Search Results (154)

The phenomenon of transgene silencing was first observed shortly after the generation of the initial transgenic plants. The vast body of experimental data accumulated since then constitutes an invaluable resource for dissecting the mechanisms of epigenetic gene regulation. Silencing operates at either the transcriptional (TGS) or post-transcriptional (PTGS) level and is predominantly mediated by small interfering RNAs (siRNAs). Although these two epigenetic pathways involve distinct sets of proteins and enzymes, they share fundamental mechanistic features: the generation of double-stranded RNA (dsRNA), its processing into siRNAs by DICER-LIKE (DCL) enzymes, and the assembly of an Argonaute-centered effector ribonucleoprotein complex (RISC). Guided by sequence-specific siRNAs, this complex identifies complementary target sequences with high precision. A comprehensive understanding of these regulatory pathways enables the targeted induction or suppression of specific plant genes. This review traces the history of experimental findings regarding the loss of recombinant gene activity in transformants and their progeny, which collectively established the foundation for elucidating the molecular mechanisms of transgene silencing. Full article

Dicer is crucial for the generation of microRNAs (miRNAs), which are essential for regulating gene expression and keeping neuronal health. Dicer’s conditional deletion cuts all spiral ganglion neurons but spares a small fraction of vestibular ganglion neurons, innervating the utricle and part of the saccule. Hair cells develop in the utricle, saccule, posterior crista, and the cochlea in Pax2^Cre; Dicer^f/f. Cochlear hair cells develop at the base and expand the OHC and IHC in the middle, or split into a base/middle and the apex. In contrast, Foxg1^Cre; Dicer^f/f cuts all canal cristae and cochlea hair cells, leaving a reduced utricle and an exceedingly small saccule. Likewise, Foxg1^Cre; Gata3^f/f shows no cochlear hair cells and is absent in the horizontal and reduced in the posterior crista. In contrast, the utricle, saccule, and anterior crista are nearly normal, underscoring the intricate regulatory networks involved in hair cell and neuronal development. The central projections have been described as the topology of various null deletions. Still, without spiral ganglion neurons, fibers from Dicer null mice navigate to the cochlear nuclei and expand into the vestibular nuclei to innervate the caudal brainstem. Beyond a ramification around the CN, no fibers expand to reach the cerebellum, likely due to Pax2 and Foxg1 that cut these neurons. Genetic alterations, such as Dicer deletion, can lead to hearing loss and impairments in auditory signal processing, illustrating the critical role of microRNAs in the development and function of auditory and vestibular neurons. Further studies on this topic could help in understanding potential therapeutic targets for hearing loss associated with neuronal degradation of miRNA. Full article

The RNA interference machinery is crucial for regulating the activity of both native and foreign genes across all eukaryotes. The core protein families involved in this process are Dicer-like, Argonaute, and RNA-dependent RNA polymerase. However, plants exhibit remarkable diversity within each family and extensively use RNA interference mechanisms in their intricate immune responses. This review examines the role of RNA interference in plant interactions with various pathogens, including viruses, viroids, fungi, oomycetes, and bacteria. Plant diseases cause an estimated $220 billion in annual damage, with microorganisms accounting for approximately $150 billion. Hence, the focus is on the most severe plant diseases, specifically those caused by fungi and viruses. Additionally, recent biotechnological advancements are discussed, with an emphasis on the application of RNA interference for the development of novel plant defence strategies. Full article

Background: Myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) are clonal stem cell disorders in which disrupted post-transcriptional regulation contributes to aberrant hematopoiesis and leukemic transformation. The miRNA biogenesis machinery, which comprises Drosha, DGCR8, Dicer, TARBP2, and AGO1, ensures the precise maturation of miRNAs that control lineage commitment and proliferation. However, the extent to which alterations in this pathway reshape hematopoietic gene networks during myeloid disease evolution remains largely unexplored. Methods: Bone marrow samples from newly diagnosed, untreated MDS and AML patients and matched healthy controls were analyzed for the expression of five key miRNA biogenesis genes using quantitative real-time PCR. Statistical comparisons, correlation matrices, and ROC analyses were performed to characterize gene-expression differences. These results were integrated with multigene logistic modeling, decision-curve analysis, and exploratory random forest/SHAP approaches to evaluate molecular interactions and diagnostic relevance. Results: DROSHA, DICER1, and TARBP2 were significantly downregulated in both MDS and AML, suggesting impaired miRNA maturation and a loss of global post-transcriptional control. DGCR8 expression increased across higher-risk MDS groups, suggesting compensatory activation of the Microprocessor complex, whereas AGO1 levels remained relatively stable, consistent with partial maintenance of RISC function. Correlation analyses revealed a co-regulated DROSHA–TARBP2–AGO1 module. ROC, logistic, and machine learning models identified DGCR8 and DICER1 as the strongest diagnostic discriminators. The integrated five-gene signature achieved high discriminative performance (AUC ≈ 0.98) and showed promise but remains preliminary potential for clinical application. Conclusions: Our findings suggest that defects in miRNA biogenesis disrupt hematopoietic homeostasis, reflecting common mechanisms in MDS and AML. The dysregulation of DICER1, DGCR8, and TARBP2 offers insights into miRNA-driven leukemogenesis and may pave the way for miRNA-based diagnostic and therapeutic strategies, pending validation in larger cohorts. Although transcript-level data are provided, future studies should include functional validation to determine the impact on downstream miRNA processing and hematopoietic pathways. Full article

Background: Hepatocellular carcinoma (HCC) remains a major global health challenge with limited therapeutic options. Although RNA interference (RNAi) enables precise gene silencing, its clinical application is restricted by siRNA instability, inefficient cellular uptake, and the requirement for potentially toxic delivery carriers. To address these limitations, a dual-targeted branched siRNA nanostructure (GT-multi-siRNA) was developed to simultaneously silence two HCC-related oncogenes, GP73 and hTERT. Methods: GT-multi-siRNA was synthesized in Escherichia coli and characterized for particle size, stability, Dicer processing efficiency, intracellular retention, and cytotoxicity. Its therapeutic effects were evaluated through gene-silencing assays, proliferation and migration assays in Hep3B cells, and intratumoral administration in a xenograft mouse model. Histopathology and cytokine profiling were conducted to assess biosafety. Results: GT-multi-siRNA formed uniform nanoparticles (50–100 nm) with moderate physicochemical stability and minimal cytotoxicity at concentrations ≤ 200 ng/μL. The nanostructure was efficiently processed by Dicer into functional siRNAs and remained detectable intracellularly for at least 36 h. In Hep3B cells, GT-multi-siRNA reduced GP73 and hTERT mRNA and protein levels by approximately 50%, accompanied by significant inhibition of cell proliferation and migration. In vivo, a single intratumoral dose suppressed tumor growth, while a two-dose regimen markedly limited tumor progression. No liver toxicity was observed, and cytokine analysis showed selective IL-4 upregulation without influencing IL-6 levels. Conclusions: GT-multi-siRNA demonstrates potent dual-gene silencing activity and favorable biosafety, providing a promising RNAi-based therapeutic strategy for targeted HCC treatment. Full article

Backgrounds: Objective of this study is to conduct a genome-wide association study (GWAS) of first-parity reproductive traits in Suzi pigs to identify significant single-nucleotide polymorphisms (SNPs) or candidate genes influencing these traits. Methods: This research employed technologies including the Zhongxin 50K SNP chip, simplified genome sequencing, resequencing, and the 100K SNP liquid chip to perform genome-wide SNP detection on 898 Suzi sows. Genotype data and phenotypic data were combined to do GWAS, gene annotation, and enrichment analysis. Results: Results showed that this study obtained phenotypes of 33 first-parity reproductive traits from 574 sows. GWAS results indicated there were 10 first-parity reproductive traits significantly associated with SNPs, and these traits were AFS, AFF, NNB, NH, NW, NS, NM, ND, PB, and CCN. These 10 traits were significantly associated with 60 SNPs, with 15 (25%) located on chromosome 2-the highest proportion. The SNPs significantly associated with AFS and AFF were largely identical. Genome-wide variance component analysis revealed that among the 10 traits with significantly associated SNPs in GWAS, there were 5 traits that exhibited genome-wide heritability ≥ 0.01. Trait of NM showed the highest heritability (0.65–0.7). These significantly associated SNPs annotated 20 candidate genes, including ADAMTS19, PROP1, ZNF354B, PCARE, LUZP2, VIRMA, EPHA5, AAAS, SLCO3A1-SV2B, KIF18A-BDNF, SERGEF, DYNLRB2, HNF4G, CATSPERD, HSD11B1L, DICER1, RARG, PCDHAC2, KRT79, and HSD17B2. GO analysis of candidate genes revealed that the top three biological processes were cell adhesion, positive regulation of cell projection organization, and positive regulation of neuron projection development. KEGG results showed the top three pathways were inositol phosphate metabolism, glutamatergic synapse, and phosphatidylinositol signaling system. Conclusions: These findings provide a foundation for the reproductive breeding of Suzi pigs and offer new insights into biological breeding in pigs. Full article

Background: Posttraumatic growth (PTG) refers to positive psychological change following trauma. While its psychological aspects are well-documented, the biological mechanisms remain unclear. Epigenetic changes, such as DNA methylation (DNAm), may offer insight into PTG’s neurobiological basis. Aims: This study aimed to identify epigenetic markers associated with PTG using an epigenome-wide association study (EWAS), the first of its kind in a trauma-exposed population. Methods: A longitudinal EWAS design was used to assess DNAm before and after trauma exposure in first-year paramedicine students (n = 39). Genome-wide methylation data were analyzed for associations with PTG, applying epigenome-wide and gene-wise statistical thresholds. Pathway enrichment analysis was also conducted. Results: The study identified two CpGs (cg09559117 and cg05351447) within the PCDHA1/PCDHA2 and PDZD genes significantly associated with PTG at the epigenome-wide threshold (p < 9.42 × 10^–8); these were replicated in an independent sample. DNAm in 5 CpGs across known PTSD candidate genes ANK3, DICER1, SKA2, IL12B and TPH1 were significantly associated with PTG after gene-wise Bonferroni correction. Pathway analysis revealed that PTG-associated genes were overrepresented in the Adenosine triphosphate Binding Cassette (ABC) transporters pathway (p = 2.72 × 10⁻⁴). Conclusions: These results identify genes for PTG, improving our understanding of the neurobiological underpinnings of PTG. Full article

Beyond well-known genetic drivers, microRNA dysregulation has emerged as a key contributor to thyroid tumorigenesis. Central to this process is Dicer1, a ribonuclease essential for microRNA maturation, whose expression is often reduced in papillary thyroid carcinoma (PTC). Evidence from previous studies suggest Dicer1 functions as a context-dependent haplo-insufficient tumor suppressor gene: partial loss may promote tumor development, whereas complete loss may disrupt essential cellular functions, causing cell death and tumor suppression. However, the effects of partial or complete Dicer1 loss in thyroid cancer remain unclear. To explore this, we genetically inactivated one (heterozygous) or both (homozygous) Dicer1 alleles specifically in thyroid follicular cells of a RET/PTC3 transgenic mouse model using an inducible Cre-Lox system. Our findings deepen the current understanding of the RET/PTC3-driven PTC model by revealing an increased number of vimentin-positive cells and disruption in redox homeostasis. Additionally, whereas heterozygous Dicer1 loss did not alter tumor progression in RET/PTC3 mice, total loss reduced tumor growth and led to accumulated DNA damage and cell death. These findings highlight the crucial role of Dicer1 dosage in thyroid cancer progression and underscore its potential as a therapeutic target for aggressive PTC and other malignancies characterized by aberrant Dicer1 expression. Full article

DICER1 syndrome is a hereditary cancer predisposition syndrome, characterized by a large range of benign and malignant neoplasms. Patients with DICER1 syndrome have a broad phenotype, with pleuropulmonary blastoma, Sertoli–Leydig cell tumor, cystic nephroma, cervical embryonal rhabdomyosarcoma, cystic lung lesions, and thyroid follicular nodular disease being the most prevalent manifestations. The syndrome is caused by loss-of-function germline variants in the DICER1 gene, and DICER1-related tumors are characterized by second somatic hotspot variants in the RNase IIIb domain of DICER1. DICER1 encodes an endoribonuclease, which is important for RNA interference. This review describes the molecular mechanism of DICER1 function and the pathogenetic mechanisms of tumorigenesis. The purpose of this review is to describe the pathogenesis, genotype–phenotype correlation and tissue specificity of DICER1 syndrome. We conclude that there is a lack of knowledge about the exact molecular mechanisms of DICER1 function and more research is needed to determine the exact role of this altered protein in relation to pathogenesis. Full article

Plant viruses have been traditionally considered pathogens restricted to plant hosts. However, recent studies have shown that some plant viruses can infect and replicate in filamentous fungi and oomycetes, suggesting that their host range is broader than previously thought, and that their ecological interactions are more complex. In this study, we investigated the ability of the well-characterized positive-sense RNA plant virus Tobacco mosaic virus (TMV) to replicate in four major phytopathogenic fungi from different taxonomic groups: Botrytis cinerea, Fusarium oxysporum f. sp. lycopersici, Verticillium dahliae, and Monilinia fructicola. Using a recombinant TMV-based vector expressing a green fluorescent protein (TMV-GFP-1056) as reporter, we demonstrated that TMV can enter, replicate, and persist within the mycelia of B. cinerea and V. dahliae—at least through the first subculture. However, it cannot replicate in F. oxysporum f. sp. lycopersici and M. fructicola. RNA interference (RNAi) is a conserved eukaryotic epigenetic mechanism that provides an efficient defence against viruses. We explored the role of RNAi in the interaction between TMV and the mycelia of V. dahliae and B. cinerea. Our results revealed a strong induction of the Dicer-like 1 and Argonaute 1 genes, which are key compounds of the RNA silencing pathway. This RNAi-based response impaired TMV-GFP replication in both fungi. Notably, despite viral replication and RNAi activation, the virulence of V. dahliae and B. cinerea on their respective host plants remained unaffected. These findings reinforce the emerging recognition of cross-kingdom virus transmission and interactions, which likely play a crucial role in pathogen ecology and viral evolution. Understanding these virus–fungus interactions not only sheds light on RNAi interference silencing mechanisms but also suggests that plant viruses like TMV could serve as simple and effective tools for functional genomic studies in fungi, such as in V. dahliae and B. cinerea. Full article

(1) Background: Sertoli–Leydig cell tumors (SLCTs) are rare ovarian neoplasms that account for less than 0.5% of all ovarian tumors. They usually affect young women and often present with androgenic symptoms. We report a unique case of a 40-year-old woman diagnosed with both SLCT and clear cell papillary renal cell carcinoma (CCP-RCC), a rare tumor association with unclear pathogenesis. (2) Methods: Both tumors were treated surgically. The diagnostic workup included hormonal testing, imaging studies, and extensive genetic testing, including DICER1 mutation analysis and multiplex ligation-dependent probe amplification (MLPA), as well as the examination of a next-generation sequencing (NGS) panel covering ~280 cancer-related genes. (3) Results: Histopathologic examination confirmed a well-differentiated SLCT and CCP-RCC. No pathogenic variants in DICER1 were identified by WES or MLPA. No clinically relevant changes were found in the extended NGS panel either, so a known hereditary predisposition could be ruled out. The synchronous occurrence of both tumors without genomic alterations could indicate a sporadic event or as yet unidentified mechanisms. (4) Conclusions: This case highlights the importance of a multidisciplinary approach in the management of rare tumor compounds. The exclusion of DICER1 mutations and the absence of genetic findings adds new evidence to the limited literature and underscores the importance of long-term surveillance and further research into potential shared oncogenic pathways. Full article

TDP-43 is an RNA-binding protein linked to amyotrophic lateral sclerosis (ALS), possibly associated with a role in miRNA biogenesis, which is still not fully understood. Herein we investigated the impact of the Drosophila homolog of TDP-43, TBPH, on genes related to miRNA biogenesis. A TBPH knockout significantly reduced mRNA transcription and protein levels of DCR-1 and DCR-2, whereas an overexpression of DCR-1 and DCR-2 in a TBPH knockdown background exacerbated compound eye damage, with variations in severity that were sex-dependent. Neuronal TBPH RNAi consistently shortened lifespan, with males and females exhibiting distinct survival profiles. DCR-1 and DCR-2 knockdown worsened the locomotor defects induced by TBPH deficiency, thus reinforcing the functional link between TBPH and DCR. In TBPH-deficient flies, the pharmacological activation of Dicer promoted reverse locomotion behavior, with a preference for backward movement. Overall, we show that TBPH is a key regulator of DCR protein expression, highlighting its conserved role in miRNA dysregulation associated with motor function and cytotoxicity in ALS-like pathology in Drosophila models. Full article

RNA silencing regulates diverse cellular processes in plants. Argonaute (AGO), Dicer-like (DCL), and RNA-dependent RNA polymerase (RDR) proteins are core components of RNA interference (RNAi). Despite their functional significance, the systematic identification and characterization of these families have remained largely unexplored in Siraitia grosvenorii. Using HMMER and Pfam analyses, we identified six SgAGO, four SgDCL, and six SgRDR genes. Phylogenetic analysis classified SgAGOs, SgDCLs, and SgRDRs into five, four, and four clades, respectively, all of which clustered closely with homologs from other Cucurbitaceae species, demonstrating lineage-specific evolutionary conservation. Promoter cis-element analysis revealed the significant enrichment of hormonal (methyl jasmonate, abscisic acid) and stress-responsive (light, hypoxia) elements, indicating their roles in environmental adaptation. Tissue-specific expression profiling showed that most SgAGO, SgDCL, and SgRDR genes were highly expressed in flowers and mid-stage fruits (35 days after pollination), while SgAGO10.1 exhibited stem-specific expression. By contrast, SgRDR1.2 displayed no tissue specificity. Notably, sex-biased expression patterns in dioecious flowers suggested the RNAi-mediated regulation of gametophyte development and their potential roles in reproductive and secondary metabolic processes. This study lays the foundation for further exploration of RNAi machinery’s role in coordinating mogroside biosynthesis and stress resilience in S. grosvenorii while providing potential targets for genetic improvement. Full article

Aedes aegypti mosquitoes are critical vectors of arboviruses, responsible for transmitting pathogens that pose significant public health challenges. Serine hydroxymethyltransferase (SHMT), a key enzyme in one-carbon metabolism, plays a vital role in various biological processes, including DNA synthesis, energy metabolism, and cell proliferation. Although SHMT is expressed at low levels in the midgut of Aedes aegypti, its silencing has been shown to inhibit blood meal digestion. The precise mechanisms by which SHMT regulates midgut physiology in mosquitoes remain poorly understood. In this study, we employed small RNA sequencing and quantitative PCR to identify differentially expressed miRNAs (DEMs) following SHMT downregulation. We focused on a subset of DEMs—miR-2940-5p, miR-2940-3p, miR-2941, and miR-306-5p—to explore their potential biological functions. To further elucidate the molecular mechanisms underlying the miRNA response to SHMT downregulation, we analyzed the expression levels of key genes involved in the miRNA biogenesis pathway. Our results demonstrated that several critical enzymes, including Drosha, Dicer1, and AGO1, exhibited significant changes in expression upon SHMT silencing. This study provides new insights into the molecular mechanisms through which SHMT influences the biological functions and nutritional metabolism of the mosquito midgut. By linking SHMT activity to miRNA regulation, our findings highlight a potential pathway by which SHMT modulates midgut physiology, offering a foundation for future research into mosquito biology and vector control strategies. Full article

DICER1 tumor predisposition syndrome is a genetic condition that increases the risk of developing certain cancer types. While thyroid tumors are the main tumors caused by this condition in adult oncology, children and adolescents with DICER1 germline mutations may suffer from a broader spectrum of tumors, including Sertoli-Leydig cell tumors, pleuropulmonary blastomas, embryonal rhabdomyosarcomas, and pineoblastomas. Although these diseases—many of which are hallmark tumors of DICER1 syndrome and rarely occur sporadically—have been known for several years, the more recent identification of DICER1 mutations in embryonal tumors with multilayered rosettes (ETMR) and DICER1-associated intra- and extracranial sarcomas has expanded the spectrum of tumor types potentially linked to DICER1 syndrome. This review sought to investigate the presence and characteristics of DICER1 mutations in rare CNS tumors and to discuss their potential implications for early recognition of DICER1-related syndromes. To address this, we conducted a comprehensive systematic literature review and analyzed data from our nationwide German database (CNS-InterREST) regarding these entities. When present, DICER1 mutation status, mutation type (somatic vs. germline), and localization within the gene were recorded. Demographic and clinical data—including age at diagnosis and tumor localization—were also evaluated where available. We found that the prevalence of DICER1 mutations in the cohort of ETMR patients included in the CNS-InterREST study was exceedingly low (1/31). The distribution of DICER1 mutations in patients with ETMR or intracranial sarcomas is comparable to that in other previously identified DICER1-mutant tumors. Our literature review demonstrates that within the 248 cases, which include three intracranial DICER1-mutated neoplasias and one reference group, most somatic mutations accumulate in the RNase IIIb domain, while germline mutations are usually evenly distributed throughout the gene. Overall, further research is necessary to unravel the cell-of-origin of the respective tumor types and whether other, hitherto undescribed, genetic factors may contribute to the development of ETMR and DICER1-associated intracranial sarcomas. Full article