Down-regulation Of Gene Expression Research Articles

Vitamin A and D3 combinations reduce breast cancer tumor load in a postmenopausal MCF-7 xenograft mouse model in a dose- and time- dependent manner

Introduction: Earlier, we documented that a combination of vitamins A and D3 synergistically inhibited the growth of MCF-7, T48:A18 and SKBR3 breast cancer cells with the best activity seen in the ER+ cell line MCF-7. Transcriptomic analysis of treated MCF-7 cells also showed that the combination significantly upregulated the apoptosis and unfolded protein response canonical pathways, and reduced estrogen signaling. Objective: This study aimed to explore the impact of increasing vitamin A and D3 dose combinations over time in a postmenopausal model of breast cancer using ovariectomized athymic female mice bearing MCF-7 xenografts and further analyze mechanisms of action in MCF-7 cells using RNA-seq analysis. Methods: MCF-7 breast cancer cells were grown in culture for the xenograft experiments. Athymic female mice were injected with MCF-7 cells (1 x 10^6 in 100 µl of 50% Matrigel mixed with sterile PBS) via subcutaneous injection. Once the tumors reached an average volume of 100 mm³, the mice were randomly divided into four groups and treated with different vitamin A and D3 combinations. Tumor sizes and mouse body weights were monitored on a biweekly basis. After the treatment period, the mice were euthanized, and the tumors were surgically removed and measured. RNA-seq data from the treated MCF-7 cells were then further evaluated using IPA. Results: As compared with controls, treatment with vitamin A (25,000 IU) and vitamin D (10,000 IU) led to a significant reduction in tumor volume >70%, (p < 0.05-0.01) in OVX athymic mice with MCF-7 xenografts as determined by a two-tailed Student T test. Over the treatment period, the tumor volume in mice treated with vitamin A (10,000 IU) and vitamin D (5,000 IU) or vitamin A (25,000 IU) and vitamin D (5,000 IU) also trended downward and was statistically significant using one-way analysis of variance (ANOVA) followed by Dunnett’s multiple comparison test (p<0.05 and p<0.0001, respectively) but was not significant using a two-tailed Student T test. In cultured MCF-7 cells, Ingenuity Pathway Analysis of mRNA-seq data showed that the vitamin A and D combination significantly altered the expression of 101 genes out of 864 in the molecular mechanisms in cancer canonical pathway, downregulating gene expression in the integrin/P13K/Akt/mTOR pathway. Conclusions: The findings showed that the combination of vitamins A and D3 effectively reduced tumor burden in a postmenopausal MCF-7 xenograft mouse model, with effects that were both dose-dependent and time-dependent. The combination also significantly altered the expression of genes in the molecular mechanisms of cancer canonical pathway in cultured MCF-7 cells. These preclinical data support the use of vitamins A and D3 in the management of estrogen-dependent breast cancers, with the caveat that higher doses and longer treatment periods may be needed to observe anti-tumor effects. Keywords: Apoptosis, autophagy, breast cancer, cell cycle, integrin, postmenopausal, P13K, tumor load, xenograft

Expression and functional analysis of adipokinetic hormone reveal its different roles in larval development and female fecundity in Panonychus citri (McGregor) (Acari: Tetranychidae).

Adipokinetic hormone (AKH), a crucial neuropeptide, participates in the important physiological processes by specially binding to its receptor to activate the AKH signalling pathway. AKH regulates energy metabolism. However, it remains unknown whether AKH affects larval development and adult reproduction by influencing energy metabolism. In the present study, the AKH was identified from Panonychus citri and contained the conserved functional domain 'Q-[LIV]-[NT]-F-[ST]-X (2)-W' that characterises the AKH family. The relative expression levels of PcAKH revealed different patterns of AKH expression at different developmental stages of P. citri. Feeding of double-standard RNA against PcAKH induced decreased fecundity and reduced survival, which was accompanied by the down-regulation of vitellogenin gene expression. In addition, after silencing the PcAKH, lipid metabolism and carbohydrate homeostasis were disrupted, manifested by increased body width and weight, and fasting phenomenon. Further investigation found that compared with the control, physiological changes in trehalose and triglyceride contents were accompanied by variations in the mRNA expression levels of genes related to lipid metabolism and carbohydrate metabolism. The disorder of lipid and carbohydrate metabolism may affect adult female reproduction, which may lead to insufficient vitellogenin deposition. Moreover, the silencing of PcAKH seriously affected the growth and development of larvae, which was manifested as delayed development period and difficulty in moulting. Conclusively, all these results in current study demonstrated that double-stranded RNA silencing system targeting PcAKH effectively inhibited larval development and female fecundity by disturbing lipid and carbohydrate metabolism, and PcAKH is a specific RNAi target for control of P. citri in the design and development of biopesticide in sustainable agriculture.

Effect of Liquid Blood Concentrates on Cell Proliferation and Cell Cycle- and Apoptosis-Related Gene Expressions in Nonmelanoma Skin Cancer Cells: A Comparative In Vitro Study.

Nonmelanoma skin cancer (NMSC) presents a significant challenge to global healthcare due to its rising incidence, prompting the search for innovative treatments to overcome the limitations of current therapies. Our study aims to explore the potential effects of the liquid blood concentrate platelet-rich fibrin (PRF) on basal cell carcinoma cells (BCCs) and squamous cell carcinoma cells (SCCs) in order to obtain results that may lead to new possible adjunctive therapies for managing localized skin cancers, particularly NMSC. Basal cell carcinoma (BCC) cells and squamous cell carcinoma (SCC) cells were indirectly treated with PRF generated via different relative centrifugation forces, namely high and low RCF PRF, for 7 days. PRF-treated cells were comparatively analyzed for cell viability, proliferation and cell cycle- and apoptosis-related gene expression. Analysis of MTS assay results revealed a significant decrease in cell viability in both BCC and SCC cells following PRF treatment for 7 days. Ki-67 staining showed a decreased percentage of Ki-67-positive cells in both BCC and SCC cells after 2 days of treatment compared to the control group. The downregulation of CCND1 gene expression in both cell types at 2 days along with the upregulation of p21 and p53 gene expression in SCC cells demonstrated the effect of PRF in inhibiting cell proliferation and inducing cell cycle arrest, especially during the initial phases of treatment. Increased expression of caspase-8 and caspase-9 was observed, indicating the activation of both extrinsic and intrinsic apoptotic pathways by PRF treatment. Although the exact immunomodulatory properties of PRF require further investigation, the results of our basic in vitro studies are promising and might provide a basis for future investigations of PRF as an adjunctive therapy for managing localized skin cancers, particularly NMSC.

Antimicrobial Susceptibility of Fructophilic Lactic Acid Bacteria on PHZM Gene of Pseudomonas Aeruginosa Isolates from Wounds Infected

Abstract Introduction The study was to isolate and characterize fructophilic lactic acid bacteria (FLAB) species from the honey bee gut. Based on the results of this study, it was found that the FLAB species obtained from honey were gram-positive and catalase-negative, and this identification was confirmed through 16S rRNA gene sequencing. Materials and methods The results indicated that yeast extract was the most effective nitrogen source, while glucose was the preferred carbon source for cell-free supernatant (CFS) production. The optimal pH for CFS production was found to be 5, and the incubation period of 72 hours was determined to be the most suitable for obtaining a high yield of CFS. Another aspect of the study aimed to identify multidrug-resistant P. aeruginosa isolates from burn wound infections. The isolates were identified using the VITEK 2 system, and the phzM gene was detected in all nine strains. Furthermore, the study evaluated the effect of the CFS of the selected strain (E5) on the expression of the phzM gene. Results The study showed a significant down-regulation of phzM gene expression in multidrug-resistant P. aeruginosa isolates following exposure to the CFS, indicating the potential of E. faecium as an effective antimicrobial agent against P. aeruginosa infections that are resistant to multiple drugs. We performed a primary screening to evaluate the effect of the CFS obtained from E. faecium (E5), and it was observed that the CFS showed a high inhibition zone of 23 mm against multidrug-resistant P. aeruginosa, as determined by the agar well diffusion assay. The study also investigated further to determine the optimal conditions for producing CFS. Conclusion Down-regulation and up-regulation in the expression of the genes following exposure to CFS indicate the potential of E. faecium as an effective antimicrobial agent against multi-drug resistant (MDR) P. aeruginosa infections.

Enhanced HSP70 binding to m6A-methylated RNAs facilitates cold stress adaptation in mango seedlings

BackgroundCold stress poses a serious challenge to tropical fruit production, particularly in mango. N6-methyladenosine (m6A) modifications are key regulators of gene expression, enabling plants to respond to stress responses, enhance adaptation and improve resilience to environmental challenges.ResultsIn our study, transcriptome-wide m6A methylation profiling under cold stress identified 6,499 differentially methylated m6A peaks and 2,164 differentially expressed genes (DEGs) in mango seedlings. Among these genes, six exhibited both significant increases in m6A modification levels and gene expression, 21 showed a significant increase in m6A levels but a concurrent downregulation of gene expression, and 26 showed reduced m6A levels but exhibited increased gene expression, highlighting distinct regulatory patterns in m6A-mediated gene expression control. Gene Ontology (GO) enrichment analysis revealed significant involvement in pathways such as potassium ion import, nitrate response, and transcription regulation. Notably, HSP70 was one of the upregulated genes in response to cold stress. RNA immunoprecipitation (RNA-IP) assays confirmed the association of HSP70 with m6A-modified RNAs in vivo, supporting its role in regulating stress-responsive transcripts. Additionally, immunofluorescence analysis demonstrated the formation of HSP70 condensates in plant cells under cold stress, indicating a potential mechanism for localized RNA stabilization. Fluorescence polarization assays demonstrated that HSP70 binds preferentially to m6A-modified RNAs, suggesting its role in forming protective condensates under cold conditions. This interaction between m6A modification and HSP70 points to a potential mechanism that helps stabilize stress-responsive transcripts, contributing to the plant’s enhanced cold tolerance.Conclusionsm6A modifications play a vital role in regulating gene expression under cold stress, offering new insights into mango’s stress responses and potential breeding strategies for cold tolerance.

Fumigation with dimethyl trisulfide to inhibit Aspergillus flavus growth, aflatoxin B1 production and virulence.

Aspergillus flavus is a common saprophytic aerobic fungus in oil crops that poses a serious threat worldwide with the carcinogenic aflatoxin. Prevention of aflatoxin B1 contamination has great significance to ensure food safety and reduce the economic loss. The present work focuses on the antagonistic activity against A. flavus growth in peanuts by fumigation with dimethyl trisulfide. The results indicated that dimethyl trisulfide exhibits great antifungal activity against A. flavus. The conidial germination and mycelial growth of A. flavus were completely suppressed after exposure to 15 and 20µl/L of dimethyl trisulfide, respectively. Numerous deformed conidia were found after exposure to dimethyl trisulfide at high concentration (≥ 20µl/L). SEM observation demonstrated that dimethyl trisulfide induced severely shrinking mycelia of A. flavus. The results of OD-260nm absorption and rhodamine-123 fluorescent staining indicated that cell membrane and mitochondria may be legitimate antifungal targets of dimethyl trisulfide. Dimethyl triethyl has a significant inhibitory effect on A. flavus infection in peanuts. In addition, dimethyl trisulfide could reduce production of aflatoxin B1 via downregulation of toxin synthesis and regulatory gene expression. Dimethyl trisulfide can be a tremendous potential agent for the biological control of A. flavus, and deepened our understanding of anti-fungal mechanisms of volatile organic compounds.

'The effect of neuropeptide Y1 receptor agonist on hypothalamic neurogenesis in rat experimental depression model'.

Depression is responsible for neuropathies such as decreased neurogenesis and increased dendritic atrophy. There is information that antidepressant treatments have an effect by increasing hippocampal neurogenesis and neurotrophic factor expression. The neuropeptide Y1 (NPY1R) receptor agonist has been suggested to have anxiolytic effects. Based on this information, it was aimed to investigate the effect of NPY1R agonist on depression in rats with depression using the CMS model and to determine how depression affects cell proliferation in the hypothalamus and hypothalamic peptide levels. Forty-eight adult, male Wistar albino rats were divided into groups as Control, Depression (D), Depression + NPY1R and NPY1R. Various stressors were applied to D for 30 days. An open field test (OFT) and forced swim test (FST) were performed to check whether the animals were depressed. On the 16th day, an osmotic mini pump was placed under the skin and NPY1R (130 ul/kg/day) was applied for 15 days. Behavioral tests were performed, hypothalamic peptide gene expression levels were analyzed by quantitative RT-PCR and statistical evaluations were made using ANOVA. A decrease in the percentage of movement in the D and control groups were noted in the OFT, an increase in the immobility time in the D group in the FST, and an increase in swimming behavior in the DNPY1R group. The animals did not display any anxiety behavior based on the elevated plus maze test results. It caused a decrease in IGF1R, FGF2, POMC, NPY and GLUT2 gene expression in the hypothalamus of depression group animals, and an increase in NPY gene expression in NPY1R treatment. This study compellingly demonstrated that exposure to chronic mild stress simultaneously downregulates gene expression in the hypothalamus; we observed that NPY receptor NPY1R treatment increased the effect of NPY. Therefore, adjunctive treatments with appropriate molecules such as NPY, Y1 receptor agonists or pharmacological derivatives may have significant potential in the treatment of depression.

The effect of silicate on polyamine oxidase genes in Skeletonema dohrnii

By using Skeletonema dohrnii as the experimental algal species, we investigated how silicate concentration impacts the polyamine metabolism of diatoms in our experiment. Three different silicate concentrations were set for cultivation, and Skeletonema dohrnii at the exponential growth phase was selected to analyze basic physiological parameters, polyamine content, and Polyamine oxidase (PAO) gene expression under varying silicate concentrations. Results showed that low silicate concentrations led to reduced growth rate and polyamine content, with down-regulation of PAO gene expression. Conversely, high silicate concentrations did not significantly increase growth rate but did increase polyamine content and up-regulate the PAO gene. These findings suggested that changes in silicate concentration impact the growth rate and polyamine content of Skeletonema dohrnii, with the PAO gene potentially playing a role in regulating the algal response to silicate concentration variations. This study provides a foundation for further exploration of the PAO gene function in Skeletonema dohrnii.

Pathomic and bioinformatics analysis of clinical-pathological and genomic factors for pancreatic cancer prognosis

Pancreatic cancer exhibits a high degree of malignancy with a poor prognosis, lacking effective prognostic targets. Utilizing histopathological methodologies, this study endeavors to predict the expression of pathological features in pancreatic ductal adenocarcinoma (PAAD) and investigate their underlying molecular mechanisms. Pathological images, transcriptomic, and clinical data from TCGA-PAAD were collected for survival analysis. Image segmentation using unsupervised machine learning was employed to extract features, perform clustering, and establish models. The prognostic value of pathological features and associated clinical risk factors were evaluated; the correlation between pathological features and molecular mechanisms, gene mutations, and immune infiltration was analyzed. By clustering 45 effective pathological features, we divided PAAD patients into two groups: cluster 1 and cluster 2. Significant associations with poor prognosis were found for cluster 2 in both the training group (n = 113) and validation group (n = 75) (p = 0.006), with pathological stages II-IV identified as potential synergistic risk factors (HR = 2.421, 95% CI = 1.263–4.639, p = 0.008). Subsequently, through multi-omics correlation analysis, we further revealed a close association between cluster 2 and the oxidative phosphorylation mechanism. Within the cluster 2 group, 28 oxidative phosphorylation genes exhibited reduced expression, CDKN2A gene mutations were upregulated, and there was significant downregulation of Tregs infiltration and related immune gene expression. The pathomic model constructed using machine learning serves as a valuable prognostic target for PAAD. The histopathological features cluster 2 are closely associated with the downregulation of oxidative phosphorylation levels and Tregs immune infiltration.

Chlorogenic acid improves urogenital dysfunction induced by exposure to ambient particulate matter.

Oxidative stress is a well-known underlying mechanism for several diseases in response to environmental pollution. Although there is a lack of evidence on the relationship between air pollution and an established risk factor for urogenital dysfunction. The aim of this study was to investigate the mechanism of particulate matter (PM) on urogenital function and evaluate the potential efficacy of chlorogenic acid (CGA) in preventing urogenital damage in rats. Forty Wistar rats were divided into five groups (n = 8): control, particulate matter exposure (animals were exposed to fine dust in an inhalation chamber for 4 weeks, 3 days a week, for 3 h, PM10 concentration adjusted to 500-2000 µg/m3), and particulate matter plus 3 concentrations of chlorogenic acid (100, 200, and 400 mg/kg, gavage, 4 weeks, 3 days a week). At the end of the study, kidney biomarkers, oxidative stress markers, antioxidant enzymes, the oxidation resistance 1 (OXR1) and its downstream gene expression, sperm count, gonadotropin hormones, and the structure of the kidney, epididymis, and seminal vesicle were evaluated in response to PM exposure and CGA treatment in all groups. The data obtained from the current study showed that PM exposure led to kidney dysfunction and inhibition of oligospermia through oxidative stress, as evidenced by an increase in MDA and a decrease in TAC, SOD, CAT, and GSH concentration levels in blood samples. These results were consistent with the down-regulation of OXR1, Nrf2, and P21 gene expression. In contrast, CGA improved urogenital biomarkers and histopathology structures of the kidney, epididymis, and seminal vesicle by enhancing antioxidant defense system enzymes and modulating the OXR1 signaling pathway. Our findings suggest that environmental air pollution contributes to kidney dysfunction and urogenital damage. Modulation of oxidative stress through the OXR1, P21, and Nrf2 signaling pathways may be the underlying mechanism. Furthermore, chlorogenic acid supplementation could be recommended as a new protective or treatment strategy to safeguard urogenital function against exposure to particulate matter.

A microenvironment-modulating dressing with proliferative degradants for the healing of diabetic wounds.

Diabetic wounds are usually entangled in a disorganized and self-perpetuating microenvironment and accompanied by a prolonged delay in tissue repair. Sustained and coordinated microenvironment regulation and tissue regeneration are key to the healing process of diabetic wounds, yet they continue to pose a formidable challenge. Here we report a rational double-layered dressing design based on chitosan and a degradable conjugated polymer polydiacetylene, poly(deca-4,6-diynedioic acid) (PDDA), that can meet this intricate requirement. With an alternating ene-yne backbone, PDDA degrades when reacting with various types of reactive oxygen species (ROS), and more importantly, generates proliferative succinic acid as a major degradant. Inheriting from PDDA, the developed PDDA-chitosan double layer dressing (PCD) can eliminate ROS in the microenvironment of diabetic wounds, alleviate inflammation, and downregulate gene expression of innate immune receptors. PCD degradation also triggers simultaneous release of succinic acid in a sustainable manner, enabling long-term promotion on tissue regeneration. We have validated the biocompatibility and excellent performance of PCD in expediting the wound healing on both diabetic mouse and porcine models, which underscores the significant translational potential of this microenvironment-modulating, growth-promoting wound dressing in diabetic wounds care.

Utilizing the apical-out enteroids in vitro model to investigate intestinal glucose transport, barrier function, oxidative stress, and inflammatory responses in broiler chickens.

Conventional 2D intestinal epithelial cell lines have been widely used in investigating intestinal functions, yet with limitations in recapitulating the in vivo gut physiology of chickens. A recently established chicken enteroid model with apical-out nature and the presence of leukocyte components represents intestinal mucosal functions. The objectives of this study were to 1) evaluate basic gut nutrient transport and barrier functions in this model and 2) identify the model's effectiveness in studying inflammation and oxidative stress responses. Enteroids were generated from individual villus units isolated from the small intestine of Cobb500 broiler embryos. Enteroid viability, morphology, and epithelial cell markers were monitored; barrier function was evaluated based on the permeability to fluorescein isothiocyanate-dextran (FD4) with or without EDTA and lipopolysaccharide (LPS) challenges; nutrient transport was evaluated by fluorescence-labeled glucose (2NBD-G) with or without transporter blockade; the oxidative status was indicated by reactive oxygen species (ROS). Inflammatory and oxidative challenges were induced by LPS and menadione treatment, respectively. Selected marker gene expressions, including tight junction proteins (CLDN-1, CLDN-2, ZO-1, and OCCL), epithelial cell markers (Lgr-5, LYZ, and MUC-2), cytokines (IL-1β, IL-6, IL-8, IL-10, TNF-α, and INF-γ), and antioxidant enzymes (Nrf-2, catalase, and SOD), were determined by using RT-qPCR. Data were analyzed by one-way ANOVA among treatment groups. Enteroid cell activity was stable from day (d) 2 to d 6 and declined at d 7. Epithelial cell marker and cytokine expressions were stable from d 4 to d 6. FD4 permeability was increased after the EDTA treatment (P ≤ 0.05). Transporter-mediated 2NBD-G absorption was observed, which was reduced with glucose transporter blockade (P ≤ 0.05). Enteroids showed classic responses to LPS challenges, including upregulated gene expressions of IL-1β and IL-6, downregulated gene expressions of ZO-1 and OCCL, and increased FD4 permeability (P ≤ 0.05). Enteroids showed increased ROS generation (P ≤ 0.05) in response to oxidative stress. In conclusion, this apical-out enteroid model is a stable alternative in vitro model that exhibits intestinal barrier, nutrient transport, oxidation, and inflammation functions. With this enteroid model, we developed two challenge protocols for evaluating intestinal functions under oxidative stress and inflammation conditions.

Gene-Based Targeting for Treatment of Hypercholesterolemia and Prevention of Atherosclerotic Cardiovascular Disease

Familial hypercholesterolemia, characterized by high levels of LDL cholesterol is a monogenic metabolic disorder linked to atherosclerotic cardiovascular disease. Several genetic mutations in genes such as LDLR and PSK9 are thought to cause familial hypercholesterolemia. This ultimately causes dysfunction of the LDLR pathway, increasing circulating LDL levels. Current treatment revolves around decreasing LDL cholesterol levels in the blood. Statins are the current gold standard while sterol absorption inhibitors (ezetimibe) and PCSK9 inhibitors (evolocumab) are either used as primary treatment in individuals with statin intolerance, or supplementary treatment otherwise. However, CRISPR-Cas9 offers an upstream therapeutic intervention, inducing mutations in pathogenic genes (such as LDLR) to upregulate or downregulate gene expression and subsequently reduce LDL cholesterol levels. This technology thus has great potential as a two-fold treatment option, offering an effective solution for familial hypercholesterolemia, while simultaneously diminishing the risk of atherosclerotic cardiovascular disease. A limitation to current research exists in the sole analysis of monogenic factors in genetic screening, thus polygenic, multifactorial analyses are required to assess more holistic treatment plans. Furthermore, there exist current limitations to CRISPR-Cas9 including ethical limitations and social considerations revolving around the perpetuation of social inequities through technology necessitating future research on global health policies.

ELF1 serves as a potential biomarker for the disease activity and renal involvement in systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is an autoimmune disease that affects multiple organs, yet its underlying mechanisms remain unclear, and precise biomarkers are lacking. In this study, we employed Mendelian randomization and HEIDI tools to comprehensively analyze large-scale Genome-Wide Association Study (GWAS) and expression Quantitative Trait Loci (eQTL) data, leading to the identification of seven novel potential functional genes associated with SLE, including BLK, ELF1, STIM1, B3GALT6, APOLD1, INPP5B, and FHL3. Subsequent investigations revealed a significant downregulation of ELF1 gene expression in CD4+ T cells of SLE patients compared to healthy controls. Moreover, within various SLE subgroups, such as those with decreased serum complement C3 levels, positive urinary protein, new-onset skin rashes, and SLE Disease Activity Index (SLEDAI) scores ≥ 5, ELF1 expression displayed a consistent decreasing trend. Notably, ROC curve analysis highlighted the diagnostic potential of ELF1 expression in SLE (AUC = 0.9493), as well as its value in assessing disease activity (AUC = 0.6852) and renal involvement (AUC = 0.7363). In conclusion, this study underscores the potential of ELF1 as a SLE biomarker for diagnosis and evaluation, offering insights into the underlying mechanisms of SLE and paving the way for future therapeutic research.

The CRISPR-dCas9 interference system suppresses inhA gene expression in Mycobacterium smegmatis

CRISPR-dead Cas9 interference (CRISPRi) has become a valuable tool for precise gene regulation. In this study, CRISPRi was designed to target the inhA gene of Mycobacterium smegmatis (Msm), a gene necessary for mycolic acid synthesis. Our findings revealed that sgRNA2 induced with 100 ng/ml aTc achieved over 90% downregulation of inhA gene expression and inhibited bacterial viability by approximately 1,000-fold. Furthermore, CRISPRi enhanced the susceptibility of M. smegmatis to isoniazid and rifampicin, which are both 50% and 90% lower than those of the wild-type strain or other strains, respectively. This study highlights the ability of CRISPRi to silence the inhA gene, which impacts bacterial viability and drug susceptibility. The findings provide valuable insights into the utility of CRISPRi as an alternative tool for gene regulation. CRISPRi might be further assessed for its synergistic effect with current anti-tuberculosis drugs and its possible implications for combating mycobacterial infections, especially drug-resistant tuberculosis.

Evolutionary divergent clusters of transcribed extinct truncated retroposons drive low mRNA expression and developmental regulation in the protozoan Leishmania

BackgroundThe Leishmania genome harbors formerly active short interspersed degenerated retroposons (SIDERs) representing the largest family of repetitive elements among trypanosomatids. Their substantial expansion in Leishmania is a strong predictor of important biological functions. In this study, we combined multilevel bioinformatic predictions with high-throughput genomic and transcriptomic analyses to gain novel insights into the diversified roles retroposons of the SIDER2 subfamily play in Leishmania genome evolution and expression.ResultsWe show that SIDER2 retroposons form various evolutionary divergent clusters, each harboring homologous SIDER2 sequences usually located nearby in the linear sequence of chromosomes. This intriguing genomic organization underscores the importance of SIDER2 proximity in shaping chromosome dynamics and co-regulation. Accordingly, we show that transcripts belonging to the same SIDER2 cluster can display similar levels of expression. SIDER2 retroposons are mostly transcribed as part of 3'UTRs and account for 13% of the Leishmania transcriptome. Genome-wide expression profiling studies underscore SIDER2 association generally with low mRNA expression. The remarkable link of SIDER2 retroposons with downregulation of gene expression supports their co-option as major regulators of mRNA abundance. SIDER2 sequences also add to the diversification of the Leishmania gene expression repertoire since ~ 35% of SIDER2-containing transcripts can be differentially regulated throughout the parasite development, with a few encoding key virulence factors. In addition, we provide evidence for a functional bias of SIDER2-containing transcripts with protein kinase and transmembrane transporter activities being most represented.ConclusionsAltogether, these findings provide important conceptual advances into evolutionary innovations of transcribed extinct retroposons acting as major RNA cis-regulators.

Gamma irradiation green synthesis of (polyacrylamide/chitosan/silver nanoparticles) hydrogel nanocomposites and their using as antifungal against Candida albicans and anti-cancer modulator

Silver nanoparticles-loaded hydrogel nanocomposites are exploited for medicinal and pharmaceutical applications. Hydrogel nanocomposites were prepared from acrylamide (Am), chitosan (CS) and AgNO3 utilizing gamma rays. Diverse variables were applied in preparation of silver nanoparticles-laoded hydrogel nanocomposites of (PAm/CS)-AgNPs such as influence of radiation dose and influnece of CS concentration. Diverse techniques were utilized to characterize hydrogel nanocomposites; Fourier transform infrared spectroscopy (FTIR), thermal gravimetric analysis (TGA), X-ray diffraction (XRD), Transmission electron microscopy (TEM), energy dispersive X-ray (EDX) and scanning electron microscopy (SEM). Results confirmed formation of silver nanoparticles-loaded hydrogel nanocomposites of (PAm/CS)-AgNPs. Antifungal activity of (PAm/CS)-AgNPs hydrogel nanocomposites on viability of C. albicans was esitmated. Results displayed the efficient microbial inhibition activity of treatment against C. albicans compared to control. Furthermore, (PAm/CS)-AgNPs hydrogel nanocomposite against cervical cancer HeLa cell line was investigated. Cytotoxicity of (PAm/CS)-AgNPs hydrogel nanocomposites on prior cancer cell line empolyed to prohibition of cell growth assesssed by MTT test. HeLa cancer cell is treated by (PAm/CS)-AgNPs for 48 h exposed a potential apoptotic activity by noticeable up-regulation of p53 gene expression. Moreover, anticancer activity was investigated by down-regulation of platelet-based growth variable receptor beta (PDGFR-β), Bcl2, Cathepsine, and MMP-2 gene expression. antioxidant activity was investigated and results showed antioxidant activity of (PAm/CS) hydrogel and (PAm/CS)-AgNPs hydrogel nanocomposite are 87.8% and 62.9%, respectively.

Statins have profound effects on the epicardial fat transcriptome

Abstract Background Epicardial adipose tissue (EAT) has direct contact with the myocardium, which enables a common microcirculation allowing bidirectional signaling between the tissues. It is possible that a change in the balance of protective and damaging mediators produced by EAT is a major driver for myocardial dysfunction. Notably, EAT volume and thickness associate with increased pro-inflammatory secretome and with coronary artery disease (CAD). Purpose This aim of this study was to analyze the total transcriptome in EAT and relate putative differences between patient groups to metabolic parameters as well as ongoing medications. Methods Between 2011 and 2016, 44 patients (mean age 68.0 years, 18.2% women) had a biopsy taken from the epicardial fat during coronoray by-pass surgery (CABG, n=36), or during elective aortic valvular replacement due to aortic stenosis (AVR, n=8). RNA from epicardial fat biopsis was extracted and sequenced. Differentially expressed genes were obtained by custom scripts that performed a negative binomial distribution test on effective counts. Multivariate regression analysis with orthogonal partial least-squares-discriminant analysis (OPLS-DA) was applied to extract and interpret the systematic variation in the resolved RNA sequencing profiles. To identify enrichment of biologically relevant functional gene sets, our data were entered in evidence-based network enrichment analysis (EviNet). Results The CABG surgery was performed approximately 7 days after an acute coronary event (75% acute MI), and 44% of them had previously known CAD. None of the AVR cases had significant CAD. At surgery, 97% of the CABG cases were prescribed statins, and 36% of them had statins alredy before the actual admission (long-term statin treatment). 63% of the AVR cases were on statins at admission. The OPLS analysis revealed only one medication with significant outcome, i.e., patients with long-term treatment with statins (n=18) versus patients without (n=26). Long-term statin treatment associated with down-regulated gene expression involved in beta-oxidation and triglyceride biosynthesis whereas gene expression involved in extracellular matrix organization were up-regulated. Gene expression involved in MHC class II presentation and interferon signalling were also reduced in patients with long-term treatment with statisn. A downregulation of genes in the interleukin- and complement cascade genes among CABG patient (versus AVR patients) without long-term statin treatment showed normal levels in statin pretreated patients. Conclusion Long-term statin treatment has a major influence on transcriptional regulation of genes involved in beta-oxidation, triglyceride biosynthesis, extracellular matrix composition, MHC class II presentation and interferon signalling in epicardial adipose tissue. These findings support important metabolic and immune effects of statins beyond the lipid-lowering function.

Construction of a tumor mutational burden-derived LncRNA prognostic computational framework associated with therapy sensitivity in skin cutaneous melanoma

BackgroundSkin cutaneous melanoma (SKCM) poses a significant public health challenge due to its aggressive nature and limited treatment options. To address this, the study introduces the Tumor Mutational Burden-Derived Immune lncRNA Prognostic Index (TILPI) as a potential prognostic tool for SKCM.MethodsTILPI was developed using a combination of gene set variation analysis, differential expression analysis, and COX regression analysis. Additionally, functional experiments were conducted to validate the findings, focusing on the effects of STARD4-AS1 knockdown on SKCM tumor cell behavior. These experiments encompassed assessments of tumor cell proliferation, gene and protein expression, migration, invasion, and in vivo tumor growth.ResultsThe results demonstrated that knockdown of STARD4-AS1 led to a significant reduction in tumor cell proliferation and impaired migration and invasion abilities. Moreover, it resulted in the downregulation of ADCY4, PRKACA, and SOX10 gene expression, as well as decreased protein expression of ADCY4, PRKACA, and SOX10. In vivo experiments further confirmed the efficacy of STARD4-AS1 knockdown in reducing tumor growth.ConclusionsThis study elucidates the mechanistic role of STARD4-AS1 and its downstream targets in SKCM progression, highlighting the importance of the ADCY4/PRKACA/SOX10 pathway. The integration of computational analysis with experimental validation enhances the understanding of TILPI and its clinical implications. Overall, the findings underscore the potential of novel computational frameworks like TILPI in predicting and managing SKCM, particularly through targeting the ADCY4/PRKACA/SOX10 pathway.

Bidirectional Impact of Varying Severity of Acute Kidney Injury on Calcium Oxalate Stone Formation

Introduction: Acute kidney injury (AKI) is a prevalent renal disorder. The occurrence of AKI may promote the formation of renal calcium oxalate stones by exerting continuous effects on renal tubular epithelial cells (TECs). We aimed to delineate the molecular interplay between AKI and nephrolithiasis. Methods: A mild (20 min) and severe (30 min) renal ischemia-reperfusion injury model was established in mice. Seven days after injury, calcium oxalate stones were induced using glyoxylate (Gly) to evaluate the impact of AKI on the formation of kidney stones. Transcriptome sequencing was performed on TECs to elucidate the relationship between AKI severity and kidney stones. Key transcription factors (TFs) regulating differential gene transcription levels were identified using motif analysis, and pioglitazone, ginkgetin, and fludarabine were used for targeted therapy to validate key TFs as potential targets for kidney stone treatment. Results: Severe AKI led to increased deposition of calcium oxalate crystals in renal, impaired kidney function, and upregulation of kidney stone-related gene expression. In contrast, mild AKI was associated with decreased crystal deposition, preserved kidney function, and downregulation of similar gene expression. Transcriptomic analysis revealed that genes associated with inflammation and cell adhesion pathways were significantly upregulated after severe AKI, while genes related to energy metabolism pathways were significantly upregulated after mild AKI. An integrative bioinformatic analysis uncovered a TF regulatory network within TECs, pinpointing that PKNOX1 was involved in the upregulation of inflammation-related genes after severe AKI, and inhibiting PKNOX1 function with pioglitazone could simultaneously reduce the increase of calcium oxalate crystals after severe AKI in kidney. On the other hand, motif analysis also revealed the protective role of STAT1 in the kidneys after mild AKI, enhancing the function of STAT1 with ginkgetin could reduce kidney stone formation, while the specific inhibitor of STAT1, fludarabine, could eliminate the therapeutic effects of mild AKI on kidney stones. Conclusion: Inadequate repair of TECs after severe AKI increases the risk of kidney stone formation, with the upregulation of inflammation-related genes regulated by PKNOX1 playing a role in this process. Inhibiting PKNOX1 function can reduce kidney stone formation. Conversely, after mild AKI, effective cell repair through upregulation of STAT1 expression can protect TEC function and reduce stone formation, and activating STAT1 function can also achieve the goal of treating kidney stones.