Search Results (154)

Tetranychus urticae, commonly known as the two-spotted spider mite, is a highly adaptable and polyphagous arthropod in the family Tetranychidae, capable of feeding on over 1200 plant species, including strawberries (Fragaria × ananassa Duch.). The fitness and microbiota of herbivorous arthropods can vary significantly across different plant species and cultivars. In this study, we investigated the fecundity, longevity, growth rate, and microbiota composition of T. urticae reared on seven Chinese strawberry cultivars: Hongyan (HY), Yuexiu (YX), Tianshi (TS), Ningyu (NY), Xuetu (XT), Zhangjj (ZJ), and Xuelixiang (XLX). Our findings revealed significant differences among cultivars: mites reared on the XT cultivar exhibited the highest fecundity (166.56 ± 7.82 eggs), while those on XLX had the shortest pre-adult period (7.71 ± 0.13 days). Longevity was significantly extended in mites reared on XLX, XT, and NY cultivars (25.95–26.83 days). Microbiota analysis via 16S rRNA sequencing showed that Proteobacteria dominated (>89.96% abundance) across all mite groups, with Wolbachia as the predominant symbiont (89.58–99.19%). Male mites exhibited higher bacterial diversity (Shannon and Chao1 indices) than females, though Wolbachia abundance did not differ significantly between sexes or cultivars. Functional predictions highlighted roles of microbiota in biosynthesis, detoxification, and energy metabolism. These findings underscore the influence of host plant variety on T. urticae fitness and microbiota composition, suggesting potential strategies for breeding resistant strawberry cultivars and leveraging microbial interactions for pest management. Full article

The selective regulation of gene expression at the RNA level represents a rapidly evolving field offering substantial clinical potential. This review examines the molecular mechanisms of intracellular enzymatic systems that utilize single-stranded nucleic acids to downregulate specific RNA targets. The analysis encompasses antisense oligonucleotides and synthetic mimics of small interfering RNA (siRNA), microRNA (miRNA), transfer RNA-derived small RNA (tsRNA), and PIWI-interacting RNA (piRNA), elucidating their intricate interactions with crucial cellular machinery, specifically RNase H1, RNase P, AGO, and PIWI proteins, mediating their biological effects. The functional and structural characteristics of these endonucleases are examined in relation to their mechanisms of action and resultant therapeutic outcomes. This comprehensive analysis illuminates the interactions between single-stranded nucleic acids and their endonuclease partners, covering antisense inhibition pathways as well as RNA interference processes. This field of research has important implications for advancing targeted RNA modulation strategies across various disease contexts. Full article

Hypopharyngeal carcinoma is a highly aggressive malignancy in the head and neck region with poor prognosis due to challenges in early diagnosis, high invasiveness, recurrence rate, and metastatic potential. Small non-coding RNAs (sncRNAs) play crucial roles in tumorigenesis and progression and hold potential as clinical diagnostic biomarkers and therapeutic targets. However, the ability of traditional RNA-sequencing technologies to detect modified sncRNAs is limited, potentially leading to the failure to accurately identify some functionally relevant sncRNAs. In this study, we employed PANDORA-seq technology for the first time to systematically profile sncRNA expression in cancerous and adjacent normal tissues from five patients with hypopharyngeal carcinoma. Our results revealed dynamic changes in sncRNA expression in hypopharyngeal carcinoma tissues and found 4798 significantly differentially expressed sncRNAs. Among these, differentially expressed miRNAs and tsRNAs were primarily involved in key signaling pathways, including MAPK, FoxO, and TGF-β. Additionally, we validated the differential expression of eight sncRNAs in hypopharyngeal carcinoma tissues, which may represent potential diagnostic biomarkers and therapeutic targets. This study lays the foundation for the application of PANDORA-seq technology in human cancers and offers new directions for exploring the underlying molecular mechanisms of hypopharyngeal carcinoma and potential targets for its clinical diagnosis and treatment. Full article

RNA polymerase III (Pol III) transcribes a broad spectrum of non-coding RNAs, including transfer RNAs (tRNAs), 5S ribosomal RNA (5S rRNA), U6 small nuclear RNA (U6 snRNA), and a range of regulatory RNAs (7SK, 7SL, RMRP, RPPH1, Y RNA, vault RNA, Alu, BC200, snaR, and nc886). These RNAs are integral to fundamental cellular processes, including transcription and translation, RNA processing and stability, and cytoplasmic protein targeting. Among them, tRNA-derived small RNAs (tsRNAs) have recently emerged as critical regulators across a wide array of biological contexts. Increasing evidence links the dysfunction of Pol III transcripts to human diseases, particularly genetic disorders and cancer. In this review, we provide a comprehensive overview of Pol III-transcribed RNAs, their biogenesis and regulatory mechanisms, and their biological functions. We also explore emerging insights into the disease relevance of Pol III-transcribed RNAs and discuss their potential implications for future research and therapeutic development. Full article

Hypoxia leads to endothelial dysfunction and increased blood–brain barrier (BBB) permeability, promoting the incidence of diseases such as stroke and acute high-altitude illness. Brain microvascular endothelial cells (BMECs) are important structural and functional components of the BBB; however, the molecular changes that occur in BMECs during hypoxia remain unknown. We reported the molecular and functional changes in BMECs under hypoxia through whole-transcriptome sequencing, small RNA microarray, TMT quantitative proteomic, and untargeted metabolomic analyses. We found that hypoxia affected pathways such as ncRNA processing, the HIF-1 signaling pathway, the cell cycle, DNA replication, glucose metabolism, protein synthesis, and inflammation pathways. ncRNA processing was significantly downregulated. However, the levels of some miRNAs, tRNAs, tsRNAs, snoRNAs, lncRNAs, and circRNAs were significantly upregulated under hypoxia. These results suggest that ncRNAs may play an important role in oxidative stress and cellular adaptation to hypoxia, helping us understand the pathological process of BBB injury and providing potential targets for the treatment of BBB-related cerebrovascular diseases. Full article

Background: Although extensive resection improves the prognosis of gliomas, it risks impairing critical brain functions. Photodynamic therapy (PDT) utilizing talaporfin sodium (TS) targets tumor cells upon light activation. Despite its approval in Japan, TS application remains restricted, and factors influencing its efficacy are unclear. We aimed to identify TS efficacy determinants to optimize treatment outcomes. Methods: Data from 171 patients with grade 4 glioma who underwent surgery and PDT at Tokyo Women’s Medical University Hospital between January 2017 and March 2024 were retrospectively analyzed. Clinical variables evaluated included age, sex, genotype, Karnofsky Performance Status (KPS), serum albumin (Alb) levels, MIB-1 expression levels, and medication history. TS concentrations in tumor tissues were quantitatively assessed in 82 patients (41 primary, 41 recurrent). Survival outcomes were analyzed. RNA-seq was performed on the three highest and three lowest TS concentration samples with significant TS concentration variations to investigate corresponding gene expression changes. Results: Multivariate analysis identified KPS (hazard ratio [95% confidence interval]: 0.96 [0.93–0.99], p = 0.01) and Alb (3.68 [1.05–13.76], p = 0.047) as independent prognostic factors. In recurrent cases, higher TS concentrations were significantly associated with improved survival (p = 0.0454). RNA-seq analysis indicated decreased expression of ACTB and PDPN genes in samples with lower TS concentrations, suggesting potential resistance mechanisms. Conclusions: TS concentration is a critical determinant of PDT efficacy, especially in recurrent glioma, highlighting its prognostic significance. Alb may affect treatment outcomes by mediating TS binding. RNA-seq findings imply that low TS concentrations may suppress immune and stress response-related genes, potentially diminishing PDT sensitivity. Full article

Emerging small non-coding RNAs (sncRNAs), including tRNA-derived small RNAs (tsRNAs) and rRNA-derived small RNAs (rsRNAs), are critical in various biological processes, such as neurological diseases. Traditional sncRNA-sequencing (seq) protocols often miss these sncRNAs due to their modifications, such as internal and terminal modifications, that can interfere with sequencing. We recently developed panoramic RNA display by overcoming RNA modification aborted sequencing (PANDORA-seq), a method enabling comprehensive detection of modified sncRNAs by overcoming the RNA modifications. Using PANDORA-seq, we revealed a previously unrecognized sncRNA profile enriched by tsRNAs/rsRNAs in the mouse prefrontal cortex and found a significant downregulation of mitochondrial tsRNAs and rsRNAs in an Alzheimer’s disease (AD) mouse model compared to wild-type controls, while this pattern is not present in the genomic tsRNAs and rsRNAs. Moreover, our integrated analysis of gene expression and sncRNA profiles reveals that those downregulated mitochondrial sncRNAs negatively correlate with enhanced lysosomal activity, suggesting a crucial interplay between mitochondrial RNA dynamics and lysosomal function in AD. Given the versatile tsRNA/tsRNA molecular actions in cellular regulation, our data provide insights for future mechanistic study of AD with potential therapeutic strategies. Full article

The epidermis of the skin and oral mucosa is constantly exposed to various environmental stimuli, including temperature changes. In particularly extreme conditions, such as excess heat or cold, significant injury may occur. Oral and skin keratinocytes exhibit tissue-specific differences in wound healing outcomes and the transcriptomic response to injury. This study investigated if skin and oral keratinocytes also have differential responses to heat- and cold-induced injury. Oral keratinocytes (TIGKs) were found to exhibit an enhanced viability following heat-induced injury compared to skin keratinocytes (HaCaTs). However, there were no discernible differences between skin and oral keratinocyte viability following cold-induced injury. To examine the transcriptomic differences between skin and oral keratinocytes in response to temperature-induced injury, we generated an mRNA-sequencing gene expression dataset. Differentially expressed genes (DEGs) including heat shock proteins (HSPs) were identified between HaCaTs and TIGKs at baseline (37 °C) and after heat- (60 °C) or cold-induced (−25 °C) injury. Our comparative analyses suggest that skin and oral keratinocytes exhibit transcriptomic differences at baseline and in their responses to heat or cold exposure. The enhanced heat tolerance of TIGKs relative to HaCaTs may be due to an advantageous expression of a subset of HSPs at baseline in TIGKs. Our work also provides a source of skin and oral keratinocyte gene expression data following heat- and cold-induced injury that can be used for future analyses. Full article

Transfer RNA is a class of non-coding RNA that plays a role in amino acid translocation during protein synthesis. After specific modification, the cleaved fragment is called tRNA-derived small RNA. The advancement of bioinformatics technology has led to an increase in the visibility of small RNA derived from tRNA, and their functions in biological processes are being revealed. These include gene silencing, transcription and translation, epigenetics, and cell death. These properties have led to the implication of tsRNAs in various diseases. Although the current research mainly focuses on the role of tRNA-derived small RNA in cancer, there is mounting evidence that they are also strongly associated with cardiovascular disease, including cardiac hypertrophy, atrial fibrillation, heart failure, and myocarditis. Therefore, the regulatory role of tRNA-derived small RNA in cardiovascular disease will become an emerging therapeutic strategy. This review succinctly summarizes the characteristics, classification, and regulatory effect of tsRNA. By exploring the mechanism of tsRNA, it will provide a new tool for the diagnosis and prognosis of cardiovascular disease. Full article

Background/Objectives: Duloxetine, despite being a leading treatment option for major depressive disorder (MDD), exhibits a relatively low adequate response rate when used as a monotherapy, and the fundamental molecular mechanisms remain largely elusive. tRNA-derived small RNA (tsRNA) is a particularly interesting and new class of molecules that is becoming increasingly noticeable for investigation. Methods: We integrated small RNA sequencing with bioinformatics approaches to dissect the expression profiles of tsRNAs and decipher their functional roles post-duloxetine treatment. Subsequently, molecular docking experiments were carried out to validate the potential functions. Results: Ten tsRNAs significantly changed in the duloxetine response group after an 8-week therapy. Correlation analyses revealed that these tsRNAs predominantly interacted with miRNAs across multiple biological pathways and processes, such as the ECM-receptor interaction and B cell activation. Molecular docking analysis corroborated the binding capabilities of duloxetine with key proteins associated with ECM1 and BAFF, respectively. Conclusions: The identified changes in tsRNAs can precisely mirror the response of duloxetine in MDD treatment, offering novel insights into the underlying mechanisms of duloxetine action. Full article

Background: Mesoporous titanium dioxide nanoparticles (mTiNPs) are known for their chemical stability, non-toxicity, antimicrobial and anticancer effects, as well as for their photocatalytic properties. When this material is subjected to UV radiation, its electronic structure shifts, and during that process, reactive oxygen species are generated, which in turn exert apoptotic events on the cancer cells. Objectives: We evaluated the cytotoxic effects of UV-irradiated mTiNPs on prostate cancer (PCa) cell line PC3 with the aim of demonstrating that the interaction between UV-light and mTiNPs positively impacts the nanomaterial’s cytotoxic efficiency. Moreover, we assessed the differential expression of key oncomiRs and tumor suppressor (TS) miRNAs, as well as their associated target genes, in cells undergoing this treatment. Methods: PBS-suspended mTiNPs exposed to 290 nm UV light were added at different concentrations to PC3 cells. Cell viability was determined after 24 h with a crystal violet assay. Then, the obtained IC₅₀ concentration of UV-nanomaterial was applied to a new PC3 cell culture, and the expression of a set of miRNAs and selected target genes was evaluated via qRT-PCR. Results: The cells exposed to photo-activated mTiNPs required 4.38 times less concentration of the nanomaterial than the group exposed to non-irradiated mTiNPs to achieve the half-maximal inhibition, demonstrating an improved cytotoxic performance of the UV-irradiated mTiNPs. Moreover, the expression of miR-18a-5p, miR-21-5p, and miR-221-5p was downregulated after the application of UV-mTiNPs, while TS miR-200a-5p and miR-200b-5p displayed an upregulated expression. Among the miRNA target genes, PTEN was found to be upregulated after the treatment, while BCL-2 and TP53 were underexpressed. Conclusions: Our cytotoxic outcomes coincided with previous reports performed in other cancer cell lines, strongly suggesting UV-irradiated mTiNPs as a promising nano-therapeutic approach against PCa. On the other hand, to the best of our knowledge, this is the first report exploring the impact of UV-irradiated mTiNPs on key onco- and TS microRNAs in PCa cells. Full article

tRNA molecules are among the most fundamental and evolutionarily conserved RNA types, primarily facilitating the translation of genetic information from mRNA into proteins. Beyond their canonical role as adaptor molecules during protein synthesis, tRNAs have evolved to perform additional functions. One such non-canonical role for tRNAs is through the generation of tRNA-derived fragments via specific cleavage processes. These tRNA-derived small RNAs (tsRNAs) are present across all three domains of life, including in protozoan parasites. They are formed through the cleavage of the parent tRNA molecules at different sites, resulting in either tRNA halves or smaller fragments. The precise mechanisms underlying the synthesis of various tRNA-derived fragments, including the specific RNases involved, as well as their distinct functions and roles in parasite physiology, are not yet fully understood and remain an active area of ongoing research. However, their role in modulating gene expression, particularly during stress responses, is becoming increasingly evident. In this context, we discuss recent findings on the roles of tRNA-derived small RNA in various protozoan parasites. Furthermore, we investigate how these tsRNAs either modulate gene expression within the parasite itself or are packaged into extracellular vesicles to alter host gene expression, thereby promoting parasite survival and adaptation. Full article

Turner syndrome (TS) can be determined by karyotype analysis, marked by the loss of one X chromosome in females. However, the genes involved in autoimmunity in TS patients remain unclear. In this study, we aimed to analyze differences in immune gene expression between a patient with TS, a healthy female, and a female patient with Graves’ disease using single-cell RNA sequencing (scRNA-seq) analysis of antigen-specific CD4(+) T cells. We identified 43 differentially expressed genes in the TS patient compared with the healthy female and the female patient with Graves’ disease. Many of these genes have previously been suggested to play a role in immune system regulation. This study provides valuable insights into the differences in immune-related gene expression between TS patients, healthy individuals, and those with autoimmune diseases. Full article

Tail fat is essential for sheep survival in extreme environments, yet its significance is often overlooked, leading to the decline of fat-tailed breeds. This study identified a novel lncRNA, lncRSFD1 (TCONS_00054953), through transcriptome sequencing, showing differential expression in the tail adipose tissues of Lanzhou Fat-Tailed (LFT) sheep and Tibetan (TS) sheep. Highly expressed in adipose tissues, lncRSFD1 inhibits preadipocyte proliferation and promotes 3T3-L1 differentiation, suggesting its role in regulating fat deposition. Located in both the cytoplasm and nucleus, lncRSFD1 targets the neighboring gene PDE4DIP and may function as a molecular sponge for conserved miRNAs, including oar-miR-30a-3p, oar-miR-329b-5p, and oar-miR-431, which are known to influence fat and muscle-related physiological processes. Moreover, the core promoter of lncRSFD1 (−2607 bp to −1776 bp) harbors four SNPs (g.-2429G>A, g.-2030T>C, g.-2016C>T, g.-2015G>A) significantly associated with growth traits such as body height in Guiqian Semi-Fine Wool (GSFW) sheep. These findings suggest lncRSFD1 plays a key role in fat deposition and growth regulation, offering new insights into the molecular mechanisms of lncRNAs in sheep. It provides a potential target for genetic improvement and molecular breeding to enhance fat deposition and adaptability in sheep breeds. Full article

The RNA-binding S1 domain is a β-barrel with a highly conserved RNA-binding site on its surface. This domain is an important part of the structures of different bacterial, archaeal, and eukaryotic proteins. A distinctive feature of the S1 domain is multiple presences (structural repeats) in proteins and protein complexes. Here, we have analyzed all available protein sequences in the UniProt database to obtain data on the distribution of bacterial, eukaryotic and archaeal proteins containing the S1 domain. Mainly, the S1 domain is found in bacterial proteins with the number of domains varying from one to eight. Eukaryotic proteins contain from one to fifteen S1 domains, while in archaeal proteins, only one S1 domain is identified. Analysis of eukaryotic proteins containing S1 domains revealed a group of chloroplast S1 ribosomal proteins (ChRpS1) with characteristic properties of bacterial S1 ribosomal proteins (RpS1) from the Cyanobacteria. Also, in a separate group, chloroplast and mitochondrial elongation factor Ts containing two S1 structural domains were assigned. For mitochondrial elongation factor Ts, the features of S1 in comparison with the RpS1 from Cyanobacteria phylum and the Alphaproteobacteria class were revealed. The data obtained allow us to consider the S1 domain as one of the evolutionary markers of the symbiogenesis of bacterial and eukaryotic organisms. Full article