Two RNA-binding proteins mediate the sorting of miR223 from mitochondria into exosomes

Unveiling the origin and functions of diagnostic circulating microRNAs in lung cancer

BACKGROUND

Circulating microRNAs (c-miRs) were shown to be effective biomarkers for lung cancer early detection. However, the understanding of c-miRs origin and their biological functions still remains elusive.

METHODS

We analysed miRNA expression in a large panel of lung cancer (LC) and hematopoietic cell lines (N = 252; CCLE database) coupled with c-miR profile of a large cohort of serum samples (N = 975), from high-risk subjects underwent annual LD-CT for 5 years. Furthermore, we examined intracellular and extracellular miR-29a-3p/223-3p expression profile in lung adenocarcinoma (LUAD) tissues, in matched serum samples and in LC and stromal cell lines. Lastly, through the modulation of expression of selected c-miRs by using mimic (OE) or antisense microRNA (KD), we explored their impact on lung cancer transcriptome and cancer and immune phenotypes.

RESULTS

Here, we investigated the origin of an extensively validated 13 c-miRs signature diagnostics for asymptomatic lung cancer (LC) in high-risk subjects (smokers, >20 packs/y; >50 y old). Overall, we found a mixed origin of these c-miRs, originating both from tumour cells and the tumour microenvironment (TME). Intriguingly, we revealed that circulating miR-29a-3p and miR-223-3p are abundantly released from LC epithelial cells and immune cells, respectively. In particular, we found that miR-223-3p triggered several lung cancer related phenotypes such as invasion, migration and tumour-promoting inflammation.

CONCLUSIONS

Our study highlights a mixed tumour epithelial and stroma-associated origin of LC c-miRs with new evidences on the multifaceted role of miR-223-3p in LC pathogenesis and immune modulation.

Therapeutic and diagnostic potential of extracellular vesicle (EV)-mediated intercellular transfer of mitochondria and mitochondrial components

Extracellular vesicles (EVs) facilitate the transfer of biological materials between cells throughout the body. Mitochondria, membrane-bound organelles present in the cytoplasm of nearly all eukaryotic cells, are vital for energy production and cellular homeostasis. Recent studies highlight the critical role of the transport of diverse mitochondrial content, such as mitochondrial DNA (mt-DNA), mitochondrial RNA (mt-RNA), mitochondrial proteins (mt-Prots), and intact mitochondria by small EVs (<200 nm) and large EVs (>200 nm) to recipient cells, where these cargos contribute to cellular and mitochondrial homeostasis. The interplay between EVs and mitochondrial components has significant implications for health, metabolic regulation, and potential as biomarkers. Despite advancements, the mechanisms governing EV-mitochondria crosstalk and the regulatory effect of mitochondrial EVs remain poorly understood. This review explores the roles of EVs and their mitochondrial cargos in health and disease, examines potential mechanisms underlying their interactions, and emphasizes the therapeutic potential of EVs for neurological and systemic conditions associated with mitochondrial dysfunction.

Cell surface RNA biology: new roles for RNA binding proteins

Much of our understanding of RNA-protein interactions, and how these interactions shape gene expression and cell state, have come from studies looking at these interactions in vitro or inside the cell. However, recent data demonstrates the presence of extracellular and cell surface-associated RNA such as glycosylated RNA (glycoRNA), suggesting an entirely new environment and cellular topology in which to study RNA-RNA binding protein (RBP) interactions. Here, we explore emerging ideas regarding the landscape of cell surface RNA and RBPs. We also discuss open questions concerning the trafficking and anchoring of RBPs to the cell surface, whether cell surface RBPs (csRBPs) directly interact with cell surface RNA, and how changes in the presentation of csRBPs may drive autoimmune responses.

Macrophage-derived exosomes in cancer: a double-edged sword with therapeutic potential

Solid cancer contains a complicated communication network between cancer cells and components in the tumor microenvironment (TME), significantly influencing the progression of cancer. Exosomes function as key carriers of signaling molecules in these communications, including the intricate signalings of tumor-associated macrophages (TAMs) on cancer cells and the TME. With their natural lipid bilayer structures and biological activity that relates to their original cell, exosomes have emerged as efficient carriers in studies on cancer therapy. Intrigued by the heterogeneity and plasticity of both macrophages and exosomes, we regard macrophage-derived exosomes in cancer as a double-edged sword. For instance, TAM-derived exosomes, educated by the TME, can promote resistance to cancer therapies, while macrophage-derived exosomes generated in vitro have shown favorable potential in cancer therapy. Here, we depict the reasons for the heterogeneity of TAM-derived exosomes, as well as the manifold roles of TAM-derived exosomes in cancer progression, metastasis, and resistance to cancer therapy. In particular, we emphasize the recent advancements of modified macrophage-derived exosomes in diverse cancer therapies, arguing that these modified exosomes are endowed with unique advantages by their macrophage origin. We outline the challenges in translating these scientific discoveries into clinical cancer therapy, aiming to provide patients with safe and effective treatments.

The cell biology of Extracellular Vesicles: A jigsaw puzzle with a myriad of pieces

Extracellular vesicle (EV) research has expanded beyond traditional boundaries, evolving into an inter-kingdom endeavor. First described over 50 years ago, EVs are now recognized as playing diverse roles in basic cellular functions, such as intercellular communication, transport, and cell migration. Their biogenesis and secretion involve complex molecular processes, with cargos that include proteins, lipids, and genetic material. Despite advances, isolation and purification methods are still developing. EVs are present in all body fluids, with different subtypes fulfilling distinct roles. Nonetheless, in biological ecosystems, vesicle diversity can be seen as a strength where each one complements the other in the dialogue between cells and tissues. The involvement of EVs in homeostasis and disease and their well-recognized potential for diagnosis and therapeutics will continue to boost investigations to reveal their fundamental biology.

Translational Regulators in Pulmonary Fibrosis: MicroRNAs, Long Non-Coding RNAs, and Transcript Modifications

Fibrosing disorders including idiopathic pulmonary fibrosis (IPF) are progressive irreversible diseases, often with poor prognoses, characterized by the accumulation of excessive scar tissue and extracellular matrix. Translational regulation has emerged as a critical aspect of gene expression control, and the dysregulation of key effectors is associated with disease pathogenesis. This review examines the current literature on translational regulators in IPF, focusing on microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and RNA transcript modifications including alternative polyadenylation and chemical modification. Some of these translational regulators potentiate fibrosis, and some of the regulators inhibit fibrosis. In IPF, some of the profibrotic regulators are upregulated, and some of the antifibrotic regulators are downregulated. Correcting these defects in IPF-associated translational regulators could be an intriguing avenue for therapeutics.

Breaking barriers in targeted Therapy: Advancing exosome Isolation, Engineering, and imaging

Exosomes have emerged as promising tools for targeted drug delivery in biomedical applications and medicine. This review delves into the scientific advancements, challenges, and future prospects specifically associated with these technologies. In this work, we trace the research milestones that led to the discovery and characterization of exosomes and extracellular vesicles, and discuss strategies for optimizing the synthetic yield and the loading of these particles with various therapeutics. In addition, we report the current major issues affecting the field and hampering the clinical translation of these technologies. Highlighting the pivotal role of imaging techniques, we explore how they drive exosome therapy and development by offering insights into biodistribution and cellular trafficking dynamics. Methodologies for vesicle isolation, characterization, loading, and delivery mechanisms are thoroughly examined, alongside strategies aimed at enhancing their therapeutic efficacy. Special emphasis was dedicated to their therapeutic properties, particularly to their ability to deliver biologics into the cytoplasm. Furthermore, we delve into the intricate balance between surface modifications and targeting properties including also transgenic methods aimed at their functionalization and visualization within biological systems. This review underscores the transformative potential of these carriers in targeted drug delivery and identifies crucial areas for further research and clinical translation.

Enzymatic tools for mitochondrial genome manipulation

Mutations in mitochondrial DNA (mtDNA) can manifest phenotypically as a wide range of neuromuscular and neurodegenerative pathologies that are currently only managed symptomatically without addressing the root cause. A promising approach is the development of molecular tools aimed at mtDNA cutting or editing. Unlike nuclear DNA, a cell can have hundreds or even thousands of mitochondrial genomes, and mutations can be present either in all of them or only in a subset. Consequently, the developed tools are aimed at reducing the number of copies of mutant mtDNA or editing mutant nucleotides. Despite some progress in the field of mitochondrial genome editing in human cells, working with model animals is still limited due to the complexity of their creation. Furthermore, not all existing editing systems can be easily adapted to function within mitochondria. In this review, we evaluate the mtDNA editing tools available today, with a particular focus on specific mtDNA mutations linked to hereditary mitochondrial diseases, aiming to provide an in-depth understanding of both the opportunities and hurdles to the development of mitochondrial genome editing technologies.

Beyond the Bubble: A Debate on microRNA Sorting Into Extracellular Vesicles

Over the past decade, a scientific field has been developed demonstrating microRNAs (miRNAs) to be actively sorted into extracellular vesicles via specific nucleotide motifs that interact with discrete RNA-binding proteins. These miRNAs are proposed to be transported into recipient cells in which they can regulate specific cellular pathways. This mechanism could have enormous potential in explaining how cells signal and regulate other cells nearby or at a distance. Tens of studies have built this theme of a regulated transport of miRNAs. However, some concerns exist about this field. Taken together, there are concerns of a lack of a consistent motif, RNA-binding protein, or preferential miRNA involved in this process. In this study, we provide an expert and extensive analysis of the field that makes the cases for and against an active sorting mechanism. We provide potential explanations on why there is a lack of agreement. Most importantly, we provide ideas on how to move this field forward with more rigor and reproducibility. It is hoped that by engaging in a scientific debate of the pros and cons of this field, more rigorous experiments can be performed to conclusively demonstrate this biological activity.

Extracellular vesicles and microRNAs in cancer progression

Extracellular vesicles (EVs) have emerged as critical mediators of intercellular communication in cancer. These membranous structures, secreted by normal and cancerous cells, carry a cargo of bioactive molecules including microRNAs (miRNAs) that modulate various cellular processes. miRNAs are small non-coding RNAs that play pivotal roles in post-transcriptional gene regulation and have been implicated in cancer initiation, progression, and metastasis. In cancer, tumor-derived EVs transport specific miRNAs to recipient cells, modulating tumorigenesis, growth, angiogenesis, and metastasis. Dysregulation of miRNA expression profiles within EVs contributes to the acquisition of cancer hallmarks that include increased proliferation, survival, and migration. EV miRNAs influence the tumor microenvironment, promoting immune evasion, remodeling the extracellular matrix, and establishing pre-metastatic niches. Understanding the complex interplay between EVs, miRNAs, and cancer holds significant promise for developing novel diagnostic and therapeutic strategies. This chapter provides insights into the role of EV-mediated miRNA signaling in cancer pathogenesis, highlighting its potential as a biomarker for cancer detection, prognosis, and treatment response assessment.

Bubble Ticket Trip: Exploring the Mechanism of miRNA Sorting into Exosomes and Maintaining the Stability of Tumor Microenvironment

Exosomes are vesicles ranging from 30 to 100 nanometers in size that show great potential as carriers for therapeutic uses and drug delivery. Enriching a specific set of miRNAs in exosomes emphasizes the existence of particular sorting mechanisms that manage the targeted cargo packaging. The molecular mechanism for miRNA sorting has not been understood. It is crucial to understand the mechanism of exosome encapsulation to develop its therapeutic potential. In this review, we will explore the particular processes through which exosomes naturally encapsulate miRNA, as well as discuss the effect on tumors after encapsulation of miRNAs. We also summarize the effects of targeted drug delivery using genetic engineering and chemical methods to modify exosome-encapsulated miRNA. Finally, gaining insight into how exosome cargo is sorted could be applied in clinical settings for precise drug delivery and to hinder the progression of diseases.

miRNA packaging into small extracellular vesicles and implications in pain

Extracellular vesicles (EVs) are a heterogenous group of lipid bilayer bound particles naturally released by cells. These vesicles are classified based on their biogenesis pathway and diameter. The overlap in size of exosomes generated from the exosomal pathway and macrovesicles that are pinched off from the surface of the plasma membrane makes it challenging to isolate pure populations. Hence, isolated vesicles that are less than 200 nm are called small extracellular vesicles (sEVs). Extracellular vesicles transport a variety of cargo molecules, and multiple mechanisms govern the packaging of cargo into sEVs. Here, we discuss the current understanding of how miRNAs are targeted into sEVs, including the role of RNA binding proteins and EXOmotif sequences present in miRNAs in sEV loading. Several studies in human pain disorders and rodent models of pain have reported alterations in sEV cargo, including miRNAs. The sorting mechanisms and target regulation of miR-939, a miRNA altered in individuals with complex regional pain syndrome, is discussed in the context of inflammation. We also provide a broad overview of the therapeutic strategies being pursued to utilize sEVs in the clinic and the work needed to further our understanding of EVs to successfully deploy sEVs as a pain therapeutic.

Extracellular Vesicle lncRNAs as Key Biomolecules for Cell-to-Cell Communication and Circulating Cancer Biomarkers

Extracellular vesicles (EVs) are secreted by almost every cell type and are considered carriers of active biomolecules, such as nucleic acids, proteins, and lipids. Their content can be uptaken and released into the cytoplasm of recipient cells, thereby inducing gene reprogramming and phenotypic changes in the acceptor cells. Whether the effects of EVs on the physiology of recipient cells are mediated by individual biomolecules or the collective outcome of the total transferred EV content is still under debate. The EV RNA content consists of several types of RNA, such as messenger RNA (mRNA), microRNA (miRNA), and long non-coding RNA (lncRNA), the latter defined as transcripts longer than 200 nucleotides that do not code for proteins but have important established biological functions. This review aims to update our insights on the functional roles of EV and their cargo non-coding RNA during cancer progression, to highlight the utility of EV RNA as novel diagnostic or prognostic biomarkers in cancer, and to tackle the technological advances and limitations for EV RNA identification, integrity assessment, and preservation of its functionality.

Exploring the roles and molecular mechanisms of RNA binding proteins in the sorting of noncoding RNAs into exosomes during tumor progression

BACKGROUND

RNA binding proteins (RBPs) play a role in sorting non-coding RNAs (ncRNAs) into exosomes. These ncRNAs, carried by exosomes, are involved in regulating various aspects of tumor progression, including metastasis, angiogenesis, control of the tumor microenvironment, and drug resistance. Recent studies have emphasized the importance of the RBP-ncRNA-exosome mechanism in tumor regulation.

AIM OF REVIEW

This comprehensive review aims to explore the RBP-ncRNA-exosome mechanism and its influence on tumor development. By understanding this intricate mechanism provides novel insights into tumor regulation and may lead to innovative treatment strategies in the future.

KEY SCIENTIFIC CONCEPTS OF REVIEW

The review discusses the formation of exosomes and the complex relationships among RBPs, ncRNAs, and exosomes. The RBP-ncRNA-exosome mechanism is shown to affect various aspects of tumor biology, including metastasis, multidrug resistance, angiogenesis, the immunosuppressive microenvironment, and tumor progression. Tumor development relies on the transmission of information between cells, with RBPs selectively mediating sorting of ncRNAs into exosomes through various mechanisms, which in turn carry ncRNAs to regulate RBPs. The review also provides an overview of potential therapeutic strategies, such as targeted drug discovery and genetic engineering for modifying therapeutic exosomes, which hold great promise for improving cancer treatment.

RNAs in tumour-derived extracellular vesicles and their significance in the tumour microenvironment

Small extracellular vesicles (sEVs) secreted by various types of cells serve as crucial mediators of intercellular communication within the complex tumour microenvironment (TME). Tumour-derived small extracellular vesicles (TDEs) are massively produced and released by tumour cells, recapitulating the specificity of their cell of origin. TDEs encapsulate a variety of RNA species, especially messenger RNAs, microRNAs, long non-coding RNAs, and circular RNAs, which release to the TME plays multifaced roles in cancer progression through mediating cell proliferation, invasion, angiogenesis, and immune evasion. sEVs act as natural delivery vehicles of RNAs and can serve as useful targets for cancer therapy. This review article provides an overview of recent studies on TDEs and their RNA cargo, with emphasis on the role of these RNAs in carcinogenesis.

Roles of Exosomal miRNAs in Asthma: Mechanisms and Applications

Asthma is a chronic inflammatory disorder of the airways, characterized by a complex interplay of genetic, environmental, and immunological factors that contribute to its onset and progression. Recent advances in researches have illuminated the critical role of exosomal microRNAs (miRNAs) in the pathogenesis and development of asthma. Exosomes are nano-sized extracellular vesicles that facilitate intercellular communication by transporting a variety of bioactive molecules, including miRNAs, and play a crucial role in regulating gene expression and immune responses, which are central to the inflammatory processes underlying asthma. Exosomal miRNAs are emerging as key players in asthma due to their involvement in various aspects of the disease, including the regulation of inflammation, airway hyperresponsiveness, and remodeling. Their ability to influence the behavior of target cells and tissues makes them valuable both as diagnostic biomarkers and as potential therapeutic targets. This review aims to provide a comprehensive overview of the biogenesis of exosomes, the functional roles of exosomal miRNAs in asthma, and their clinical potential. It will explore the mechanisms by which these miRNAs contribute to asthma pathophysiology, discuss their utility in diagnosing and monitoring the disease, and highlight ongoing research efforts to harness their therapeutic potential.

Progress in extracellular vesicle homeostasis as it relates to cardiovascular diseases

Extracellular vesicles (EVs) are involved in both physiological and pathological processes in many organ systems and are essential in mediating intercellular communication and maintaining organismal homeostasis. It is helpful to propose new strategies for disease treatment by elucidating the mechanisms of EV release and sorting. An increasing number of studies have shown that there is specific homeostasis in EVs, which is helpful for the human body to carry out physiological activities. In contrast, an EV homeostasis im-balance promotes or accelerates disease onset and development. Alternatively, regulating the quality of EVs can maintain homeostasis and even achieve the purpose of treating conditions. An analysis of the role of EV homeostasis in the onset and development of cardiovascular disease is presented in this review. This article also summarizes the methods that regulate EV homeostasis and their application in cardiovascular diseases. In particular, this study focuses on the connection between EV steady states and the cardiovascular system and the potential value of EVs in treating cardiovascular diseases.

Milk-derived exosome nanovesicles: recent progress and daunting hurdles

Raw milk is the foundation of quality and safety in the dairy industry, and improving milk source management is the fundamental guarantee. Milk-derived exosomes (MDEs) are nanoscale information transfer molecules secreted by mammary cells with unique content and high stability, which can be used not only as potential markers to analyze key traits of lactation, reproduction, nutrition and health of animals, but also help farm managers to take timely interventions to improve animal welfare, milk quality, and functional traits. Our review first outlines the latest advances in MDEs isolation and purification, compositional analysis and characterization tools. We then provide a comprehensive summary of recent applications of MDEs liquid biopsy in breed selection, disease prevention and control, and feeding management. Finally, we evaluate the impact of processing on the stability of MDEs to offer guidance for dairy production and storage. The limitations and challenges in the development and use of MDEs markers are also discussed. As a noninvasive marker with high sensitivity and specificity, the MDEs-mediated assay technology is expected to be a powerful tool for measuring cow health and raw milk quality, enabling dynamic and precise regulation of dairy cows and full traceability of raw milk.

A Group of Highly Secretory miRNAs Correlates with Lymph Node Metastasis and Poor Prognosis in Oral Squamous Cell Carcinoma

MicroRNAs (miRNAs) in oral squamous cell carcinoma (OSCC)-derived small extracellular vesicles (sEVs) play a pivotal role in modulating intercellular communications between tumor cells and other cells in the microenvironment, thereby influencing tumor progression and the efficacy of therapeutic interventions. However, a comprehensive inventory of these secretory miRNAs in sEVs and their biological and clinical implications remains elusive. This study aims to profile the miRNA content of OSCC cell line sEVs and computationally elucidate their biological and clinical relevance. We conducted miRNA sequencing to compare the miRNA profiles of OSCC cells and their corresponding sEVs. Our motif enrichment analysis identified specific sorting motifs that are implicated in either cellular retention or preferential sEV secretion. Target cell analysis suggested that the sEV miRNAs potentially interact with various immune cell types, including natural killer cells and dendritic cells. Additionally, we explored the clinical relevance of these miRNAs by correlating their expression levels with TNM stages and patient survival outcomes. Intriguingly, our findings revealed that a distinct sEV miRNA signature is associated with lymph node metastasis and poorer survival in patients in TCGA-HNSC dataset. Collectively, this research furthers our understanding of the miRNA sorting mechanisms in OSCC and underscores their clinical implications.

The effects of intracellular and exosomal ncRNAs on cancer progression

Altered gene expression as well as mislocalization of a gene's encoded product (proteins or noncoding RNAs (ncRNAs)) can lead to disease and cancer formation. Multiple studies have indicated that exosomes and their contents act as cell-to-cell communicators and play a key role in cancer progression. Moreover, exosomes contain several functional molecules, including ncRNAs. NcRNAs function as master regulators to coordinate cell growth, cell motility and drug resistance. However, intracellular ncRNAs, which can be transferred to recipient cells via exosomes (exosomal ncRNAs), mediate common/distinct downstream molecules, signaling pathways and functions that are less emphasized concepts in cancer development research. In this study, by using exosomes as a model, we comprehensively discuss the current knowledge regarding (1) the functional role of ncRNAs, both their intracellular and exosomal forms, in cancer progression, (2) the possible mechanism of ncRNA incorporation into exosomes and (3) the therapeutic applications and limitations of exosomes based on current knowledge.