer activity against various cancers. However, studies on PPI use and ovarian cancer are limited, and the potential mechanisms remain unclear. This study explored the effects of anti-ovarian cancer and the potential mechanisms of action of PPI. Methods such as MTT, colony formation, three-dimensional spheroid formation, flow cytometry, and western blotting were employed to assess the anti-proliferative effects of PPI on different ovarian cancer cell lines. RNA sequencing was used to discover potential mechanisms by evaluating the effects of PPI on transcriptional signatures and identifying differences in gene expression patterns. The results indicate that PPI demonstrated dose- and time-dependent anti-proliferative effects on ovarian cancer cell lines. PPI also up-regulated 1518 genes and down-regulated 800 genes. The genes showed enrichment in the "apoptosis" gene sets, while exhibiting negative enrichment in the "cell cycle" and "Myc signaling pathway" gene sets. PPI caused cell cycle arrest at the G0/G1 phase by increasing the expression of p21 and p27 and inhibiting the activity of the CDK2/cyclin E complex. PPI triggered cell apoptosis, which was associated with elevated cellular reactive oxygen species and mitochondrial membrane potential depolarization. Finally, PPI reduced c-Myc protein levels and affected mRNA levels of c-Myc pathway-related genes. PPI effectively suppressed ovarian cancer cell proliferation, indicating its potential as a treatment option for ovarian cancer.

Cocaine use disorder is characterized by persistent drug-seeking behavior and a high risk of relapse, driven in part by lasting molecular and circuit adaptations in the nucleus accumbens. To explore the transcriptomic changes underlying these alterations, we employed fluorescence-activated nucleus sorting coupled with single-nucleus RNA sequencing to analyze D1 and D2 medium spiny neurons in this brain region of male mice subjected to acute cocaine exposure or to prolonged withdrawal from repeated cocaine exposure without or with an acute cocaine rechallenge. This approach allowed us to precisely delineate and contrast transcriptionally distinct neuronal subpopulations─or ensembles─across various treatment conditions. We identified significant heterogeneity within both D1 and D2 MSNs, revealing distinct clusters with unique transcriptional profiles. Notably, we identified a discrete D1 MSN population characterized by the upregulation of immediate early genes, as well as another group of D1 MSNs linked to prolonged withdrawal, uncovering novel regulators of withdrawal-related transcriptome dynamics. Our findings provide a high-resolution transcriptomic map of D1 and D2 MSNs, illustrating the dynamic changes induced by cocaine exposure and withdrawal. These insights into the molecular mechanisms underlying cocaine use disorder highlight potential targets for therapeutic intervention aimed at preventing relapse.

Cannabis is among the most used illicit substances in the world, and approximately 10% of regular cannabis users are estimated to be susceptible to developing cannabis use disorder (CUD). We examined the effect of different concentrations of delta-9-tetrahydrocannabinol (THC) on the epigenetic DNA modifiers DNA methyltransferases (DNMTs) and ten-eleven translocation enzymes (TETs); cannabinoid CB1 and CB2 receptors; and the cytokines IL-1β, IL-6, IL-10, and TNF-α. We used two in vitro study designs on human peripheral blood mononuclear cells (PBMCs) collected from healthy donors: (a) repeated THC incubations and (b) repeated THC incubations followed by an "abstinence" period and a THC challenge incubation. We observed no significant effects on DNMTs and TETs mRNA levels, enzymatic activity, or CB1 and CB2 mRNA levels at an average THC concentration (50 ng/ml, n = 8 donors). However, repeated incubations at a high THC concentration (200 ng/ml, n = 16 donors) significantly downregulated DNMTs and upregulated TETs, CB1, and CB2 mRNA levels. Both THC concentrations upregulated the gene expression of IL-1β, IL-6, and IL-10, but had no effect on TNF-α gene expression. At the genome-wide level, repeated THC incubations resulted in a significant number of differentially hydroxymethylated genes being hyperhydroxymethylated. An additional THC challenge shifted the hyperhydroxymethylated state to hypohydroxymethylation. The genes with the strongest associations with THC exposure were found to be functionally significant for various signaling pathways. These findings suggest that repeated incubations with high concentrations of THC may affect the expression of genes critical for the development of CUD through aberrant demethylation.

The emergence and rapid spread of multidrug-resistant pathogens have caused a need for alternative antimicrobials, and bacteriocins are considered promising alternatives due to their lower risk of resistance development. Regarding this, we aimed to investigate the long-term subinhibitory and semisubinhibitory concentrations of a commonly used bacteriocin (nisin) in Staphylococcus aureus using an experimental evolution approach followed by genome sequencing. We then performed RT-qPCR to examine changes in the expression level of the biofilm-related icaA gene in evolved lines. We found that while nisin treatment did not significantly elevate the base-substitution rates, there was a significant decrease in the insertion/deletion rate in the lines exposed to the subinhibitory concentration of nisin. We also revealed an increase in nonsynonymous mutations in specific genes (e.g. sarS and cap8) associated with resistance and virulence mechanisms. Importantly, we observed a transition bias in the nisin-treated lines for the first time, and it may be related to the resistance development to nisin. RT-qPCR analysis of the icaA gene showed a reduced expression levels in nisin-treated groups, although the results were not statistically significant. These findings show the potential outcomes of nisin exposure in S. aureus and emphasize the need for careful consideration of bacteriocins in clinical practice.

The poor prognosis of clear cell renal cell carcinoma (ccRCC) is primarily attributed to inherent resistance and malignant progression, yet the underlying mechanism and effective strategies remain poorly understood. Renal drug transporters play an indispensable role in regulating the intracellular concentration of tumor cells. Therefore, this study aims to investigate the role of proton-coupled oligopeptide transporter 2 (PEPT2) in ccRCC. PEPT2 was found to be downregulated in ccRCC tissues and cell lines, and its low expression was associated with an unfavorable prognosis in ccRCC patients. Overexpression of PEPT2 inhibited cell proliferation and metastasis both in vitro and in vivo. Furthermore, the transcriptional repression of PEPT2 was attributed to DNMT3A/B mediated methylation of its promoter, which could be reversed by the epigenetic inhibitor decitabine, leading to the restored expression and functional transport activity of PEPT2. Importantly, the combination treatment with decitabine (an epigenetic inhibitor) and a lenalidomide-dipeptide conjugate (a substrate for PEPT2) significantly enhanced cytotoxicity against ccRCC cells both in vitro and in vivo. Our investigation into the epigenetic repression of PEPT2 promoters has revealed a significant role in the progression of ccRCC. Furthermore, our findings demonstrate that the combination of PEPT2-targeted lenalidomide with epigenetic therapy effectively enhances cytotoxicity in ccRCC cells. This study provides compelling experimental evidence for the potential therapeutic benefit of targeting PEPT2 in the treatment of ccRCC.

Exosomes (Exos) derived from mesenchymal stem cells (MSCs) are known to influence cancer cell behavior; however, the clinical use of MSCs is limited due to the gradual loss of their differentiation potential with continuous passaging. Induced mesenchymal stem cells (iMSCs) have emerged as a promising alternative source, but the effects of Exos derived from iMSCs (iMSC-Exos) on cancer cells remain incompletely understood. This study aims to compare the effects of iMSC-Exos with ADMSC-Exos derived from adipose tissue-derived mesenchymal stem cells (ADMSCs) on the viability, invasion, and migration of breast (MCF7) and lung (A549) cancer cells. Conditioned media from iMSCs and ADMSCs were collected for isolation and characterization of Exos. MCF7 and A549 cell lines were treated with iMSC- and ADMSC-Exos, and Exos uptake, cell viability, migration, senescence, and expression of BAX and BCL-2 genes were evaluated. iMSCand ADMSC-Exos were successfully internalized into cancer cells, with a higher efficiency of ADMSC-Exos uptake in MCF7 cells. Cell viability decreased and migration increased in both cancer cell lines upon treatment. BAX expression was significantly reduced in MCF7 cells following ADMSC-Exos treatment and in A549 cells after iMSC-Exos treatment. In contrast, BCL-2 expression was significantly reduced in MCF7 cells treated with both iMSC- and ADMSC-Exos, while it significantly increased in A549 cells after ADMSC-Exos treatment. A549 lung cancer cells showed a higher level of senescence than MCF7 breast cancer cells, particularly when treated with iMSC-Exos. Minimal overall differences were observed in viability, apoptosis, and migration assays between iMSC- and ADMSC-Exos in MCF7 and A549 cells. However, significant differences were observed in the senescence and expression of BAX and BCL-2 genes across cancer cell lines. These findings highlight the importance of further investigation into the distinct effects of iMSC- and ADMSC-Exos on cancer cell biology.

Glyphosate-based herbicides (GBHs) can be found in waterbodies and may affect aquatic populations, resulting in physiological and behavioral impairments. In Colombia, white cachama (Piaractus orinoquensis) are frequently found in areas subjected to glyphosate aerial fumigation. This study aims to investigate changes in c-Fos protein expression in P. orinoquensis telencephalic hemispheres after exposure to 0, 1, 5, and 10 mg/L glyphosate for 30, 60, and 90 min. For this purpose, 5 lm paraffin sections were obtained and used for c-Fos immunodetection. To define the effect of xenobiotics on c-Fos expression, nuclei were taken from the dorsal dorsal (Dd), dorsomedial (Dm), dorsal posterior (Dp), dorsolateral (Dl), ventral (Vv), dorsoventral (Vd), and ventrolateral (Vl) regions of P. orinoquensis telencephalic hemispheres. Except for Dd nuclei, other nuclei showed an initial increase in c-Fos+ cells, followed by a progressive decrease toward values similar to those observed in unexposed individuals. In Dd nuclei, the initial tendency was toward a reduced number of c-Fosexpressing cells, followed by an increase in unexposed values. As changes in the number of cells containing c-Fos can be related to changes in neuronal activity, GBH exposure may potentially affect the fish's behavioral and sensorial performance, resulting in a reduced survival probability in its natural environment.

Metarhizium rileyi is an entomopathogenic fungus that is widely used to control agricultural pests. However, maintaining an efficient and stable yield of M. rileyi conidia is challenging. In this study, M. rileyi sporulation was inhibited on media with 4 % glucose. M. rileyi conidial production was elevated with increasing the maltose on media. Transcriptome and proteome resulted in 3154 differentially expressed genes and 1263 differentially expressed proteins between 4 % glucose and 4 % maltose groups. Combined transcriptome and proteome data revealed that glucose-mediated sporulation inhibition was found to be enriched in catalytic activity, oxidoreductase activity, metabolic pathways, carbon metabolism, and TCA cycle. Major transcription factor (TF) families were Pkinase, WD40, and adh_short. Protein-protein interaction network and core targets analyses identified the vital target TFs: OAA51986.1, OAA39667.1, and OAA47593.1. The present study will lay a theoretical foundation for commercial production of fungal conidia and provide more products for biological control of agricultural pests.

Plant viruses threaten global food security by subverting host defenses, necessitating sustainable solutions. Carbon quantum dots (CQDs)-nanoscale materials with tunable optoelectronic properties and biocompatibility, offer promise in antiviral therapy, but their mechanisms in plant immunity remain unclear. This study comprehensively mapped CQDs-modulated transcriptional reprogramming of antiviral responses in association with the diversity and patterns of alternative splicing (AS) events in cotton leaf curl Multan virus CLCuMuV (DNA-A + β)-infected Nicotiana benthamiana. Transcriptomic analysis revealed that at 5 days post-inoculation (dpi) with CLCuMuV (DNA-A + β), the CQDs upregulated antiviral immunity-related genes (Ca+2/calmodulin-dependent protein kinase (CaMK), WRKY transcription factors, mitogen-activated protein kinase (MAPK), and serine/threonine protein kinases (STPKs) and stress-responsive immunity pathways. At 20 dpi, the transcriptional response shifted to reflect reduced virus-induced stress. Moreover, the CQDs differentially impacted AS patterns by increasing exon skipping and modulating intron retention, mainly at later stages of viral infection. Structural modeling revealed that the CQDs induced conformational changes in the RRM domain-containing heterogeneous nuclear ribonucleoprotein (hnRNP), enhancing protein druggability and binding capacity. These findings indicate the dynamic role of CQDs in the modulation of antiviral immune responses and the transcriptomic plasticity of plants during viral infection which is reflected by regulation of gene expression and alternative splicing. CQDs showed strong antiviral potential in alleviating symptoms of CLCuMuV via reprogramming transcriptional responses and differential AS events in N. benthamiana. These findings underscore CQDs as effective tools for enhancing plant resilience against viral pathogens. Future research should explore field efficacy of CQDs and their nanoscale interactions with viral proteins and their broader applications in sustainable crop protection.

The objective of this review is to examine the direct evidence implicating epigenetic mechanisms in manganese (Mn)-induced neurotoxicity, with particular emphasis on the modulation of non-coding RNA (ncRNA) expression and histone modifications. Existing data demonstrate that Mn exposure modulates expression of various types of ncRNAs, especially micro RNAs (miRNAs or miRs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). Through regulation of target gene expression, these differentially expressed ncRNAs likely mediate Mn-induced neuronal oxidative stress, ferroptosis, apoptosis, autophagy, inflammation, as well as α-synuclein expression. Additionally, Mn exposure affects histone acetylation in neurons by modulating enzymes such as histone deacetylases (HDACs) and histone acetyltransferases (HATs). These Mn-induced changes in histone acetylation enhance neuronal oxidative stress by down-regulating antioxidant gene expression and promoting neuroinflammation. Alterations in HDACs activity and the ensuing histone acetylation modifications play a role in Mn-induced down-regulation of glutamate transporter 1 (GLT-1) and glutamate-aspartate transporter (GLAST) expression which results in reduced glutamate uptake and ensuing excitotoxicity. Additionally, Mn exposure impacts the methylation of genes involved in neuroinflammation, neurogenesis, neuronal migration, signal transduction, mitochondrial functioning, cell cycle, and DNA damage response, as well as apoptosis. Detailed analysis reveals that Mn-induced DNA methylation leads to the down-regulation of brain-derived neurotrophic factor (BDNF) expression and the up-regulation of p53. Collectively, current evidence indicates that epigenetic mechanisms are key mediators of manganese (Mn)-induced neurotoxicity in both in vivo and in vitro models. However, the specific target genes and downstream signaling pathways involved in Mn-associated epigenetic regulation have yet to be fully characterized.

The primary treatment for Celiac disease (CeD) is a gluten-free diet (GFD), which presents challenges. Studies on the anti-inflammatory properties of Curcumin, Quercetin, Vitamin D, Zinc, and Eicosapentaenoic acid (EPA) offer hope for patients. This study evaluated their effects on immune reactivity in gliadin-stimulated Caco-2 cells.

Mast cells are key drivers of allergic inflammation. We have previously shown that butyrate, a short-chain fatty acid derived from dietary fibers, inhibits human mast cell activation and degranulation. Here, we characterized the mechanisms underlying butyrate-mediated control of mast cell activity. To this end, we assessed the genome-wide impact of butyrate, a histone deacetylase (HDAC) inhibitor, on the epigenomic control of mast cell gene expression by integrating transcriptome and histone acetylation (H3K27Ac) profiles obtained from butyrate-treated primary human mast cells. Butyrate affected a selective set of genes and gene regulatory elements in mast cells. Most prominent was the hypoacetylation of promoter regions of highly expressed genes and super-enhancers controlling key mast cell identity genes. Perturbation of super-enhancer activity via pharmacological bromodomain inhibition suppressed degranulation of primary human mast cells, evoking repression of key mast cell identity genes that resembled the inhibitory effects of butyrate. Our data indicate that butyrate inhibits human mast cell activity via surprisingly selective targeting of super-enhancers to regulate the core mast cell transcriptional program.

Major depressive disorder is a prevalent and debilitating psychiatric condition. Understanding its molecular mechanisms can aid in the development of more effective treatments. Gap junctions (GJs), composed of connexin (CX) proteins, facilitate direct intercellular communication and have been implicated in the pathophysiology of depression. In particular, connexin 36 (CX36) and connexin 43 (CX43) play key roles in neuronal and glial interactions, respectively. This study aimed to investigate whether fluoxetine modulates the expression of CX36 and CX43 in specific limbic regions, including the ventral hippocampus (v Hip), medial prefrontal cortex (m PC), and basolateral amygdala (BLA) of rats subjected to chronic unpredictable stress (CUS).

Recent years have seen increased focused on developing new anti-parasitic drugs that are both highly effective and low in toxicity, as the widespread use of existing anti-parasitic drugs has raised growing concerns. Natural products have gained significant interest due to their diverse biological activities with minimal toxic side effects. Our previous studies have already demonstrated the good anti-E. tenella effect of Perillyl Alcohol. To further investigate its efficacy against other protozoa, we selected Toxoplasma gondii as the researchsubject.

Glioblastoma multiforme (GBM) is a deadly disease known for its genetic heterogeneity. LTR12C is an endogenous retrovirus-derived regulator of pro-apoptotic genes and is normally silenced by epigenetic regulation. In this study, we found that the treatment of two glioblastoma cell lines, T98-G and U87-MG, with DNA methyltransferase (DNMT) and histone deacetylase (HDAC) inhibitors activated LTR12C expression. Combined treatment with these epigenetic drugs exerted a synergistic action on the LTR12C activation in both cell lines, while treatment with each drug as a single agent had a far weaker effect. A strong induction of the expression of the TP63 gene was seen in both cell lines, with the pro-apoptotic isoform GTA-p63 accounting for most of this increase. Coherently, downstream targets of p63, such as p21 and PUMA, were also induced by the combined treatment. Furthermore, we observed a significant reduction in the GBM cell growth and viability following the dual DNMT/HDAC inhibition. These findings reveal that the reactivation of LTR12C expression has the potential to modulate survival pathways in glioblastoma and provide information regarding possible epigenetic mechanisms that can be used to treat this deadly disease.

To investigate how dysregulated transient receptor potential canonical channels (TRPCs) are associated with Alzheimer's disease (AD), we challenged primary neurons with amyloid-β (Aβ). Both the naturally secreted or synthetic Aβ oligomers (AβOs) induced long-lasting increased TRPC3 and downregulated the TRPC6 expression in mature excitatory neurons (CaMKIIα-high) via a Ca2+-dependent calcineurin-coupled NFAT transcriptionally and calpain-mediated protein degradation, respectively. The TRPC3 expression was also found to be upregulated in pyramidal neurons of human AD brains. The selective downregulation of the Trpc6 gene induced synaptotoxicity, while no significant effect was observed from the Trpc3-targeting siRNA, suggesting potentially differential roles of TRPC3 and 6 in modulating the synaptic morphology and functions. Electrophysiological recordings of mouse hippocampal slices overexpressing TRPC3 revealed increased neuronal hyperactivity upon the TRPC3 channel activation by its agonist. Furthermore, the AβO-mediated synaptotoxicity appeared to be positively correlated with the degrees of the induced dendritic Ca2+ flux in neurons, which was completely prevented by the co-treatment with two pyrazole-based TRPC3-selective antagonists Pyr3 or Pyr10. Taken together, our findings suggest that the aberrantly upregulated TRPC3 is another ion channel critically contributing to the process of AβO-induced Ca2+ overload, neuronal hyperexcitation, and synaptotoxicity, thus representing a potential therapeutic target of AD.

Despite affecting millions worldwide, major depressive disorder (MDD) remains a therapeutic challenge, with approximately one-third of patients failing to respond to standard treatments. The need for innovative, molecularly driven therapies has turned attention to ketamine and its enantiomers. While S-ketamine is clinically approved for treatment-resistant depression (TRD), it has various psychoactive side effects and potential for abuse. Hence, it is necessary to identify alternative compounds, such as R-ketamine, and their metabolites (e.g., 2S,6S-hydroxynorketamine and 2R,6R-hydroxynorketamine, collectively referred to as HNKs). Emerging evidence suggests that the pathophysiology of MDD involves two processes regulated by the unfolded protein response (UPR): endoplasmic reticulum (ER) stress and neuroinflammation. As such, they represent promising therapeutic targets. The study provides the first direct comparison of ketamine enantiomers and their metabolites in modulating ER stress and inflammatory signaling in human microglial cells (HMC3), which play key roles in neuroimmune communication. Both S-ketamine and R-ketamine, along with their metabolites, significantly reduced both the expression and protein levels of CHOP and GRP78-two critical UPR components-under tunicamycin-induced ER stress conditions. Additionally, the compounds significantly decreased IL-6 levels and, to a lesser extent, IL-8 levels in lipopolysaccharide (LPS)-stimulated microglia, indicating anti-inflammatory potential. Taken together, these findings highlight a novel glia-targeted mechanism by which ketamine and its metabolites modulate ER stress and neuroinflammation. CHOP and GRP78 appear to be stress-responsive molecular markers within the UPR pathway. These results justify further in vivo validation and support the development of antidepressants with fewer psychoactive effects.

Traumatic brain injury (TBI) leads to persistent pro-inflammatory microglial activation implicated in neurodegeneration. Idebenone, a coenzyme Q10 analogue that interacts with both mitochondria and the tyrosine kinase adaptor SHC1, inhibits aspects of microglial activation in vitro. We used the NanoString Neuropathology Panel to test the hypothesis that idebenone post-treatment mitigates TBI-pathology-associated acute gene expression changes by moderating the pro-inflammatory microglial response to injury. Controlled cortical impact to adult male mice increased the microglial activation signature in the peri-lesional cortex at 24 h post-TBI. Unexpectedly, several microglial signature genes upregulated by TBI were further increased by post-injury idebenone administration. However, idebenone significantly attenuated TBI-mediated perturbations to gene expression associated with behavior, particularly in the gene ontology-biological process (GO:BP) pathways "ephrin receptor signaling" and "dopamine metabolic process". Gene co-expression analysis correlated levels of microglial complement component 1q (C1q) and the neurotrophin receptor gene Ntrk1 to large (>3-fold) TBI-induced decreases in dopamine receptor genes Drd1 and Drd2 that were mitigated by idebenone treatment. Bioinformatics analysis identified SUZ12 as a candidate transcriptional regulator of idebenone-modified gene expression changes. Overall, the results suggest that idebenone may enhance TBI-induced microglial number within the first 24 h of TBI and identify ephrin-A and dopamine signaling as novel idebenone targets.