Specific Target Genes Research Articles

LBF-MI: Limited Boolean Functions and Mutual Information to Infer a Gene Regulatory Network from Time-Series Gene Expression Data

Background: In the realm of system biology, it is a challenging endeavor to infer a gene regulatory network from time-series gene expression data. Numerous Boolean network inference techniques have emerged for reconstructing a gene regulatory network from a time-series gene expression dataset. However, most of these techniques pose scalability concerns given their capability to consider only two to three regulatory genes over a specific target gene. Methods: To overcome this limitation, a novel inference method, LBF-MI, has been proposed in this research. This two-phase method utilizes limited Boolean functions and multivariate mutual information to reconstruct a Boolean gene regulatory network from time-series gene expression data. Initially, Boolean functions are applied to determine the optimum solutions. In case of failure, multivariate mutual information is applied to obtain the optimum solutions. Results: This research conducted a performance-comparison experiment between LBF-MI and three other methods: mutual information-based Boolean network inference, context likelihood relatedness, and relevance network. When examined on artificial as well as real-time-series gene expression data, the outcomes exhibited that the proposed LBF-MI method outperformed mutual information-based Boolean network inference, context likelihood relatedness, and relevance network on artificial datasets, and two real Escherichia coli datasets (E. coli gene regulatory network, and SOS response of E. coli regulatory network). Conclusion: LBF-MI’s superior performance in gene regulatory network inference enables researchers to uncover the regulatory mechanisms and cellular behaviors of various organisms.

Discovery of potential ferroptosis and osteoporosis biomarkers through TMT proteomics and bioinformatics analysis

BackgroundPrimary osteoporosis has increasingly emerged as a major issue affecting human health, with a complex specific pathogenic mechanism. As a research hotspot, ferroptosis plays a vital role in the pathogenesis of primary osteoporosis, aiming to explore the link and specific target genes between ferroptosis and primary osteoporosis.MethodsBy utilizing TMT proteomics and bioinformatics analyses, we elucidated the linkages and key targets of the ferroptosis pathway in an ovariectomized osteoporotic rat model. Forty 12-week-old SD female rats were employed in the study, of which 20 female SD rats were ovariectomized as the OVX group and 20 female SD rats were employed as the SHAM group. At the end of the experiments, the femurs of the rats were excised for computed tomography tests and used for hematoxylin and eosin staining. Finally, we extracted bone tissue proteins for TMT proteomics analysis and protein blotting verification.ResultsThe proteomics results of the VX and SHAM groups showed that 133 proteins were significantly changed, of which 91 proteins were upregulated and 42 proteins were downregulated, including TXN, TMSB4X, TFRC, TF, RELA, PARP14, CP, CAPG, and ADIPOQ. The expression of key proteins in the bone tissues was detected by protein blotting. The expression of TFR1, TFRC and TF was upregulated, whereas the expression of Cp, TXN and BMP-2 was downregulated.ConclusionsTMT proteomics and functional enrichment analyses in our study substantiated that in osteoporosis, disturbances in lipid metabolism lead to the emergence of oxidative stress with iron homeostasis imbalance.

Deciphering temporal gene expression dynamics during epilepsy development using a rat model of focal neocortical epilepsy.

Epilepsy involves significant changes in neural cells during epileptogenesis. Although the molecular mechanism of epileptogenesis remains obscure, changes in gene regulation play a crucial role in the evolution of epilepsy. This study aimed to compare changes in a subset of specific genes during epilepsy development, focusing on the period after the first spontaneous seizure, to identify critical time windows for targeting different regulators. Using a rat model of acquired focal neocortical epilepsy induced by tetanus toxin, we characterized gene expression at acute, subacute, and chronic stages (48-72 h, 2 weeks, and 30 days after first spontaneous seizure, respectively), focusing on genes' potential contribution to epilepsy progression. We observed dynamic changes in the expression of these genes throughout the period after the first spontaneous seizure. Astrocytic reactions primarily occur early, before epilepsy is well established. Changes in Mtor (mammalian target of rapamycin) and Rest (repressor element 1 silencing transcription factor) signaling pathways are highly dynamic and correlated with the progression of epilepsy development. Ccl2 (chemokine C-C-motif ligand) is upregulated at the chronic stage, indicating activation of the neuroinflammatory pathway. Finally, Gabra5 (γ-aminobutyric acidergic signaling) is downregulated at the late stage after epilepsy is established. Surprisingly, changes in the expression of specific genes are linked to the time since the first seizure, rather than seizure frequency or duration. These results suggest that the regulation of specific genes is essentially stage-dependent during the development of epilepsy, highlighting the importance of targeting specific genes at appropriate stages of epilepsy development.

Comparison Between Electroporation at Different Voltage Levels and Microinjection to Generate Porcine Embryos with Multiple Xenoantigen Knock-Outs.

In the context of xenotransplantation, the production of genetically modified pigs is essential. For several years, knock-out pigs were generated through somatic cell nuclear transfer employing donor cells with the desired genetic modifications, which resulted in a lengthy and cumbersome procedure. The CRISPR/Cas9 system enables direct targeting of specific genes in zygotes directly through microinjection or electroporation. However, these techniques require improvement to minimize mosaicism and low mutation rates without compromising embryo survival. This study aimed to determine the gene editing potential of these two techniques to deliver multiplexed ribonucleotide proteins (RNPs) to generate triple-knock-out porcine embryos with a multi-transgenic background. We designed RNP complexes targeting the major porcine xenoantigens GGTA1, CMAH, and B4GALNT2. We then compared the development of mosaicism and gene editing efficiencies between electroporation and microinjection. Our results indicated a significant effect of voltage increase on molecule intake in electroporated embryos, without it notably affecting the blastocyst formation rate. Our gene editing analysis revealed differences among delivery approaches and gene loci. Notably, employing electroporation at 35 V yielded the highest frequency of biallelic disruptions. However, mosaicism was the predominant genetic variant in all RNP delivery methods, underscoring the need for further research to optimize multiplex genome editing in porcine zygotes.

Major components of RNAi gene families in Oryza sativa cultivar Kitaake: In-silico discovery and characterization

BackgroundThe Oryza sativa cultivar Kitaake is a promising new model rice for research due to its short life cycle (9 weeks), adaptability to greenhouse conditions, readily accepts foreign genes, and its complete genome sequence is accessible, providing a valuable blueprint for researchers. However, its major RNA interference (RNAi) gene families (DCLs, AGOs, RDRs) have not yet been studied. These gene families influence target-specific protein-coding gene expression and biotic and abiotic stresses, regulating plant growth and development. ObjectivesThis study aims to identify and characterize RNAi gene families from the Kitaake rice. MethodsThis study has been designed by in-silico analysis to explore major RNAi genes highlighting their molecular functions, phylogenetic groups, regulatory factors, and other vital characteristics of Kitaake rice corresponding to OsRNAi genes. ResultsThis study has identified 10 DCLs, 21 AGOs, and 7 RDRs as major RNAi proteins of Kitaake rice corresponding to OsRNAi by BLASTP search. Domain analysis has been revealed the RNase III, PAZ, and Piwi domains are related to gene silencing processes. According to synteny study, Kitaake and rice have the most homology in 33 RNAi gene pairs, suggesting they share a chromosomal order and similar functions. The majority of OsKRNAi proteins have been located in the nucleus and chloroplast, which are related to gene silencing. Gene silencing and ribonuclease III activity are key terms from gene ontology (GO) analysis, which is part of the gene silencing process. Gene regulatory analysis has identified some important transcription factors including ERE, which participates in DNA binding and microRNAs (miRNAs) including 'Osa-MIR168' improves rice resistance to blast disease. The investigation of cis-acting regulatory elements in OsKRNAi genes has shown various crucial components, including MBS, W-box, LTR, ABRE, ARE that are linked with the different stresses. Genes (such as OsKAGO1d) were found to be overexpressed in target of rapamycin (TOR), increasing susceptibility to pathogens. ConclusionThe findings of this study may be useful resources for further experimental investigation on the improvement of Kitaake rice crop against different stresses.

Comprehensive Exploration of CRISPR and Gene Editing Technologies: Applications, Ethical Considerations, and Future Implications in Genetic Research

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and other gene-editing technologies have revolutionized genetic research by enabling precise, targeted modifications of DNA sequences. This paper provides a comprehensive exploration of CRISPR technology, detailing its development, mechanism of action, and versatility in diverse applications. From advancements in medicine, including therapeutic interventions for genetic disorders, to innovations in agriculture aimed at enhancing crop resilience and yield, CRISPR's transformative potential is vast. However, the rapid evolution of gene editing presents significant ethical and societal challenges, particularly concerning human germline editing, ecological impacts, and issues of accessibility and equity. This paper examines these ethical considerations, emphasizing the need for robust regulatory frameworks and responsible scientific practices. It also projects the future trajectory of gene editing technologies, speculating on emerging trends, possible breakthroughs, and the global implications of CRISPR in fields such as personalized medicine, synthetic biology, and biotechnology. By critically analyzing current applications and addressing ethical concerns, this study aims to provide a balanced perspective on CRISPR's potential to reshape genetic research while advocating for ethical governance and public engagement in its ongoing development. CRISPR’s ability to target specific genes with high accuracy has made it an invaluable tool not only in research laboratories but also in clinical settings, where it shows promise in treating previously incurable diseases. Recent advancements have extended CRISPR’s applications beyond simple gene knockout, allowing for base editing, prime editing, and epigenetic modifications that expand the possibilities for genetic correction and enhancement. As scientists explore using CRISPR in complex organisms, the precision and control required for safe and effective treatments become a key focus, particularly in addressing off-target effects that could lead to unintended genetic consequences.

MicroRNA‑374a‑5p/ANLN axis promotes malignant progression of Oral squamous cell carcinoma

Background: Recent research has revealed a significant association between Anillin (ANLN) and miR-374a‑5p with the progression of tumors. Additionally, bioinformatics analysis indicated an inverse relationship in transcript expression levels between ANLN and miR-374a-5p. However, the specific mechanisms driving the miR-374a-5p/ANLN signaling axis in oral squamous cell carcinoma (OSCC) have not been thoroughly explored. Methods: ANLN and miR-374a‑5p expression were evaluated within OSCC cell lines and tissues by RT-qPCR. Using bioinformatics databases, it has been demonstrated that the ANLN gene could be a target of miR-374a-5p. MiR-374a‑5p and ANLN correlation could be assessed via the dual-luciferase reporter assay and western blotting techniques. Functional studies were employed to investigate the behavioral patterns of miR-374a‑5p within OSCC cells. Results: miR-374a‑5p expression could be remarkably downregulated within both OSCC tissues and cells, coinciding with high ANLN expression. ANLN was a specific target gene for miR-374a‑5p by luciferase function assay. The expression of miR-374a‑5p could serve as a diagnostic biomarker and independently predict a poor prognosis in patients with OSCC, and the counteractive effect of upregulating miR-374a‑5p was observed on the proliferative, migratory, and invasive capabilities of OSCC cells. Conclusions: The findings suggest that the miR-374a‑5p/ANLN signaling axis potentially modulates the advancement of OSCC, and miR-374a‑5p may serve as potential therapeutic targets of oral cancer.

Discovery of Kuraridin as a Potential Natural Anti-Melanogenic Agent: Focusing on Specific Target Genes and Multidirectional Signaling Pathways.

Abnormal melanogenesis upon UV exposure causes excessive oxidative stress, leading to hyperpigmentation disorders. As a key rate-limiting enzyme in melanogenesis, tyrosinase is considered a primary target for depigmenting agents. Sophora flavescens is used as a food and in traditional medicine as a valuable source of prenylated flavonoids. The present study aimed to elucidate the anti-melanogenic effect and potential mechanism of kuraridin, one of the major prenylated flavonoids. Kuraridin showed anti-tyrosinase activity with an IC50 value in the nanomolar range, superior to that of kojic acid, a positive control. It significantly reduced tyrosinase activity with the least cytotoxicity, suppressing melanogenesis in α-MSH-induced B16F10 cells. Furthermore, kuraridin considerably reduced melanogenesis in a 3D human skin model. To elucidate the anti-melanogenic mechanism of kuraridin, target genes (KIT, MAP2K1, and PRKCA) and pathways (c-KIT and ETB-R pathways) were identified using network pharmacology. KIT and MAP2K1 are simultaneously involved in the c-KIT cascade and are considered the most important in melanogenesis. PRKCA acts directly on MITF and its downstream enzymes through another pathway. Docking simulation showed strong interactions between kuraridin and c-KIT, ERK1/2, and PKC encoded by target genes. Overall, the present study showed kuraridin to be a novel natural anti-melanogenic agent in hyperpigmentation disorders.

8490 The mRNA for the Nonsyndromic Deafness Gene Atp2b2 Is Reduced Following Developmental Hypothyroidism

Abstract Disclosure: E.A. Gregersen: None. R.P. Peeters: None. D. Forrest: None. D.S. Sharlin: None. Thyroid hormone (TH) is essential for auditory system development. In rodent models, low levels of TH during the early postnatal period delay cochlear tissue remodeling and alter ion channel function required for normal auditory function. TH receptors are ligand-dependent transcription factors that regulate gene expression. Considering this, auditory deficits observed in hypothyroidism are thought to be largely the result of altered expression of specific TH target genes. However, few TH-regulated genes in the developing cochlea have been reported. TH is reported to impact calcium signaling in several tissues, but whether regulators of calcium signaling are altered following developmental hypothyroidism in the cochlea is largely unexplored. In this report, we investigated the spatial and temporal expression of the ATPase, Ca++ transporting, plasma membrane 2 (Atp2b2) gene in a mouse model of developmental hypothyroidism. Timed-pregnant dams were treated with thyroid gland inhibitors to induce developmental TH insufficiency from embryonic day 12.5 (E12.5) through post-natal day 15 (P15). Untreated timed-pregnant dams served as euthyroid controls. Control and experimental cochleae were collected over a developmental period ranging from embryonic day 18.5 (E18.5) through P15. Cochleae were then processed to detect Atp2b2 mRNA by in situ hybridization or quantitative real-time PCR. In situ hybridization showed that Atp2b2 localizes to inner and outer hair cells as expected, but Atp2b2 was also observed at lower levels in the greater epithelial ridge and spiral ganglion. Quantification of Atp2b2 mRNA revealed an effect of postnatal day and treatment on Atp2b2. In euthyroid animals, Atp2b2 expression gradually increased until P10, then decreased slightly by P15. In hypothyroid animals, Atp2b2 mRNA was consistently decreased (2-2.5 fold). Hypothyroidism similarly impacted expression regardless of sex. The reduction in Atp2b2 mRNA expression in the hypothyroid animals suggests that Atp2b2 is developmentally regulated in part by thyroid hormone signaling. This study characterizes the relationship between TH and Atp2b2 expression during early cochlear development while providing insight into abnormal cochlear development due to hypothyroidism. Presentation: 6/3/2024

B-205 Performance of a Novel Fluorogenic Assay for Detection of Carbapenemase-producing Enterbacteriaceae

Abstract Background In recent years, under the selective challenge of antibiotics, the variety and number of drugresistant pathogenic microorganisms have increased significantly, which brings great challenges to clinical diagnosis and treatment, especially the infection caused by carbapenem resistant Enterobacteriaceae (CRE). Carbapenemases production is the main mechanism of drug resistance of Enterobacteriaceae to carbapenems. Drug resistance of Carbapenems can be caused by three mechanisms, resulting in the production of five major Carbapenemases. These are Klebsiella pneumoniae enzyme (KPC), New Delhi metal β-lactamase (NDM), carbapenem hydrolyzed oxalase (OXA-48 like), integrin-encoded metal β- lactamase (VIM) and IMP (Imipenemase). The real-time fluorescence quantitative PCR (qPCR) method based on molecular beacons was combined with the melting curve analysis to identify five drug resistance genes simultaneously by a single PCR reaction, with rapid detection, high sensitivity and strong specificity. Based on this principle, we developed the novel fluorogenic assay for rapid detection of Carbapenemases in multidrug-resistant Enterobacteriaceae (Dynamiker Biotechnology (Tianjin) Co., Ltd.). Methods We evaluated the performance of the novel fluorogenic assay for rapid detection of Carbapenemases in multidrug-resistant Enterobacteriaceae, including the limit of detection (LoD) and cross-reactivity, and compared it with the lateral flow immunochromatography assay (LFA). Results The LoD ranged from 75-450 CFU/mL for the five carbapenemase genes. The analytical specificity for target genes was 100%, as assessed with a panel of 15 pathogens, which indicated no cross-reactions. Comparison of qPCR and LFA results from twenty-three CRE clinical isolates with characterized carbapenemase content demonstrated a complete agreement (Table 1). Conclusions The novel fluorogenic assay for rapid detection of Carbapenemases in multidrug-resistant Enterobacteriaceae is an accurate and rapid method to identify KPC, NDM, VIM, IMP and OXA-48-like carbapenemases in the clinical microbiology laboratory, which can guide infection control programs to limit the spread of these organisms.

Cooperativity among clustered κB sites within promoters and enhancers dictates transcriptional specificity of NF-κB-RelA along with specific cofactors.

The functional role of weak DNA binding sites for transcription factor (TF) recruitment and gene expression remains largely unknown. Our study reveals that the weak NF-κB DNA binding sites, which are abundant in gene promoters and enhancers, appear in clusters and exhibit minimal to undetectable NF-κB binding activity in isolation in vitro, yet they play prominent roles in gene regulation within native context in cells. We found nuclear concentration of RelA/p65, the predominant NF-κB, is approximately 0.2 µM in stimulated cells, challenging the idea that these weak κB sites operate through mass action-dependent binding mechanisms. Through proteomic analysis, we identified a range of nuclear factors, including various other TFs, interacting with RelA at these κB-sites. ChIP-seq, RNA-seq and phase-separated condensation analyses suggest these additional TFs, referred to as the cofactors of NF-κB, facilitate dynamic recruitment of NF-κB to clustered κB sites of specific target genes. Overall, our findings demonstrate the collective contribution of both strong and weak κB sites in occupancy of NF-κB at the promoters and enhancers, with the recruitment facilitated by a variety of cofactors. This congregation of multiple factors forming larger dynamic complexes appearing as a transcription condensate is likely to be common to all transcriptional programs.

Environmental surveillance for Salmonella Typhi in rivers and wastewater from an informal sewage network in Blantyre, Malawi.

Environmental surveillance for Salmonella Typhi may provide information on the community-level dynamics of typhoid fever in resource poor regions experiencing high disease burden. Many knowledge gaps concerning the feasibility of ES remain, especially in areas lacking formal sewage systems. We implemented protocols for S. Typhi ES, including site selection and catchment population estimation, sample concentration and testing using qPCR for S. Typhi specific gene targets. Between May 2021 and May 2022, we collected grab samples and Moore swabs from 43 sites in Blantyre, Malawi. Catchment characteristics, water quality, and human faecal contamination (qPCR for Bacteroides HF183) were also recorded. Their association with S. Typhi detection was investigated using a logistic mixed-effects regression analysis. Prevalence of S. Typhi in ES samples was 2.1% (1.1-4.0%) and 3.9% (1.9-7.9%) for grab and Moore swab samples, respectively. HF183 was associated S. Typhi positivity, with a unit increase in log genome copies/microlitre increasing the odds of detection of S. Typhi by 1.56 (95% CI: 1.29-1.89) and 1.33 (1.10-1.61) in Moore swabs and grab samples, respectively. The location and timing of S. Typhi detection through ES was not associated with the incidence of typhoid fever reported in associated catchment populations. During this period of relatively low typhoid fever incidence, wastewater surveillance continued to detect S. Typhi in human sewage and wastewater suggesting that ES using natural river systems can be a sensitive indicator of transmission.

Multidrug-Resistant Proteus mirabilis and Other Gram-Negative Species Isolated from Native Egyptian Chicken Carcasses.

Poultry carcasses may be reservoirs for the zoonotic transmission of antimicrobial-resistant bacteria to humans and pose a major public health hazard. During the isolation of Salmonella from poultry and other foods, many of the presumptive typical Salmonella colonies on xylose lysine deoxycholate (XLD) agar were found to lack the invA gene, which is the specific target gene for Salmonella spp. Therefore, the current study aimed to estimate the prevalence and antimicrobial resistance profiles of extensively drug-resistant invA-negative non-Salmonella isolates recovered from native Egyptian chicken carcasses as presumptive Salmonella colonies on XLD agar. The non-Salmonella isolates were detected in 84% (126/150) of the examined native Egyptian chicken carcasses and classified into five genera, with prevalence rates of 64% (96/150), 14% (21/150), 6.7% (10/150), 3.3% (5/150), and 1.3% (2/150) for Proteus, Citrobacter, Shigella, Pseudomonas, and Edwardsiella, respectively. One hundred and ninety-five invA-negative, non-verified presumptive Salmonella isolates were recovered and classified at the species level into Proteus mirabilis (132/195; 67.7%), Proteus vulgaris (11/195; 5.6%), Citrobacter freundii (26/195; 13.3%), Shigella flexneri (8/195; 4.1%), Shigella sonnei (6/195; 3.1%), Shigella dysenteriae (3/195; 1.5%), Pseudomonas fluorescens (6/195; 3.1%), and Edwardsiella tarda (3/195; 1.5%). All (195/195; 100%) of these isolates showed resistance against cefaclor and fosfomycin. Additionally, these isolates showed high resistance rates of 98%, 92.8%, 89.7%, 89.2%, 89.2%, 86.7%, 80%, 78.5%, 74.4%, and 73.9% against cephalothin, azithromycin, vancomycin, nalidixic acid, tetracycline, sulfamethoxazole/trimethoprim, cefepime, gentamicin, cefotaxime, and ciprofloxacin, respectively. Interestingly, all (195/195; 100%) of the identified isolates were resistant to at least five antibiotics and exhibited an average MAR (multiple antibiotic resistance) index of 0.783. Furthermore, 73.9% of the examined isolates were classified as extensively drug-resistant, with an MAR index equal to 0.830. The high prevalence of extensively drug-resistant foodborne Proteus, Citrobacter, Shigella, Pseudomonas, and Edwardsiella isolated from native chicken carcasses poses a great hazard to public health and necessitates more monitoring and concern about the overuse and misuse of antibiotics in humans and animals. This study also recommends the strict implementation of GHP (good hygienic practices) and GMP (good manufacturing practices) in the chicken meat supply chain to protect consumer health.

Altered expression of insulin-like growth factor 2 mRNA binding protein 2 is associated with periodontal disease- a case-control analysis

Background/PurposePeriodontitis has a multifactorial pathogenesis involving genetic and epigenetic factors. Insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) is an N6-methyladenosine (m6A) reader that enhances messenger RNA (mRNA) stability in an m6A-dependent manner. It is being considered as a potential target for treating inflammatory diseases. However, its role in periodontitis and its specific target genes affected by m6A modification are not yet well understood. This study aims to investigate the expression of IGF2BP2 and its potential involvement in periodontitis. Materials and methodsSeventy participants were recruited, including 35 patients with periodontitis and 35 healthy controls. Clinical examination and radiography were performed to confirm a diagnosis of periodontitis. Gingival tissue samples were collected from each participant, and IGF2BP2 expression was measured using real-time PCR and western blotting. In addition, in silico tools were used to identify the IGF2BP2 network pathway and its functions. ResultsIGF2BP2 expression was significantly higher in the periodontitis group than in the healthy control group (p < 0.0001). Functional enrichment analysis revealed that the IGF2BP2 pathway network plays a crucial role in periodontal pathogenesis. In addition, pro-inflammatory cytokines, including IL-1β and IL-6, were significantly increased in the periodontitis group (p < 0.0001) and were positively correlated with IGF2BP2 expression and m6A methylation sites. ConclusionOur study demonstrated that increased IGF2BP2 expression is associated with periodontitis, which may regulate proinflammatory cytokine production in an m6A-dependent manner. Further functional studies are required to understand the mechanism of action of IGF2BP2 in periodontitis.

Estrogen receptor alpha mediated repression of PRICKLE1 destabilizes REST and promotes uterine fibroid pathogenesis.

Uterine fibroids (leiomyomas), benign tumors of the myometrial smooth muscle layer, are present in over 75% of women, often causing severe pain, menorrhagia and reproductive dysfunction. The molecular pathogenesis of fibroids is poorly understood. We previously showed that the loss of REST (RE-1 Silencing Transcription factor), a tumor suppressor, in fibroids leads to activation of PI3K/AKT-mTOR pathway. We report here a critical link between estrogen receptor alpha (ERα) and the loss of REST, via PRICKLE1. PRICKLE1 expression is markedly lower in leiomyomas, and the suppression of PRICKLE1 significantly down regulates REST protein levels. Conversely, overexpression of PRICKLE1 resulted in the restoration of REST in cultured primary leiomyoma smooth muscle cells (LSMCs). Crucially, mice exposed neonatally to environmental estrogens, proven risk factors for fibroids, expressed lower levels of PRICKLE1 and REST in the myometrium. Using mice that lack either endogenous estrogen (Lhb -/- mice) or ERα (Esr1 -/- mice), we demonstrate that Prickle1 expression in the myometrium is suppressed by estrogen through ERα. Enhancer of zeste homolog 2 (EZH2) is known to participate in the repression of specific ERα target genes. Uterine leiomyomas express increased levels of EZH2 that inversely correlate with the expression of PRICKLE1. Using chromatin immunoprecipitation, we provide evidence for association of EZH2 with the PRICKLE1 promoter and for hypermethylation of H3K27 within the regulatory region of PRICKLE1 in leiomyomas. Additionally, siRNA mediated knockdown of EZH2 leads to restoration of PRICKLE1 in LSMCs. Collectively, our results identify a novel link between estrogen exposure and PRICKLE1/REST-regulated tumorigenic pathways in leiomyomas.

Casticin suppresses self-renewal related stemness via miR-342-3p-mediated FoxM1 downregulation in cervical cancer cells

BackgroundCasticin (CAS), a natural flavonoid found in Viticis Fructus, Viticis Cannabifoliae Fructus, and Semen Euphorbiae, shows anti-inflammatory activity and efficacy against various cancers. However, its effect on stemness associated with self-renewal in cervical cancer (CC) cells remains unclear, as well as the underlying mechanism. PurposeThe primary objective of this study was to examine the effect of CAS on CC stemness and to explore the underpinning regulatory mechanism. MethodsHeLa cells underwent treatment with varying concentrations of CAS (0, 10, 30, 100 nM). To evaluate the impacts of CAS on CC stemness and tumorigenicity, sphere- and colony-formation assays and a xenograft model were employed. The study involved screening for changes in miRNAs and their target genes. The miRNA array identified an upregulation in miRNAs, whereas the mRNA array detected a downregulation of specific target genes. The latter genes were found to regulate stem cell-related genes through miR-342-3p in HeLa cells administered CAS. Next, whether miR-342-3p directly targets FOXM1 when upregulated by CAS was assessed by the luciferase reporter assay. qRT-PCR was performed to analyze miR-342-3p expression. Additionally, immunoblotting was conducted to assess the protein amounts of FoxM1 and stemness-related factors (CD133, CD49f, Nanog, and Sox2). Function rescue experiments were conducted to determine the mechanism of CAS in stemness regulation. These experiments involved utilizing a miR-342-3p inhibitor and overexpressing FOXM1 in HeLa cells. ResultsCAS decreased in vitro stemness, suppressing sphere- and colony-formation capabilities of CC. It also dose-dependently downregulated the expression of stemness-associated proteins, including CD133, CD49f, Nanog, and Sox2. Moreover, CAS inhibited in vivo carcinogenesis, remarkably reducing tumor growth in mice bearing HeLa cell xenografts. Analysis revealed downregulated FOXM1 expression in HeLa cells treated with CAS. In the luciferase reporter assay, miR-342-3p was found to directly target FOXM1 in CAS-treated HeLa cells. Additionally, miR-342-3p inhibitor transfection successfully rescued CAS’ suppressive impact on stemness. Furthermore, overexpression of FOXM1 did not induce changes in miR-342-3p expression. However, it effectively rescued CAS’ suppressive effects on stemness. Moreover, CAS also inhibited stemness, upregulated miR-342-3p, and lowered FOXM1 expression in the SiHa cell line. ConclusionCAS suppresses self-renewal-associated stemness by targeting FOXM1 via miR-342-3p upregulation. These findings suggest CAS is promising as a novel therapeutic candidate in CC.

Unraveling DNA Triplex Assembly: Mass Spectrometric Investigation of Modified Triplex Forming Oligonucleotides for Enhanced Gene Targeting.

Deoxyribonucleic acid triplexes have potential roles in a range of biological processes involving gene and transcriptional regulation. A major challenge in exploiting the formation of these higher-order structures to target genes in vivo is their low stability, which is dependent on many factors including the length and composition of bases in the sequence. Here, different DNA base modifications have been explored, primarily using native mass spectrometry, in efforts to enable stronger binding between the triplex forming oligonucleotide (TFO) and duplex target sites. These modifications can also be used to overcome pyrimidine interruptions in the duplex sequence in promoter regions of genomes, to expand triplex target sequences for antigene therapies. Using model sequences with a single pyrimidine interruption, triplex forming oligonucleotides containing locked nucleic acid base modifications were shown to have a higher triplex binding propensity than DNA-only and dSpacer-containing TFOs. However, the triplex forming ability of these systems was limited by the competitive formation of multiple higher order assemblies. Triplex forming sequences that correspond to specific gene targets from the Pseudomonas aeruginosa genome were also investigated, with LNA-containing TFOs the only variant able to form triplex using these sequences. This work indicates the advantages of utilizing synthetically modified TFOs to form triplex assemblies in vivo for potential therapeutic applications and highlights the advantages of native mass spectrometry for the study of their formation.

The Cutting-edge of CRISPR for Cancer Treatment and its Future Prospects.

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a versatile technology that allows precise modification of genes. One of its most promising applications is in cancer treatment. By targeting and editing specific genes involved in cancer development and progression, CRISPR has the potential to become a powerful tool in the fight against cancer. This review aims to assess the recent progress in CRISPR technology for cancer research and to examine the obstacles and potential strategies to address them. The two most commonly used CRISPR systems for gene editing are CRISPR/Cas9 and CRISPR/Cas12a. CRISPR/Cas9 employs different repairing systems, including homologous recombination (HR) and nonhomologous end joining (NHEJ), to introduce precise modifications to the target genes. However, off-target effects and low editing efficiency are some of the main challenges associated with this technology. To overcome these issues, researchers are exploring new delivery methods and developing CRISPR/Cas systems with improved specificity. Moreover, there are ethical concerns surrounding using CRISPR in gene editing, including the potential for unintended consequences and the creation of genetically modified organisms. It is important to address these issues through rigorous testing and strict regulations. Despite these challenges, the potential benefits of CRISPR in cancer therapy cannot be overlooked. By introducing precise modifications to cancer cells, CRISPR could offer a targeted and effective treatment option for patients with different types of cancer. Further investigation and development of CRISPR technology are necessary to overcome the existing challenges and harness its full potential in cancer therapy.

Association between the Exposure to Phthalates and the Risk of Endometriosis: An Updated Review.

Endometriosis is a chronic gynecological disease, primarily associated with pelvic pain and infertility, that affects approximately 10% of the women of reproductive age. Estrogen plays a central role in endometriosis, and there is growing evidence that endocrine disruptors, such as phthalates, may contribute to its development. This review aimed to determine whether there is a causal relationship between phthalate exposure and the development of endometriosis, as well as the possible effects of phthalates on fertility, by analyzing epidemiological data. After a literature search with a combination of specific terms on this topic, we found that although there are limitations to the current studies, there is a clear association between phthalate exposure and endometriosis. Phthalates can interfere with the cellular processes of the endometrium; specifically, they can bind to PPAR and ER-α and activate TGF-β, promoting different signaling cascades that regulate the expression of specific target genes. This may lead to inflammation, invasion, cytokine alteration, increased oxidative stress, and impaired cell viability and proliferation, culminating in endometriosis. Nevertheless, future research is important to curb the progression and development of endometriosis, and strategies for prevention, diagnosis, and treatment are a priority. In this regard, public policies and recommendations to reduce exposure to phthalates and other endocrine disruptors should be promptly implemented.

Two-polarized roles of transcription factor FOSB in lung cancer progression and prognosis: dependent on p53 status

BackgroundActivator protein-1 (AP-1) represents a transcription factor family that has garnered growing attention for its extensive involvement in tumor biology. However, the roles of the AP-1 family in the evolution of lung cancer remain poorly characterized. FBJ Murine Osteosarcoma Viral Oncogene Homolog B (FOSB), a classic AP-1 family member, was previously reported to play bewilderingly two-polarized roles in non-small cell lung cancer (NSCLC) as an enigmatic double-edged sword, for which the reasons and significance warrant further elucidation.Methods and ResultsBased on the bioinformatics analysis of a large NSCLC cohort from the TCGA database, our current work found the well-known tumor suppressor gene TP53 served as a key code to decipher the two sides of FOSB – its expression indicated a positive prognosis in NSCLC patients harboring wild-type TP53 while a negative one in those harboring mutant TP53. By constructing a panel of syngeneically derived NSCLC cells expressing p53 in different statuses, the radically opposite prognostic effects of FOSB expression in NSCLC population were validated, with the TP53-R248Q mutation site emerging as particularly meaningful. Transcriptome sequencing showed that FOSB overexpression elicited diversifying transcriptomic landscapes across NSCLC cells with varying genetic backgrounds of TP53 and, combined with the validation by RT-qPCR, PREX1 (TP53-Null), IGFBP5 (TP53-WT), AKR1C3, and ALDH3A1 (TP53-R248Q) were respectively identified as p53-dependent transcriptional targets of FOSB. Subsequently, the heterogenous impacts of FOSB on the tumor biology in NSCLC cells via the above selective transcriptional targets were confirmed in vitro and in vivo. Mechanistic investigations revealed that wild-type or mutant p53 might guide FOSB to recognize and bind to distinct promoter sequences via protein-protein interactions to transcriptionally activate specific target genes, thereby creating disparate influences on the progression and prognosis in NSCLC.ConclusionsFOSB expression holds promise as a novel prognostic biomarker for NSCLC in combination with a given genetic background of TP53, and the unique interactions between FOSB and p53 may serve as underlying intervention targets for NSCLC.