Search Results (588)

Nucleic acid-based gene-interfering molecules, such as antisense oligonucleotides, ribozymes, and small interfering RNA (siRNA), represent exciting gene-targeting agents for therapeutic applications. RNase P ribozymes derived from M1 RNA, the catalytic RNA subunit of RNase P in Escherichia coli, have shown great promise as a novel nucleic acid-based gene interference approach to modulate gene expression. When M1 RNA is covalently linked to a guide sequence (GS), it can be engineered into a sequence-specific endonuclease M1GS ribozyme, which can hydrolyze any mRNA that base-pairs with the guide sequence. M1GS activity enhancement has been achieved through an in vitro selection process that introduced mutations into M1 RNA. This selection process generated ribozyme variants with improved cleavage efficiency and substrate affinity. Hepatitis B virus (HBV) chronically infects more than 250 million people worldwide and is the leading cause of cirrhosis and liver cancer globally. Current FDA-approved drugs cannot completely eliminate HBV chronic infections. RNase P ribozymes have recently been demonstrated to effectively inhibit HBV gene expression and replication in human cells. This review summarizes the recent progress in using RNase P ribozymes to inhibit HBV infection and discusses prospects for developing engineered RNase P ribozymes for therapeutic applications against HBV infection and associated diseases. Full article

The study aim was to apply murine double minute 2 (MDM2)-siRNA to a biodegradable siRNA delivery vector, ternary complex, for treating colorectal cancer peritoneal dissemination. The ternary complex containing MDM2-siRNA (MDM2-siRNA complex) was constructed by mixing MDM2-siRNA, dendrigraft poly-L-lysine, and γ-polyglutamic acid. Cellular uptake of the ternary complex and suppressive effect on MDM2-mRNA were determined in a mouse colorectal cancer cell line. Tumor-growth inhibition by the MDM2-siRNA complex was evaluated in peritoneal dissemination model mice. The MDM2-siRNA complex, with an approximately 177 nm particle size and −35 mV ζ-potential, prevented degradation of the inner siRNA by RNase. In the in vitro study, the ternary complex was highly taken up by the cells, and 2 μg/mL of the MDM2-siRNA complex significantly decreased MDM2-mRNA to about 30% of control cells. Intraperitoneal administration in colorectal cancer peritoneal dissemination model mice showed little effect of the ternary complex containing scramble-siRNA on cancer growth in the peritoneal cavity. Conversely, the MDM2-siRNA complex significantly reduced peritoneal dissemination to less than 1/1000th of control mice and successfully prolonged survival time. In this study, we found that the biodegradable MDM2-siRNA complex had a suppressive effect on MDM2-mRNA in cancer cells and tumor growth of peritoneal dissemination. Full article

Apricot (Prunus armeniaca L.) exhibits a gametophytic self-incompatibility (GSI) system. To identify the S-genotypes of the main apricot cultivars, including 133 native Chinese cultivars and 35 foreign accessions, PCR was performed using a combination of five primers based on the conserved regions of Prunus S-RNase genes. After cloning and sequencing the PCR products, the S-genotypes of all 168 apricot cultivars were determined. A total of 46 different S-RNase alleles, with 15 new alleles, were identified. For all 168 accessions, the top five most frequent S-alleles were S₈, S₁₁, S₉, S₁₆, and S₅₃. S₁₁, S₈, and S₁₆ were the most frequent in Chinese cultivars, and S₉, S₈, and S₂ were mostly found in European accessions. For Chinese apricot cultivars, the distribution of S-alleles among five geographic regions was also investigated. In Northwest China, S₁₆ was the most frequent S-allele. In the Xinjiang region, S₆₆, S₄₉, and S₁₄ were the top three most frequent S-alleles. In North China, S₈, S₁₁, and S₅₃ were the top three most frequent S-alleles. In addition, the self-compatible type, S_C, was not detected in these 133 Chinese accessions. Finally, the phylogenetic tree of apricot S-alleles indicated that there are four groups of S-RNase genes (S₉₇/S₁₀₆, S₁₄/S_14a/S₆₆, S₉/S₁₇/S₄₄, and S₂₃/S₅₃) presenting a very close relation. These results provide more data on the S-genotypes of apricot accessions, which can support future breeding programs by aiding in the selection of the appropriate parents and contributing to efficient orchard design by combining cultivars with suitable pollinizers. 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

Stachys duriaei (Lamiaceae) remains unexplored despite its pharmacological potential. In this study, for the first time, the antiproliferative, pro-apoptotic, cell cycle arrest, and vasorelaxant effects of the n-butanolic extract (BESD) and a VLC fraction (BF1SD) of Stachys duriaei were investigated. Antiproliferative activity was evaluated on PC3 and MDA-MB-231 cell lines via MTT assay (72 h). Apoptosis (Annexin V-FITC/PI) and cell cycle arrest (PI/RNase) were assessed by flow cytometry (24 h, 250–1000 µg/mL). Vasorelaxant effects were studied ex vivo on rat aortic rings. LC-HRMS/MS was used for phytochemical analysis. BESD showed higher antiproliferative activity (IC₅₀: 196 ± 6 µg/mL for PC3, 182 ± 8 µg/mL for MDA-MB-231) than BF1SD (IC₅₀: 281 ± 6 µg/mL and 273 ± 3 µg/mL, respectively). Apoptosis was dose-dependent, with BF1SD displaying a stronger effect at 1000 µg/mL (67.3 ± 0.5% vs. 49.9 ± 0.7% for BESD). BESD induced G2/M arrest, while BF1SD caused G0/G1 and G2/M arrest. Vasorelaxation was endothelium-dependent, likely mediated by NO. Identified compounds (hyperoside, luteolin-7-glucoside, and rutin) may contribute to these effects. BESD and BF1SD exhibit anticancer and vasorelaxant properties, indicating potential therapeutic use against cancer and cardiovascular diseases. Further studies are needed to isolate active compounds and confirm their effects in vivo. Full article

Caenorhabditis elegans, a free-living nematode model, secretes neuropeptides, but the ecological roles of its peptide exudates in regulating rhizosphere microbial activity remain largely unexplored. We identified six short peptides (P1, P9, P19, P20, P25, and P26) from C. elegans exudates that significantly enhanced indole-3-acetic acid (IAA) production by the plant growth-promoting bacterium Arthrobacter pascens ZZ21. These peptides were heat-labile and proteinase K-sensitive but unaffected by DNase I or RNase A, confirming their proteinaceous (peptide) nature rather than nucleic acid origin. The retention of bioactivity in n-butanol extracts further supported their hydrophilic, peptide-like properties. LC-MS/MS identified 30 linear peptides, including the six bioactive ones, which exhibited distinct dose-dependent effects, suggesting diverse regulatory mechanisms. Despite their relatively low abundance, these peptides strongly promoted IAA production in the bacterial culture system across multiple concentrations. These findings reveal an unrecognized mechanism whereby free-living nematodes regulate rhizobacterial metabolism via secreted peptides, offering new insights into nematode-mediated chemical signaling. Therefore, this study advances understanding of plant–microbe–nematode interactions and highlights strategies for manipulating rhizosphere microbiota in sustainable agriculture. Full article

The peach landrace ‘Liuyefeitao’ exhibits the unique reproductive trait of self-compatibility combined with cross-incompatibility, contrasting with typical Prunus species in this way. In preliminary studies involving controlled pollination assays, we showed complete pollen tube arrest in cross-pollinated styles, whereas self-pollination enabled full tube elongation. S-genotyping identified a homozygous S₂S₂ genotype with intact S₂-RNase but a truncated PpSFB2 due to a frameshift mutation. Transcriptome profiling of the styles revealed 7937 differentially expressed genes (DEGs) between self- and cross-pollination treatments, with significant enrichment in plant MAPK signaling, plant–pathogen interactions, and plant hormone signaling transduction pathways (|Fold Change| ≥ 2, FDR < 0.01). Notably, PpSLFL3 (a pollen F-box gene) showed down-regulation in cross-pollinated styles, as validated by means of qRT-PCR. Protein interaction assays revealed direct binding between PpSLFL3 and S₂-RNase via Y2H and BiFC analysis, suggesting its role in mediating SCF complex-dependent degradation. We propose that insufficient PpSLFL3 expression during cross-pollination disrupts SCF ubiquitin ligase complex-mediated degradation of non-self S₂-RNase, leading to the toxic degradation of RNA in pollen tubes by S₂-RNase. This mechanism is mechanistically similar to unilateral reproductive barriers in Solanaceae but represents a novel regulatory module in Rosaceae. Our findings provide critical insights into the evolution of cross-incompatibility systems and molecular breeding strategies for Prunus species. Full article

Adipose tissue development plays a critical role in determining carcass quality and meat production efficiency in swine; however, the regulatory mechanisms governing fat deposition remain incompletely understood. Circular RNAs (circRNAs), characterized by high stability and resistance to RNase R degradation, have emerged as important epigenetic regulators of livestock traits. This study investigated the regulatory role of circIDH2 in adipogenic differentiation of porcine preadipocytes and the underlying molecular mechanisms. Functional assays revealed that silencing circIDH2 markedly promoted preadipocyte proliferation while inhibiting differentiation and lipid accumulation; conversely, circIDH2 overexpression produced the opposite effects. Mechanistically, circIDH2 acted as a molecular sponge for miR-193a-5p through complementary base pairing, thereby relieving the repression of its target gene RASGRP4, a positive regulator of adipogenesis. Furthermore, this study demonstrated that miR-193a-5p promoted proliferation but suppressed the differentiation of porcine preadipocytes, whereas RASGRP4 inhibited proliferation while promoting adipogenic differentiation. Rescue experiments further confirmed the regulatory relationship among circIDH2, miR-193a-5p, and RASGRP4. In summary, the findings indicated that circIDH2 functioned as a key regulator of adipogenesis by modulating the miR-193a-5p/RASGRP4 axis, thereby suppressing preadipocyte proliferation and promoting adipogenic differentiation. These results provide a theoretical foundation for future investigations into the regulatory mechanisms of adipose tissue development. Full article

Objectives: A thorough understanding of pharmacokinetics and metabolism is critical during early drug development. This study investigates the absorption, distribution, metabolism, and excretion (ADME) profile of R14, a novel compound, using a combination of in vitro and in vivo approaches. Methods: In vitro studies included Caco-2 permeability assays, metabolic stability evaluations in liver microsomes and hepatocytes, and identification of CYP isoforms responsible for R14 metabolism. In vivo pharmacokinetic and metabolic profiling was conducted in rats following oral administration. R14 was quantified using UHPLC-MS/MS. Metabolites were identified using high-resolution UHPLC- QTOF MS/MS, and relative exposure was estimated using peak area-derived AUCs. Results: R14 exhibited low oral bioavailability (13.4%) and high systemic clearance (2.63 L/h/kg), indicating high hepatic extraction. A total of 21 plasma and 38 urine metabolites were identified. Major metabolic pathways included initial hydroxylation and hydrogenation, followed by sequential methylation and Phase II conjugations (glucuronidation and sulfation). Key metabolites (M3, M4, M22, M38) accounted for the majority of systemic exposure. Less than 1% of the unchanged drug was excreted in urine, confirming extensive metabolism. Notably, discrepancies between in vitro and in vivo metabolite profiles suggested rapid further transformation of initial metabolites in vivo, which were not fully captured in vitro. Conclusions: This study demonstrates an efficient and integrated strategy for early-phase ADME characterization. The combined use of in vitro assays and in vivo studies, guided by advanced analytical techniques, provides a robust framework for understanding drug metabolism. These findings can inform drug optimization and help minimize risks in later stages of development. Full article

Contact unmodified antisense DNA biotechnology (CUADb), developed in 2008, employs short antisense DNA oligonucleotides (oligos) as a novel approach to insect pest control. These oligonucleotide-based insecticides target pest mature rRNAs and/or pre-rRNAs and have demonstrated high insecticidal efficacy, particularly against sap-feeding insect pests, which are key vectors of plant DNA viruses and among the most economically damaging herbivorous insects. To further explore the potential of CUADb, this study evaluated the insecticidal efficacy of short 11-mer antisense DNA oligos against Coccus hesperidum, in comparison with long 56-mer single-stranded and double-stranded DNA sequences. The short oligos exhibited higher insecticidal activity. By day 9, the highest mortality rate (97.66 ± 4.04%) was recorded in the Coccus-11 group, while the most effective long sequence was the double-stranded DNA in the dsCoccus-56 group (77.09 ± 6.24%). This study also describes the architecture of the DNA containment (DNAc) mechanism, highlighting the intricate interactions between rRNAs and various types of DNA oligos. During DNAc, the Coccus-11 treatment induced enhanced ribosome biogenesis and ATP production through a metabolic shift from carbohydrates to lipid-based energy synthesis. However, this ultimately led to a ‘kinase disaster’ due to widespread kinase downregulation resulting from insufficient ATP levels. All DNA oligos with high or moderate complementarity to target rRNA initiated hypercompensation, but subsequent substantial rRNA degradation and insect mortality occurred only when the oligo sequence perfectly matched the rRNA. Both short and long oligonucleotide insecticide treatments led to a 3.75–4.25-fold decrease in rRNA levels following hypercompensation, which was likely mediated by a DNA-guided rRNase, such as RNase H1, while crucial enzymes of RNAi (DICER1, Argonaute 2, and DROSHA) were downregulated, indicating fundamental difference in molecular mechanisms of DNAc and RNAi. Consistently, significant upregulation of RNase H1 was detected in the Coccus-11 treatment group. In contrast, treatment with random DNA oligos resulted in only a 2–3-fold rRNA decrease, consistent with the normal rRNA half-life maintained by general ribonucleases. These findings reveal a fundamental new mechanism of rRNA regulation via complementary binding between exogenous unmodified antisense DNA and cellular rRNA. From a practical perspective, this minimalist approach, applying short antisense DNA dissolved in water, offers an effective, eco-friendly and innovative solution for managing sternorrhynchans and other insect pests. The results introduce a promising new concept in crop protection: DNA-programmable insect pest control. Full article

The potent and selective ‘genetic zipper’ method for insect pest control consists of three essential components: an antisense DNA (the finder), its complementary mature rRNA or pre-rRNA of the pest (the target), and the host’s endogenous DNA-guided rRNase (the degrader). Although this approach has been validated, the spectrum of effective rRNA targets remains insufficiently explored. In this study, we report for the first time the insecticidal efficacy of a novel oligonucleotide insecticide, Eriola-11, which targets the mitochondrial 16S rRNA of the woolly apple aphid Eriosoma lanigerum Hausmann. We hypothesized that the antisense-mediated silencing of mitochondrial rRNA would impair aphid viability and lead to physiological disruptions associated with mitochondrial energy metabolism. Eriola-11 was applied either once or twice (with a 24 h interval) to aphid-infested plants, and aphid mortality was recorded over 14 days. Mitochondrial 16S rRNA expression levels were quantified using molecular assays, and the degradation kinetics of Eriola-11 were assessed in aphid tissue homogenates. Results showed significant insecticidal activity, with 67.55% mortality after a single treatment and 83.35% after two treatments. Treated aphids exhibited the loss of their characteristic white woolly wax covering, and mitochondrial 16S rRNA expression was reduced 0.66-fold relative to the control. Additionally, Eriola-11 was fully degraded by aphid DNases from tissue homogenates within 3 h, highlighting its rapid biodegradability. These findings establish mitochondrial 16S rRNA as a viable target for antisense insecticides and expand the catalogue of potential rRNA-based targets, offering a promising avenue for environmentally sustainable pest control strategies. Full article

Variants in ELAC2, a gene encoding the mitochondrial RNase Z enzyme essential for mitochondrial tRNA processing, have been associated with severe pediatric-onset mitochondrial dysfunction, primarily presenting with developmental delay, hypertrophic cardiomyopathy (HCM), and lactic-acidosis. We hereby report the case of a 25-year-old young woman presenting with dilated cardiomyopathy (DCM) and peripheral sensorimotor polyneuropathy, harboring a homozygous variant in ELAC2. The same variant has been reported only once so far in a case of severe infantile-onset form of HCM and mitochondrial respiratory chain dysfunction, with in vitro data showing a moderate reduction in the RNase Z activity and supporting the current classification as C4 according to the American College of Medical Genetics (ACMG) criteria (PS3, PM2, PM3, PP4). Our extensive clinical, imaging, histological, and genetic investigations support a causal link between the identified variant and the patient’s phenotype, despite the fact that the latter might be considered atypical according to the current state of knowledge. A detailed review of the existing literature on ELAC2-related disease is also provided, highlighting the molecular mechanisms underlying tRNA maturation, mitochondrial dysfunction, and the variable phenotypic expression. Our case further expands the clinical spectrum of ELAC2-related cardiomyopathies to include a relatively late onset in young adulthood and underscores the importance of comprehensive genetic testing in unexplained cardiomyopathies with multisystem involvement. Full article

Cherry laurel (Prunus laurocerasus) is an understudied, highly polyploid (22×) species that is widely used as an ornamental shrub and as a fruit-bearing plant in Türkiye. We analyzed 43 accessions—33 ornamental cultivars and 10 fruit-bearing selections—by examining size variations in 10 simple sequence repeat (SSR) markers and the first intron region of the self-incompatibility ribonuclease (S-RNase) gene. A total of 498 alleles were detected across 11 loci, with the highest number of alleles observed at the S-locus. The SSR loci amplified between 4 (ASSR63) and 17 (BPPCT039) alleles per accession, with eight of the 11 primers generating more than 12 alleles per accession. Two markers, BPPCT040 and CPSCT021, uniquely distinguished all tested accessions. Of the alleles, only 178 (36%) were shared between the ornamental and fruit-bearing groups, reflecting significant genetic differentiation. A dendrogram and principal coordinate analysis revealed three distinct groups. Group 1 included most Hungarian and some European cultivars. Groups 2 (Western European cultivars) and 3 (Turkish selections) exhibited higher average allele numbers, suggesting greater genetic diversity in these groups. Our results indicate that cultivated cherry laurels originate from a broad genetic base and show clear genetic divergence between ornamental and fruit-bearing selections, likely due to differing long-term selection pressures. The observed genetic variability is consistent with the polyploid nature of the species and supports the presumed self-incompatible phenotype. This is the first study to report SSR fingerprints for ornamental cultivars and fruit-bearing selections, providing a potential tool for use in breeding programs. Full article

Circular RNA (CircRNA) is a single-stranded RNA arising from back splicing. CircRNAs interact with mRNA, miRNA, and proteins. These interactions regulate various life processes, including transcription, translation, cancer progression, anticancer drug resistance, and metabolism. Due to a lack of cap and poly(A) tails, circRNAs show exceptional stability and resistance to RNase degradation. CircRNAs exhibit dysregulated expression patterns in various cancers and influence cancer progression. Stability and regulatory roles in cancer progression make circRNAs reliable biomarkers and targets for the development of anticancer therapeutics. The dysregulated expression of circRNAs is associated with resistance to anticancer drugs. Enhanced glycolysis by circRNAs leads to resistance to anticancer drugs. CircRNAs have been known to regulate the response to chemotherapy drugs and immune checkpoint inhibitors. Exogenous circRNAs can encode antigens that can induce both innate and adaptive immunity. CircRNA vaccines on lipid nanoparticles have been shown to enhance the sensitivity of cancer patients to immune checkpoint inhibitors. In this review, we summarize the roles and mechanisms of circRNAs in anticancer drug resistance and glycolysis. This review discusses clinical applications of circRNA vaccines to overcome anticancer drug resistance and enhance the efficacy of immune checkpoint inhibitors. The advantages and disadvantages of circRNA vaccines are also discussed. Overall, this review stresses the potential value of circRNAs as new therapeutic targets and diagnostic/prognostic biomarkers for cancer Full article

Parkinson’s disease (PD) is the second most common neurodegenerative disease. It primarily affects the motor system but is also associated with a range of cognitive impairments that can manifest early in disease progression, indicating its multifaceted nature. In this paper, we performed a meta-analysis of transcriptomics and proteomics data using MultiOmicsIntegrator to gain insights into the post-transcriptional modifications and deregulated pathways associated with this disease. Our results reveal differential isoform usage between control and PD patient brain samples that result in enriched alternative splicing events, including an extended UTR length, domain loss, and the upregulation of non-coding isoforms. We found that Inositol-Requiring Enzyme 1 (IRE1) is active in PD samples and examined the role of its downstream signaling through X-box binding mRNA 1 (XBP1) and regulated IRE1-dependent decay (RIDD). We identified several RIDD candidates and showed that the enriched alternative splicing events observed are associated with RIDD. Moreover, in vitro mRNA cleavage assays demonstrated that OSBPL3, C16orf74, and SLC6A1 mRNAs are targets of IRE1 RNAse activity. Finally, a pathway enrichment analysis of both XBP1s and RIDD targets in the PD samples uncovered associations with processes such as immune response, oxidative stress, signal transduction, and cell–cell communication that have previously been linked to PD. These findings highlight a potential regulatory role of IRE in PD. Full article