Abstract:Previously we reported that LIM1863 colorectal cancer (CRC) cells secrete three distinct extracellular vesicle subtypes – two subpopulations of exosomes (apical EpCAM-Exos and basolateral A33-Exos) and shed microvesicles (sMVs) – with distinct protein and miRNA signatures. Here, we extend our omics approach to understand the fundamental role of LIM1863-derived EVs by performing a comprehensive analysis of their mRNAs and long non-coding RNAs (lncRNAs) using RNA-Seq. We show that 2,389 mRNAs, 317 pseudogene tra… Show more
“…In exosomes, the two most common species were also lincRNAs and antisense RNAs, although the abundance of mRNAs was significantly reduced. It has been already shown that the distribution of long noncoding RNAs in exosomes is strongly related to the parent cell type (Chen et al 2016) and that it can be regulated by disease and by changes in the cellular environment (Hewson et al 2016;Lang et al 2017;Pan et al 2017). Exosomal lncRNAs have also been widely studied as biomarkers (Wang et al 2014;Işin et al 2015;Li et al 2015;Liu et al 2016) and it has been hypothesized that they may act as microRNA sponges to promote their export (Ahadi et al 2016).…”
Exosomes are small extracellular vesicles of around 100 nm of diameter produced by most cell types. These vesicles carry nucleic acids, proteins, lipids, and other biomolecules and function as carriers of biological information in processes of extracellular communication. The content of exosomes is regulated by the external and internal microenvironment of the parent cell, but the intrinsic mechanisms of loading of molecules into exosomes are still not completely elucidated. In this study, by the use of next-generation sequencing we have characterized in depth the RNA composition of healthy endothelial cells and exosomes and provided an accurate profile of the different coding and noncoding RNA species found per compartment. We have also discovered a set of unique genes preferentially included (or excluded) into vesicles. Moreover, after studying the enrichment of RNA motifs in the genes unequally distributed between cells and exosomes, we have detected a set of enriched sequences for several classes of RNA. In conclusion, our results provide the basis for studying the involvement of RNA-binding proteins capable of recognizing RNA sequences and their role in the export of RNAs into exosomes.
“…In exosomes, the two most common species were also lincRNAs and antisense RNAs, although the abundance of mRNAs was significantly reduced. It has been already shown that the distribution of long noncoding RNAs in exosomes is strongly related to the parent cell type (Chen et al 2016) and that it can be regulated by disease and by changes in the cellular environment (Hewson et al 2016;Lang et al 2017;Pan et al 2017). Exosomal lncRNAs have also been widely studied as biomarkers (Wang et al 2014;Işin et al 2015;Li et al 2015;Liu et al 2016) and it has been hypothesized that they may act as microRNA sponges to promote their export (Ahadi et al 2016).…”
Exosomes are small extracellular vesicles of around 100 nm of diameter produced by most cell types. These vesicles carry nucleic acids, proteins, lipids, and other biomolecules and function as carriers of biological information in processes of extracellular communication. The content of exosomes is regulated by the external and internal microenvironment of the parent cell, but the intrinsic mechanisms of loading of molecules into exosomes are still not completely elucidated. In this study, by the use of next-generation sequencing we have characterized in depth the RNA composition of healthy endothelial cells and exosomes and provided an accurate profile of the different coding and noncoding RNA species found per compartment. We have also discovered a set of unique genes preferentially included (or excluded) into vesicles. Moreover, after studying the enrichment of RNA motifs in the genes unequally distributed between cells and exosomes, we have detected a set of enriched sequences for several classes of RNA. In conclusion, our results provide the basis for studying the involvement of RNA-binding proteins capable of recognizing RNA sequences and their role in the export of RNAs into exosomes.
“…The expression level of exosomal lncRNAs varies from its donor cells (51–54). The level of the oncogenic lncRNA TUC339 is dramatically different in EV, including exosomes, compared to HCC donor cells (53).…”
“…Moreover, using RNA-Seq, Chen et al , confirmed that exosomes from LIM1863, a polarized colon carcinoma cell line with cryptic-like structure, are preferentially enriched in 2,389 mRNAs, 317 pseudogenes, 1,028 lncRNAs, and 206 short ncRNAs compared to parental LIM1863 whole cell lysates. They further classified the exosomes in apical and basolateral type and demonstrated the RNA signature differs between the two subclasses (54). …”
Neoplastic cells use various intercellular communication mechanisms in order to adapt to the local microenvironment, manipulate the immune system, and facilitate metastasis. Exosomes release is a new mechanism of cell-to-cell communication. These nanovesicles enclose various types of molecules including lipids, proteins, DNA, messenger RNA (mRNA) and non-coding RNAs [microRNA and long non-coding RNA (lncRNA)]. lncRNAs are over 200 nt long transcripts, that exhibit no coding potential, but are crucial regulators of physiological processes and are deregulated in cancer. In this review, we will discuss the role of exosomal lncRNAs in cancer, which is an incipient research field that could bring new insights to the vast domain of intercellular communication. Exosomal lncRNAs seem to be promising biomarkers for any type of cancer. The exact role of exosomal lncRNAs is not fully revealed. Several studies show that cancer derived exosomal lncRNAs are functional and can transmit to neighboring cells different phenotypic patterns, like drug resistance and increased angiogenesis. We further discuss the mechanistic function of exosomal lncRNAs, and hypothesize that the crowded exosomal content can be a suitable place of RNA species crosstalk. Finally, we assume that lncRNAs could be a loading vehicle for miRNAs, mRNAs and other complex molecules into the exosome but future studies are required to confirm these hypotheses.
“…We identified a high proportion of antisense and coding messenger RNA sequences, as well as abundant lincRNA sequences (Figure 8(a)), but a very low relative abundance of miRNAs (0.014%). The largest proportion of identified RNAs (34.4%) mapped to non-coding RNA (rfam [51]) with the most abundant species belonging to the Signal Recognition Particle RNA family, universally conserved ribonucleoprotein complexes involved in protein trafficking [52]. 10.1080/20013078.2018.1456888-F0008Figure 8.EV RNA profiles as determined by RNA sequencing.…”
Newts can regenerate amputated limbs and cardiac tissue, unlike mammals which lack broad regenerative capacity. Several signaling pathways involved in cell proliferation, differentiation and survival during newt tissue regeneration have been elucidated, however the factors that coordinate signaling between cells, as well as the conservation of these factors in other animals, are not well defined. Here we report that media conditioned by newt limb explant cells (A1 cells) protect mammalian cardiomyocytes from oxidative stress-induced apoptosis. The cytoprotective effect of A1-conditioned media was negated by exposing A1 cells to GW4869, which suppresses the generation of extracellular vesicles (EVs). A1-EVs are similar in diameter (~100–150 nm), structure, and share several membrane surface and cargo proteins with mammalian exosomes. However, isolated A1-EVs contain significantly higher levels of both RNA and protein per particle than mammalian EVs. Additionally, numerous cargo RNAs and proteins are unique to A1-EVs. Of particular note, A1-EVs contain numerous mRNAs encoding nuclear receptors, membrane ligands, as well as transcription factors. Mammalian cardiomyocytes treated with A1-EVs showed increased expression of genes in the PI3K/AKT pathway, a pivotal player in survival signaling. We conclude that newt cells secrete EVs with diverse, distinctive RNA and protein contents. Despite ~300 million years of evolutionary divergence between newts and mammals, newt EVs confer cytoprotective effects on mammalian cardiomyocytes.
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