Non-Coding RNA最新文献

Introduction: Anal squamous cell carcinoma (ASCC) is a rare but increasingly common gastrointestinal malignancy, mainly associated with oncogenic human papillomaviruses (HPVs). The role of non-coding RNAs (ncRNAs) in tumorigenesis is recognized, but the impact of viral ncRNAs on host gene expression remains unclear. Methods: We re-analyzed total RNA-Seq data from 70 anal biopsies: 31 low-grade squamous intraepithelial lesions (LGSIL), 16 high-grade SIL (HGSIL), and 23 ASCC cases. Microbial composition was assessed taxonomically. Novel viral miRNAs were predicted using vsRNAfinder and linked to host targets using TargetScan and expression correlation analyses. Results: Microbial profiling revealed significant differences in abundance, with Alphapapillomaviruses types 9, 10, and 14 enriched across lesion grades. We identified 90 novel viral miRNAs and 177 significant anti-correlated miRNA-mRNA interactions. Target genes were enriched in pathways related to cell cycle, epithelial-mesenchymal transition, lipid metabolism, immune modulation, and viral replication. Discussion: Our findings suggest that HPV-derived miRNAs, including those from low-risk types, may contribute to neoplastic transformation by modulating host regulatory networks. Conclusion: This study highlights viral miRNAs as potential drivers of HPV-related anal cancer and supports their utility as early biomarkers and therapeutic targets in ASCC.

The poultry farming industry encounters considerable obstacles stemming from viral diseases, resulting in elevated mortality rates and substantial economic losses. Current research highlights the significant involvement of long non-coding RNAs (lncRNAs) in the interactions between hosts and pathogens by enhancing antiviral responses at different levels, such as the activation of pathogen recognition receptors, as well as through epigenetic, transcriptional, and post-transcriptional modifications. Specific long non-coding RNAs (lncRNAs), including ERL lncRNA, linc-GALMD3, and loc107051710, have been recognized as significant contributors to the antiviral immune response to multiple avian viral pathogens. Understanding the mechanisms by which long non-coding RNAs (lncRNAs) act offers valuable insights into prospective diagnostic and therapeutic approaches aimed at improving disease resistance in poultry. Differentially expressed lncRNAs may also be utilized as biomarkers for both prognosis and diagnosis of avian viral diseases. This review delves into the various roles of long non-coding RNAs (lncRNAs) in the context of viral diseases in chickens, such as avian leukosis, Marek's disease, infectious bursal disease, avian influenza, infectious bronchitis, and Newcastle disease. It highlights the pivotal role of lncRNAs in the complex dynamics between the host and viral pathogens, particularly their interactions with specific viral proteins. Understanding these interactions may provide valuable insights into the spatial and temporal regulation of lncRNAs, aid in the identification of potential drug targets, and reveal the expression patterns of lncRNA and coding gene transcripts in response to different viral infections in avian species.

Background/Objectives: Exposure of high-fat diet (HFD)-fed mice to polychlorinated biphenyls (PCBs) results in metabolic dysfunction-associated steatotic liver disease (MASLD) and progression to metabolic dysfunction-associated steatohepatitis (MASH). The mechanisms by which HFD diet and PCBs increase MASLD are unclear. Previously, we identified differences in HFD-fed mouse liver tRNA modifications with single oral exposures to the dioxin-like PCB126, the non-dioxin-like PCB mixture Aroclor 1260 (Ar1260), or the combination of Ar1260 + PCB126. Methods: Here, we used small RNA sequencing and the tRNA analysis of expression (tRAX) pipeline to examine if PCB exposures alter the tRNA transcriptome, including tRNA-derived fragments (tRFs), in the livers of the PCB-exposed mice. Results: Each PCB exposure produced distinct hepatic tRNA transcriptomes with more tRNAs decreased than increased. Only tRNA-Glu-TTC-1 was reduced with all three PCB exposures. More changes in tRFs were identified with Ar1260 alone or in combination with PCB126 than with PCB126 alone. Four tRF-3s were upregulated in both PCB126 and Ar1260 + PCB126 co-exposed mice, suggesting PCB126 as responsible for this increase. We previously reported that PCB126 exposure increased hepatic Angiogenin (ANG) protein which generates tRF-3s. Four previously reported tRNA modifications corresponded to positions of PCB-associated tRNA modifications identified by tRAX: m1A, m6A, ms2t6A, and Ψ. Conclusions: Overall, the differences in hepatic tRNAs and tRFs with three different PCB exposures suggest that PCB exposures play an unexplored role in regulating translation in mouse liver.

Seyedeh Elnaz Banijamali was not included as an author in the original publication [...].

Background/Objectives: SINEs (short interspersed elements) are eukaryotic non-autonomous retrotransposons. They are transcribed by RNA polymerase III (pol III) and generate non-coding RNAs. The 3' end of many mammalian SINEs contains a polyadenylation signal (AATAAA), a pol III transcription terminator, and an A-rich tail. Studies have shown that, in human HeLa cells that have been transiently transfected with such SINEs, short pol III-generated SINE transcripts undergo polyadenylation, resulting in the addition of a long poly(A)-tail. Notably, this AAUAAA-dependent polyadenylation is not characteristic of any other transcripts synthesized by pol III. B2 SINEs, found in the genomes of mouse-like rodents, exemplify all these features. Methods: In this study, we implemented a novel approach to sequencing pol III-generated B2 transcripts from mouse cell cultures (L929 and 4T1) and organs (brain and testis). Results: Transcription occurred in 16,000-20,000 B2 copies in each cell type, 51-62% of which were transcribed in all four cell types. Effective transcription terminators (e.g., TCT_>3 and T_≥4) were found in approximately 40% of the transcribed B2 copies. The transcripts of these B2 copies contained a truncated terminator sequence, as pol III transcriptional arrest is known to occur within the terminator, with a poly(A)-tail immediately downstream. Such a tail could only have formed through RNA polyadenylation. Conclusions: These results demonstrate that B2 transcripts synthesized by pol III are capable of polyadenylation in mouse cells. We discuss the transcription of B2 copies with and without moderately efficient pol III terminators (TCTTT) and provide examples of the polyadenylation of such transcripts.

Background: Platelet-derived Extracellular Vesicles, or "Platelet Dust" (PD), are reported as the most-abundant extracellular vesicles in plasma. However, the PD molecular content, especially the small RNA profile, is still poorly characterized. This study aims to characterize PD and other extracellular vesicles (EVs) in patients with non-small-cell lung cancer (NSCLC), focusing on their small RNA signatures and diagnostic potential. Methods: The EVs were isolated directly from the plasma of healthy donors and patients with NSCLC using the surface markers CD9, CD63, CD81 (overall EVs), and CD61 (PD). Small RNA sequencing was then performed to comprehensively profile the miRNAs. Results: Our analysis revealed distinct small RNA profiles in the EVs and the PD from the patients with NSCLC. The EVs (CD9-, CD63-, and CD81-positive) showed the enrichment of four miRNAs and the depletion of ten miRNAs, while the PD (CD61-positive) exhibited a more complex profile, with nineteen miRNAs enriched and nine miRNAs depleted in the patients with NSCLC compared to those of the healthy controls. Conclusions: This exploratory study enhances our understanding of miRNA composition within different plasma vesicle populations, shedding light on the biology of plasma vesicles and their contents. Furthermore, utilizing an extracellular vesicle isolation method with potential clinical applicability offers the prospect of improved cancer characterization and detection by selecting the most informative subpopulation of plasma vesicles.

Objectives: Periodontitis is a chronic inflammatory disease that could influence the pathophysiology of cardiovascular diseases through immunoinflammatory and epigenetic mechanisms. MicroRNAs (miRNAs) could be key mediators in this interaction, regulating gene expression and the synthesis of inflammatory molecules. The objective of this systematic review was to evaluate the relationship between periodontitis and cardiovascular diseases by analyzing the expression of miRNAs involved in both pathologies.

Methods: A systematic search was performed in the PubMed, Scopus, Embase, and Web of Science databases following the PRISMA guidelines. A total of 320 studies were identified, of which seven were included after applying eligibility criteria. Data on study design, sample characteristics, periodontal and cardiovascular diagnostic methodology, and the analyzed miRNAs were extracted.

Results: The included studies were observational case-control studies in humans (n = 5) and experimental studies in animal models (n = 3). The miRNAs selected by the studies to link both pathologies were miR-155, miR-155-5p, miR-146a, miR-143, miR-145, and miR-23b. Most studies observed the overexpression of these miRNAs in patients with periodontitis and cardiovascular disease, with miR-146a being the most frequently associated.

Conclusions: The findings suggest that certain miRNAs, particularly miR-146a, may play a key role in the connection between periodontitis and cardiovascular disease. Its overexpression in patients with both pathologies reinforces the hypothesis of its involvement in the inflammatory processes associated with both conditions. It would be interesting to conduct studies to validate their clinical applicability as biomarkers of susceptibility to cardiovascular disease.

Bacterial pathogens have evolved diverse strategies to infect hosts, evade immune responses, and establish successful infections. While the role of transcription factors in bacterial virulence is well documented, emerging evidence highlights the significant contribution of small regulatory RNAs (sRNAs) in bacterial pathogenesis. These sRNAs function as posttranscriptional regulators that fine-tune gene expression, enabling bacteria to adapt rapidly to challenging environments. This review explores the multifaceted roles of bacterial sRNAs in host-pathogen interactions. Firstly, it examines how sRNAs regulate pathogenicity by modulating the expression of key virulence factors, including fimbriae, toxins, and secretion systems, followed by discussing the role of sRNAs in bacterial stress response mechanisms that counteract host immune defenses, such as oxidative and envelope stress. Additionally, this review investigates the involvement of sRNAs in antibiotic resistance by regulating efflux pumps, biofilm formation, and membrane modifications, which contribute to multi-drug resistance phenotypes. Lastly, this review highlights how sRNAs contribute to intra- and interspecies communication through quorum sensing, thereby coordinating bacterial behavior in response to environmental cues. Understanding these regulatory networks governed by sRNAs is essential for the development of innovative antimicrobial strategies. This review highlights the growing significance of sRNAs in bacterial pathogenicity and explores their potential as therapeutic targets for the treatment of bacterial infections.

Dimorphism of sex chromosomes often leads to a need for dosage compensation. In eutherian mammals, XIST, a long non-coding RNA, is expressed from the X chromosome that will be silenced, triggering X-chromosome inactivation (XCI). XIST originated from the ancestral protein-coding Lnx3 gene with contributions from various mobile elements that contributed to the striking domains of tandem repeats within the first and sixth exons. Modular domains of XIST are now involved in recruiting heterochromatic marks and proteins essential for XCI initiation and maintenance. This review presents a comparative analysis of human XIST with five other eutherian mammals-chimpanzees, cats, pigs, sheep, and mice-examining conservation across exons as well as the tandem repeats. Notably, repeats exhibited higher conservation than exons, underscoring their functional importance. Additionally, a species-specific G repeat, previously described in pigs, was also identified in sheep and cats. These findings provide insights into the domains of XIST, a cis-acting silencer that has been used to proposed to alleviate the impact of a supernumerary chromosome in Down syndrome.

Background/Objectives: Competing endogenous RNAs (ceRNA) are molecules that compete for the binding to a microRNA (miR). Usually, there are two ceRNA, one of which is a protein-coding RNA (mRNA), with the other being a long non-coding RNA (lncRNA). The miR role is to inhibit mRNA expression, either promoting its degradation or impairing its translation. The lncRNA can "sponge" the miR, thus impeding its inhibitory action on the mRNA. In their easier configuration, these three molecules constitute a regulatory axis for protein expression. However, each RNA can interact with multiple targets, creating branched and intersected axes that, all together, constitute what is known as a competing endogenous RNA network (ceRNET). Methods: In this systematic review, we collected all available data from PubMed about experimentally verified (by luciferase assay) regulatory axes in endometrial cancer (EC), excluding works not using this test; Results: This search allowed the selection of 172 bibliographic sources, and manually building a series of ceRNETs of variable complexity showed the known axes and the deduced intersections. The main limitation of this search is the highly stringent selection criteria, possibly leading to an underestimation of the complexity of the networks identified. However, this work allows us not only to hypothesize possible gap fillings but also to set the basis to instruct artificial intelligence, using adequate prompts, to expand the EC ceRNET by comparing it with ceRNETs of other cancers. Moreover, these networks can be used to inform and guide research toward specific, though still unidentified, axes in EC, to complete parts of the network that are only partially described, or even to integrate low complexity subnetworks into larger more complex ones. Filling the gaps among the existing EC ceRNET will allow physicians to hypothesize new therapeutic strategies that may either potentiate or substitute existing ones. Conclusions: These ceRNETs allow us to easily visualize long-distance interactions, thus helping to select the best treatment, depending on the molecular profile of each patient, for personalized medicine. This would yield higher efficiency rates and lower toxicity levels, both of which are extremely relevant factors not only for patients' wellbeing, but also for the legal, regulatory, and ethical aspects of miR-based innovative treatments and personalized medicine as a whole. This systematic review has been registered in PROSPERO (ID: PROSPERO 2025 CRD420251035222).