Role of extracellular vesicle-carried ncRNAs in the interactive 'dialogue' within the brain and beyond: emerging theranostic epigenetic modifiers in brain-derived nanoplatforms

Abstract

Proper brain function and overall health critically rely on the bidirectional communications among cells in the central nervous system and between the brain and other organs. These interactions are widely acknowledged to be facilitated by various bioactive molecules present in the extracellular space and biological fluids. Extracellular vesicles (EVs) are an important source of the human neurosecretome and have emerged as a novel mechanism for intercellular communication. They act as mediators, transferring active biomolecules between cells. The fine-tuning of intracellular trafficking processes is crucial for generating EVs, which can significantly vary in composition and content, ultimately influencing their fate and function. Increasing interest in the role of EVs in the nervous system homeostasis has spurred greater efforts to gain a deeper understanding of their biology. This review aims to provide a comprehensive comparison of brain-derived small EVs based on their epigenetic cargo, highlighting the importance of EV-encapsulated non-coding RNAs (ncRNAs) in the intercellular communication in the brain. We comprehensively summarize experimentally confirmed ncRNAs within small EVs derived from neurons, astrocytes, microglia, and oligodendrocytes across various neuropathological conditions. Finally, through in-silico analysis, we present potential targets (mRNAs and miRNAs), hub genes, and cellular pathways for these ncRNAs, representing their probable effects after delivery to recipient cells. In summary, we provide a detailed and integrated view of the epigenetic landscape of brain-derived small EVs, emphasizing the importance of ncRNAs in brain intercellular communication and pathology, while also offering prognostic insights for future research directions.

Keywords: Brain; CirRNA; Epigenetic; Exosomes; LncRNA; MiRNAs.

Fig. 1

Communications between donor and recipient cells via exosomes. EVs released from donor cells can deliver their contents to recipient cells through three main pathways, including paracrine signaling (EVs are delivered to neighboring cells in the vicinity), endocrine signaling (EVs enter the bloodstream and are transferred throughout the body), and autocrine signaling (EVs are taken up by the same donor cell that released them). In each pathway, EVs can be taken up by recipient cells through fusion (directly merging with the plasma membrane of the recipient cell, and releasing contents into the cell), classic endocytosis (engulfed by the recipient cell through formation of vesicles), or receptor-mediated endocytosis (RME). Exosome content can be highly heterogeneous, including a variety of cargos such as nucleic acids and different kinds of proteins. Figure was created using BioRender (BioRender.com) and is used with permission

Fig. 2

Different methodologies and experiments can be integrated to comprehensively characterize exosomes. The cellular origin of EVs extracted from biological fluids can be determined through bioinformatic and computational analyses, by labeling them in individual cells before release or sorting them according to unique signatures during or after extraction. The signature of cell-specific EVs can be validated in vitro in cultures of primary cells or cell lines. Figure was created using BioRender (BioRender.com) and is used with permission

Fig. 3

The role of brain-derived exosomes in the synaptic cleft. EVs, such as exosomes, exert various functions within the synaptic cleft, facilitating intercellular communication and potentially impacting synaptic function. They participate in the transmission of signaling molecules, clearance of neurotoxic proteins, modulation of neuroinflammatory responses, and regulation of synaptic development and plasticity. However, their confirmation remains elusive, as depicted by question marks in this illustration. Figure was created using BioRender (BioRender.com) and is used with permission

Fig. 4

Variability in ncRNA distribution across BDEVs. a ADEVs exhibit the greatest diversity, containing 45 confirmed miRNAs, 3 circRNAs, and 6 lncRNAs, followed by NDEVs, which contain 29 confirmed miRNAs, one circRNA, and four lncRNAs. b Among the 110 confirmed BDEV miRNAs, 34 were exclusive to ADEVs, 21 to NDEVs, and 27 to MDEVs. c Further screening of these 82 miRNAs identified 61 miRNAs enriched in BDEVs and absent in EVs from other cell types. d Next, human miRNAs and animal miRNAs with 100% sequence similarity to human miRNAs were selected, narrowing the final list to 29 miRNAs for further analysis. Eight mRNAs were commonly targeted by 17 miRNAs, with SESN3 and DCUN1D3 being the most targeted, each interacting with 12 miRNAs. Four other mRNAs were targeted by at least seven miRNAs. e PPI network analysis of all target genes identified STAT3 and CDKN1A as the most interactive hub genes. f Pathway analysis of these hub genes highlights the involvement of HIF-1, p53, and JAK-STAT signaling pathways. Further analysis of the JAK-STAT pathway PPI network confirmed STAT3 and CDKN1A as key hub genes

Fig. 5

Identification of targets of BDEV miRNAs. Common gene targets of miRNAs were predicted in a cell-specific manner, followed by PPI network and cellular pathways analysis. a In NDEVs, five miRNAs targeted 14 common genes, with Let7-c-5p interacting with all of them, while DCUN1D3 was also targeted by ADEV-derived miRNAs. b In ADEVs, six miRNAs targeted 25 common genes, with miR-17-5p interacting with all, while CLOCK and IGF2BP1 were also targeted by MDEV-derived miRNAs. c In MDEVs, six miRNAs targeted 18 common genes, with miR-129-5p interacting with 17 of them. PPI network analysis identified STAT3 as the top hub protein for NDEV miRNAs, and CCND1 emerged as the top hub protein for ADEV miRNAs. CDKN1A is among the top 10 hub proteins for both NDEV and ADEV miRNAs. For MDEVs, RBX1 was the predominant hub protein. Cellular pathways associated with the hub proteins include inflammatory-related pathways predominantly involved in NDEVs (a), glioma-related pathways in ADEVs (b), and neuronal and cytokine-related pathways in MDEVs (c)

Fig. 6

Target evaluation of lncRNAs and circRNAs in BDEVs. a A comprehensive miRNA-target prediction analysis was conducted for three selected circRNAs (circSHOC2, circOGHD, and circ_0012381) and six selected lncRNAs (CAND1.11, lncRNA-NKILA, lncRNA-ATB, lncRNA-aHIF, lncRNA-CCAT2, and lncRNA-POU3F3) with available complete sequences. Particularly, two of these miRNAs, let-7c and miR-145, are also contained in BDEVs. b PPI network was constructed for miRNAs targeted by each circRNA. For circOGHD, the top hub proteins identified are STAT3 and EEF2, with the JAK-STAT signaling pathway showing the most significant relevance. For circSHOC2, the top hub proteins are CD4 and RHOA, with the SNARE vesicular transport pathway showing notable relevance. For circ_0012381, PRKACB and IL4R are identified as key hub, with the cytokine-cytokine receptor interaction pathway showing the most significant relevance. c Common miRNA-target predictions were performed for the six selected lncRNAs. Among these, only four lncRNAs share common miRNA interactions. Notably, CAND1 and aHIF were predicted to target a significant number of 38 miRNAs, among which let-7b, miR-145, miR-190b, and miR-495 have been detected in BDEVs. PPI network constructed for miRNAs targeted by these lncRNAs reveal that EGFR, CCND1, and PIK3CA are three top hub genes. These hub genes are significantly enriched in key cellular pathways, including miRNAs in cancer, axon guidance, and the PI3K-Akt signaling pathway. Interestingly, when focusing on miRNAs involved in cancer, the same three hub proteins (EGFR, CCND1, and PIK3CA) were once again highlighted, emphasizing their crucial role in both cancer-related and neuroinflammatory regulatory networks