Search Results (245)

Background: DEAD/H box 5 (DDX5) serves as a transcriptional coactivator for several transcription factors including E2F1, the primary target of the tumor suppressor pRB. E2F1 physiologically activated by growth stimulation activates growth-related genes and promotes cell proliferation. In contrast, upon loss of pRB function due to oncogenic changes, E2F1 is activated out of restraint by pRB (deregulated E2F1) and stimulates tumor suppressor genes such as ARF, which activates the tumor suppressor p53, to suppress tumorigenesis. We have recently reported that DDX5 augments deregulated E2F1 activity to induce tumor suppressor gene expression and apoptosis. During the analyses, we noted that over-expression of E2F1 increased DDX5 expression, suggesting a feed forward loop in E2F1 activation through DDX5. Objective: We thus examined whether the DDX5 gene is a target of deregulated E2F1. Method: For this purpose, we performed promoter analysis and ChIP assay. Result: The DDX5 promoter did not possess typical E2F binding consensus but contained several GC repeats observed in deregulated E2F1 targets. Insertion of point mutations in these GC repeats decreased responsiveness to deregulated E2F1 induced by over-expression of E2F1, but scarcely affected responsiveness to growth stimulation. ChIP assays showed that deregulated E2F1 induced by over-expression of E2F1 or expression of E1a, which binds pRB and releases E2F1, bound to the DDX5 gene, while physiological E2F1 induced by growth stimulation did not. Conclusions: These results suggest that the DDX5 gene is a target of deregulated E2F1, generating a feed forward loop mediating tumor suppressive E2F1 activity. Full article

Stress granule formation is a type of liquid–liquid phase separation in the cytoplasm, leading to RNA–protein condensates that are associated with various cellular stress responses and implicated in numerous pathologies, including cancer, neurodegeneration, inflammation, and cellular senescence. One of the key components of mammalian stress granules is the DEAD-box RNA helicase DDX3, which unwinds RNA in an ATP-dependent manner. DDX3 is involved in multiple steps of RNA metabolism, facilitating gene transcription, splicing, and nuclear export and regulating cytoplasmic translation. In this study, we investigate the role of the RNA helicase DDX3’s enzymatic activity in shaping the RNA content of ribonucleoprotein (RNP) condensates formed during arsenite-induced stress by inhibiting DDX3 activity with RK-33, a small molecule previously shown to be effective in cancer clinical studies. Using the human osteosarcoma U2OS cell line, we purified the RNP granule fraction and performed RNA sequencing to assess changes in the RNA pool. Our results reveal that RK-33 treatment alters the composition of non-coding RNAs within the RNP granule fraction. We observed a DDX3-dependent increase in circular RNA (circRNA) content and alterations in the granule-associated intronic RNAs, suggesting a novel role for DDX3 in regulating the cytoplasmic redistribution of non-coding RNAs. Full article

This study aimed to identify genetic variants using a customized next-generation sequencing (NGS) panel for pediatric myelodysplastic syndrome (pMDS) and to explore their associations with cytogenetic and clinical characteristics. Cytogenetic analyses were conducted using G-banding and fluorescence in situ hybridization. NGS was performed with the Ion Torrent Personal Genome Machine for the following genes: GATA2, RUNX1, CEBPA, ANKRD26, ETV6, SAMD9, SAMD9L, PTPN11, NRAS, SETBP1, DDX41, TP53, FLT3, SRP72, and JAK3. Analyses were performed with Ion Reporter 5.20.8.0 software. Genetic variants were classified using the dbSNP, 1000 Genomes, COSMIC, and Varsome databases. We analyzed 25 cases of pMDS; 15 presented abnormal karyotypes, and 19 showed genetic variants. Among the 29 variants identified across 12/15 genes, 27% were pathogenic and 14% were likely pathogenic, with NRAS and GATA2 most frequently associated with disease progression. A new somatic variant of uncertain significance in SETBP1 was detected in seven patients showing heterogeneous clinical outcomes. Genetic variants were found in 7/10 patients with normal karyotypes, indicating that submicroscopic alterations can shed light on disease biology. Our results highlight the critical role of a targeted NGS panel in identifying molecular alterations associated with pMDS pathogenesis, thereby enhancing diagnostic precision, prognosis, and aiding in treatment selection. Full article

Black rockfish (Sebastes schlegelii) is a marine ovoviviparous teleost that exhibits significant sexual dimorphism, with females growing faster and reaching larger sizes than males. Establishing stable oogonial stem cells (OSCs) is critical for understanding germline stem cell dynamics and facilitating all-female breeding. In this study, we successfully isolated and cultured OSCs from S. schlegelii for 12 passages. These cells exhibited alkaline phosphatase activity, expressed germline marker genes (ddx4, cdh1, klf4), and maintained a diploid karyotype (2n = 48). Transcriptomic comparisons between early (P3) and late (P12) passages revealed significant metabolic dysfunction and cell cycle arrest in the late-passage cells. Specifically, the down-regulation of glutathione-related and glycolysis-related genes (gstm3, gstt1, mgst3, gsta1, gsta4, gsto1, gapdh) and key mitotic regulators (cdk1, chk1, cdk4, e2f3, ccne2, ccnb1) suggested that metabolic imbalance contributes to oxidative stress, resulting in cell cycle inhibition and eventual senescence. This study provides a marine fish model for investigating metabolism-cell cycle interactions in germline stem cells and lays the foundation for future applications in germ cell transplantation and all-female breeding. Full article

Urolithin A, which is a natural gut microbial metabolite, exerts multiple beneficial effects upon supplementation, including prolonging lifespan, mitigating diseases, restoring the quality of aged oocytes and alleviating drug toxicity. The study aims to investigate the ovarian protective role of Urolithin A using a neonatal mouse ovarian in vitro culture and chemotherapy model, with a particular focus on its mechanisms for inhibiting primordial follicle activation and mitigating cyclophosphamide (CY) or 4-hydroperoxy (4-HC)-induced follicle apoptosis. The results showed that Urolithin A significantly decreased the number of growing follicles and downregulated the expression of oocyte growth-related genes (Gdf9 and Zp3) and protein (DDX4), as well as Ki-67 and BrdU-positive signals. Further studies revealed that Urolithin A significantly downregulated the levels of phosphorylated Akt and FOXO3a and decreased the percentage of oocytes with FOXO3a nuclear export. Molecular docking showed a strong binding ability between Urolithin A and its downregulated gene Pik3cg. Moreover, Urolithin A significantly decreased CY- and 4-HC-induced increases in cleaved Caspase-3- and PARP1-positive signals. Meanwhile, RNA-seq analysis indicated that Urolithin A significantly downregulated CY-induced expression of DNA damage-related genes (Trp73 and Trim29). In short, Urolithin A inhibits primordial follicle activation by reducing PI3K/Akt signaling reactivity. Furthermore, Urolithin A prevents CY-induced follicle apoptosis. The study provides valuable insights into Urolithin A treatment for chemotherapy-induced infertility. Full article

GIGYF2 (Grb10-interacting GYF protein 2) functions as a versatile adaptor protein that regulates gene expression at various levels. At the transcriptional level, GIGYF2 facilitates VCP/p97-mediated extraction of ubiquitylated Rpb1 from stalled RNA polymerase II complexes during DNA damage response. In mRNA surveillance, GIGYF2 participates in ribosome collision-induced quality control, nonsense-mediated decay, no-go decay, and non-stop decay pathways. Furthermore, GIGYF2 interacts with key factors including 4EHP, TTP, CCR4-NOT, DDX6, ZNF598, and TNRC6A to mediate translational repression and mRNA degradation. Additionally, dysregulation of GIGYF2 has been implicated in various pathological conditions, including metabolic diseases, vascular aging, viral infections, and neurodegenerative disorders. This review summarizes the structural and functional characteristics of GIGYF2, highlighting its importance in transcriptional regulation, mRNA surveillance, translational inhibition, and mRNA degradation, while also elucidating its potential as a therapeutic target for disease treatment. Full article

Autism spectrum disorder (ASD) is a neurodevelopmental impairment that occurs due to mutations related to the formation of the nervous system, combined with the impact of various epigenetic and environmental factors. This necessitates the identification of the genetic variations involved in ASD pathogenesis. We performed whole exome sequencing (WES) in a cohort of 22 Bulgarian male and female individuals showing ASD features alongside segregation analyses of their families. A targeted panel of genes was chosen and analyzed for each case, based on a detailed examination of clinical data. Gene analyses revealed that specific variants concern key neurobiological processes involving neuronal architecture, development, and function. These variants occur in a number of genes, including SHANK3, DLG3, NALCN, and PACS2 which are critical for synaptic signaling imbalance, CEP120 and BBS5 for ciliopathies, SPTAN1 for spectrins structure, SPATA5, TRAK1, and VPS13B for neuronal organelles trafficking and integrity, TAF6, SMARCB1, DDX3X, MECP2, and SETD1A for gene expression, CDK13 for cell cycle control, ALDH5A1, DPYD, FH, and PDHX for mitochondrial function, and PQBP1, HUWE1, and WDR45 for neuron homeostasis. Novel single nucleotide variants in the SPATA5, CEP120, BBS5, SETD1A, TRAK1, VPS13B, and DDX3X genes have been identified and proposed for use in ASD diagnostics. Our data contribute to a better understanding of the complex neurobiological features of autism and are applicable in the diagnosis and development of personalized therapeutic approaches. Full article

Acute Myeloid Leukemia (LAML) is a life-threatening hematological malignancy, and the DEAD-box helicase 3 X-linked (DDX3X) gene is a potential yet underexplored target gene for LAML. Biomolecules derived from medicinal plants like Aerva javanica offer a great source of therapeutic candidates. This study aimed to investigate the role of DDX3X in LAML and identify plant-derived biomolecules that could inhibit DDX3X using computational approaches. Pan-cancer mutational profiling, a transcriptomic analysis, survival, protein–protein interaction networks, and a principal component analysis (PCA) were employed to elucidate functional associations and transcriptomic divergence. Subsequently, biomolecules from A. javanica were subjected to in silico screening using molecular docking and ADMET profiling. The docking protocol was validated using RK-33, a known DDX3X inhibitor. DDX3X was found to be linked to key leukemogenic pathways, including Wnt/β-catenin and MAPK signaling, indicating it to be a potential target. Molecular docking of A. javanica compounds revealed CIDs 15559724, 5490003, and 74819331 as potent DDX3X inhibitors with strong binding affinity and favorable pharmacokinetic and toxicity profiles compared to RK-33. This study highlights the importance of DDX3X in LAML pathogenesis and suggests targeting it using plant-derived inhibitors, which may require further in vitro and in vivo validation. Full article

HIV-1 infection in microglia induces HIV-associated neurocognitive disorder (HAND). Recent evidence suggests that microglia can be infected with HIV-1 in the active, persistent, or latent replication stages. The molecular mechanisms governing these stages of infection are still the subject of continuous study. In this study, we analyzed the relationship between HIV-1 infection and two lncRNAs, NEAT1 and ZBTB11-AS1, on different days post-infection. We found that on days 1 and 4 post-infection, HIV-1 was actively replicating; meanwhile, by day 21, HIV-1 had entered a persistent stage. We also noted that the expression levels of NEAT1 and ZBTB11-AS1 varied during these different stages of HIV-1 infection in microglia, as did their subcellular localization. We performed an interaction network analysis and identified DDX3X and ZC3HAV1 as hypothetically related to NEAT1 and ZBTB11-AS1 in the C20 human microglial cell line. Additionally, we determined that IL-6, a cytokine regulated by DDX3X and ZC3HAV1, exhibits changes in protein expression levels during both active and persistent HIV-1 infection. Full article

Background/Objectives: DDX41, DEAD-box RNA helicase 41 gene located on chromosome 5q25.3, is one of the most mutated genes in patients with germline predisposition to myeloid neoplasms. Germline and somatic mutations often have different locations and patterns of mutation, with some hotspots displaying diversity based on ethnicity. We aimed to explore clinical outcomes in patients with various DDX41 hot-spot mutations. Methods: This was a retrospective study of patients at Mayo Clinic with DDX41 mutation identified through Next Generation Sequencing (NGS) between 2018 and 2024. We completed unadjusted comparisons using continuous or categorical variables, and survival rates were assessed using the Kaplan–Meier method and cox regression analysis. Results: Overall survival appears to be higher in those with p.M1| when compared to p.Asp140GlyFs*2 and p.Arg525His, with comparable survival between p.Arg525His and p.Asp140GlyFs*2. Among males with p.M1| who underwent bone marrow transplant, those who underwent bone marrow transplant appeared to have lower survival rates, although not statistically significant. Our study was limited by a small sample size, therefore limiting our ability to reach significance. Conclusions: Our findings suggest potential implications for clinical outcomes based on DDX41 mutation hot-spots. Full article

Glioblastoma (GBM) is a fatal brain cancer known for its rapid and aggressive growth, with some studies indicating that females may have better survival outcomes compared to males. While sex differences in GBM have been observed, the underlying biological mechanisms remain poorly understood. Feature selection can lead to the identification of discriminative key biomarkers by reducing dimensionality from high-dimensional medical datasets to improve machine learning model performance, explainability, and interpretability. Feature selection can uncover unique sex-specific biomarkers, determinants, and molecular profiles in patients with GBM. We analyzed high-dimensional proteomic and metabolomic profiles from serum biospecimens obtained from 109 patients with pathology-proven glioblastoma (GBM) on NIH IRB-approved protocols with full clinical annotation (local dataset). Serum proteomic analysis was performed using Somalogic aptamer-based technology (measuring 7289 proteins) and serum metabolome analysis using the University of Florida’s SECIM (Southeast Center for Integrated Metabolomics) platform (measuring 6015 metabolites). Machine learning-based feature selection was employed to identify proteins and metabolites associated with male and female labels in high-dimensional datasets. Results were compared to publicly available proteomic and metabolomic datasets (CPTAC and TCGA) using the same methodology and TCGA data previously structured for glioma grading. Employing a machine learning-based and hybrid feature selection approach, utilizing both LASSO and mRMR, in conjunction with a rank-based weighting method (i.e., GLIO-Select), we linked proteomic and metabolomic data to clinical data for the purposes of feature reduction to identify molecular biomarkers associated with biological sex in patients with GBM and used a separate TCGA set to explore possible linkages between biological sex and mutations associated with tumor grading. Serum proteomic and metabolomic data identified several hundred features that were associated with the male/female class label in the GBM datasets. Using the local serum-based dataset of 109 patients, 17 features (100% ACC) and 16 features (92% ACC) were identified for the proteomic and metabolomic datasets, respectively. Using the CPTAC tissue-based dataset (8828 proteomic and 59 metabolomic features), 5 features (99% ACC) and 13 features (80% ACC) were identified for the proteomic and metabolomic datasets, respectively. The proteomic data serum or tissue (CPTAC) achieved the highest accuracy rates (100% and 99%, respectively), followed by serum metabolome and tissue metabolome. The local serum data yielded several clinically known features (PSA, PZP, HCG, and FSH) which were distinct from CPTAC tissue data (RPS4Y1 and DDX3Y), both providing methodological validation, with PZP and defensins (DEFA3 and DEFB4A) representing shared proteomic features between serum and tissue. Metabolomic features shared between serum and tissue were homocysteine and pantothenic acid. Several signals emerged that are known to be associated with glioma or GBM but not previously known to be associated with biological sex, requiring further research, as well as several novel signals that were previously not linked to either biological sex or glioma. EGFR, FAT4, and BCOR were the three features associated with 64% ACC using the TCGA glioma grading set. GLIO-Select shows remarkable results in reducing feature dimensionality when different types of datasets (e.g., serum and tissue-based) were used for our analyses. The proposed approach successfully reduced relevant features to less than twenty biomarkers for each GBM dataset. Serum biospecimens appear to be highly effective for identifying biologically relevant sex differences in GBM. These findings suggest that serum-based noninvasive biospecimen-based analyses may provide more accurate and clinically detailed insights into sex as a biological variable (SABV) as compared to other biospecimens, with several signals linking sex differences and glioma pathology via immune response, amino acid metabolism, and cancer hallmark signals requiring further research. Our results underscore the importance of biospecimen choice and feature selection in enhancing the interpretation of omics data for understanding sex-based differences in GBM. This discovery holds significant potential for enhancing personalized treatment plans and patient outcomes. Full article

Colorectal cancer remains one of the leading causes of cancer-related deaths globally. Non-protein coding RNAs, including microRNAs, have emerged as crucial regulators in cancer progression. Herein, we analyzed publicly available datasets for miRNA expression in healthy controls, adenomatous polyps, and colorectal cancer and identified their regulatory networks using HCT116 and HT-29 CRC models. Differentially expressed miRNAs in adenomatous polyps and colorectal cancer were identified, highlighting their role in colorectal cancer initiation and progression. Notably, miR-218-5p was significantly downregulated in adenomatous polyps and colorectal cancer, suggesting a role in colorectal cancer initiation. Functional investigations revealed a tumor suppressive role for miR-218-5p in HCT116 and HT-29 CRC cell models, affecting cell proliferation and three-dimensional organoid formation and promoting cell death. RNA-Seq and bioinformatics identified BIRC5 and DDX21 as bona fide gene targets for miR-218-5p, validated by reverse transcription quantitative PCR and Western blotting. Further investigation into the genomic location of miR-218-5p, embedded within the SLIT2 and SLIT3 introns on chromosome 4 and chromosome 5, respectively, revealed epigenetic silencing through promoter hypermethylation in colorectal cancer cell models. These findings highlight epigenetic silencing of miR-218-5p in colorectal cancer, suggesting its potential as a biomarker and therapeutic target for early detection and intervention. Full article

Introduction: Bell’s palsy is a common acute peripheral neurological disorder causing unilateral facial paralysis. Its exact etiology remains unknown, but it is linked to inflammation, immune responses, infections, and ischemia. This study explores the potential causal relationship between Bell’s palsy and peripheral blood inflammatory proteins, metabolites, and immune cell characteristics. Methods: Genetic data for Bell’s palsy were obtained from the Finnish database (version R10) and IEU OpenGWAS. A two-sample Mendelian randomization (MR) approach was applied, analyzing 4907 plasma proteins, 731 immune cell traits, 91 inflammatory proteins, and 1400 metabolites. The Finnish dataset served as the discovery cohort, while the IEU OpenGWAS dataset acted as the validation cohort. Bioinformatics analyses included protein–protein interaction (PPI) networks, Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, colocalization, and Linkage Disequilibrium Score Regression (LDSC) to identify candidate proteins and explore potential therapeutic targets. Results: MR analysis identified 70 inflammatory proteins, 77 metabolites, and 26 immune cell traits as potentially causally associated with Bell’s palsy. After external validation, BLVRB, HMOX2, TNFRSF12A, DEFB128, ITM2A, VEGF-A, and DDX58 remained significantly associated (p < 0.05). PPI network analysis led to 31 candidate proteins, and six core proteins (JAK2, IL27RA, OSM, CCL19, SELL, VCAM-1) were identified. Conclusions: Our study identifies causal relationships between inflammatory proteins, metabolites, immune cells, and Bell’s palsy, highlighting that the JAK/STAT signaling pathway may be a potentially critical target for intervention in Bell’s palsy, and that its modulation may provide new directions and opportunities for therapeutic strategies and drug discovery for the disease. Full article

Background and Clinical Significance: We report on an infant with Snijders Blok–Campeau syndrome (psychomotor developmental delay, CNS malformations) and a complex heart defect with pulmonary arterial hypertension. Case Presentation: A DDX3X mutation encoding for RNA helicase was detected, which may suggest an association between Snijders Blok–Campeau syndrome and the development of pulmonary vasculopathy. However, further validation is required. Conclusions: We suggest an important role for DDX3X in the development of the pulmonary vasculature. Full article

Much remains to be understood about COVID-19, but the protective role of antibodies (Igs) is widely accepted in SARS-CoV-2 infection. Igs’ functions are mainly carried out by receptors that bind to their Fc portion (FcR), and less attention has been dedicated to the cytoplasmic members of this family. In this work, we used single-cell RNA sequencing (scRNA-seq) data to discern cell populations in bronchoalveolar lavage fluid obtained from healthy individuals and patients with mild or severe COVID-19. Then, we evaluated the transcription of neonatal FcR (FcRn, FCGRT gene) and tripartite motif-containing protein 21 (TRIM21) and its downstream signaling components. The TRIM21 pathway is vital for virus infections as it has a dual function, leading opsonized viruses to degradation by proteasomes and the activation of innate inflammatory anti-virus response. The transcriptional level of FCGRT showed no statistical differences in any cell population comparing the three groups of patients. On the other hand, TRIM21 transcription was significantly higher in myeloid cells collected from patients with mild COVID-19. When comparing mild with severe cases, there was no statistical difference in TRIM21 transcription in lung adaptive lymphoid cells and innate lymphoid cells (ILC). Yet, we analyzed the transcription of all downstream signaling molecules in myeloid and, as most cells expressed the receptor, in adaptive lymphoid cells. Moreover, ILCs from mild cases and all cell populations from severe cases were missing most downstream components of the pathway. We observed that members of the ubiquitin–proteasome system (UPS) and other components associated with TRIM21 proteasomal degradation were transcribed in mild cases. Despite the transcription of the danger sensors DDX58 and IFIH1, the transcriptional level of inflammatory IL1B and IL18 was generally very low, along with the NLRP3 danger sensor, members of the NF-κB pathway, and TNF. Therefore, our data suggest that TRIM21 may contribute to SARS-CoV-2 protection by reducing the viral load, while the inflammatory branch of the pathway would be silenced, leading to no pathogenic cytokine production. Full article