Search Results (105)

Transfer RNA-derived fragments (tRFs) have been recently recognized for their multiple roles in gene expression, including modulation of translation, mRNA stability, and cellular signaling pathways. Sensory organs, such as the eyes, skin, and oral cavity, are continuously exposed to environmental stressors, including oxidative stress, ultraviolet radiation, microbial challenges, and mechanical stimuli, making them particularly susceptible to dysregulation of RNA-mediated processes. This review comprehensively summarizes current evidence on the role of tRFs in sensory organ physiology and pathology with a focus on their involvement in key processes, such as angiogenesis, inflammation, immune regulation, and fibrosis. tRFs have been shown to influence critical signaling pathways that are central to diseases such as retinal neovascularization, inflammatory skin conditions, wound healing, tissue remodeling, etc. Despite these advances, the field remains limited by a lack of experimentally validated tRF-target interactions, as most available data rely on computational predictions. The findings from the literature emphasize the need for rigorous functional validation in disease-relevant models of tRFs in biofluids, such as saliva and serum, to support their potential as minimally invasive biomarkers. Further translational studies are required to fully elucidate their biological roles and explore their potential in diagnostic and therapeutic applications. Full article

Small noncoding RNAs play critical regulatory roles in development across organisms. This study profiled microRNAs (miRNAs) and tRNA-derived fragments (tRFs) during bovine conceptus elongation. Elongating conceptuses were obtained via superovulation of eight Angus heifers. Twenty samples from ovoid (OV, n = 6; 0.5–3 mm), tubular (TUB, n = 7; 5–15 mm), and filamentous (FIL, n = 7; 20–34 mm) stages underwent small RNA sequencing. Differential expression of miRNAs and tRFs was analyzed using DESeq2, accounting for donor-sire effects. No tRFs showed differential abundance across any pairwise comparisons. For miRNAs, the expressions of six miRNAs were upregulated in OV versus TUB conceptuses (padj < 0.05), including four let-7 family members (bta-let-7g, bta-let-7f, bta-let-7a-5p, and bta-let-7c) and two additional miRNAs (bta-miR-224 and bta-miR-449a). Furthermore, there were 3 miRNAs differently abundant between the ovoid and filamentous transition (padj < 0.04), including two members of the let7 family (bta-let-7g and bta-let-7f) and bta-miR-449a. Predicted targets of these differentially abundant miRNAs were identified using miRanda. Enrichment analyses of the targeted genes included pathways regulating cellular proliferation, pathways in cancer, and immune-related pathways. The let-7 family, along with miR-449a and miR-224, are candidate regulators of the balance between cellular proliferation and differentiation during elongation, based on their differential abundance and in silico target predictions. Full article

Pedicularis henryi is a hemiparasitic species within Orobanchaceae (Lamiales). In this study, the mitochondrial genome of P. henryi was assembled and characterized. The mitogenome is 251,317 bp in length with a GC content of 44.32%, containing 36 protein-coding genes, 24 tRNAs, and three rRNAs. Codon usage analysis revealed a marked preference for A/U-terminated codons. A total of 196 repetitive elements were identified, with interspersed repeats as the most abundant type. We detected 293 C-to-U RNA editing sites across 31 protein-coding genes, predominantly causing non-synonymous substitutions. Eighteen chloroplast-derived fragments totaling 35,894 bp were found, accounting for 15.0% of the mitogenome. Nucleotide diversity analysis among three Pedicularis species showed an average π of 0.0018, with core respiratory genes highly conserved. Synteny analysis revealed extensive structural rearrangement in P. henryi compared to P. chinensis. This study provides mitochondrial genomic resources for Orobanchaceae and insights into mitogenome evolution in hemiparasitic plants. Full article

Loss of ovarian hormones following menopause or ovariectomy is associated with increased anxiety, cognitive impairment, and dysregulation of hypothalamic neuroendocrine pathways. MicroRNAs (miRNAs) and tRNA-derived fragments (tRFs) are emerging classes of small non-coding RNAs that act as post-transcriptional regulators of stress, inflammation, and synaptic function; however, their coordinated involvement in estradiol-mediated hypothalamic regulation remains poorly understood. In this study, adult female mice were assigned to control, estradiol-treated, ovariectomized (OVX), or OVX plus estradiol groups. Anxiety- and cognition-related behaviors were assessed using the open field, Y-maze, and elevated plus maze tests. Circulating estradiol levels and hypothalamic gonadotropin-releasing hormone (GnRH) expression were quantified by ELISA. Hypothalamic mRNA, miRNA, and tRF expression profiles were analyzed by RNA sequencing, followed by differential expression analysis, functional enrichment, integrative network construction, and quantitative real-time PCR validation. Ovariectomy induced anxiety-like behaviors, impaired working memory, reduced estradiol levels, and increased hypothalamic GnRH expression, all of which were reversed by estradiol treatment. Transcriptomic analysis identified 376 differentially expressed miRNAs, 182 differentially expressed tRFs, and 439 differentially expressed mRNAs, enriched in pathways related to stress responses, neuroendocrine regulation, synaptic signaling, metabolic homeostasis, and neuroinflammation. Integrated miRNA–mRNA and tRF–mRNA network analyses revealed several estradiol-responsive miRNAs (including miR-200a-5p, miR-182/183-5p, miR-381-3p, miR-148a-3p, and miR-10 family members) predicting key hub genes such as Gcg, Wnt4, Prkacb, Sgk1, Fpr2, and Aldoa, and key tRFs like tRFdb-1003, tRFdb-1013, tRFdb-1026, tRFdb-3001a and tRFdb-5020a, targeting hub genes such as Wnt4, Prkacb, Sh3rf2, Hpse, Cxcr2 and Zbtb16 respectively. Collectively, these findings demonstrate that estradiol ameliorates OVX-induced behavioral and endocrine dysfunction by reorganizing hypothalamic miRNA- and tRF-mediated regulatory networks involved in stress adaptation, synaptic homeostasis, and neuroimmune signaling. Full article

Background: Diagnostic discrimination between ischemic stroke (IS) and hemorrhagic stroke (HS) is required for successful intervention with time-critical acute treatments. The available data on blood-based RNA biomarkers and discrimination between IS and HS are limited. This systematic review aimed to examine and summarize the existing literature on potentially useful blood-based RNA biomarkers that may aid in preclinical acute diagnosis. Methods: We systematically reviewed the literature on the ability of blood-based RNA biomarkers to discriminate between IS and HS according to PRISMA guidelines. We searched PubMed, EMBASE, The Cochrane Library, and The Web of Science for eligible randomized controlled trials, observational studies, and case–control studies published in the English language without time limitation. The risk of bias was evaluated using the Newcastle–Ottawa Scale. Results: We included eight studies with a total of 728 patients (436 with IS and 292 with HS) in our review. The study quality was good in five and fair in three investigations. No meta-analysis was performed due to high heterogeneity in methods and study endpoints. Reported biomarkers include miRNA-124-3p, miRNA-16, miRNA-340-5p, lncRNA XIST (X-inactive specific transcript), PFKFB3 mRNA (6-phosphofructo-2-kinase/fructose-2,6-biphosphatase), tRNA derivatives, tRNA fragments, extracellular miRNAs, transcriptome changes, and MCEMP1 gene expression. Assessment techniques varied widely across studies, ranging from RNA sequencing to qPCR, microarray, human transcriptome array, and ELISA. MicroRNA-124-3p, miRNA-340-5p, lncRNA XIST, PFKFB3 mRNA, and MCEMP1 gene expression differed significantly between IS and HS. In one study, principal component analysis and unsupervised learning demonstrated the utility of hierarchical clustering of differentially expressed exons to discriminate between HS and IS. Conclusions: This review demonstrates the utility of single RNA-based targets and clusters that may have diagnostic value in distinguishing IS from HS. However, the current body of evidence is limited by considerable methodological heterogeneity between studies. Registration: This systematic review was prospectively registered on PROSPERO on 21 April 2023 (CRD42023411203). Full article

Background/Objectives: Human milk is a complex biological fluid containing not only macro- and micronutrients but also diverse bioactive molecules, including extracellular RNAs. Although RNA has been detected in milk for decades, only a subset of RNA species has been characterized in detail, and abundant families such as tRNA-, yRNA-, and rRNA-derived fragments remain underexplored. This study aimed to define the composition, fragmentation patterns, stability, and exploratory functional activity of these highly abundant RNAs in human milk. Methods: We performed small RNA sequencing on skim milk samples and analyzed the resulting profiles in comparison with publicly available milk and biofluid datasets. RNA stability assays, Northern blotting, and RT-qPCR were conducted to validate RNA abundance and degradation kinetics. Extracellular vesicles (EVs) and non-vesicular fractions were analyzed to determine the subcellular distribution of RNA species. Exploratory functional assays using synthetic RNA fragments were carried out to assess their ability to modulate cellular responses in vitro. Results: Human milk was found to be highly enriched in small RNA fragments derived from tRNA, yRNA, and rRNA, dominated by a limited set of discrete sequences. These profiles were highly reproducible across independent datasets and distinct biofluids. Orthologal validation assays confirmed their abundance and stability, with RNA levels exceeding those of serum by over two orders of magnitude. Full-length transcripts were enriched in EVs, whereas shorter fragments predominated in the non-vesicular fraction. Synthetic milk-derived exRNAs showed detectable pro-survival activity under stress conditions in vitro. Conclusions: This study reveals that human milk carries a limited set of highly abundant stable sRNA molecules, primarily derived from tRNAs, yRNAs, and rRNAs. These findings provide new insights into the RNA cargo of human milk and offer preliminary evidence that selected sRNA fragments can modulate cellular stress responses in in vitro models. Full article

Background: Gynostemma pentaphyllum (Thunb.) Makino is an important medicinal plant within the Cucurbitaceae family. Despite its economic and pharmacological importance, genomic resources for this species remain limited. Methods: We sequenced and assembled the complete mitochondrial genome of G. pentaphyllum. Comparative analyses were conducted to investigate the genomic structure, gene content, RNA editing events, and intracellular gene transfer (IGT) from chloroplasts. Additionally, phylogenomic relationships, synteny, and the selective pressure on mitochondrial genes were evaluated against related species within Cucurbitaceae. Results: The ~324 kb mitogenome has a multipartite architecture of six circular-mapping molecules. It encodes the typical complement of mitochondrial protein-coding genes, tRNAs, and rRNAs found in angiosperms. Extensive C-to-U RNA editing, including events that generate functional start and stop codons, points to substantial post-transcriptional regulation. We also detected multiple chloroplast-derived fragments, including several intact genes, indicating active intracellular gene transfer. Phylogenomic analyses of conserved mitochondrial genes place G. pentaphyllum firmly within Cucurbitaceae, clustering it with Thladiantha cordifolia and Momordica charantia, whereas synteny comparisons reveal pronounced structural rearrangements with respect to these close relatives. While most genes evolve under strong purifying selection, rps1, sdh3, and sdh4 show signatures of accelerated evolution; furthermore, haplotype networks based on conserved loci further corroborate the close affinity with T. cordifolia. Conclusions: This study provides the first high-resolution mitogenome resource for G. pentaphyllum and candidate mitochondrial markers for species authentication, evolutionary studies, and breeding in Gynostemma and related cucurbits. Full article

Rare genetic ocular diseases represent a heterogeneous group of disorders that significantly impair visual function and quality of life. Despite their clinical relevance, many of these conditions remain insufficiently characterized due to complex molecular mechanisms and diagnostic limitations. Recent advances in molecular diagnostics, particularly Next-Generation Sequencing (NGS), have enabled comprehensive and accurate identification of pathogenic variants, offering novel insights into genotype–phenotype correlations and supporting precision medicine approaches. In parallel, the use of alternative biological matrices such as tear fluid has emerged as a promising non-invasive strategy for biomarker discovery and disease monitoring. Tear-based omics, including proteomics and transcriptomics, have identified diagnostic signatures and pathogenic mediators such as non-coding RNAs, microRNAs, and tRNA-derived fragments (tRFs). Among these, tRF-1001 has shown potential both as a biomarker and therapeutic target in ocular neovascular conditions through its modulation of angiogenic pathways. The objective of this review is to show the integration of two rapidly advancing yet frequently isolated fields: next-generation sequencing-based genomics and tear-fluid molecular profiling, positioning them as complementary foundations of precision ophthalmology for rare inherited retinal and optic nerve disorders. Previous reviews have mainly concentrated on either genetic diagnosis or ocular surface biomarkers separately; however, we have introduced a convergent model wherein genomic data furnish diagnostic and prognostic clarity, while tear-omics deliver dynamic, minimally invasive assessments of disease activity, treatment efficacy, and persistent neurovascular stress. By explicitly connecting these two aspects, we have delineated how multi-matrix, multi-omics approaches can expedite early diagnosis, facilitate personalized longitudinal monitoring, and direct focused treatment interventions in rare ocular genetic illnesses. Full article

Transfer RNA-derived fragments (tRFs) have become a significant category of small non-coding RNAs that likely play vital roles in various cellular functions. Initially, research on small RNAs overlooked tRFs as simple byproducts of tRNA degradation, but recent findings show they are precisely produced molecules that regulate gene expression. Studies have demonstrated that tRFs regulate genes and proteins through various mechanisms, from miRNA-like targeting that relies on Argonaute (AGO) protein to lesser-known modes of action. Recent reports also suggest that tRFs are involved in multiple diseases, including cancer, where they may be utilized as biomarkers. Notably, tRFs can be transported between different cells and tissues of an organism or even across different organisms, further emphasizing their biological significance. Although evidence increasingly indicates that tRFs may function as new regulatory agents in health and disease, their biogenesis and underlying mechanisms are not yet fully understood. Conducting a thorough exploratory analysis of the tRF modes of action could be a valuable resource for advancing this growing field. Our goal in this review is to gather and examine the latest research on tRF biology, focusing on its diverse and dynamic molecular mechanisms discovered in different disease contexts, with a view toward potential applications in medicine. We aim to gain a deeper understanding of tRFs and explore their potential for new therapeutic breakthroughs by combining insights from molecular studies, disease models, and clinical research. Full article

Metabolic dysfunction-associated steatotic liver disease (MASLD) is an increasingly prevalent condition linked to obesity, diabetes, and metabolic syndrome, and can progress to fibrosis, cirrhosis, and hepatocellular carcinoma. Current diagnostic standards such as liver biopsy are invasive and unsuitable for routine screening. Liquid biopsy, particularly through analysis of extracellular RNAs (exRNAs), including microRNAs (e.g., miR-122, miR-21, miR-34a), long non-coding RNAs, and tRNA-derived fragments, offers a promising non-invasive alternative. These exRNAs, released from hepatocytes and carried in blood via extracellular vesicles or protein complexes, can be detected using techniques like RNA sequencing, qRT-PCR, and droplet digital PCR. These biomarkers correlate with histologic severity, fibrosis stage, and treatment response, and have shown promising diagnostic utility; however, their performance may differ across various populations and disease stages. Despite their potential, clinical translation is limited by a lack of standardization and large-scale validation. This review outlines recent advances in exRNA-based diagnostics for MASLD and MASH, emphasizing their role in early detection, disease monitoring, and the shift toward personalized hepatology. Full article

Transfer RNA-derived small RNAs (tDRs) are increasingly being recognized as versatile regulators, yet their physiological landscape remains poorly charted. We analyzed tDR expression in seven adult mouse tissues to explore tissue-specific tDR enrichment using a tDR-optimized library preparation methodology. We catalogued 26,901 unique nuclear tDRs (ntDRs) and 5114 mitochondrial tDRs (mtDRs). Clustering analysis segregated the tissues, with the spleen and lungs forming a distinct immune cluster. Tissue-versus-all and pairwise differential analysis showed the spleen harboring unique ntDRs and mtDRs. Tissue-enriched tDRs arose from specific isoacceptor and isodecoder tRNAs, independent of mature tRNA abundance, suggesting selective biogenesis rather than bulk turnover. G-quadruplex prediction revealed a pronounced enrichment of potentially quadruplex-forming ntDRs in the kidneys, heart, and spleen, predominantly derived from i-tRFs and tRF3 fragments, suggesting structure-dependent functions in immune regulation. We also benchmarked our library strategy against the PANDORA-seq method. Despite comparable or lower sequencing depth, our method detected ~3–10-fold more unique ntDRs and we observed a clearer representation of tRF-3 fragments and greater isotype diversity. Our tissue atlas and improved tDR sequencing method reveal extensive tissue-specific heterogeneity in tDR biogenesis, sequencing, and structure, providing a framework for understanding the context-dependent regulatory roles of tDRs. Full article

Background/Objectives: Transfer RNA-derived fragments (tRFs) are small non-coding RNAs increasingly implicated in gene regulation and disease, yet their target specificity and disease relevance remain poorly understood. This is an exploratory study that investigates the phenomenon of identical tRF sequences reported in distinct disease contexts and evaluates the consistency between experimental findings and predictions from both target-based and abundance-based tRF databases. Methods: Five tRFs with identical sequences across at least two peer-reviewed disease studies were selected from a recent systematic review. Their validated targets and disease associations were extracted from the literature. Motifs and predicted targets were cross-referenced using three target-oriented databases: tatDB, tRFTar, and tsRFun. In parallel, the abundance enrichment of cancer-associated tRFs was assessed in OncotRF and MINTbase using TCGA-based abundance data. Results: Among the five tRFs, only LeuAAG-001-N-3p-68-85 showed complete alignment between experimental data and both tatDB and tRFTar predictions. Most of the other four displayed at least partial overlaps in motif/binding regions with some of validated targets. tRF abundance data from MINTbase and OncotRF showed inconsistent enrichment, with only AlaAGC-002-N-3p-58-75 exhibiting concordance with its experimentally validated cancer type. Most functionally relevant tRFs were not strongly represented in abundance-only databases. Conclusions: Given the limited number of tRFs analyzed, this study serves primarily as a pilot analysis designed to generate hypotheses and guide future in-depth research, rather than offering comprehensive conclusions. We did, however, illustrate how the analysis of tRFs can benefit from utilizing currently available databases. Target-based databases more closely reflected experimental evidence for mechanistic details when a tRF or a motif match is found. Yet all database types are incomplete, including the abundance-focused tools, which often fail to capture disease-specific regulatory roles of tRFs. These findings underscore the importance of using integrated data sources for tRF annotation. As a pilot analysis, the study provides insights into how identical tRF sequences might function differently across disease contexts, highlighting areas for further investigation while pointing out the limitations of relying on expression data alone to infer functional relevance. Full article

Cell-based therapies emerge as potential treatment options for various debilitating diseases. Preclinical research and clinical studies involving cells increased exponentially in the past decade. In addition to cell-based approaches, the use of extracellular vesicles (EVs), which are released by nearly all cell types, emerged as a promising cell-free alternative. Those approaches are also being explored in the field of ophthalmology. Several clinical trials involving EVs are underway to develop potential treatments for advanced ocular surface diseases, including corneal disorders, injuries, and dry eye disease. The cargo carried by EVs has been shown to include a diverse array of functional molecules such as transcription factors, cytokines, growth factors, mRNA, tRNA, rRNA, miRNA, and fragments of dsDNA. While the molecular composition of EVs is already well characterised, the specific activity of these molecules upon delivery to recipient cells remains poorly understood. In this review, we summarise recent studies investigating the bioactive molecules within EVs shown to influence or modulate cellular activity on the ocular surface. Among these, various miRNAs have most commonly been identified as therapeutic agents targeting distinct molecular pathways. The EVs studied were predominantly derived from various mesenchymal stem cells. Full article

Background/Objectives: Myelodysplastic syndrome (MDS) is a heterogeneous clonal hematopoietic disorder characterized by ineffective hematopoiesis and leukemic transformation risk. Current therapies show limited efficacy, with ~50% of patients failing hypomethylating agents. This review aims to synthesize recent discoveries through an integrated network model and examine translation into precision therapeutic approaches. Methods: We reviewed breakthrough discoveries from the past three years, analyzing single-cell multi-omics technologies, epitranscriptomics, stem cell architecture analysis, and precision medicine approaches. We examined cell-type-specific splicing aberrations, distinct stem cell architectures, epitranscriptomic modifications, and microenvironmental alterations in MDS pathogenesis. Results: Four interconnected mechanisms drive MDS: genetic alterations (splicing factor mutations), aberrant stem cell architecture (CMP-pattern vs. GMP-pattern), epitranscriptomic dysregulation involving pseudouridine-modified tRNA-derived fragments, and microenvironmental changes. Splicing aberrations show cell-type specificity, with SF3B1 mutations preferentially affecting erythroid lineages. Stem cell architectures predict therapeutic responses, with CMP-pattern MDS achieving superior venetoclax response rates (>70%) versus GMP-pattern MDS (<30%). Epitranscriptomic alterations provide independent prognostic information, while microenvironmental changes mediate treatment resistance. Conclusions: These advances represent a paradigm shift toward personalized MDS medicine, moving from single-biomarker to comprehensive molecular profiling guiding multi-target strategies. While challenges remain in standardizing molecular profiling and developing clinical decision algorithms, this systems-level understanding provides a foundation for precision oncology implementation and overcoming current therapeutic limitations. Full article

Hippophae rhamnoides subsp. sinensis is extensively found in China, where the annual precipitation ranges from 400 to 800 mm. It is the most dominant species in natural sea buckthorn forests and the primary cultivar for artificial ecological plantations. Additionally, it exhibits significant nutritional and medicinal value, making it a renowned eco-economic tree species. Despite extensive research into its ecological functions and health benefits, the mitochondrial genome of this widespread species has not yet been published, and knowledge of the mitochondrial genome is crucial for understanding plant environmental adaptation, evolution, and maternal inheritance. Therefore, the complete mitochondrial genome was successfully assembled by aligning third-generation sequencing data to the reference genome sequence using the Illumina NovaSeq 6000 platform and Nanopore Prometh ION technologies. Additionally, the gene structure, composition, repeat sequences, codon usage bias, homologous fragments, and phylogeny-related indicators were also analyzed. The results showed that the length of the mitochondrial genome is 454,489 bp, containing 30 tRNA genes, three rRNA genes, 40 PCGs, and two pseudogenes. A total of 411 C-to-U RNA editing sites were identified in 33 protein-coding genes (PCGs), with higher frequencies observed in ccmFn, ccmB, nad5, ccmC, nad2, and nad7 genes. Moreover, 31 chloroplast-derived fragments were detected, accounting for 11.86% of the mitochondrial genome length. The ccmB, nad4L, and nad7 genes related to energy metabolism exhibited positive selection pressure. The mitochondrial genome sequence similarity between H. rhamnoides subsp. sinensis and H. tibetana or H. salicifolia was 99.34% and 99.40%, respectively. Fifteen shared gene clusters were identified between H. rhamnoides subsp. sinensis and H. tibetana. Phylogenetically, the Rosales order showed close relationships with Fagales, Fabales, Malpighiales, and Celastrales. These findings provide fundamental data for exploring the widespread distribution of H. rhamnoides subsp. sinensis and offer theoretical support for understanding the evolutionary mechanisms within the Hippophae genus and the selection of molecular breeding targets. Full article