Review
Open Access
RNA modifications in mammals: from basic research to biotechnological application
Yihang LiYongle LiuHongyuan GuoZheng Fu

DOI:10.55092/exrna20250006

Received

27 Nov 2024

Accepted

17 Mar 2025

Published

21 Mar 2025
PDF
RNA, a crucial molecule in protein synthesis and gene expression regulation, plays an essential role in organisms. RNA modifications, acting as epigenetic marks, subtly adjust the structure, stability, and function of RNA, thereby regulating gene expression and exerting profound effects on cellular functions and organismal health. These natural modifications, together with RNA editing that alters nucleotide sequence of mRNA, constitute the epitranscriptome, which is vital for cellular metabolism. With the rapid advancement of biotechnology, RNA-based therapies and technologies have emerged as a frontier in biotech research. Various RNA drugs, including small interfering RNA (siRNA), antisense oligonucleotides (ASO), mRNA vaccines, and the small guide RNA (sgRNA) required for CRISPR gene editing, have been continuously developed. It has been widely demonstrated that RNA modifications can alter the physicochemical properties of RNA, enhance resistance to nucleases, reduce immunogenicity, and optimize in vivo functionality, leading to their extensive application in RNA-related biotechnologies. Furthermore, the variety of RNA modifications has expanded beyond natural modifications with the invention of an increasing number of artificial modifications. This review delves into the common types of RNA modifications, including base, ribose, and phosphate modifications, discussing their impact on RNA structure and how these modifications influence the biological characteristics of RNA. The current applications of these modifications in the biotechnology field are summarized, highlighting their significance in RNA-based therapies.
Article
Open Access
Influence of pre-analytical conditions on cell-free microRNA stability in blood plasma samples
Brayann Martínez PabónIvan ZaporozhchenkoMaria KonoshenkoEkaterina MurinaOlga BryzgunovaPavel Laktionov

DOI:10.55092/exrna20250005

Received

18 Nov 2024

Accepted

07 Mar 2025

Published

12 Mar 2025
PDF
Numerous preanalytical variables (sample collection, pretreatment and storage conditions, miRNA extraction, etc.) can influence miRNA detection. Understanding the various properties of miRNA, especially its stability in biofluids, is important in various types of miRNA studies, both fundamental and applied. This study aimed to evaluate the influence of plasma storage conditions and certain RNA extraction parameters on stability of endogenous miRNAs in human blood plasma. We report stability kinetics of four endogenous miRNAs (-16, -19b, -23a, -451a) and cel-miR-39 as exogenous miRNA under short and long-term incubation at different temperatures as well as the effect of long-term storage on extracellular vesicles miRNAs stability. The most stable of the endogenous ones was miRNA-23a. When studying archival samples (1–2 and 9–10 years of storage) of blood plasma from healthy donors, it was shown, that the concentrations of all endogenous miRNAs are steadily decreasing. These findings further show that endogenous miRNA levels do not remain stable during prolonged storage at −20°C. Although packaging of miRNA in extracellular vesicles stabilizes miRNA to some extent, it nevertheless the level decreases over a period of time from 6 months to 6 years. We have also evaluated the effect of the reagents used in the extraction process on miRNA recovery. The addition of guanidine isothiocyanate containing denaturation buffer alone prevented degradation of the synthetic cel-miR-39 miRNA spiked-in to blood plasma. In the presence of denaturation buffer with or without 2-mercaptoethanol the yields were higher than with just 2-mercaptoethanol or in the absence of any agents. Addition of the commercial RNA-stabilizing agent RNAlater did not result in significant retention of miRNA in plasma, but significantly worsened the efficiency of miRNA isolation. Thus, the degradation rate of miRNAs can be affected by their structure and packaging. Addition of various stabilization solutions to biofluids can affect the efficiency of miRNA extraction.
Review
Open Access
Exosomal RNAs in macrophage polarization-mediated resilience to ischemic disease
Jun HuangYujie WuHaiyi LiuYonghui YuanChenyang JingYang WangDihan Zhu

DOI:10.55092/exrna20250004

Received

29 Nov 2024

Accepted

27 Feb 2025

Published

07 Mar 2025
PDF
The polarization of macrophages towards an anti-inflammatory and/or pro-tissue repairing phenotype has shown promising potential in the treatment of ischemic diseases. Macrophages play a crucial role in promoting the growth of new blood vessels in ischemic tissue by clearing apoptotic debris caused by hypoxia, recruiting immune cells that support tissue repair, and releasing a variety of cytokines and growth factors. However, there is still a significant knowledge gap regarding the effective induction of this specific macrophage polarization. Non-coding RNAs have demonstrated promise in regulating macrophage activity, although there is a need for more efficient delivery system. Exosomes, which are cell-derived extracellular vesicles ranging from 30 nm to 200 nm in size, have emerged as promising carriers of non-coding RNAs for regulating macrophage activity. This review will discuss the important role of macrophage polarization in ischemic diseases and explore the potential of non-coding RNAs delivered by exosomes in modulating macrophage polarization.
Review
Open Access
RNA cargo in motion: the exosomal connection to head and neck cancers
Vasanth Kanth Thasma LoganathanSrisri SatishkartikShriya PattabiramAswini Suresh KumarSayantani ChattopadhyayVanshikaa KarthikeyanKruthika PrakashKirubakaran RangasamyKandasamy Nagarajan ArulJothi

DOI:10.55092/exrna20250003

Received

30 Sep 2024

Accepted

14 Feb 2025

Published

27 Feb 2025
PDF
Head and neck cancers (HNCs) are malignant tumors that differ from carcinomas in their biological behaviour and require a different diagnostic and treatment approach, especially in cancers like lung, breast, and prostate. Exosomal RNA (exRNA), particularly miRNA, mRNA, and lncRNA in blood or other body fluids through liquid biopsy, is emerging as a non-invasive biomarker for early cancer detection, prognosis, and treatment monitoring. Exosomal RNA modulates key signalling pathways like NF-κB, EGFR, PI3K/AKT/mTOR, and TP53 and contributes to the development, progression and therapeutic resistance of cancers. In this review, we focus on the roles of exosomal RNA in the growth and evolution of head and neck squamous cell carcinoma (HNSCC) as well as the emerging therapeutic strategies targeting exosomal RNA to improve clinical outcomes in HNC patients.
Article
Open Access
MicroRNA profiling as novel biomarkers for detecting gutter oil using machine learning
Jiaxin LiLin CongYuyu LiuLimin LiYujing Zhang

DOI:10.55092/exrna20250002

Received

19 Nov 2024

Accepted

17 Feb 2025

Published

21 Feb 2025
PDF
Gutter oil, a major public health concern in East Asia, is often indistinguishable from pure edible oils using conventional physical and chemical methods. In this study, we present a novel approach for detecting gutter oil using microRNAs (miRNAs) as biomarkers. We proved that miRNAs exist in edible oils and can be used to differentiate between pure and recycled oils. A combination of qRT-PCR and machine learning techniques was employed to characterize miRNA profiles across commercial vegetable oils, animal oils, and gutter oil. Specifically, the relative abundances of miR-16 and let-7a were found to be significantly different among these oils, allowing for accurate differentiation via a support vector machine (SVM) model. The results indicate that miRNAs such as miR-16 and let-7a serve as reliable biomarkers, enabling classification of gutter oil even when it complies with national standards. This research provides a feasible and effective method for detecting gutter oil, with potential implications for improving food safety and public health.
Review
Open Access
MSC-derived exosomes for small RNA delivery in disease treatment: a narrative review
Ruoyan ZhangXu Guo

DOI:10.55092/exrna20250001

Received

23 Oct 2024

Accepted

23 Dec 2024

Published

06 Feb 2025
PDF
Mesenchymal stem cells (MSCs) are known for their ability to differentiate and self-renew, playing a critical role in tissue homeostasis and repair. Despite their therapeutic potential, clinical applications of MSCs face challenges, including safety concerns and uncertain effects on tumors. In contrast, MSC-derived exosomes (MSC-EXOs) have shown comparable or superior efficacy across various diseases, primarily due to their cargo of functional RNAs and proteins. These natural nanovesicles offer a promising drug delivery platform, combining the advantages of both MSCs and exosomes. Genetic engineering approaches, such as surface modification and drug loading, further enhance their therapeutic capabilities. Small RNA drugs present novel opportunities for expanding therapeutic targets, but efficient delivery remains a significant challenge. MSC-EXOs, either natural or engineered, provide a safe and effective solution for delivering small RNA drugs, holding great promise for both research and translational applications. However, large-scale production of MSC-EXOs remains a key hurdle, and ongoing efforts focus on optimizing strategies for producing high-quality MSC-EXOs in sufficient quantities for industrial and clinical use. This review examines the role of MSC-EXOs in small RNA drug delivery, highlighting the associated challenges and potential solutions for scalable production.