Altered Expression Levels Research Articles

Evolution and functional characterization of Populus salt stress-responsive calcineurin B-like protein-interacting protein kinases.

Identification of salt-responsive calcineurin B-like protein-interacting protein kinases(CIPKs) in Populus. Calcineurin B-like protein-interacting protein kinases (CIPKs) play vital roles in plant growth and abiotic stress responses. Currently, the regulatory mechanisms underlying these processes mediated by CIPK proteins are not completely understood in woody species. This study provided the first systematic analysis of 31 Populus CIPK genes and investigated their evolutionary relationships, gene structures, motif compositions, and salt stress responses. A total of 11 pairs of paralogous PtCIPK genes were identified, of which three pairs may be resulted from whole genome duplication, and two pairs that may be created bytandem duplications. RT-qPCR analysis revealed that 93.5% (29/31) genes showed altered expression levels in roots after salt treatment. Ectopic expression of PdCIPK21 or PdCIPK31 in Arabidopsis resulted in significant increases of seed germination, root elongation and fresh weight under salt stressconditions. Cytological observation revealed that PdCIPK21/31 overexpression lines showed increased number, lumen area and cell wall thickness of xylem vessels, and higher lignin content in stems compared with the wild type, with decreased sensitivity to long-term salt stress treatment. Our results suggest that PdCIPK21/31 serve as candidate genes for improving wood production and enhancing salt tolerance of tree species.

Changes in Circulating Levels of Long Non-Coding RNA p5549 and p19461 Following Metabolic Bariatric Surgery (MBS): A Prospective Study.

Obesity is attributed to a combination of factors such as lifestyle, environmental influences, and genetic background. Nowadays, the issue of obesity has grown to an epidemic scale. Environmental changes, having contributed to the sharp rise in obesity prevalence, are not the only contributing etiologic factors. Inherent biological variables interact with environmental factors resulting in obesity. Epigenetic mechanisms may explain part of obesity heritability. One of the recently discovered epigenetic mechanisms for controlling gene expression is long non-coding RNAs (lncRNAs). Circulating lncRNA p5549 and p19461 levels were reported to be significantly lower in individuals with obesity. This study aimed to evaluate whether weight loss following metabolic/bariatric surgery (MBS) can be related to altered expression levels of those lncRNAs, which have been reported to be reduced in individuals with obesity. Comparison of circulating levels of lncRNA p5549 and p19461 before and 12weeks after MBS in thirty-four patients was conducted to evaluate whether MBS can revert the altered levels of these lncRNAs. None of the participating patients were lost to follow-up, and all underwent re-evaluation of post-surgical expression levels. lncRNA p5549 expression levels in serum were found to increase significantly in the postoperative samples compared to preoperative samples (fold increase: 4.63 ± 7.68, p = 0.014). Epigenetic changes in patients with obesity, specifically lncRNA-p5549 expression levels, are reversed after MBS. The postoperative increase in the expression levels of lncRNA- p19461 was not statistically significant.

A structure-based in silico analysis of the Kell blood group system

Kell is one of the most complex blood group systems, with a highly polymorphic genetic background. Extensive allelic variations in the KEL gene affect the encoded erythrocyte surface protein Kell. Genetic variants causing aberrant splicing, premature termination of protein translation, or specific amino acid exchanges lead to a variety of different phenotypes with altered Kell expression levels or changes in the antigenic properties of the Kell protein. Using an in silico structural model of the Kell protein, we analyzed the biophysical and structural context of all full-length Kell variants of known phenotype. The results provided insights regarding the 3D co-localization of antigenic Kell variants and led us to suggest several conformational epitopes on the Kell protein surface. We found a number of correlations between the properties of individual genetic variants in the Kell protein and their respective serological phenotypes, which we used as a search filter to predict potentially new immunogenic Kell variants from an in-house whole exome sequencing dataset of 19,772 exomes. Our analysis workflow and results aid blood group serologists in predicting whether a newly identified Kell genetic variant may result in a specific phenotype.

Study of gene expression of the Toll-like receptor system in the forebrain cortex of rat pups with prenatal alcohol exposure and pharmacologic correction with rifampicin

Ethanol causes changes in the toll-like receptor (TLR) system in the brain promoting activation of neuroinflammatory pathways. Alcohol consumption during pregnancy induces neuroinflammatory processes in the fetus, which can lead to the development of symptoms of fetal alcohol spectrum disorder (FASD). Modeling prenatal alcohol exposure in our experiment resulted in changes in the expression of TLR system genes (Tlr3, Tlr4, Hmgb1, Trif, cytokine genes) in the forebrain cortex of baby rats. The administration of rifampicin (from the first to the seventh day of neonatal development) normalized the altered expression level of the studied genes. This suggests that rifampicin may prevent the development of persistent neuroinflammatory phenomena in the forebrain cortex of baby rats.

The role of p16 gene and P16INK4a protein in hematologic malignancies and therapeutic implications: A systematic review.

Hematological malignancies encompass a diverse group of cancers affecting the blood, bone marrow and lymph nodes. The p16 gene, encoding the P16INK4A protein, plays a pivotal role in cell cycle regulation and tumor suppression. Understanding the involvement of p16 in the development and progression of hematological malignancies is crucial for advancing therapeutic strategies. This systematic review aims to elucidate the multifaceted roles of the p16 gene and P16INK4A protein in hematological malignancies, focusing on their impact on disease pathogenesis, prognostic significance and therapeutic implications. A comprehensive search was conducted across electronic databases, including PubMed, Scopus and Google Scholar, using predefined search terms related to p16, P16INK4A, hematological malignancies, and therapy. Studies published up to 2023 were included, encompassing clinical trials, observational studies, meta-analyses, and preclinical research. The review synthesizes evidence highlighting the dysregulation of the p16 pathway in various hematological cancers. Alterations in p16 expression levels, genetic mutations and epigenetic modifications contribute to disease initiation and progression. Moreover, the prognostic significance of p16 status in predicting therapeutic outcomes and patient survival is explored. The p16 gene and P16INK4A protein emerge as promising biomarkers and therapeutic targets in hematological malignancies. Integrating knowledge of p16 dysregulation into clinical practice holds the potential to optimize treatment strategies, enhance patient outcomes and pave the way for personalized medicine approaches in the management of these challenging diseases.

Clusterin Deficiency Promotes Cellular Senescence in Human Astrocytes.

The glycoprotein clusterin (CLU) is involved in cell proliferation and DNA damage repair and is highly expressed in tumor cells. Here, we aimed to investigate the effects of CLU dysregulation on two human astrocytic cell lines: CCF-STTG1 astrocytoma cells and SV-40 immortalized normal human astrocytes. We observed that suppression of CLU expression by RNA interference inhibited cell proliferation, triggered the DNA damage response, and resulted in cellular senescence in both cell types tested. To further investigate the underlying mechanism behind these changes, we measured reactive oxygen species, assessed mitochondrial function, and determined selected markers of the senescence-associated secretory phenotype. Our results suggest that CLU deficiency triggers oxidative stress-mediated cellular senescence associated with pronounced alterations in mitochondrial membrane potential, mitochondrial mass, and expression levels of OXPHOS complex I, II, III and IV, indicating mitochondrial dysfunction. This report shows the important role of CLU in cell cycle maintenance in astrocytes. Based on these data, targeting CLU may serve as a potential therapeutic approach valuable for treating gliomas.

Long-chain perfluoroalkylether carboxylic acids PFO5DoA and PFO4DA alter glucose, bile acid, and thyroid hormone homeostasis in fetal rats from 5-day maternal oral exposure

Chemical monitoring studies in North Carolina, USA and Shandong, China have reported detections of perfluoroalkylether carboxylic acids of increasing chain length with ether bonds between each fluorinated carbon. Despite detection there is limited hazard data available to inform risk assessment. Here, we exposed pregnant Sprague-Dawley rats to two of these compounds, perfluoro-3,5,7,9-butaoxadecanoic acid (PFO4DA) and perfluoro-3,5,7,9,11-pentaoxadodecanoic acid (PFO5DoA), from gestation days 18-22 across a series of doses (0.3-62.5mg/kg/d) via oral gavage. PFO5DoA was acutely toxic to rat dams and fetuses at the top two doses (30 and 62.5mg/kg), while PFO4DA did not cause acute toxicity at any doses tested. PFO5DoA significantly increased maternal liver weight (≥3mg/kg; 28% increase at 10mg/kg) while PFO4DA did not affect maternal liver weight up to 62.5mg/kg. PFO4DA and PFO5DoA both significantly reduced serum total thyroxine in maternal (≥10mg/kg for both) and fetal (≥1mg/kg) rats. Both compounds significantly reduced fetal liver glycogen concentrations, increased fetal serum total bile acids, and altered expression levels of multiple genes associated with glucose metabolism in the fetal liver. Serum concentrations of PFO5DoA were higher than PFO4DA in both rat dams and fetuses at equivalent maternal oral doses indicating greater accumulation. Dose response modelling of several fetal endpoints as a function of serum molar concentration indicates PFO5DoA was ∼3-4-fold more potent than PFO4DA. PFO5DoA and PFO4DA produced maternal and fetal toxicity from short-term oral maternal exposure indicating need for additional toxicity data to evaluate potential human health risks.

Transcriptome profiling of maize transcription factor mutants to probe gene regulatory network predictions.

Transcription factors (TFs) play important roles in regulation of gene expression and phenotype. A variety of approaches have been utilized to develop gene-regulatory networks (GRNs) to predict the regulatory targets for each TF, such as yeast-one-hybrid (Y1H) screens and gene co-expression network (GCN) analysis. Here we identified potential TF targets and used a reverse genetics approach to test the predictions of several GRNs in maize. Loss-of-function mutant alleles were isolated for 22 maize TFs. These mutants did not exhibit obvious morphological phenotypes. However, transcriptomic profiling identified differentially expressed genes in each of the mutant genotypes, and targeted metabolic profiling indicated variable phenolic accumulation in some mutants. An analysis of expression levels for predicted target genes based on Y1H screens identified a small subset of predicted targets that exhibit altered expression levels. The analysis of predicted targets from GCN-based methods found significant enrichments for prediction sets of some TFs, but most predicted targets did not exhibit altered expression. This could result from false-positive GCN predictions, a TF with a secondary regulatory role resulting in minor effects on gene regulation, or redundant gene regulation by other TFs. Collectively, these findings suggest that loss-of-function for single uncharacterized TFs might have limited phenotypic impacts but can reveal subsets of GRN predicted targets with altered expression.

Association between the variations in metabolic pathways and oral cancer risk: results from a Pakistani case-control study.

Oral cancer (OC) is a significant global health concern, with Pakistan ranking 5th worldwide in OC incidence. Given the poor prognosis, early detection of at-risk individuals is crucial. Genetic factors, particularly single nucleotide polymorphisms (SNPs) in metabolic genes, may influence OC susceptibility. This study investigated the association between SNPs in CYP1A1, COX2, SOD2, and HIF1a genes and OC risk in the Pakistani population. A prospective study was conducted from October 2019 to March 2022, enrolling 215 newly diagnosed OC patients and 410 controls. Genetic variations were analyzed using High-Resolution Melting (HRM)analysis and Sanger sequencing, with protein expression evaluated by ELISA. No significant associations were found between the studied SNPs and OC risk. However, a non-significant trend was observed for the SOD2 variant (rs4880), where the G allele was associated with a higher OC risk than the A allele (p = 0.20). Elevated COX2 and HIF1α levels (p-values of 0.014 and <0.001, respectively) and reduced SOD2 levels (p < 0.0001) were observed in OC patients, while CYP1A1 levels remained similar in both controls and cases. Although SNPs in CYP1A1, COX2, SOD2, and HIF1α were not significantly associated with OC risk in the Pakistani population, altered protein expression levels of COX2, HIF1α and SOD2 suggest additional regulatory mechanisms. Further investigation into post-transcriptional modifications and epigenetic factors could lead to novel biomarkers and therapeutic targets for OC in Pakistan.

Impact of hydroxycarbamide treatment on the whole‐blood transcriptome in sickle cell disease

SummaryHydroxycarbamide (HC) is the most widely used therapeutic for individuals with sickle cell disease (SCD, including sickle cell anemia and other forms of the disease). HC's clinical benefits are primarily associated with its ability to induce foetal haemoglobin (HbF); this limited view of HC's therapeutic potential may lead to its discontinuation when a modest amount of HbF is induced. A better understanding of the HbF‐independent effects of HC on genes and pathways relevant to SCD pathophysiology is therefore needed. In this study, we performed bulk RNA‐Seq on whole blood samples collected from a cohort of 25 paediatric patients with SCD to identify genes and pathways that are affected by treatment with HC. At the maximum tolerated dose (MTD) of HC, patients showed altered expression levels of several genes and biological pathways. Pathways related to haeme metabolism, interferon‐alpha response, and interferon‐gamma response were significantly downregulated at HC MTD relative to the matched pre‐HC samples. Pathways linked with IL2‐STAT5 signalling and TNFα signalling via NF‐Kβ were observed to be up‐regulated at HC MTD. These results illustrate the range of effects exerted by HC during therapy for SCD and pave the way for an improved understanding of the HbF induction‐independent benefits of HC.

Acid Sphingomyelinase Activation and ROS Generation Potentiate Antiproliferative Effects of Mitomycin in HCC.

Sphingolipids play a major role in the regulation of hepatocellular apoptosis and proliferation. We have previously identified sphingolipid metabolites as biomarkers of chronic liver disease and hepatocellular carcinoma. Human hepatocellular carcinoma cell lines were transfected with a plasmid vector encoding for acid sphingomyelinase. Overexpressing cells were subsequently treated with mitomycin and cell proliferation, acid sphingomyelinase activity, sphingolipid concentrations, and generation of reactive oxygen species were assessed. The stimulation of acid sphingomyelinase-overexpressing cell lines with mitomycin showed a significant activation of the enzyme (p < 0.001) followed by an accumulation of various ceramide species (p < 0.001) and reactive oxygen radicals (p < 0.001) as compared to control transfected cells. Consequently, a significant reduction in cell proliferation was observed in acid sphingomyelinase-overexpressing cells (p < 0.05) which could be diminished by the simultaneous application of antioxidant agents. Moreover, the application of mitomycin induced significant alterations in mRNA expression levels of ceramidases and sphingosine kinases (p < 0.05). Our data suggest that the overexpression of the acid sphingomyelinase in human hepatoma cell lines enhances the in vitro antiproliferative potential of mitomycin via accumulation of ceramide and reactive oxygen species. The selective activation of acid sphingomyelinase might offer a novel therapeutic approach in the treatment of hepatocellular carcinoma.

Impact of sleep problems on the cardiometabolic risks: an integrated epidemiological and metabolomics study

BackgroundWe investigated the association between sleep problems and cardiometabolic risks and the potential linking effect of metabolites and metabolic pathways based on multi-layered research, including observational, mendelian randomization (MR), and metabolomics analysis.MethodsA cross-sectional analysis of the 2015–2018 National Health and Nutrition Examination Survey (NHANES) dataset was conducted to identify the association between sleep problems and cardiometabolic risks. A subsequent MR study based on genetic data was performed to explore the causal correlation of significant associations in the NHANES study. The underlying alteration of metabolism was explored by constructing zebrafish models and wide-targeted metabolomics analysis.ResultsThe cross-sectional analysis of the NHANES database revealed a significant association of snoring with obesity [OR = 2.65, 95% confidence intervals (CI): 1.87, 3.74]; sleep apnea with hypertension (OR = 1.68, 95% CI: 1.14, 2.48) and obesity (OR = 1.44, 95% CI: 1.05, 1.96); trouble sleeping with hypertension (OR = 1.84, 95% CI: 1.18, 2.86), obesity (OR = 1.56, 95% CI: 1.07, 2.26), and type 2 diabetes (T2DM) (OR = 1.52, 95% CI: 1.02, 2.25). MR analysis verified the causal relationship between genetically proxied sleep apnea or snoring and obesity. The decreased activity levels and altered expression levels of six circadian genes (bmal1b, cry1aa, cry1ab, clock1a, per1b, per2) were identified in the zebrafish of the sleep disorder group. Multiple metabolites related to disturbed glucose metabolism (e.g., 20-HETE), lipid metabolism (e.g., inosine), and vascular-related metabolites (e.g., riboflavin) were finally identified, indicating the latent effect of metabolism.ConclusionsThis study identified the chain of sleep-circadian rhythm-metabolism-cardiometabolic risks. These findings can promote improved prevention implementation and therapeutic strategies.

An integrative lipidomics and transcriptomics study revealing Bavachin and Icariin synergistically induce idiosyncratic liver injury

Objectives: Reports of traditional Chinese medicine (TCM)-related liver injury have increased over recent years; however, identifying susceptibility-related components and biomarkers remains challenging due to the heterogeneous nature of TCM and idiosyncratic drug-induced liver injury (IDILI). Psoraleae Fructus (PF) and Epimedii Folium (EF), commonly found in TCM prescriptions, have been implicated in IDILI, but their constituents and underlying mechanisms are poorly understood. Methods: In this study, we identified bavachin (Bav) and icariin (Ica) as susceptibility components for IDILI in PF and EF using a TNF-α-mediated mouse model. Lipidomics and transcriptomics were used to investigate their related mechanism. Results: Liver biochemistry and histopathology analyses revealed that co-exposure to Bav, Ica, and a non-toxic dose of TNF-α prestimulation induced significant liver injury, while Bav and Ica alone did not. Lipidomics identified seven differentially abundant metabolites in the Bav/Ica/TNF-α group compared to the Ica/TNF-α or Bav/TNF-α groups, mainly enriched in alpha-linolenic acid (ALA), arachidonic acid (AA), and linoleic acid (LA) metabolic pathways. Additionally, transcriptomics revealed 49 differentially expressed genes (DEGs) in the Bav/TNF-α vs Bav/Ica/TNF-α and Ica/TNF-α vs Bav/Ica/TNF-α groups, primarily associated with the PI3K/AKT/mTOR signaling pathway and sphingolipid metabolism. Integrative lipidomics and transcriptomics analyses identified significant positive correlations between five differential metabolites (DMs) – PC (O-16:0_14:1), PG (22:1_20:3), PI (16:0_14:1), PS (18:0_19:2), and TG (17:0_18:2_22:5) – and ten DEGs – Nr0b2, Btbd19, Btg2, Fam222a, Fam83f, Gtse1, Anln, Gja4, Srrm4, and Zfp13. Conslusions: Collectively, these results suggest that alterations in intracellular metabolism and gene expression levels may contribute to the synergistic induction of IDILI by the incompatible pair Bav and Ica in the presence of TNF-α.

Effects of branched-chain amino acid imbalance and dietary valine and isoleucine supplementation in modified corn-soybean meal diets with corn distillers dried grains with solubles on growth performance, carcass quality, intestinal health, and cecal microbiome in Cobb 500

One important feature of corn distillers dried grains with solubles (DDGS) is its high leucine:lysine ratio, which can inhibit chicken growth by causing branched-chain amino acid (BCAA) antagonism. The current study was conducted to investigate the effects of BCAA imbalance of inclusion of DDGS and whether additional dietary valine and isoleucine could alleviate the negative effects in broilers. A total of 640 0-d-old male Cobb 500 broilers were allocated into 4 treatments with 8 replicates and reared until d 42. The four different dietary groups were as follows: 1) control (CON) group (corn-soybean meal-based diet); 2) 30% DDGS (30D) group (replacing soybean meal with 30% DDGS); 3) 30D + additional valine and isoleucine (30DB) group; and 4) the group of 30DB + additional valine and isoleucine to provide the same leucine:valine and leucine:isoleucine ratios as the CON group (30DBB). The analyzed leucine:lysine ratios of the CON group were 1.36/1.41/1.46 (starter/grower/finisher phase), whereas the average leucine:lysine ratios of the 30% DDGS groups were 1.61/1.70/1.78 (starter/grower/finisher phase). The 30% DDGS groups (30D, 30DB, and 30DBB) negatively affected body weight (BW) from d 7 to 42 and BW gain (BWG), feed intake, carcass weight, breast muscle weight, and jejunal and ileal villus height:crypt depth during the overall period (d 0 to 42) (P < 0.05). Furthermore, the 30% DDGS groups significantly altered expression levels of jejunal tight junction proteins, breast muscle mechanistic target of rapamycin (mTOR) pathway-related genes, BCAA catabolism genes, and AA transporters compared to the CON (P < 0.01). The 30% DDGS groups showed differences in beta-diversity indices compared to the CON group (P < 0.05). The 30DBB group showing the lowest d 21 and 42 BW and overall BWG had the largest differences compared to the CON group in most measurements. In conclusion, excessive replacement of soybean meal with DDGS can significantly increase leucine levels, which may negatively affect chicken growth. Additionally, inappropriate ratios of valine and isoleucine can further decrease growth performance.

Combined administration of catalpol, puerarin, gastrodin, and borneol modulates the Tlr4/Myd88/NF-κB signaling pathway and alleviates microglia inflammation in Alzheimer's disease.

Alzheimer's Disease (AD) is a progressive neurodegenerative disorder affecting millions of people worldwide, with no effective treatment currently available. In recent decades, various traditional Chinese medicines (TCMs) and their active ingredients have shown the potential to attenuate the pathogenesis of AD in cellular and animal models. However, the effects of TCM formulas, which are typically administered in practice, have been less studied. This study aims to investigate the therapeutic effects of several formulas consisting of 4 components herbal components: catalpol, puerarin, gastrodin, and borneol, on streptozotocin (STZ)-induced AD models in cells and rats. The new object recognition (NOR), elevated plus maze (EMP), and Morris water maze (MWM) tests were used to evaluate the cognitive functions of rats. Golgi staining, Haematoxylin and Eosin (HE) staining, and Nissl staining analyses were employed assess the physiology of hippocampal tissues. Gene expression profiles were analyzed used transcriptomics and reverse transcription quantitative polymerase chain reaction analysis, while protein expression levels were determined using immunoblotting, immunohistochemical, and immunofluorescence. The production of cytokines was evaluated with enzyme-linked immunosorbent assay. The results demonstrated that the combined administration of these 4 components (CPGB) had superior mitigating effects on AD cell model, as evidenced by the reduced pro-inflammatory cytokine production and decreased deposition of Aβ protein. Further in vivo and in vitro experiments confirmed that varying doses of CPGB formula effectively ameliorated STZ-induced cognitive deficits, as shown by NOR, MWM, and EMP tests, as well as pathological changes in hippocampal tissues and a 3-dimensional brain neurovascular unit (3D-NVU) model, including decreased deposition of Aβ protein and formation of plaques. Transcriptome sequencing and analysis identified 35 genes with significantly altered expression levels due to STZ and CPGB treatment in hippocampal tissues, which were enriched in the Tlr4/Myd88/NF-κB signaling pathway. Interference with this pathway significantly influenced the therapeutic effects of CPGB in the 3D-NVU model. Collectively, these findings suggest that the combined administration of catalpol, puerarin, gastrodin, and borneol offers superior therapeutic effects on AD by modulating the Tlr4/Myd88/NF-κB signaling pathway. This study strengthens the theoretical foundation for using TCMs to treat AD, proving new insights and references for alleviating and treating AD.

Laparoscopic Salpingectomy Regulates The Expression of Endometrial Homeobox Genes (HOXA9, HOXA10, HOXA11, HOXD10) and HOX Transcript Antisense Intergenic RNA in Women with Communicating Hydrosalpinx: A Prospective Study.

This study aimed to determine the alteration of endometrial expression levels of HOXA9/HOXA10/ HOXA11/HOXD10 genes and HOX transcript antisense intergenic RNA (HOTAIR) in mid-luteal phase endometrium in patients with hydrosalpinx before and after salpingectomy. In this prospective study, 14 infertile women with unilateral hydrosalpinx who were scheduled for laparoscopic salpingectomy were evaluated. The presence of hydrosalpinx was confirmed by hysterosalpingography or transvaginal 2D-ultrasonography. All patients had normal hormonal profiles, body mass index, and regular menstrual cycles identified by mid-luteal serum progesterone. Fourteen healthy fertile age-matched women with a successful pregnancy history were considered the control group. Mid-luteal-phase endometrial biopsies were performed at the time of surgery and during the mid-luteal phase of the fourth treatment cycle by Pipelle. After tissue collection, RNA extraction and cDNA synthesis were performed. Real-time polymerase chain reaction (PCR) technique was used for quantitative gene expression of HOXA9/HOXA10/ HOXA11/ HOXD10 and lnc HOTAIR. The endometrial expression of HOXA9 (P<0.001), HOXA10 (P=0.001), HOXA11 (P=0.003), and HOXD10 (P=0.004) were significantly lower in the patients with hydrosalpinx compared to the controls. After salpingectomy, we observed a significant increase in the endometrial HOXA9 (P=0.006) and HOXA10 (P=0.023) mRNA expression levels compared to before salpingectomy samples. Similarly, a significant upregulation in endometrial HOXA11 (P= 0.013) and HOXA10 mRNA expression levels (P=0.012) were detected in postoperative samples compared to preoperative tissue. Moreover, the lnc HOTAIR was significantly higher in the endometrium-induced hydrosalpinx fluid than in controls (P=0.020), which had a 2.89-fold decrease following salpingectomy (P=0.010). Elevated endometrial lncRNA HOTAIR may disrupt the expression of endometrial receptivity HOX genes in women with hydrosalpinx. However, our results failed to show a significant inverse correlation between HOTAIR and HOX genes due to limited sample size. Further studies with larger sample sizes are required to investigate HOTAIR inverse co-expression with HOX genes in these subjects.

CRISPR/Cas9-mediated knockout of DYRK1B in triple-negative breast cancer cells: implications for cell proliferation, apoptosis, and therapeutic sensitivity

Breast cancer is the most common cancer among women worldwide, with the triple-negative subtype (TNBC) having a poor prognosis and limited treatment options. DYRK1B is a dual-specificity kinase that regulates the cell cycle and quiescence. While its role in several cancers has been characterized, its role in TNBC remains unknown. In this study, we used CRISPR/Cas9 to delete DYRK1B in MDA-MB-231 cells, a model of TNBC and investigated its effects on cell proliferation, apoptosis, invasion, migration, angiogenesis, and response to Paclitaxel. The DYRK1B knockout (KO) was confirmed by PCR, Real-time qPCR, and Sanger sequencing. KO cells showed a significant reduction in cell proliferation, colony formation, invasion, and migration. Additionally, there were alterations in mRNA expression levels of several genes related to the cell cycle, angiogenesis, and cell motility, such as CCND1, MCM2, PCNA, CDKN1B, HIF1A, VEGFA, and WASF3, compared to MDA-MB-231 wild type (WT) cells. Immunocytochemistry results assessing Ki67 expression, a marker of cell proliferation, indicated that DYRK1B knockout cells had significantly lower Ki67 expression than WT cells. Furthermore, KO cells exhibited increased apoptosis and sensitivity to contact inhibition. Additionally, the IC50 for Paclitaxel was significantly decreased in KO cells. These results suggest that DYRK1B plays an important role in the survival and invasion of TNBC cells and might be a potential candidate as a new therapeutic target for this disease.

Su(H) Modulates Enhancer Transcriptional Bursting in Prelude to Gastrulation.

Transcriptional regulation, orchestrated by the interplay between transcription factors (TFs) and enhancers, governs gene expression dynamics crucial for cellular processes. While gross qualitative fluctuations in transcription factor-dependent gene expression patterning have a long history of characterization, the roles of these factors in the nuclei retaining expression in the presence or absence of these factors are now observable using modern techniques. Our study investigates the impact of Suppressor of Hairless (Su(H)), a broadly expressed transcription factor, on enhancer-driven transcriptional modulation using Drosophila early embryos as a model system. Building upon previous findings, we employ super-resolution microscopy to dissect Su(H)'s influence on sog-Distal (sogD) enhancer activity specifically in nuclei with preserved sogD-driven expression in the absence of Su(H) binding. We demonstrate that Su(H) occupancy perturbations alter expression levels and bursting dynamics. Notably, Su(H) absence during embryonic development exhibits region-specific effects, inhibiting expression dorsally and stabilizing expression ventrally, implying a nuanced role in enhancer regulation. Our findings shed light on the intricate mechanisms that govern transcriptional dynamics and suggest a critical patterning role for Notch/Hairless signaling in sog expression as embryos transition to gastrulation.

Decoding Cancer through Silencing the Mitochondrial Gatekeeper VDAC1.

Mitochondria serve as central hubs for regulating numerous cellular processes that include metabolism, apoptosis, cell cycle progression, proliferation, differentiation, epigenetics, immune signaling, and aging. The voltage-dependent anion channel 1 (VDAC1) functions as a crucial mitochondrial gatekeeper, controlling the flow of ions, such as Ca2+, nucleotides, and metabolites across the outer mitochondrial membrane, and is also integral to mitochondria-mediated apoptosis. VDAC1 functions in regulating ATP production, Ca2+ homeostasis, and apoptosis, which are essential for maintaining mitochondrial function and overall cellular health. Most cancer cells undergo metabolic reprogramming, often referred to as the "Warburg effect", supplying tumors with energy and precursors for the biosynthesis of nucleic acids, phospholipids, fatty acids, cholesterol, and porphyrins. Given its multifunctional nature and overexpression in many cancers, VDAC1 presents an attractive target for therapeutic intervention. Our research has demonstrated that silencing VDAC1 expression using specific siRNA in various tumor types leads to a metabolic rewiring of the malignant cancer phenotype. This results in a reversal of oncogenic properties that include reduced tumor growth, invasiveness, stemness, epithelial-mesenchymal transition. Additionally, VDAC1 depletion alters the tumor microenvironment by reducing angiogenesis and modifying the expression of extracellular matrix- and structure-related genes, such as collagens and glycoproteins. Furthermore, VDAC1 depletion affects several epigenetic-related enzymes and substrates, including the acetylation-related enzymes SIRT1, SIRT6, and HDAC2, which in turn modify the acetylation and methylation profiles of histone 3 and histone 4. These epigenetic changes can explain the altered expression levels of approximately 4000 genes that are associated with reversing cancer cells oncogenic properties. Given VDAC1's critical role in regulating metabolic and energy processes, targeting it offers a promising strategy for anti-cancer therapy. We also highlight the role of VDAC1 expression in various disease pathologies, including cardiovascular, neurodegenerative, and viral and bacterial infections, as explored through siRNA targeting VDAC1. Thus, this review underscores the potential of targeting VDAC1 as a strategy for addressing high-energy-demand cancers. By thoroughly understanding VDAC1's diverse roles in metabolism, energy regulation, mitochondrial functions, and other cellular processes, silencing VDAC1 emerges as a novel and strategic approach to combat cancer.

BONCAT-iTRAQ Labelling Reveals Molecular Markers of Adaptive Responses in Toxoplasma gondii to Pyrimethamine Treatment.

We employed a BONCAT-iTRAQ labelling approach to investigate newly synthesised proteins (NSPs) in Toxoplasma gondii subjected to varying concentrations of the antifolate drug pyrimethamine. Our results reveal that numerous NSPs exhibited altered expression levels in response to the drug, with significant upregulation observed at higher concentrations. Key proteins involved in protein synthesis, stress responses, energy metabolism, and cytoskeletal dynamics were identified, indicating that T. gondii undergoes complex adaptive responses to pyrimethamine treatment. While some of the identified pathways reflect a generic stress response, this study provides important molecular markers and mechanistic insights specific to the parasite's adaptation strategies. These findings contribute to understanding how T. gondii modulates its proteome in response to drug-induced stress and lay the groundwork for further investigations into potential therapeutic targets.