HIV-1 infection establishes a reservoir of long-lived cells with integrated proviral DNA that can persist despite antiretroviral therapy (ART). Certain reservoir cells can be reactivated to reinitiate infection. The mechanisms governing proviral latency and transcriptional regulation of the provirus are complex. Here, we identify a role for histone H3 citrullination, a post-translational modification catalyzed by protein-arginine deiminase type-4 (PADI4), in HIV-1 transcription and latency. PADI4 inhibition by the small molecule inhibitor GSK484 reduces HIV-1 transcription after T cell activation in ex vivo cultures of CD4+ T cells from people living with HIV-1 in a cross-sectional study. The effect is more pronounced in individuals with active viremia compared to individuals under effective ART. Cell models of HIV-1 latency show that citrullination of histone H3 occurs at the HIV-1 promoter upon T cell stimulation, which facilitates proviral transcription. HIV-1 integrates into genomic regions marked by H3 citrullination and these proviruses are less prone to latency compared to those in non-citrullinated chromatin. Inhibiting PADI4 leads to compaction of the HIV-1 promoter chromatin and an increase of heterochromatin protein 1α (HP1α)-covered heterochromatin, in a mechanism partly dependent on the HUSH complex. Our data reveal a novel mechanism to explain HIV-1 latency and transcriptional regulation.

The present study presents a novel approach combining a tetracycline-inducible system (Tet-On) and CRISPR-Cas9 techniques to investigate the function of two essential genes in Phytophthora sojae. We constructed a donor vector in which the reverse tetracycline transactivator (rtTA) is driven by an oomycete promoter. Additionally, it contains a fused TetR binding site and the minimum oomycete promoter, as well as 1000-bp homologous arms of the promoter upstream and downstream sequences. The promoter of the target gene was replaced with a tetracycline-responsive promoter (Ptet) using a CRISPR-Cas9 system. In the native transformants, the target gene was induced by the administration of tetracycline and repressed in its absence. Using the Tet-On/CRISPR-Cas9 system, we obtained inducible transformants of PsAF5 and PsCesA3. The phenotype of PsAF5 inducible transformants without doxycycline was consistent with that of ΔPsAF5 transformants, specifically characterised by an increase in oospore production and heightened sensitivity to H2O2. PsCesA3 inducible transformants could not grow in the absence of doxycycline, which means PsCesA3 is an essential protein for P. sojae. In conclusion, the Tet-On/CRISPR-Cas9 system represents an effective approach for investigating crucial genes in P. sojae.

Acute myeloid leukemia (AML) is associated with the accumulation of acquired genetic disorders. Moreorver chromosomal and molecular changes are independent prognostic factors that are taken into account to determine prognosis and treatment. MicroRNAs are novel gene regulators, which have been recognized to play an important role in pathological leukemogenesis. This study is aimed to analyze the possible role of micro RNAs as a markers predicting the outcome to induction chemotherapy based on cytarabine.

Ataxia telangiectasia mutated (ATM) blockage can induce apoptosis in ovarian cancer. However, the molecular mechanisms underlying this process remain poorly understood. In this study, ovarian cancer cells (SKOV3) were treated with an ATM inhibitor (KU60019) for 24 hours, and the fold changes of DGAT1 and hsa-miR-1273g-3p were quantified by real-time quantitative polymerase chain reaction (RT-qPCR). Gene Ontology (GO) and pathway enrichment analyses of DGAT1-associated functions were performed. Hsa-miR-1273g-3p mimics were used to investigate the relationship between DGAT1 and hsa-miR-1273g-3p in ovarian cancer cells under ATM inhibitor treatment, and cell apoptosis rate, viability, and migration were detected. The DGAT1 inhibitor reversed KU60019-induced migration impairment in SKOV3 cells. Finally, Kaplan-Meier analysis showed the correlation between DGAT1 level and survival in ovarian cancer patients. We found that ATM blockage significantly suppressed hsa-miR-1273g-3p level and elevated DGAT1 level in SKOV3 cells. DGAT1 was enriched in cytokine receptor interaction, T cell receptor signaling pathway, and cell apoptosis. Hsa-miR-1273g-3p mimics reversed suppression of DGAT1 and impaired cell viability induced by KU60019. Higher levels of DGAT1 associated with worse survival in ovarian cancer patients. KU60019 induced ovarian cancer cell impairment by enhancing DGAT1 level and suppressing hsa-miR-1273g-3p level. Our results demonstrate the antitumor effect of KU60019 in ovarian cancer depended on miR1273g-3p/DGAT1 axis.

Epigenetic alterations are emerging as a major driver of acquired cisplatin (CDDP) resistance in bladder cancer (BCa). The study investigated whether GSK343, an inhibitor of Enhancer of Zeste Homolog 2 (EZH2), can overcome CDDP resistance in BCa. CDDP-resistant T24 and 5637 cells were treated GSK343 (5, 10, or 20µM) for 48 h. Cell viability was assessed using CCK-8 assays, clonogenic survival using colony formation assays, migration capacity using wound healing (scratch) assays, invasion using Transwell assays, and apoptosis using flow cytometry. CDDP-resistant cells exhibited significantly higher EZH2 and H3K27me3 expression levels than parental T24 and 5637 cells. Treatment with 20 µM GSK343 markedly reduced EZH2 and H3K27me3 expression in resistant cells compared to vehicle control, with greater efficacy than lower concentrations (5 or 10 µM). Following 20 µM GSK343 treatment, resistant cells showed significantly reduced viability, fewer colonies, impaired migration, and decreased invasion compared to vehicle control. Furthermore, the apoptosis rate was significantly increased in resistant cells treated with 20 µM GSK343. The study demonstrates that GSK343 inhibits EZH2-mediated H3K27me3 and overcomes acquired CDDP resistance in BCa cells, suggesting its therapeutic potential for BCa patients with limited benefit from chemotherapy.

Sea cucumber represents a potential marine source of high value compounds with medicinal properties especially its anti-cancer activity. Sea cucumbers contain numerous biomolecules, including sulfated polysaccharides (Ps) which have enormous therapeutic and nutraceutical potential. This study aimed to investigate anticancer effect of Ps extracted from sea cucumbers on hepatocellular carcinoma. This study was in vitro study conducted on HepG-2 cells and normal wish cells that were divided into four groups: Group I including untreated cells, Group II including cells treated with different concentrations of 5-FU, Group III including cells treated with various concentrations of Ps extract. Group IV including cells treated with different concentrations of combined 5-FU and Ps extract. The extracted Ps were characterized using FT-IR, HPLC, and GC-MS. The anticancer effect of Ps extract was determined using cytotoxicity MTT assay, DNA fragmentation assay, wound healing assay, colony formation and soft agar assay. Also, the effect of Ps extract on VEGF, survivin, BAX and BID gene expression was determined by qRT-PCR and its effect on Bcl2 and BAK protein level was determined by western blotting technique. The results indicated that sea cucumber Ps extract either alone or in combination with 5-FU reduced HepG-2 and wish cell viability with higher selectivity index. Also, it inhibited both adherent and non-adherent colony forming ability and cell migration of HepG-2 cells. Moreover, it was significantly downregulated VEGF, survivin and Bcl2 while, it was significantly upregulated BAX, BAK and BID. In conclusion, sea cucumber Ps extract may be an effective chemotherapeutic agent against HCC.

Pilocytic astrocytomas (PA), the most common pediatric low-grade gliomas (pLGGs), are characterized by genetic MAPK pathway alterations leading to constitutive activation and oncogene-induced senescence (OIS) accompanied with the senescence-associated secretory phenotype (SASP). This study investigates the molecular mechanisms of signaling pathways regulating OIS and SASP in pLGGs using a multi-omics approach. We utilized senescent DKFZ-BT66 cells derived from a primary KIAA1549::BRAF-fusion positive PA to generate RNA-sequencing and phospho-/proteomic datasets before and after treatment with the MEK inhibitor trametinib. Multi-omics factor analysis (MEFISTO) and single sample gene set enrichment analysis (ssGSEA) were employed to identify key OIS effectors and differentially regulated pathways upon MAPK inhibition. Trametinib treatment inhibited MAPK activity, OIS and SASP signatures across all omics levels, functionally underscored by reduced sensitivity towards senolytic drugs. We constructed a pathway network using a prior knowledge approach, mapping n = 106 upregulated and n = 84 downregulated direct downstream effectors of MAPK leading to OIS/SASP. These effectors are associated with better progression-free survival in pLGG patients, independent of tumor site, level of resection, and genetic aberration. Several compounds targeting signaling nodes (SOD-1, IRS1, CDK1/2, CK2) involved in OIS and under MAPK control were identified, of which n = 4 were validated in an additional primary KIAA1549::BRAF fusion pLGG model as potential new therapeutic vulnerabilities for the treatment of pLGG. Our unbiased multi-omics signaling pathway analysis identifies a specific and comprehensive network of MAPK-OIS-SASP interdependencies in pLGGs and suggests new therapeutic strategies for these tumors.

Improving sperm quality is essential for enhancing the reproductive efficiency of Oreochromis niloticus. This study evaluated the effect of three dietary antioxidant supplements, kaolinite-doped zinc oxide (ZnO-K), citrus essential oil (CEO), and pumpkin seed oil (PSO), on sperm quality parameters. A suite of integrative assessments, including Computer-Assisted Semen Analysis (CASA) parameters, spermatozoa DNA integrity, antioxidant enzyme assays, and gene expression profiling, was applied to validate sperm quality. A total of 192 adult males (mean weight 421.31 g ± 30.41 SD) were assigned to four dietary groups, each with three replicates. The control group received a basal diet without supplementation. The experimental groups were fed diets supplemented with ZnO-K (0.06 g kg⁻1), CEO (10 g kg⁻1), or PSO (15 g kg⁻1). ZnO-K supplementation significantly (P < 0.05) increased milt volume (1.40 ± 0.10 ml) and sperm concentration (5.676 × 109 sperm ml-1), along with marked improvements in CASA parameters (sperm motility and velocity) and DNA integrity. Antioxidant enzymes, catalase, CAT, glutathione peroxidase, GPX, and superoxide dismutase, SOD, were also significantly elevated in the ZnO-K group, recording activity values of 47.333 ± 1.452 U ml-1 milt, 65.667 ± 5.547 mU ml-1 milt and 60.667 ± 3.382 U ml-1 milt, respectively. Gene expression analysis revealed that CEO induced the highest upregulation of HSP70, while both CEO and ZnO-K significantly upregulated CC chemokine expression compared to control. In contrast, PSO consistently showed the lowest performance across all measured parameters. Collectively, ZnO-K supplementation most effectively enhanced sperm physiological and biochemical quality, whereas CEO predominantly supported cellular stress protection through gene expression modulation. These findings offered practical implications for optimizing artificial reproduction and sperm cryopreservation strategies in tilapia aquaculture.

CRISPR activation and interference (CRISPRa/i) are highly effective tools to regulate transcription by fusing dead Cas9 (dCas9) with transcriptional regulatory factors guided by small guide RNA (sgRNA) in mammalian cells and mice. Still, a controllable gene regulation system is desired to investigate and manipulate dynamic biological processes. Here, we reported flexible drug-responsive CRISPRa/i systems by fusing mutated human estrogen receptor (ERT2) domains, which responded to estrogen analogue tamoxifen or its active metabolite 4-hydroxy-tamoxifen (4OHT), to CRISPRa/i components for transcriptional regulation. Upon 4OHT treatment, the optimal variants, ERT2-ERT2-CRISPRa/i-ERT2 (iCRISPRa/i), showed rapid protein translocation of iCRISPRa/i from cytoplasm to nucleus and subsequent transcriptional response. The inducible transcriptional manipulation could be restored to its original level when 4OHT was withdrawn. Moreover, the efficiencies of gene expression regulation of iCRISPRa/i were comparable to those of non-inducible and doxycycline-inducible counterparts, with a lower leakage and a faster drug response activity. The iCRISPRa/i systems successfully induced phenotypic changes in various cell lines. These results highlight that iCRISPRa/i systems could achieve fast and flexible drug-responsive transcriptional modulation and phenotypic changes, and thus provide better options for gain- and loss-of-function model construction and gene therapy.

Glioblastoma multiforme (GBM) is a lethal brain tumor. With the current gold standard chemotherapy treatment, temozolomide (TMZ), many patients do not survive beyond one year. While the urgency of researching novel treatments is understandable, the prohibitively high costs and the prolonged duration of research and clinical trials significantly delay the availability of medical advancements to the general public. This highlights the urgent need for adjuvant therapies to enhance treatment effectiveness.

The aim of this study was to investigate the anticancer effects of H. pluvialis extract on breast cancer.  Methods: We evaluated the cytotoxicity, suppression of migration, and apoptosis ability of H. pluvialis alga extract MDA-MB-468 by MTT assay, scratch test, and flow cytometry, respectively. The expression patterns of MMP1 and MMP9, Bax and Bcl2, Caspase3, Caspase6, and Caspase9 were analyzed by qRT-PCR.

The current investigation evaluated the impact of the dietary addition of commercial bile acids (BAs) on growth, nutrient assimilation, immunity, antioxidant status, intestinal and hepatic histomorphometry, and gene expression of lipid metabolism in Nile tilapia (Oreochromis niloticus). In a study conducted for seventy days, 180 healthy fingerlings weighing 9 ± 0.5 g were divided into 18 hapas measuring 0.7 × 0.7 × 1.0 m. The fish were fed on six meals enriched with varied amounts of BAs: 0.0 (D1), 0.1 (D2), 0.2 (D3), 0.3 (D4), 0.4 (D5), and 0.5 (D6) g/kg diet. Nile tilapia fed the D3 diet exhibited significantly enhanced growth performance, with a specific growth rate of 1.89%/day and had the greatest feed conversion ratio (1.25), protein productive value, and energy utilization (33.28%). Fish fed the D3 exhibited significantly the highest crude protein content (64.50%). Energy content varied significantly, with D1 showing the lowest value (533.34 Kcal/100 g) and D3 the highest (604.27 Kcal/100 g). D3 improved biochemical indicators, immunological parameters, and digestive enzymes of O. niloticus. Histological analysis revealed notable liver and intestinal integrity enhancements among fish receiving BA-enriched diets, especially D3. Additionally, gene expression related to lipid metabolism in liver, peritoneal fat, and muscle tissues was upregulated in the treatment groups, especially 0.2 g/kg BAs compared to the control group. Results illustrate significant modulation of lipid metabolism gene expression parameters (Adipose triglyceride lipase; ATGL, Hormone-sensitive lipase; HSL, Peroxisome proliferator-activated receptor α; PPARα, Fatty acid synthase; FAS) by BAs treatments and were upregulated in BA-fed groups (D2-D6). Conversely, Carnitine palmitoyl transferase 1; CPT-1and Insulin-like growth factor-II; Igf-II expression declined, particularly when the BAs dose was increased. Accordingly, dietary 0.2 g/kg BAs supplementation positively influences on physiological, biochemical parameters, and lipid metabolic of Nile tilapia, making it a promising feed additive for aquaculture.

Hydroxyurea (HU) has been extensively used in laboratory settings to induce S-phase arrest and checkpoint activation. Furthermore, it has a history of clinical use as a cost-effective chemotherapeutic agent. Nevertheless, there is still uncertainty regarding its precise pharmacology, side effects, and toxicity, particularly in terms of its impact on organelle homeostasis. Here, we demonstrate that in budding yeast, HU specifically inhibits the endoplasmic reticulum-associated degradation (ERAD) of luminal misfolded proteins (ERAD-L pathway), an effect that is independent of S-phase arrest. In contrast, HU did not affect the degradation of misfolded ER membrane proteins or the degradation of cytosolic proteins. The selective inhibition of ERAD-L by HU is likely attributable to the formation of disulfide bonds in cysteine residues in luminal substrates, which must be reduced before their retrotranslocation to the cytosol. We further demonstrate that HU plays a role in alleviating reductive stress phenotypes observed in cells lacking Ero1, which is essential for oxidative protein folding in the ER. We propose that HU functions as a modulator of thiol-disulfide homeostasis in the ER lumen.

Nicotine exposure during neural development presents a significant public health concern. Nicotine, the primary addictive component of tobacco, influences the central nervous system by interacting with various cell types, including the glial cell termed astrocytes. Astrocytes are cells that are critical for supporting neurons, regulating neurotransmitter balance, and managing neuroinflammation. This current study explored nicotine's effects on astrocytes, examining cellular activity and gene expression within an acute exposure period. Murine C8D1A astrocytic (garnered as a cell line from postnatal day 8 tissue) cells were treated with nicotine (0-500 ng/mL) in vitro, with assays measuring cell viability and apoptosis at 12, 18, 24, and 48 hours to establish a critical concentration gradient for nicotine. Nicotine exposure increased astrocyte viability at later time points (24 and 48 hours), while apoptosis rose initially but declined over time allowing for the establishment of pharmacologically and clinically relevant nicotine concentrations of 25,50 and 100ng/ml for subsequent experiments. Real-time quantitative PCR revealed that nicotine influenced inflammatory signaling, with pro-inflammatory (A1) markers (IL-6, IFNγ, TNFα) increasing in a dose- and time-dependent manner, while anti-inflammatory (A2) markers (ARG1, IL-10, TGFβ) displayed a more complex pattern after nicotine exposures to astrocytes. These results suggest that nicotine disrupts astrocyte function and inflammatory balance, which may contribute to neurodevelopmental disruptions and heightened neuroinflammatory risks in adults. Further research is needed to investigate the prolonged impact of nicotine on brain health, addiction, and associated neurological conditions.

Multiple myeloma (MM) is a blood cancer marked by the abnormal clonal growth of plasma cells. Hypoxia plays a critical role in the progression and treatment resistance of MM.

Corynebacterium glutamicum serves as a pivotal industrial chassis for biomanufacturing and an ideal model for studying the phylogenetically related pathogen Mycobacterium tuberculosis. Oxidative stress poses a critical challenge to microorganisms during aerobic industrial processes and immune cell-mediated antibacterial killing by perturbing cellular redox homeostasis, affecting central metabolism, and damaging the integrity of biomacromolecules. However, the intricate mechanisms underlying the dynamic defence of C. glutamicum, despite previous transcriptomic studies on acute and adaptive responses to oxidative stresses, remain largely unclear, hindering strain engineering for industrial applications and the development of effective antimicrobial treatments. In this study, the susceptibility of C. glutamicum to hydrogen peroxide (H2O2) was evaluated, and the inhibitory dynamics of H2O2 were characterised through viable cell counting. RNA sequencing (RNA-seq) was employed to analyse gene expression changes after exposure to 720 mM H2O2. The treatment induced differential expression of 966 and 787 genes at 2 and 6 h, respectively, reflecting perturbations across a broad array of pathways, including (i) enhanced H2O2 and peroxide scavenging, mycothiol biosynthesis, and iron chelation; (ii) repressed central metabolism and enhanced anaplerosis; (iii) elevated sulphur assimilation; (iv) altered amino acid biosynthesis; and (v) altered transcriptional regulation in response to oxidative stress. Further validation by overexpression of ahpD, cysN, and exogenous supplementation with l-methionine and l-cysteine significantly enhanced bacterial tolerance to H2O2. Overall, this study provides the most comprehensive analysis to date of temporal cellular adaptation to H2O2 stress in C. glutamicum, establishing a foundation for future applications in both biomanufacturing and antimicrobial research.

KDM4-A/B/C, preferentially demethylating di- and tri-methylated lysine 9 on histone H3, are overexpressed in cancers and considered interesting therapeutic targets. Consequently, KDM4 inhibitors have been developed to block their enzymatic activity. However, the potential lack of specificity of such small molecules (epi-drugs) may contribute to dose-limiting toxicities. In the pursuit of more specific interventions, epigenetic editing (epi-editing) has emerged as a powerful tool to modulate gene expression by modifying the epigenetic profile of specific genomic locations. The recently developed CRISPRoff (dCas9 fused to DNMT3A/3L and KRAB), guided by sgRNAs, is successfully used for gene repression by introducing methylation of DNA and (indirectly) of histones at the targeted genomic region. We propose that combining epi-editing (here to prevent the expression of KDM4) with epi-drugs (to inhibit the KDM4 protein activity) may represent a novel path for synergistic anticancer effects through simultaneous inhibition of gene expression and protein activity. Upon validating the downregulation of KDM4A in HEK293T cells through epi-editing, we demonstrated its repression in colon, breast and hepatocellular carcinomas which was effective in preventing (breast, MCF7) or inhibiting (colon, HCT116) cancer cell growth. Anticancer effect was also confirmed for these cell lines using the KDM4 inhibitor QC6352. In parallel, our studies demonstrate a previously unnoticed increase in the expression of KDM4-A/B/C genes following the inhibition of protein activity using the pan-KDM4 inhibitors QC6352 and JIB-04. Importantly, this induction of gene expression was fully prevented or even further inhibited by epi-editing. Then, we assessed the efficacy of our dual-targeted silencing approach in cancer cells and demonstrated that the inhibition in cancer cell growth by epi-drug or epigenetic editing could be further improved by combining the treatments. Building upon these findings, we introduce a novel, potentially synergistic, therapeutic strategy that combines epi-drug administration with epi-editing. This innovative approach aims to reduce drug toxicity and the potential development of resistance by preventing drug-induced upregulation of target enzyme expression, thereby further increasing anticancer effects.

The intestine has molecular and functional diversity across the proximal-distal and the crypt-villus axes, so it is imperative to determine the common and compartment-specific molecular actions of vitamin D. However, very little work on vitamin D mediated gene regulation has been done in normal human intestine. Here, we examined the impact of 1,25-dihydroxyvitamin D (1,25(OH)2D3) on cultures of human intestinal epithelium derived from duodenum (Dd) and distal colon (Co) biopsies of 6 subjects per tissue.

This study investigates the molecular mechanisms underlying the inhibitory effects of 5-alkylresorcinol (5ARs) on colorectal cancer (CRC) growth.

Early studies indicated that the androgen-deprivation-therapy with antiandrogen Enzalutamide (Enz) could increase prostate cancer patients' survival by an average of 4.8 months. Yet Enz might also have some adverse effects via increasing the prostate cancer (PCa) cell invasion. Here we found Enz treatment could increase SALL4 expression to increase the cancer stem cells-like (CSC-like) population that resulted in increasing the PCa cell invasion. Mechanism dissection revealed that Enz could function via androgen receptor (AR) to transcriptionally regulate the SALL4 expression via direct binding on the SALL4 5'-promoter. The consequences of such Enz/AR/SALL4 axis could upregulate the SOX2-OCT4 expression to increase the CSC-like population and the PCa cells invasion. Together, results from multiple in vitro and in vivo experiments all conclude that Enz may induce the adverse effect of increasing PCa cells invasion via altering the AR/SALL4/SOX2-OCT4 signaling to increase the CSC-like population, and targeting SALL4 may decrease this adverse effect for further suppress the PCa progression.