Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles

MicroRNAs in Plasma-Derived Extracellular Vesicles as Non-Invasive Biomarkers for Eosinophilic Esophagitis

Eosinophilic esophagitis (EoE) is a chronic inflammatory esophageal disorder. The lack of non-invasive biomarkers currently results in dependency on endoscopy with biopsies for its diagnosis and monitoring. We aimed to identify potential non-invasive biomarkers using microRNAs (miRNAs) in plasma-derived extracellular vesicles (pEVs). This was a prospective single-center observational study of a discovery cohort of EoE patients (n = 26) with active disease (EoE.Basal) and after anti-inflammatory treatment (EoE.Post.tx) and control subjects (n = 16). Small-RNA-seq was performed to identify differentially regulated small RNAs (sRNAs). Candidate miRNAs were validated in an independent cohort (EoE patients, n = 33; controls, n = 14). The pEVs-sRNA cargo differed among conditions. Compared with controls, Ser_Comb_22, Leu_Comb_5, miR-10b-5p, and miR-125a-5p were upregulated in EoE.Basal, and miR-224-5p, miR-221-3p, let-7d-5p, and miR-191-5p were downregulated. The combination of miR-221-3p and miR-10b-5p showed the best diagnostic performance. Comparing paired EoE samples, miR-374a-5p and miR-30a-3p were upregulated in EoE.Basal, while miR-15a-5p and let-7d-5p were downregulated. Combined miR-30a-3p and miR-15a-5p showed the best AUC values, and miR-30a-3p alone was best as a monitoring biomarker (p = 0.001). In conclusion, pEVs-sRNA changed upon inflammation in EoE patients, and miR-30a-3p was proposed as a potential biomarker for monitoring the treatment. This study was the first to explore the use of pEVs as a non-invasive biomarker for EoE.

Novel Computational and Artificial Intelligence Models in Cancer Research

The ICIBM 2023 marked the 11th annual conference of its kind, with the ICIBM recently becoming the official conference of the International Association for Intelligent Biology and Medicine (IAIBM), showcasing cutting-edge advancements at the intersection of computation and biomedical research [...].

Approaches and Challenges in Characterizing the Molecular Content of Extracellular Vesicles for Biomarker Discovery

Extracellular vesicles (EVs) are lipid bilayer nanoparticles released from all known cells and are involved in cell-to-cell communication via their molecular content. EVs have been found in all tissues and body fluids, carrying a variety of biomolecules, including DNA, RNA, proteins, metabolites, and lipids, offering insights into cellular and pathophysiological conditions. Despite the emergence of EVs and their molecular contents as important biological indicators, it remains difficult to explore EV-mediated biological processes due to their small size and heterogeneity and the technical challenges in characterizing their molecular content. EV-associated small RNAs, especially microRNAs, have been extensively studied. However, other less characterized RNAs, including protein-coding mRNAs, long noncoding RNAs, circular RNAs, and tRNAs, have also been found in EVs. Furthermore, the EV-associated proteins can be used to distinguish different types of EVs. The spectrum of EV-associated RNAs, as well as proteins, may be associated with different pathophysiological conditions. Therefore, the ability to comprehensively characterize EVs' molecular content is critical for understanding their biological function and potential applications in disease diagnosis. Here, we set out to provide an overview of EV-associated RNAs and proteins as well as approaches currently being used to characterize them.

Challenges in characterization of transcriptomes of extracellular vesicles and non-vesicular extracellular RNA carriers

Since its original discovery over a decade ago, extracellular RNA (exRNA) has been found in all biological fluids. Furthermore, extracellular microRNA has been shown to be involved in communication between various cell types. Importantly, the exRNA is protected from RNases degradation by certain carriers including membrane vesicles and non-vesicular protein nanoparticles. Each type of carrier has its unique exRNA profile, which may vary depending on cell type and physiological conditions. To clarify putative mechanisms of intercellular communication mediated by exRNA, the RNA profile of each carrier has to be characterized. While current methods of biofluids fractionation are continuously improving, they fail to completely separate exRNA carriers. Likewise, most popular library preparation approaches for RNA sequencing do not allow obtaining exhaustive and unbiased data on exRNA transcriptome. In this mini review we discuss ongoing progress in the field of exRNA, with the focus on exRNA carriers, analyze the key methodological challenges and provide recommendations on how the latter could be overcome.