Selective sorting of microRNAs into exosomes by phase-separated YBX1 condensates

Transcriptomic analysis of intracellular RNA granules and small extracellular vesicles: Unmasking their overlap in a cell model of Huntington's disease

Huntington's disease (HD) arises from the abnormal expansion of a CAG repeat in the HTT gene. The mutant CAG repeat triggers aberrant RNA-protein interactions and translates into toxic aggregate-prone polyglutamine protein. These aberrant RNA-protein ineractions also seed the formation of cytoplasmic liquid-like granules, such as stress granules. Emerging evidence demonstrates that granules formed via liquid-liquid phase separation can mature into gel-like inclusions that persist within the cell and may act as precursor to aggregates that occur in patients' tissue. Thus, deregulation of RNA granules is an important component of neurodegeneration. Interestingly, both the formation of intracellular membrane-less organelles like stress granules and the secretion of small extracellular vesicles (sEVs) increase upon stress and under disease conditions. sEVs are lipid membrane-bound particles that are secreted from all cell types and may participate in the spreading of misfolded proteins and aberrant RNA-protein complexes across the central nervous system in neurodegenerative diseases like HD. In this study, we performed a comparative transcriptomic analysis of sEVs and RNA granules in an HD model. RNA granules and sEVs were isolated from an inducible HD cell model. Both sEVs and RNA granules were isolated from induced (HD) and non-induced (control) cells and analyzed by RNA sequencing. Our comparative analysis between the transcriptomics data of HD RNA granules and sEVs showed that: (I) intracellular RNA granules and extracellular RNA vesicles share content, (II) several non-coding RNAs translocate to RNA granules, and (III) the composition of RNA granules and sEVs is affected in HD cells. Our data showing common transcripts in intracellular RNA granules and extracellular sEVs suggest that formation of RNA granules and sEV loading may be related. Moreover, we found a high abundance of lncRNAs in both control and HD samples, with several transcripts under REST regulation, highlighting their potential role in HD pathogenesis and selective incorporation into sEVs. The transcriptome cargo of RNA granules or sEVs may serve as a source for diagnostic strategies. For example, disease-specific RNA-signatures of sEVs can serve as biomarker of central nervous system diseases. Therefore, we compared our dataset to transcriptomic data from HD patient sEVs in blood. However, our data suggest that the cell-type specific signature of sEV-secreted RNAs as well as their high variability may make it difficult to detect these biomarkers in blood.

Condensate-membrane interactions shape membranes, tune cytoskeletal assembly, and localize mRNAs

Biomolecular condensates have emerged as essential subcellular compartments. Although condensates organize biochemistry without a delimiting membrane, condensates frequently interact with membrane surfaces in diverse cellular contexts. Condensates and membranes reciprocally modulate each other, inducing membrane shape changes, establishing domains of distinct lipid composition, and catalyzing reactions within condensates. Here I discuss recent advancements in our understanding of the condensate-membrane interface, with a focus on membrane shaping, lipid organization, cytoskeletal regulation, and mRNA transport. I conclude by suggesting research avenues that may uncover new functions for membrane-associated condensates, with emphasis on the understudied role of RNA in the condensate-membrane interface.

piR-RCC Suppresses Renal Cell Carcinoma Progression by Facilitating YBX-1 Cytoplasm Localization

PIWI-interacting RNAs (piRNAs), a novel category of small non-coding RNAs, are widely expressed in eukaryotes and deregulated in several pathologies, including cancer. Little is known about their function and mechanism in renal cell carcinoma (RCC) progression. Herein, a down-regulated piRNA in RCC, termed piR-hsa-28489 (designated as piR-RCC), is identified to impede RCC progression both in vivo and in vitro. Mechanistically, piR-RCC directly interacts with Y-box binding protein 1 (YBX-1), thus impeding p-AKT-mediated YBX-1 phosphorylation and its subsequent nuclear translocation. Moreover, YBX-1 coordinates the transcription of ETS homologous factor (EHF) as a repressor factor. Consequently, piR-RCC enhances EHF expression, leading to the inhibition of RCC proliferation and metastasis. Based on these, a biomimetic nanoparticle platform is constructed to achieve RCC-specific targeted delivery of piR-RCC. The nanoparticles are fabricated using a cell membrane coating derived from cancer cells and used to encapsulate and deliver piR-RCC plasmids to renal orthotopic implantation in mice, hindering RCC progression. This study illustrates piR-RCC/YBX-1/EHF signaling axis in RCC, offering a promising therapeutic avenue for RCC.

Extracellular Vesicles in the Crosstalk of Autophagy and Apoptosis: A Role for Lipid Rafts

Autophagy and apoptosis are two essential mechanisms regulating cell fate. Although distinct, their signaling pathways are closely interconnected through various crosstalk mechanisms. Lipid rafts are described to act as both physical and functional platforms during the early stages of autophagic and apoptotic processes. Only recently has a role for lipid raft-associated molecules in regulating EV biogenesis and release begun to emerge. In particular, lipids of EV membranes are essential components in conferring stability to these vesicles in different extracellular environments and/or to facilitate binding or uptake into recipient cells. In this review we highlight these aspects, focusing on the role of lipid molecules during apoptosis and secretory autophagy pathways. We describe the molecular machinery that connects autophagy and apoptosis with vesicular trafficking and lipid metabolism during the release of EVs, and how their alterations contribute to the development of various diseases, including autoimmune disorders and cancer. Overall, these findings emphasize the complexity of autophagy/apoptosis crosstalk and its key role in cellular dynamics, supporting the role of lipid rafts as new therapeutic targets.

Exosome-based immunotherapy in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a significant global health concern and ranks as the third leading cause of cancer-associated mortality. Systemic therapy faces the emergence of resistance, which hinders the clinical benefits. Recent evidence suggests that exosomes, measuring between 30 and 150 nm in size, which impact the antitumor immune responses, making them a promising candidate for cancer immunotherapy. Owing to their unique physical and chemical characteristics, exosomes can be tailored and engineered for a range of therapeutic objectives. In the present review, we outline the immunomodulatory functions of exosomes in the tumor microenvironment (TME) of HCC, aiming to decipher the underlying mechanisms of exosomes in remodeling suppressive TME. Moreover, we provide detailed and intuitive resource for leveraging the potential of exosomes in immunotherapy, presenting valuable strategies to improve and optimize HCC treatment. Despite the huge therapeutic potential of exosomes, significant challenges persist, including the need for standardization in exosome production, optimization of cargo loading techniques, and the assurance of safety and effectiveness in clinical applications. Addressing these challenges may pave the way for exosome-based immunotherapy for HCC patients.

Muscle-derived small extracellular vesicles induce liver fibrosis during overtraining

The benefits of exercise for metabolic health occur in a dose-dependent manner. However, the adverse effects of overtraining and their underlying mechanisms remain unclear. Here, we show that overtraining induces hepatic fibrosis. Mechanistically, we find that excessive lactate accumulation in skeletal muscle leads to the lactylation of SH3 domain-containing 3 (SORBS3), triggering its liquid-liquid phase separation (LLPS). LLPS of SORBS3 enhances its interaction with flotillin 1 and selectively facilitates the sorting of F-box protein 2 (FBXO2) into small extracellular vesicles, referred to as "lactate bodies." Lactate bodies induce hepatocyte apoptosis followed by hepatic stellate cell activation via myeloid cell leukemia sequence 1 (MCL1)-BAX/BAK signaling. Inhibition of SORBS3 lactylation or FBXO2 disrupts lactate bodies formation and alleviates overtraining-triggered liver fibrosis. Likewise, reduction of muscle lactate bodies formation by salidroside attenuates overtraining-induced liver fibrosis. Collectively, we identify a process by which overtraining induces hepatic fibrosis, highlighting a potential therapeutic target for liver health.

N4-Acetylcytidine-Mediated CD2BP2-DT Drives YBX1 Phase Separation to Stabilize CDK1 and Promote Breast Cancer Progression

Long noncoding RNAs (lncRNAs) play critical roles in the initiation and progression of breast cancer. However, the specific mechanisms and biological functions of lncRNAs in breast cancer remain incompletely understood. Bioinformatics analysis identifies a novel lncRNA, CD2BP2-DT, that is overexpressed in breast cancer and correlates with adverse clinicopathological features and poor overall survival. Both in vivo and in vitro experiments demonstrate that CD2BP2-DT promotes proliferation of breast cancer cells. Mechanistically, NAT10 mediates the N4-acetylcytidine (ac4C) modification of CD2BP2-DT, enhancing its RNA stability and expression. More importantly, CD2BP2-DT enhances the stability of CDK1 mRNA by mediating YBX1 phase separation, thereby promoting the proliferation of breast cancer cells. In conclusion, the lncRNA CD2BP2-DT is identified as a crucial driver of breast cancer cell proliferation through the YBX1/CDK1 axis, highlighting its potential as a promising biomarker and therapeutic target for breast cancer.

Small extracellular vesicles: crucial mediators for prostate cancer

Small extracellular vesicles (sEVs) play a critical role in the progression, diagnosis, and treatment of prostate cancer (PCa), particularly within the tumor microenvironment (TME). Acting as novel biomarkers and agents for targeted biological therapy, sEVs contribute significantly to improving patient survival. These vesicles transport a variety of biomolecules, including proteins, nucleic acids, and lipids, which are instrumental in remodeling the TME, facilitating intercellular communication, and influencing key processes such as tumor growth, metastasis, and therapy resistance. A thorough understanding of sEV heterogeneity, including their biogenesis, characteristics, and potential applications, is essential. Recent advances have illuminated the origins, formation processes, and molecular cargo of PCa-derived sEVs (PCa-sEVs), enhancing our understanding of their role in disease progression. Furthermore, sEVs show promise as diagnostic markers, with potential applications in early detection and prognostic assessment in PCa. Therapeutically, natural and engineered sEVs offer versatile applications, including drug delivery, gene therapy, and immunomodulation, underscoring their potential in PCa management. This review delves into the substantial potential of sEVs in clinical practices for PCa.

p62 sorts Lupus La and selected microRNAs into breast cancer-derived exosomes

Exosomes are multivesicular body-derived extracellular vesicles that are secreted by metazoan cells. Exosomes have utility as disease biomarkers, and exosome-mediated miRNA secretion has been proposed to facilitate tumor growth and metastasis. Previously, we demonstrated that the Lupus La protein (La) mediates the selective incorporation of miR-122 into metastatic breast cancer-derived exosomes; however, the mechanism by which La itself is sorted into exosomes remains unknown. Using unbiased proximity labeling proteomics, biochemical fractionation, superresolution microscopy and genetic tools, we establish that the selective autophagy receptor p62 sorts La and miR-122 into exosomes. We then performed small RNA sequencing and found that p62 depletion reduces the exosomal secretion of tumor suppressor miRNAs and results in their accumulation within cells. Our data indicate that p62 is a quality control factor that modulates the miRNA composition of exosomes. Cancer cells may exploit p62-dependent exosome cargo sorting to eliminate tumor suppressor miRNAs and thus to promote cell proliferation.

When Extracellular Vesicles Go Viral: A Bird's Eye View

The science of extracellular vesicles (EVs) is a rapidly growing field that spans multiple aspects of normal physiology and pathophysiology. EVs play a critical role in most basic biological processes of cell-cell communications under normal conditions and in disease. EVs have "gone viral" not only in terms of research popularity, but also in our realization that they exhibit an elaborate crosstalk with viruses, particularly with the enveloped ones, which are also extracellular vesicles that are released by cells as a part of their virulence cycle yet are replicative. Here, we highlight some of the complexities underlying EV-virus crosstalk and pathways and provide our insights on key challenges from the viewpoint of EV biology.

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.

The role of exosomal non-coding RNAs in the breast cancer tumor microenvironment

The leading form of cancer affecting females globally is breast cancer, characterized by an unregulated growth of cells within the breast. Therefore, examining breast tissue is crucial in accurately identifying and treating this disease. Exosomes are very small enclosures bounded by a layer of cells and produced by a variety of cells present in the cancerous tissue surroundings. They play a crucial role in several biological functions in cancerous tumors. These exosomes carry non-coding RNAs (ncRNAs) and are discharged into the TME, where they are instrumental in the development and advancement of tumors. Additionally, the ncRNAs enclosed in exosomes act as significant mediators of communication within cells. Consequently, there is limited comprehension regarding the precise roles and targets of exosomal RNA in regulation, as research in this area is still in its preliminary phases. This piece provides a comprehensive overview of the latest studies on exosomes, delving into their impact on the behavior of cancer cells and immune cells. Moreover, it presents a compilation of the diverse forms of non-coding RNA molecules found in exosomes released by both cancerous and supportive cells, including circular RNAs, microRNAs, and long non-coding RNAs. Current research has proven the noteworthy influence that non-coding RNA molecules have on the progression, proliferation, drug resistance, and immune responses of breast cancer cells.

Strontium-Alix interaction enhances exosomal miRNA selectively loading in synovial MSCs for temporomandibular joint osteoarthritis treatment

The ambiguity of etiology makes temporomandibular joint osteoarthritis (TMJOA) "difficult-to-treat". Emerging evidence underscores the therapeutic promise of exosomes in osteoarthritis management. Nonetheless, challenges such as low yields and insignificant efficacy of current exosome therapies necessitate significant advances. Addressing lower strontium (Sr) levels in arthritic synovial microenvironment, we studied the effect of Sr element on exosomes and miRNA selectively loading in synovial mesenchymal stem cells (SMSCs). Here, we developed an optimized system that boosts the yield of SMSC-derived exosomes (SMSC-EXOs) and improves their miRNA profiles with an elevated proportion of beneficial miRNAs, while reducing harmful ones by pretreating SMSCs with Sr. Compared to untreated SMSC-EXOs, Sr-pretreated SMSC-derived exosomes (Sr-SMSC-EXOs) demonstrated superior therapeutic efficacy by mitigating chondrocyte ferroptosis and reducing osteoclast-mediated joint pain in TMJOA. Our results illustrate Alix's crucial role in Sr-triggered miRNA loading, identifying miR-143-3p as a key anti-TMJOA exosomal component. Interestingly, this system is specifically oriented towards synovium-derived stem cells. The insight into trace element-driven, site-specific miRNA selectively loading in SMSC-EXOs proposes a promising therapeutic enhancement strategy for TMJOA.

Posttranscriptional Control of Neural Progenitors Temporal Dynamics During Neocortical Development by Syncrip

The development of the mammalian neocortex is precisely regulated by temporal gene expression, yet the temporal regulatory mechanisms of cortical neurogenesis, particularly how radial glial cells (RGCs) sequentially generate deep to superficial neurons, remain unclear. Here, the hnRNP family member Syncrip (hnRNP Q) is identified as a key modulator of superficial neuronal differentiation in neocortical neurogenesis. Syncrip knockout in RGCs disrupts differentiation and abnormal neuronal localization, ultimately resulting in superficial cortical layer defects as well as learning and memory impairments in mice. Single-cell RNA sequencing analysis demonstrated that the knockout of Syncrip disrupts the late-stage neurogenesis, stalling transcriptional progression in RGCs. Mechanistically, Syncrip maintains the transcription of temporal process-related transcription factors by recruiting stabilization complexes through phase separation, crucially regulating the Notch signaling pathway that determines the fate of RGCs. Furthermore, pathogenic human mutations in Syncrip weaken its phase-separation capability, failing to form stable complexes normally. Thus, Syncrip acts as a mediator of posttranscriptional regulatory mechanisms, governing the fate progression of RGCs and the advancement of intrinsic temporal programs. This study establishes an intracellular mechanism for posttranscriptional regulation of progressive fate determination in cortical neurogenesis.

Arginine demethylation of Serine/Arginine-rich splicing factor 1 enhances miRNA enrichment in small extracellular vesicles derived from pancreatic ductal adenocarcinoma cells

Small extracellular vesicles (sEVs) are enriched in certain miRNAs, impacting the progression of pancreatic ductal adenocarcinoma (PDAC). The mechanisms involved in the selective sEV miRNA enrichment remain to be elucidated. We recently reported that Serine/Arginine-rich splicing factor 1 (SRSF1) regulates selective sEV miRNA enrichment in PDAC cells. SRSF1 is an onco-protein that is overexpressed in PDAC, and its function is dictated by posttranslational modifications such as phosphorylation and arginine methylation. The objective of this study was to examine the role of phosphorylation and arginine methylation in SRSF1-mediated sEV miRNA enrichment in PDAC cells. Treatment of PDAC cells with the protein arginine methyltransferase inhibitors AMI-5 and EPZ015666, but not with the phosphorylation inhibitor SRPIN340, selectively enhanced the level of sEV miR-1246, a miRNA known to be highly enriched in PDAC sEVs. Consistently, overexpression of the mutant SRSF1 with the three arginine residues R93, R97, and R109 being replaced with lysinaugmented sEV miR-1246 levels in both wild-type and SRSF1-knockdown PANC-1 cells. Interestingly, the binding of SRSF1 to miR-1246 was significantly reduced in PDAC cells overexpressing the mutant SRSF1, which was further confirmed using purified wild-type and the mutant SRSF1 proteins. We demonstrate that arginine demethylation of SRSF1 reduces SRSF1-miRNA binding in PDAC cells and enhances selective sEV miRNA enrichment, providing novel insight into SRSF1-mediated sEV miRNA enrichment in PDAC cells and opening up new avenues of investigation on the biology and function of extracellular vesicles in PDAC.

DeepMiRBP: a hybrid model for predicting microRNA-protein interactions based on transfer learning and cosine similarity

BACKGROUND

Interactions between microRNAs and RNA-binding proteins are crucial for microRNA-mediated gene regulation and sorting. Despite their significance, the molecular mechanisms governing these interactions remain underexplored, apart from sequence motifs identified on microRNAs. To date, only a limited number of microRNA-binding proteins have been confirmed, typically through labor-intensive experimental procedures. Advanced bioinformatics tools are urgently needed to facilitate this research.

METHODS

We present DeepMiRBP, a novel hybrid deep learning model specifically designed to predict microRNA-binding proteins by modeling molecular interactions. This innovation approach is the first to target the direct interactions between small RNAs and proteins. DeepMiRBP consists of two main components. The first component employs bidirectional long short-term memory (Bi-LSTM) neural networks to capture sequential dependencies and context within RNA sequences, attention mechanisms to enhance the model's focus on the most relevant features and transfer learning to apply knowledge gained from a large dataset of RNA-protein binding sites to the specific task of predicting microRNA-protein interactions. Cosine similarity is applied to assess RNA similarities. The second component utilizes Convolutional Neural Networks (CNNs) to process the spatial data inherent in protein structures based on Position-Specific Scoring Matrices (PSSM) and contact maps to generate detailed and accurate representations of potential microRNA-binding sites and assess protein similarities.

RESULTS

DeepMiRBP achieved a prediction accuracy of 87.4% during training and 85.4% using testing, with an F score of 0.860. Additionally, we validated our method using three case studies, focusing on microRNAs such as miR-451, -19b, -23a, -21, -223, and -let-7d. DeepMiRBP successfully predicted known miRNA interactions with recently discovered RNA-binding proteins, including AGO, YBX1, and FXR2, identified in various exosomes.

CONCLUSIONS

Our proposed DeepMiRBP strategy represents the first of its kind designed for microRNA-protein interaction prediction. Its promising performance underscores the model's potential to uncover novel interactions critical for small RNA sorting and packaging, as well as to infer new RNA transporter proteins. The methodologies and insights from DeepMiRBP offer a scalable template for future small RNA research, from mechanistic discovery to modeling disease-related cell-to-cell communication, emphasizing its adaptability and potential for developing novel small RNA-centric therapeutic interventions and personalized medicine.

Implications of intrinsic disorder and functional proteomics in the merkel cell polyomavirus life cycle

Infection with merkel cell polyomavirus (MCPyV) is implicated in the development of merkel cell carcinoma (MCC), a rare but aggressive skin cancer. MCC has a mortality rate near 50%, and incidence has been rapidly increasing in recent decades, making development of improved treatment strategies critical to addressing its growing social burden. The parallel increasing necessity for novel research to better understand MCPyV pathogenesis has prompted numerous studies in recent years, yet the role of intrinsic disorder in MCPyV proteins remains unexplored. This study carries out computational characterization of intrinsic disorder within the MCPyV proteome and suggests mechanisms that may contribute to the oncogenicity of the virus to invade and hijack host immune systems. Our analysis finds that significant levels of intrinsic disorder are present in proteins LT, ALTO, 57kT, and VP1, and suggests that regions of sT may also contain large, disordered regions. The investigation further shows correlation of disorder propensity with the outputs for functional predictors of eukaryotic linear motifs (ELMs), molecular recognition features (MoRFs), and propensity for liquid-liquid phase separation (LLPS). Our findings indicate that MCPyV may use disorder and phase condensation to alter viral function that may accentuate or provide the basis for oncogenic activities. It is intended that this study will inform future experimental validation efforts around the phase separation capacity of MCPyV and its host protein-protein interactions. Furthermore, we hope to inform other investigators on the potential role of disorder in the MCPyV life cycle toward ultimately progressing the development of novel therapeutic agents.

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.

Nanocarriers for intracellular delivery of proteins in biomedical applications: strategies and recent advances

Protein drugs are of great importance in maintaining the normal functioning of living organisms. Indeed, they have been instrumental in combating tumors and genetic diseases for decades. Among these pharmaceutical agents, those that target intracellular components necessitate the use of therapeutic proteins to exert their effects within the targeted cells. However, the use of protein drugs is limited by their short half-life and potential adverse effects in the physiological environment. The advent of nanoparticles offers a promising avenue for prolonging the half-life of protein drugs. This is achieved by encapsulating proteins, thereby safeguarding their biological activity and ensuring precise delivery into cells. This nanomaterial-based intracellular protein drug delivery system mitigates the rapid hydrolysis and unwarranted diffusion of proteins, thereby minimizing potential side effects and circumventing the limitations inherent in traditional techniques like electroporation. This review examines established protein drug delivery systems, including those based on polymers, liposomes, and protein nanoparticles. We delve into the operational principles and transport mechanisms of nanocarriers, discussing the various considerations essential for designing cutting-edge delivery platforms. Additionally, we investigate innovative designs and applications of traditional cytosolic protein delivery systems in medical research and clinical practice, particularly in areas like tumor treatment, gene editing and fluorescence imaging. This review sheds light on the current restrictions of protein delivery systems and anticipates future research avenues, aiming to foster the continued advancement in this field.

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.

The impact of exosomes on bone health: A focus on osteoporosis

Osteoporosis is a widespread chronic condition. Although standard treatments are generally effective, they are frequently constrained by side effects and the risk of developing drug resistance. A promising area of research is the investigation of extracellular vesicles (EVs), including exosomes, microvesicles, and apoptotic bodies, which play a crucial role in bone metabolism. Exosomes, in particular, have shown significant potential in both the diagnosis and treatment of osteoporosis. EVs derived from osteoclasts, osteoblasts, mesenchymal stem cells, and other sources can influence bone metabolism, while exosomes from inflammatory and tumor cells may exacerbate bone loss, highlighting their dual role in osteoporosis pathology. This review offers a comprehensive overview of EV biogenesis, composition, and function in osteoporosis, focusing on their diagnostic and therapeutic potential. We examine the roles of various types of EVs and their cargo-proteins, RNAs, and lipids-in bone metabolism. Additionally, we explore the emerging applications of EVs as biomarkers and therapeutic agents, emphasizing the need for further research to address current challenges and enhance EV-based strategies for managing osteoporosis.

Fluorogenic RNA-based biomaterials for imaging and tracking the cargo of extracellular vesicles

Extracellular vesicles (EVs), or exosomes, play important roles in physiological and pathological cellular communication and have gained substantial traction as biological drug carriers. EVs contain both short and long non-coding RNAs that regulate gene expression and epigenetic processes. To fully capitalize on the potential of EVs as drug carriers, it is important to study and understand the intricacies of EV function and EV RNA-based communication. Here we developed a genetically encodable RNA-based biomaterial, termed EXO-Probe, for tracking EV RNAs. The EXO-Probe comprises an EV-loading RNA sequence (EXO-Code), fused to a fluorogenic RNA Mango aptamer for RNA imaging. This fusion construct allowed the visualization and tracking of EV RNA and colocalization with markers of multivesicular bodies; imaging RNA within EVs, and non-destructive quantification of EVs. Overall, the new RNA-based biomaterial provides a useful and versatile means to interrogate the role of EVs in cellular communication via RNA trafficking to EVs and to study cellular sorting decisions. The system will also help lay the foundation to further improve the therapeutic efficacy of EVs as drug carriers.

Phosphorylation-regulated phase separation of syndecan-4 and syntenin promotes the biogenesis of exosomes

The biogenesis of exosomes that mediate cell-to-cell communication by transporting numerous biomolecules to neighbouring cells is an essential cellular process. The interaction between the transmembrane protein syndecan-4 (SDC4) and cytosolic protein syntenin plays a key role in the biogenesis of exosomes. However, how the relatively weak binding of syntenin to SDC4 efficiently enables syntenin sorting for packaging into exosomes remains unclear. Here, we demonstrate for the first time that SDC4 can undergo liquid-liquid phase separation (LLPS) to form condensates both in vitro and in the cell membrane and that, the SDC4 cytoplasmic domain (SDC4-CD) is a key contributor to this process. The phase separation of SDC4 greatly enhances the recruitment of syntenin to the plasma membrane (PM) despite the weak SDC4-syntenin interaction, facilitating syntenin sorting for inclusion in exosomes. Interestingly, phosphorylation at the only serine (179) in the SDC4-CD (Ser179) disrupts SDC4 LLPS, and inhibited phosphorylation or dephosphorylation restores the SDC4 LLPS to promote its recruitment of syntenin to the PM and syntenin inclusion into exosomes. This research reveals a novel phosphorylation-regulated phase separation property of SDC4 in the PM through which SDC4 efficiently recruits cytosolic syntenin and facilitates the biogenesis of exosomes, providing potential intervention targets for exosome-mediated biomedical events.

The role of liquid-liquid phase separation in defining cancer EMT

Cancer EMT is a pivotal process that drives carcinogenesis, metastasis, and cancer recurrence, with its initiation and regulation intricately governed by biochemical pathways in a precise spatiotemporal manner. Recently, the membrane-less biomolecular condensates formed via liquid-liquid phase separation (LLPS) have emerged as a universal mechanism underlying the spatiotemporal collaboration of biological activities in cancer EMT. In this review, we first elucidate the current understanding of LLPS formation and its cellular functions, followed by an overview of valuable tools for investigating LLPS. Secondly, we examine in detail the LLPS-mediated biological processes crucial for the initiation and regulation of cancer EMT. Lastly, we address current challenges in advancing LLPS research and explore the potential modulation of LLPS using therapeutic agents.

Extracellular Vesicles as Drug Delivery System for Cancer Therapy

In recent decades, the pursuit of drug delivery systems has led to the development of numerous synthetic options aimed at enhancing drug efficacy while minimizing side effects. However, the practical application of these systems is often hindered by challenges such as inefficiency, cytotoxicity, and immunogenicity. Extracellular vesicles, natural carriers for drugs, emerge as promising alternatives with distinct advantages over synthetic carriers. Notably, EVs exhibit biocompatibility, low immunogenicity, and inherent tissue-targeting capabilities, thus opening new avenues for drug delivery strategies. This review provides an overview of EVs, including their biogenesis and absorption mechanisms. Additionally, we explore the current research efforts focusing on harnessing their potential as drug carriers, encompassing aspects such as purification techniques, drug loading, and bioengineering for targeted delivery. Finally, we discuss the existing challenges and future prospects of EVs as therapeutic agents in clinical settings. This comprehensive analysis aims to shed light on the potential of EVs as versatile and effective tools for drug delivery, particularly in the realm of cancer therapy.

Exosome theranostics: Comparative analysis of P body and exosome proteins and their mutations for clinical applications

Exosomes are lipid-bilayered vesicles, originating from early endosomes that capture cellular proteins and genetic materials to form multi-vesicular bodies. These exosomes are secreted into extracellular fluids such as cerebrospinal fluid, blood, urine, and cell culture supernatants. They play a key role in intercellular communication by carrying active molecules like lipids, cytokines, growth factors, metabolites, proteins, and RNAs. Recently, the potential of exosomal delivery for therapeutic purposes has been explored due to their low immunogenicity, nano-scale size, and ability to cross cellular barriers. This review comprehensively examines the biogenesis of exosomes, their isolation techniques, and their diverse applications in theranostics. We delve into the mechanisms and methods for loading exosomes with mRNA, miRNA, proteins, and drugs, highlighting their transformative role in delivering therapeutic payloads. Additionally, the utility of exosomes in stem cell therapy is discussed, showcasing their potential in regenerative medicine. Insights into exosome cargo using pre- or post-loading techniques are critical for exosome theranostics. We review exosome databases such as ExoCarta, Expedia, and ExoBCD, which document exosome cargo. From these databases, we identified 25 proteins common to both exosomes and P-bodies, known for mutations in the COSMIC database. Exosome databases do not integrate with mutation analysis programs; hence, we performed mutation analysis using additional databases. Accounting for the mutation status of parental cells and exosomal cargo is crucial in exosome theranostics. This review provides a comprehensive report on exosome databases, proteins common to exosomes and P-bodies, and their mutation analysis, along with the latest studies on exosome-engineered theranostics.

Fundamental Aspects of Phase-Separated Biomolecular Condensates

Biomolecular condensates, formed through phase separation, are upending our understanding in much of molecular, cell, and developmental biology. There is an urgent need to elucidate the physicochemical foundations of the behaviors and properties of biomolecular condensates. Here we aim to fill this need by writing a comprehensive, critical, and accessible review on the fundamental aspects of phase-separated biomolecular condensates. We introduce the relevant theoretical background, present the theoretical basis for the computation and experimental measurement of condensate properties, and give mechanistic interpretations of condensate behaviors and properties in terms of interactions at the molecular and residue levels.

High-throughput and proteome-wide discovery of endogenous biomolecular condensates

Phase separation inside mammalian cells regulates the formation of the biomolecular condensates that are related to gene expression, signalling, development and disease. However, a large population of endogenous condensates and their candidate phase-separating proteins have yet to be discovered in a quantitative and high-throughput manner. Here we demonstrate that endogenously expressed biomolecular condensates can be identified across a cell's proteome by sorting proteins across varying oligomeric states. We employ volumetric compression to modulate the concentrations of intracellular proteins and the degree of crowdedness, which are physical regulators of cellular biomolecular condensates. The changes in degree of the partition of proteins into condensates or phase separation led to varying oligomeric states of the proteins, which can be detected by coupling density gradient ultracentrifugation and quantitative mass spectrometry. In total, we identified 1,518 endogenous condensate proteins, of which 538 have not been reported before. Furthermore, we demonstrate that our strategy can identify condensate proteins that respond to specific biological processes.

Bubbling beyond the barrier: exosomal RNA as a vehicle for soma-germline communication

'Weismann's barrier' has restricted theories of heredity to the transmission of genomic variation for the better part of a century. However, the discovery and elucidation of epigenetic mechanisms of gene regulation such as DNA methylation and histone modifications has renewed interest in studies on the inheritance of acquired traits and given them mechanistic plausibility. Although it is now clear that these mechanisms allow many environmentally acquired traits to be transmitted to the offspring, how phenotypic information is communicated from the body to its gametes has remained a mystery. Here, we discuss recent evidence that such communication is mediated by somatic RNAs that travel inside extracellular vesicles to the gametes where they reprogram the offspring epigenome and phenotype. How gametes learn about bodily changes has implications not only for the clinic, but also for evolutionary theory by bringing together intra- and intergenerational mechanisms of phenotypic plasticity and adaptation.

Autophagy in hepatic progenitor cells modulates exosomal miRNAs to inhibit liver fibrosis in schistosomiasis

Schistosoma infection is one of the major causes of liver fibrosis. Emerging roles of hepatic progenitor cells (HPCs) in the pathogenesis of liver fibrosis have been identified. Nevertheless, the precise mechanism underlying the role of HPCs in liver fibrosis in schistosomiasis remains unclear. This study examined how autophagy in HPCs affects schistosomiasis-induced liver fibrosis by modulating exosomal miRNAs. The activation of HPCs was verified by immunohistochemistry (IHC) and immunofluorescence (IF) staining in fibrotic liver from patients and mice with Schistosoma japonicum infection. By coculturing HPCs with hepatic stellate cells (HSCs) and assessing the autophagy level in HPCs by proteomic analysis and in vitro phenotypic assays, we found that impaired autophagy degradation in these activated HPCs was mediated by lysosomal dysfunction. Blocking autophagy by the autophagy inhibitor chloroquine (CQ) significantly diminished liver fibrosis and granuloma formation in S. japonicum-infected mice. HPC-secreted extracellular vehicles (EVs) were further isolated and studied by miRNA sequencing. miR-1306-3p, miR-493-3p, and miR-34a-5p were identified, and their distribution into EVs was inhibited due to impaired autophagy in HPCs, which contributed to suppressing HSC activation. In conclusion, we showed that the altered autophagy process upon HPC activation may prevent liver fibrosis by modulating exosomal miRNA release and inhibiting HSC activation in schistosomiasis. Targeting the autophagy degradation process may be a therapeutic strategy for liver fibrosis during Schistosoma infection.

ZO-1 interacts with YB-1 in endothelial cells to regulate stress granule formation during angiogenesis

Zonula occludens-1 (ZO-1) is involved in the regulation of cell-cell junctions between endothelial cells (ECs). Here we identify the ZO-1 protein interactome and uncover ZO-1 interactions with RNA-binding proteins that are part of stress granules (SGs). Downregulation of ZO-1 increased SG formation in response to stress and protected ECs from cellular insults. The ZO-1 interactome uncovered an association between ZO-1 and Y-box binding protein 1 (YB-1), a constituent of SGs. Arsenite treatment of ECs decreased the interaction between ZO-1 and YB-1, and drove SG assembly. YB-1 expression is essential for SG formation and for the cytoprotective effects induced by ZO-1 downregulation. In the developing retinal vascular plexus of newborn mice, ECs at the front of growing vessels express less ZO-1 but display more YB-1-positive granules than ECs located in the vascular plexus. Endothelial-specific deletion of ZO-1 in mice at post-natal day 7 markedly increased the presence of YB-1-positive granules in ECs of retinal blood vessels, altered tip EC morphology and vascular patterning, resulting in aberrant endothelial proliferation, and arrest in the expansion of the retinal vasculature. Our findings suggest that, through its interaction with YB-1, ZO-1 controls SG formation and the response of ECs to stress during angiogenesis.

Microglia-derived exosomes selective sorted by YB-1 alleviate nerve damage and cognitive outcome in Alzheimer's disease

BACKGROUND

Neuroinflammation is a characteristic pathological change of Alzheimer's Diseases (AD). Microglia have been reported to participate in inflammatory responses within the central nervous system. However, the mechanism of microglia released exosome (EXO) contribute to communication within AD microenvironment remains obscure.

METHODS

The interaction between microglia and AD was investigated in vitro and in vivo. RNA-binding protein immunoprecipitation (RIP) was used to investigate the mechanisms of miR-223 and YB-1. The association between microglia derived exosomal YB-1/miR-223 axis and nerve cell damage were assessed using Western blot, immunofluorescence, RT-PCR, ELISA and wound healing assay.

RESULTS

Here, we reported AD model was responsible for the M1-like (pro-inflammatory) polarization of microglia which in turn induced nerve cell damage. While M2-like (anti-inflammatory) microglia could release miR-223-enriched EXO which reduced neuroinflammation and ameliorated nerve damage in AD model in vivo and in vitro. Moreover, YB-1 directly interacted with miR-223 both in cell and EXO, and participated in microglia exosomal miR-223 loading.

CONCLUSION

These results indicate that anti-inflammatory microglia-mediated neuroprotection form inflammatory damage involves exporting miR-223 via EXO sorted by YB-1. Consequently, YB-1-mediated microglia exosomal sorting of miR-223 improved the nerve cell damage repair, representing a promising therapeutic target for AD.

Exosome, a Rising Biomarkers in Liquid Biopsy: Advances of Label-Free and Label Strategy for Diagnosis of Cancer

Cancer is commonly considered as one of the most severe diseases, posing a significant threat to human health and society due to various serious challenges. These challenges include difficulties in accurate diagnosis and a high propensity to form metastasis. Tissue biopsy remains the gold standard for diagnosing and subtyping cancer. However, concerns arise from its invasive nature and the potential risk of metastasis during these complex diagnostic procedures. Meanwhile, liquid biopsy has recently witnessed the rapid advancements with the emergence of three prominent detection biomarkers: circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and exosomes. Whereas, the very low abundance of CTCs combined with the instability of ctDNA intensify the challenges and decrease the accuracy of these two biomarkers for cancer diagnosis. While exosomes have gained widespread recognition as a promising biomarker in liquid biopsy due to their relatively low-invasive detection method, excellent biostability, rich resources, high abundance, and ability to provide valuable information about cancer. Therefore, it is crucial to systematically summarize recent advancements mainly in exosome-based detection methods for early cancer diagnosis. Specifically, this review will primarily focus on label-based and label-free strategies for detecting cancer using exosomes. We anticipate that this comprehensive analysis will enhance readers' understanding of the significance and value of exosomes in the fields of cancer diagnosis and therapy.

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.

Protein Arginine Methyltransferases in Pancreatic Ductal Adenocarcinoma: New Molecular Targets for Therapy

Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignant disease with a low 5-year overall survival rate. It is the third-leading cause of cancer-related deaths in the United States. The lack of robust therapeutics, absence of effective biomarkers for early detection, and aggressive nature of the tumor contribute to the high mortality rate of PDAC. Notably, the outcomes of recent immunotherapy and targeted therapy against PDAC remain unsatisfactory, indicating the need for novel therapeutic strategies. One of the newly described molecular features of PDAC is the altered expression of protein arginine methyltransferases (PRMTs). PRMTs are a group of enzymes known to methylate arginine residues in both histone and non-histone proteins, thereby mediating cellular homeostasis in biological systems. Some of the PRMT enzymes are known to be overexpressed in PDAC that promotes tumor progression and chemo-resistance via regulating gene transcription, cellular metabolic processes, RNA metabolism, and epithelial mesenchymal transition (EMT). Small-molecule inhibitors of PRMTs are currently under clinical trials and can potentially become a new generation of anti-cancer drugs. This review aims to provide an overview of the current understanding of PRMTs in PDAC, focusing on their pathological roles and their potential as new therapeutic targets.

Genetically engineered loaded extracellular vesicles for drug delivery

The use of extracellular vesicles (EVs) for drug delivery is being widely explored by scientists from several research fields. To fully exploit their therapeutic potential, multiple methods for loading EVs have been developed. Although exogenous methods have been extensively utilized, in recent years the endogenous method has gained significant attention. This approach, based on parental cell genetic engineering, is suitable for loading large therapeutic biomolecules such as proteins and nucleic acids. We review the most commonly used EV loading methods and emphasize the inherent advantages of the endogenous method over the others. We also examine the most recent advances and applications of this innovative approach to inform on the diverse therapeutic opportunities that lie ahead in the field of EV-based therapies.

Exosomal non-coding RNA: A new frontier in diagnosing and treating pancreatic cancer: A review

Pancreatic cancer is the most fatal malignancy worldwide. Once diagnosed, most patients are already at an advanced stage because of their highly heterogeneous, drug-resistant, and metastatic nature and the lack of effective diagnostic markers. Recently, the study of proliferation, metastasis, and drug resistance mechanisms in pancreatic cancer and the search for useful diagnostic markers have posed significant challenges to the scientific community. Exosomes carry various biomolecules (DNA, non-coding RNAs (ncRNAs), proteins, and lipids) that mediate communication between tumors and other cells. ncRNAs can be transported through exosomes to numerous relevant receptor cells and regulate local epithelial-mesenchymal transition (EMT) in tumor tissue, proliferation, drug resistance, and the establishment of pre-metastatic ecological niches in distant organs. In summary, exosomal ncRNAs promote tumor cell proliferation, invasion, and metastasis through multiple EMT, immunosuppression, angiogenesis, and extracellular matrix remodeling pathways. Moreover, we discuss the significant therapeutic significance of exosomal ncRNAs as PC biomarkers.

Apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) promotes stress granule formation via YBX1 phosphorylation in ovarian cancer

APE1 is an essential gene involved in DNA damage repair, the redox regulation of transcriptional factors (TFs) and RNA processing. APE1 overexpression is common in cancers and correlates with poor patient survival. Stress granules (SGs) are phase-separated cytoplasmic assemblies that cells form in response to environmental stresses. Precise regulation of SGs is pivotal to cell survival, whereas their dysregulation is increasingly linked to diseases. Whether APE1 engages in modulating SG dynamics is worthy of investigation. In this study, we demonstrate that APE1 colocalizes with SGs and promotes their formation. Through phosphoproteome profiling, we discover that APE1 significantly alters the phosphorylation landscape of ovarian cancer cells, particularly the phosphoprofile of SG proteins. Notably, APE1 promotes the phosphorylation of Y-Box binding protein 1 (YBX1) at S174 and S176, leading to enhanced SG formation and cell survival. Moreover, expression of the phosphomutant YBX1 S174/176E mimicking hyperphosphorylation in APE1-knockdown cells recovered the impaired SG formation. These findings shed light on the functional importance of APE1 in SG regulation and highlight the importance of YBX1 phosphorylation in SG dynamics.

A paintbrush for delivery of nanoparticles and molecules to live cells with precise spatiotemporal control

Delivery of very small amounts of reagents to the near-field of cells with micrometer spatial precision and millisecond time resolution is currently out of reach. Here we present μkiss as a micropipette-based scheme for brushing a layer of small molecules and nanoparticles onto the live cell membrane from a subfemtoliter confined volume of a perfusion flow. We characterize our system through both experiments and modeling, and find excellent agreement. We demonstrate several applications that benefit from a controlled brush delivery, such as a direct means to quantify local and long-range membrane mobility and organization as well as dynamical probing of intercellular force signaling.

YBX1 Underwent Phase Separation into Stress Granules Stimulated by Ionizing Radiation

Stress granules (SGs) are formed through liquid-liquid phase separation (LLPS), in response to external stimuli. YBX1, an integral component of SGs, plays a crucial role in tumor progression and cellular stress response. This study aims to elucidate the mechanisms and specific biological implications of YBX1 in SG formation, along with the identification of key regions and interacting proteins. Our observations indicate that YBX1 rapidly undergoes liquid-liquid phase separation, leading to SG formation in response to 8 Gy X-ray irradiation within 1 h, with SGs reverting to their original state after 5 h. There was a potential interaction between ATXN2L and YBX1, persisting YBX1 within the SGs. Our data suggested a potential interaction between ATXN2L and YBX1, and it remained associated with YBX1 within the SGs. Furthermore, our subsequent studies demonstrate that targeting ATXN2L can diminish the recruitment of YBX1 to stress granules (SGs), consequently enhancing the radiosensitivity of HeLa cells.

RNA m5C modification upregulates E2F1 expression in a manner dependent on YBX1 phase separation and promotes tumor progression in ovarian cancer

5-Methylcytosine (m5C) is a common RNA modification that modulates gene expression at the posttranscriptional level, but the crosstalk between m5C RNA modification and biomolecule condensation, as well as transcription factor-mediated transcriptional regulation, in ovarian cancer, is poorly understood. In this study, we revealed that the RNA methyltransferase NSUN2 facilitates mRNA m5C modification and forms a positive feedback regulatory loop with the transcription factor E2F1 in ovarian cancer. Specifically, NSUN2 promotes m5C modification of E2F1 mRNA and increases its stability, and E2F1 binds to the NSUN2 promoter, subsequently reciprocally activating NSUN2 transcription. The RNA binding protein YBX1 functions as the m5C reader and is involved in NSUN2-mediated E2F1 regulation. m5C modification promotes YBX1 phase separation, which upregulates E2F1 expression. In ovarian cancer, NSUN2 and YBX1 are amplified and upregulated, and higher expression of NSUN2 and YBX1 predicts a worse prognosis for ovarian cancer patients. Moreover, E2F1 transcriptionally regulates the expression of the oncogenes MYBL2 and RAD54L, driving ovarian cancer progression. Thus, our study delineates a NSUN2-E2F1-NSUN2 loop regulated by m5C modification in a manner dependent on YBX1 phase separation, and this previously unidentified pathway could be a promising target for ovarian cancer treatment.

HuR-miRNA complex activates RAS GTPase RalA to facilitate endosome targeting and extracellular export of miRNAs

Extracellular vesicles-mediated exchange of miRNA cargos between diverse types of mammalian cells is a major mechanism of controlling cellular miRNA levels and activity, thus regulating the expression of miRNA-target genes in both donor and recipient cells. Despite tremendous excitement related to extracellular vesicles-associated miRNAs as biomarkers or having therapeutic potential, the mechanism of selective packaging of miRNAs into endosomes and multivesicular bodies for subsequent extracellular export is poorly studied due to the lack of an in vitro assay system. Here, we have developed an in vitro assay with endosomes isolated from mammalian macrophage cells to follow miRNA packaging into endocytic organelles. The synthetic miRNAs, used in the assay, get imported inside the isolated endosomes during the in vitro reaction and become protected from RNase in a time- and concentration-dependent manner. The selective miRNA accumulation inside endosomes requires both ATP and GTP hydrolysis and the miRNA-binding protein HuR. The HuR-miRNA complex binds and stimulates the endosomal RalA GTPase to facilitate the import of miRNAs into endosomes and their subsequent export as part of the extracellular vesicles. The endosomal targeting of miRNAs is also very much dependent on the endosome maturation process that is controlled by Rab5 protein and ATP. In summary, we provide an in vitro method to aid in the investigation of the mechanism of miRNA packaging process for its export from mammalian macrophage cells.

How intrinsically disordered proteins order plant gene silencing

Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) possess low sequence complexity of amino acids and display non-globular tertiary structures. They can act as scaffolds, form regulatory hubs, or trigger biomolecular condensation to control diverse aspects of biology. Emerging evidence has recently implicated critical roles of IDPs and IDR-contained proteins in nuclear transcription and cytoplasmic post-transcriptional processes, among other molecular functions. We here summarize the concepts and organizing principles of IDPs. We then illustrate recent progress in understanding the roles of key IDPs in machineries that regulate transcriptional and post-transcriptional gene silencing (PTGS) in plants, aiming at highlighting new modes of action of IDPs in controlling biological processes.

Properties of biomolecular condensates defined by Activator of G-protein Signaling 3

Activator of G-protein signaling 3 (AGS3; also known as GPSM1), a receptor-independent activator of G-protein signaling, oscillates among defined subcellular compartments and biomolecular condensates (BMCs) in a regulated manner that is likely related to the functional diversity of the protein. We determined the influence of cell stress on the cellular distribution of AGS3 and core material properties of AGS3 BMCs. Cellular stress (oxidative, pHi and thermal) induced the formation of AGS3 BMCs in HeLa and COS-7 cells, as determined by fluorescent microscopy. Oxidative stress-induced AGS3 BMCs were distinct from G3BP1 stress granules and from RNA processing BMCs defined by the P-body protein Dcp1a. Immunoblots indicated that cellular stress shifted AGS3, but not the stress granule protein G3BP1 to a membrane pellet fraction following cell lysis. The stress-induced generation of AGS3 BMCs was reduced by co-expression of the signaling protein Gαi3, but not the AGS3-binding partner DVL2. Fluorescent recovery following photobleaching of individual AGS3 BMCs indicated that there are distinct diffusion kinetics and restricted fluidity for AGS3 BMCs. These data suggest that AGS3 BMCs represent a distinct class of stress granules that serve as a previously unrecognized signal processing node.

The ins-and-outs of exosome biogenesis, secretion, and internalization

Exosomes are specialized cargo delivery vesicles secreted from cells by fusion of multivesicular bodies (MVBs) with the plasma membrane (PM). While the function of exosomes during physiological and pathological events has been extensively reported, there remains a lack of understanding of the mechanisms that regulate exosome biogenesis, secretion, and internalization. Recent technological and methodological advances now provide details about MVB/exosome structure as well as the pathways of exosome biogenesis, secretion, and uptake. In this review, we outline our current understanding of these processes and highlight outstanding questions following on recent discoveries in the field.

The role and applications of extracellular vesicles in osteoporosis

Osteoporosis is a widely observed condition characterized by the systemic deterioration of bone mass and microarchitecture, which increases patient susceptibility to fragile fractures. The intricate mechanisms governing bone homeostasis are substantially impacted by extracellular vesicles (EVs), which play crucial roles in both pathological and physiological contexts. EVs derived from various sources exert distinct effects on osteoporosis. Specifically, EVs released by osteoblasts, endothelial cells, myocytes, and mesenchymal stem cells contribute to bone formation due to their unique cargo of proteins, miRNAs, and cytokines. Conversely, EVs secreted by osteoclasts and immune cells promote bone resorption and inhibit bone formation. Furthermore, the use of EVs as therapeutic modalities or biomaterials for diagnosing and managing osteoporosis is promising. Here, we review the current understanding of the impact of EVs on bone homeostasis, including the classification and biogenesis of EVs and the intricate regulatory mechanisms of EVs in osteoporosis. Furthermore, we present an overview of the latest research progress on diagnosing and treating osteoporosis by using EVs. Finally, we discuss the challenges and prospects of translational research on the use of EVs in osteoporosis.

Impact of Aging and a High-Fat Diet on Adipose-Tissue-Derived Extracellular Vesicle miRNA Profiles in Mice

BACKGROUND

Middle-aged adults have the highest obesity rates, leading to significant health complications in later years. Obesity triggers the release of altered molecules, including extracellular vesicles (EVs) from excess adipose tissue (AT), contributing to various health complications. In this study, we assessed the effects of age and a high-fat diet on AT-derived EV miRNA profiles to understand their potential roles in aging and obesity.

METHOD

C57BL/6 male mice were subjected to a normal chow diet (NCD) or a high-fat diet (HFD) for either 10-12 weeks (young mice, n = 10) or 50-61 weeks (middle-aged mice, n = 12). After evaluating metabolic characteristics, peri-gonadal white AT was isolated and cultured to obtain EVs. AT-derived EV miRNAs were profiled using a NanoString miRNA panel (n = 599).

RESULTS

Middle-aged mice exhibited obesity regardless of diet. Young mice fed an HFD showed similar metabolic traits to middle-aged mice. In the NCD group, 131 differentially expressed miRNAs (DE-miRNAs) emerged in middle-aged mice compared to young mice, including miR-21, miR-148a, and miR-29a, associated with cancer, neuro/psychological disorders, and reproductive diseases. In the HFD group, 55 DE-miRNAs were revealed in middle-aged mice compared to young mice. These miRNAs were associated with significantly suppressed IGF1R activity.

CONCLUSION

This study demonstrates the potential significant impact of miRNAs of AT EVs on aging- and obesity-related diseases.

Extracellular RNA in oncogenesis, metastasis and drug resistance

Extracellular vesicles and nanoparticles (EVPs) are now recognized as a novel form of cell-cell communication. All cells release a wide array of heterogeneous EVPs with distinct protein, lipid, and RNA content, dependent on the pathophysiological state of the donor cell. The overall cargo content in EVPs is not equivalent to cellular levels, implying a regulated pathway for selection and export. In cancer, release and uptake of EVPs within the tumour microenvironment can influence growth, proliferation, invasiveness, and immune evasion. Secreted EVPs can also have distant, systemic effects that can promote metastasis. Here, we review current knowledge of EVP biogenesis and cargo selection with a focus on the role that extracellular RNA plays in oncogenesis and metastasis. Almost all subtypes of RNA have been identified in EVPs, with miRNAs being the best characterized. We review the roles of specific miRNAs that have been detected in EVPs and that play a role in oncogenesis and metastasis.

Exosome-mediated macrophage regulation for inflammatory bowel disease repair: a potential target of gut inflammation

Inflammatory bowel disease (IBD), which includes Crohn's disease (CD) and ulcerative colitis (UC), is a complex condition without a definite cause. During IBD, immune cells such as macrophages release proinflammatory cytokines and chemokines, contributing to intestinal barrier integrity dysfunction. IBD is largely influenced by macrophages, which are classified into subtypes M1 and M2. M1 macrophages have been found to contribute to the development of IBD, whereas M2 macrophages alleviate IBD. Hence, agents that cause increased polarization of the M2 phenotype could help repair IBD. Exosomes, as ubiquitous conveyors of intercellular messages, are involved in immune responses and immune-mediated disease processes. Exosomes and their microRNA (miRNA) from healthy cells have been found to polarize macrophages to M2 to repair IBD due to their anti-inflammatory properties; however, those from inflammatory-driven cells and disease cells promote M1 macrophages to perpetuate IBD. Here, we review the biogenesis, biochemical composition, and sources of exosomes, as well as the roles of exosomes as extracellular vesicles in regulation of macrophages to repair IBD.