Non-Coding RNA最新文献

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The Emerging Applications of Artificial MicroRNA-Mediated Gene Silencing in Plant Biotechnology. 人工microrna介导的基因沉默在植物生物技术中的新应用
IF 3.6
Non-Coding RNA Pub Date : 2025-03-02 DOI: 10.3390/ncrna11020019
Luis Alberto Bravo-Vázquez, Ana Marta Castro-Pacheco, Rodrigo Pérez-Vargas, Joceline Fernanda Velázquez-Jiménez, Sujay Paul
{"title":"The Emerging Applications of Artificial MicroRNA-Mediated Gene Silencing in Plant Biotechnology.","authors":"Luis Alberto Bravo-Vázquez, Ana Marta Castro-Pacheco, Rodrigo Pérez-Vargas, Joceline Fernanda Velázquez-Jiménez, Sujay Paul","doi":"10.3390/ncrna11020019","DOIUrl":"10.3390/ncrna11020019","url":null,"abstract":"<p><p>Improving crop yield potential is crucial to meet the increasing demands of a rapidly expanding global population in an ever-changing and challenging environment. Therefore, different technological approaches have been proposed over the last decades to accelerate plant breeding. Among them, artificial microRNAs (amiRNAs) represent an innovative tool with remarkable potential to assist plant improvement. MicroRNAs (miRNAs) are a group of endogenous, small (20-24 nucleotides), non-coding RNA molecules that play a crucial role in gene regulation. They are associated with most biological processes of a plant, including reproduction, development, cell differentiation, biotic and abiotic stress responses, metabolism, and plant architecture. In this context, amiRNAs are synthetic molecules engineered to mimic the structure and function of endogenous miRNAs, allowing for the targeted silencing of specific nucleic acids. The current review explores the diverse applications of amiRNAs in plant biology and agriculture, such as the management of infectious agents and pests, the engineering of plant metabolism, and the enhancement of plant resilience to abiotic stress. Moreover, we address future perspectives on plant amiRNA-based gene silencing strategies, highlighting the need for further research to fully comprehend the potential of this technology and to translate its scope toward the widespread adoption of amiRNA-based strategies for plant breeding.</p>","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":"11 2","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11932238/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Unpaved Road of Non-Coding RNA Structure-Function Relationships: Current Knowledge, Available Methodologies, and Future Trends. 非编码RNA结构-功能关系的未知之路:当前的知识,可用的方法和未来的趋势。
IF 3.6
Non-Coding RNA Pub Date : 2025-03-02 DOI: 10.3390/ncrna11020020
Ana Lúcia Leitão, Francisco J Enguita
{"title":"The Unpaved Road of Non-Coding RNA Structure-Function Relationships: Current Knowledge, Available Methodologies, and Future Trends.","authors":"Ana Lúcia Leitão, Francisco J Enguita","doi":"10.3390/ncrna11020020","DOIUrl":"10.3390/ncrna11020020","url":null,"abstract":"<p><p>The genomes from complex eukaryotes are enriched in non-coding genes whose transcription products (non-coding RNAs) are involved in the regulation of genomic output at different levels. Non-coding RNA action is predominantly driven by sequence and structural motifs that interact with specific functional partners. Despite the exponential growth in primary RNA sequence data facilitated by next-generation sequencing studies, the availability of tridimensional RNA data is comparatively more limited. The subjacent reasons for this relative lack of information regarding RNA structure are related to the specific chemical nature of RNA molecules and the limitations of the currently available methods for structural characterization of biomolecules. In this review, we describe and analyze the different structural motifs involved in non-coding RNA function and the wet-lab and computational methods used to characterize their structure-function relationships, highlighting the current need for detailed structural studies to explore the molecular determinants of non-coding RNA function.</p>","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":"11 2","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11932211/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Secondary-Structure-Informed RNA Inverse Design via Relational Graph Neural Networks. 基于关系图神经网络的二级结构信息RNA逆设计。
IF 3.6
Non-Coding RNA Pub Date : 2025-02-26 DOI: 10.3390/ncrna11020018
Amirhossein Manzourolajdad, Mohammad Mohebbi
{"title":"Secondary-Structure-Informed RNA Inverse Design via Relational Graph Neural Networks.","authors":"Amirhossein Manzourolajdad, Mohammad Mohebbi","doi":"10.3390/ncrna11020018","DOIUrl":"10.3390/ncrna11020018","url":null,"abstract":"<p><p>RNA inverse design is an essential part of many RNA therapeutic strategies. To date, there have been great advances in computationally driven RNA design. The current machine learning approaches can predict the sequence of an RNA given its 3D structure with acceptable accuracy and at tremendous speed. The design and engineering of RNA regulators such as riboswitches, however, is often more difficult, partly due to their inherent conformational switching abilities. Although recent state-of-the-art models do incorporate information about the multiple structures that a sequence can fold into, there is great room for improvement in modeling structural switching. In this work, a relational geometric graph neural network is proposed that explicitly incorporates alternative structures to predict an RNA sequence. Converting the RNA structure into a geometric graph, the proposed model uses edge types to distinguish between the primary structure, secondary structure, and spatial positioning of the nucleotides in representing structures. The results show higher native sequence recovery rates over those of gRNAde across different test sets (eg. 72% vs. 66%) and a benchmark from the literature (60% vs. 57%). Secondary-structure edge types had a more significant impact on the sequence recovery than the spatial edge types as defined in this work. Overall, these results suggest the need for more complex and case-specific characterization of RNA for successful inverse design.</p>","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":"11 2","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11932209/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692776","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Combinatorial Analysis of miRNAs and tRNA Fragments as Potential Biomarkers for Cancer Patients in Liquid Biopsies. 液体活检中mirna和tRNA片段作为癌症患者潜在生物标志物的组合分析
IF 3.6
Non-Coding RNA Pub Date : 2025-02-14 DOI: 10.3390/ncrna11010017
Ilias Glogovitis, Silvia D'Ambrosi, Mafalda Antunes-Ferreira, Monica Chiogna, Galina Yahubyan, Vesselin Baev, Thomas Wurdinger, Danijela Koppers-Lalic
{"title":"Combinatorial Analysis of miRNAs and tRNA Fragments as Potential Biomarkers for Cancer Patients in Liquid Biopsies.","authors":"Ilias Glogovitis, Silvia D'Ambrosi, Mafalda Antunes-Ferreira, Monica Chiogna, Galina Yahubyan, Vesselin Baev, Thomas Wurdinger, Danijela Koppers-Lalic","doi":"10.3390/ncrna11010017","DOIUrl":"10.3390/ncrna11010017","url":null,"abstract":"<p><p><b>Background:</b> Liquid biopsy has gained significant attention as a non-invasive method for cancer detection and monitoring. IsomiRs and tRNA-derived fragments (tRFs) are small non-coding RNAs that arise from non-canonical microRNA (miRNAs) processing and the cleavage of tRNAs, respectively. These small non-coding RNAs have emerged as pro-mising cancer biomarkers, and their distinct expression patterns highlight the need for further exploration of their roles in cancer research. <b>Methods:</b> In this study, we investigated the differential expression profiles of miRNAs, isomiRs, and tRFs in plasma extracellular vesicles (EVs) from colorectal and prostate cancer patients compared to healthy controls. Subsequently, a combinatorial analysis using the CombiROC package was performed to identify a panel of biomarkers with optimal diagnostic accuracy. <b>Results:</b> Our results demonstrate that a combination of miRNAs, isomiRs, and tRFs can effectively di- stinguish cancer patients from healthy controls, achieving accuracy and an area under the curve (AUC) of approximately 80%. <b>Conclusions:</b> These findings highlight the potential of a combinatorial approach to small RNA analysis in liquid biopsies for improved cancer diagnosis and management.</p>","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":"11 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11858735/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143493119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Psoriasis Treatments: Emerging Roles and Future Prospects of MicroRNAs. 银屑病治疗:microrna的新作用和未来前景。
IF 3.6
Non-Coding RNA Pub Date : 2025-02-13 DOI: 10.3390/ncrna11010016
Li Tian Keane Teo, Nerissa Juantuah-Kusi, Gowtham Subramanian, Prabha Sampath
{"title":"Psoriasis Treatments: Emerging Roles and Future Prospects of MicroRNAs.","authors":"Li Tian Keane Teo, Nerissa Juantuah-Kusi, Gowtham Subramanian, Prabha Sampath","doi":"10.3390/ncrna11010016","DOIUrl":"10.3390/ncrna11010016","url":null,"abstract":"<p><p>Psoriasis, a widespread and chronic inflammatory skin disorder, is marked by its persistence and the lack of a definitive cure. The pathogenesis of psoriasis is increasingly understood, with ongoing research highlighting the intricate interplay of genetic, immunological, and environmental factors. Recent advancements have illuminated the pivotal role of microRNAs in orchestrating complex processes in psoriasis and other hyperproliferative skin diseases. This narrative review highlights the emerging significance of miRNAs as key regulators in psoriasis pathogenesis and examines their potential as therapeutic targets. We discuss current treatment approaches and the promising future of miRNAs as next-generation therapeutic agents for this condition.</p>","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":"11 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11858470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143493126","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Small Non-Coding RNA Profile of Human and Mouse Sperm. 人类和小鼠精子的非编码小RNA谱。
IF 3.6
Non-Coding RNA Pub Date : 2025-02-09 DOI: 10.3390/ncrna11010015
Yoon Sing Yap, Pasquale Patrizio, Luisa Cimmino, Konstantinos Sdrimas, Aristeidis G Telonis
{"title":"The Small Non-Coding RNA Profile of Human and Mouse Sperm.","authors":"Yoon Sing Yap, Pasquale Patrizio, Luisa Cimmino, Konstantinos Sdrimas, Aristeidis G Telonis","doi":"10.3390/ncrna11010015","DOIUrl":"10.3390/ncrna11010015","url":null,"abstract":"<p><p>Small non-coding RNAs constitute a dynamic epigenetic layer in mature spermatozoa that can exert transgenerational regulatory functions. Here, we review recent advances in the field of small RNAs in spermatozoa, how their profiles change in response to lifestyle or environmental factors, and their impact on offsprings' physiology. The profile of these RNAs changes dramatically during spermatozoa maturation. The majority of intracellular small RNAs during early spermatogenesis are miRNAs and piRNAs, but, in mature spermatozoa, tRNA- and rRNA-derived fragments (tRFs and rRFs, respectively) are the predominant forms, primarily delivered from the epididymis via extracellular vesicles. Diet, exercise, and environmental exposures have a direct effect on small RNA levels in spermatozoa, and this differential abundance can reprogram the development of the embryo. Offsprings of fathers with different lifestyles can have different phenotypes, including altered metabolism or behavior. Therefore, small RNAs in spermatozoa are emerging as an important epigenetic layer in development and transgenerational inheritance.</p>","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":"11 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11858474/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143493129","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Role of microRNA in the Regulation of Differentiation and the Functionality of Osteoblasts, Osteoclasts, and Their Precursors in Osteoporosis. microRNA在骨质疏松症成骨细胞、破骨细胞及其前体分化和功能调控中的作用。
IF 3.6
Non-Coding RNA Pub Date : 2025-02-08 DOI: 10.3390/ncrna11010014
Bulat I Yalaev, Elena I Kaletnik, Yulia S Karpova, Zhanna E Belaya, Ildar R Minniakhmetov, Natalia G Mokrysheva, Rita I Khusainova
{"title":"The Role of microRNA in the Regulation of Differentiation and the Functionality of Osteoblasts, Osteoclasts, and Their Precursors in Osteoporosis.","authors":"Bulat I Yalaev, Elena I Kaletnik, Yulia S Karpova, Zhanna E Belaya, Ildar R Minniakhmetov, Natalia G Mokrysheva, Rita I Khusainova","doi":"10.3390/ncrna11010014","DOIUrl":"10.3390/ncrna11010014","url":null,"abstract":"<p><p>Osteoporosis is a complex disease that is affected by a variety of factors, including genetic and epigenetic influences. While DNA markers for osteoporosis have been identified, they do not fully explain the hereditary basis of the disease. Epigenetic factors, such as small microRNAs (miRNAs), may provide a missing link in understanding the molecular mechanisms underlying osteoporosis. miRNAs are a class of non-coding RNAs that play a role in the epigenetic regulation of gene expression. They are known to be involved in various biological processes, including bone formation and remodelling. Differential expression of miRNAs has been linked to the pathological decrease in bone mineral density associated with osteoporosis. It has been shown that an abnormal miRNA expression pattern leads to a decrease in osteoblast activity and an increase in osteoclast activity. Further research into the role of miRNAs in osteoporosis may help to better understand this disease and identify potential therapeutic targets for treatment. Based on these assumptions, the study of miRNA expression patterns in osteoblasts, osteoclasts, and their precursors under normal and osteoporotic conditions is a rapidly growing field of scientific research. Although the results of this research are still incomplete and sometimes contradictory, they require additional scientific analysis to better understand the complex mechanisms involved. The purpose of this paper is to review the current research on miRNAs specifically expressed in osteoblasts and osteoclasts under both normal and pathological conditions. We will also discuss the potential applications of these miRNAs as biomarkers for osteoporosis diagnosis and as targets for osteoporosis treatment.</p>","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":"11 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11858178/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143493127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Circulating MicroRNAs in Patients with Vulvar Squamous Cell Carcinoma and Its Precursors. 外阴鳞状细胞癌及其前体患者的循环microrna。
IF 3.6
Non-Coding RNA Pub Date : 2025-02-07 DOI: 10.3390/ncrna11010013
Julia Rymuza, Angelika Długosz, Kamil Zalewski, Artur Kowalik, Mateusz Bujko, Magdalena Kowalewska
{"title":"Circulating MicroRNAs in Patients with Vulvar Squamous Cell Carcinoma and Its Precursors.","authors":"Julia Rymuza, Angelika Długosz, Kamil Zalewski, Artur Kowalik, Mateusz Bujko, Magdalena Kowalewska","doi":"10.3390/ncrna11010013","DOIUrl":"10.3390/ncrna11010013","url":null,"abstract":"<p><p><b>Objectives</b>: Vulvar squamous cell carcinoma (VSCC) is a rare gynecologic malignancy, with most cases arising from differentiated vulvar intraepithelial neoplasia (dVIN). Approximately one-third of VSCC cases originate from high-grade squamous intraepithelial lesions (HSILs), which are associated with persistent infection by varieties of high-risk human papillomavirus (hrHPV). This study aimed to quantify the circulating microRNAs (miRNAs) in the plasma of patients with premalignant conditions (dVIN and HSILs) and VSCC using TaqMan Low-Density Arrays. <b>Methods</b>: Plasma samples were collected from 40 patients, including those treated for HSILs, dVIN, and VSCC. Quantitative real-time PCR (qRT-PCR) identified the circulating miRNAs differentially expressed in the plasma of VSCC patients compared to patients with precancerous lesions. <b>Results</b>: A total of 31 differentially expressed miRNAs (DEMs) were found to be significantly upregulated in plasma from VSCC patients compared to precancerous cases. None of the analyzed miRNAs were able to distinguish VSCC cases based on hrHPV tumor status. <b>Conclusions</b>: This study provides strong evidence that a distinct set of miRNAs can differentiate between plasma samples from VSCC patients and those with precancerous lesions. Thus, these DEMs have potential diagnostic and prognostic value. \"Predisposing\" DEMs could be developed as biomarkers to aid in the assessment of vulvar lesions, helping to exclude or confirm progression toward cancer.</p>","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":"11 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11858568/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143493116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Cleft Palate Induced by Mycophenolate Mofetil Is Associated with miR-4680-3p and let-7c-5p in Human Palate Cells. 霉酚酸酯诱导腭裂与人腭细胞中miR-4680-3p和let-7c-5p相关
IF 3.6
Non-Coding RNA Pub Date : 2025-02-06 DOI: 10.3390/ncrna11010012
Hiroki Yoshioka, Hanane Horita, Yosuke Tsukiboshi, Hisaka Kurita, Aya Ogata, Kenichi Ogata
{"title":"Cleft Palate Induced by Mycophenolate Mofetil Is Associated with <i>miR-4680-3p</i> and <i>let-7c-5p</i> in Human Palate Cells.","authors":"Hiroki Yoshioka, Hanane Horita, Yosuke Tsukiboshi, Hisaka Kurita, Aya Ogata, Kenichi Ogata","doi":"10.3390/ncrna11010012","DOIUrl":"10.3390/ncrna11010012","url":null,"abstract":"<p><p><b>Background/Objectives</b>: Cleft palate is a birth defect associated with environmental and genetic factors. Disturbance of microRNAs (miRNAs) and exposure to medicinal agents during pregnancy can cause cleft palate. Although an association between medicine-induced cleft palate and miRNAs has been suggested, it remains to be fully elucidated. This study aimed to clarify the molecular mechanism underlying mycophenolate mofetil (MPM)-induced inhibition of cell proliferation and miRNA expression in human embryonic palatal mesenchymal (HEPM) cells. <b>Methods</b>: Cell viability, apoptosis, and cell cycle-related markers were evaluated 48 h after MPM treatment. In addition, miRNA levels and expression of their downstream genes were measured, and a rescue experiment was performed using <i>miR-4680-3p</i> and/or <i>let-7c-5p</i> inhibitors. <b>Results</b>: MPM dose-dependently reduced HEPM cell viability. Additionally, MPM treatment suppressed cyclin-D1, cyclin E1, cyclin-dependent kinase (CDK)-2, and CDK6 expression in HEPM cells. Furthermore, MPM upregulated <i>miR-4680-3p</i> and <i>let-7c-5p</i> expression and downregulated the downstream genes of each miRNA. Moreover, <i>miR-4680-3p</i> and/or <i>let-7c-5p</i> inhibitors alleviated MPM-induced inhibition of cell proliferation. <b>Conclusions</b>: These results suggest that MPM-induced cleft palate is associated with <i>miR-4680-3p</i> and <i>let-7c-5p</i> expression in HEPM cells.</p>","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":"11 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11858478/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143493118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
miRNA Library Preparation Optimisation for Low-Concentration and Low-Volume Paediatric Plasma Samples. 低浓度小体积儿科血浆样品miRNA文库制备优化
IF 3.6
Non-Coding RNA Pub Date : 2025-02-05 DOI: 10.3390/ncrna11010011
Oenone Rodgers, Chris Watson, Thomas Waterfield
{"title":"miRNA Library Preparation Optimisation for Low-Concentration and Low-Volume Paediatric Plasma Samples.","authors":"Oenone Rodgers, Chris Watson, Thomas Waterfield","doi":"10.3390/ncrna11010011","DOIUrl":"10.3390/ncrna11010011","url":null,"abstract":"<p><p><b>Background:</b> Analysing circulating miRNAs in paediatric plasma is challenging due to typically low sample volumes. The QIAseq miRNA UDI Library Kit (Qiagen, Hilden, Germany) was selected as it has a proven track record with a specific protocol for plasma and serum. The protocol, however, required optimisation for use with low-volume paediatric plasma samples before generating acceptable yields in our cohort. <b>Methods:</b> The miRNeasy Serum/Plasma kit (Qiagen) and the MagMAX miRVana Total Isolation kit (ThermoFisher Scientific, Waltham, MA, USA) were assessed following the manufacturer's instructions with 100 µL and 200 µL of paediatric plasma. Libraries were prepared using the QIAseq miRNA UDI Library Kit (Qiagen). Optimisations were made for the QIAseq miRNA UDI Library Kit (Qiagen) using total RNA extracted with the miRNeasy Serum/Plasma kit (Qiagen) from 100 µL of plasma. <b>Results:</b> Prior to optimisation, both RNA extraction kits underperformed with the QIAseq miRNA UDI Library kit, producing low miRNA library yields ranging between 0 and 1.42 ng/µL. Plasma input volumes of 100 µL and 200 µL demonstrated no significant differences. Adjusting the QIAseq protocol for low RNA concentrations improved miRNA library yields, an average of 5.6 ng/µL and a maximum of 24.3 ng/µL across 92 samples. The optimised protocol showed no age or gender biases with the QIAseq kit. <b>Conclusions:</b> Failure rates in miRNA library preparations are rarely reported, making it hard to gauge whether the 8.7% failure rate observed here is typical. However, given the challenges of using low-concentration, low-volume paediatric plasma, this represents a significant improvement over previous attempts, supporting further research in the field.</p>","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":"11 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11858269/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143493124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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