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Comparative transcriptomic analysis of human and Drosophila extracellular vesicles reveals extensive conservation

ABSTRACT: Extracellular vesicles (EVs) are membrane-enclosed nanoparticles containing specific repertoires of genetic material. In mammals, EVs can mediate the horizontal transfer of various cargos and signaling molecules, notably miRNA and mRNA species. Whether this form of intercellular communication prevails in other metazoans remains unclear. Here, we report the first parallel comparative morphologic and transcriptomic characterization of EVs from Drosophila and human cellular models. Electronic microscopy revealed that Drosophila, like human cells release exosome-like EVs with diameter ranging from 30 to 200 nm, which contain complex populations of transcripts. RNA-seq identified abundant ribosomal RNA pseudogenes and retrotransposons in human and Drosophila EVs. Vault RNAs and Y RNAs abounded in human samples, whereas small nucleolar RNAs involved in pseudouridylation were most prevalent in Drosophila EVs. Numerous mRNAs were identified, largely consisting of exonic sequences displaying full-length read coverage and enriched for translation and electronic transport chain functions. By analogy with human systems, these extensive similarities suggest that EVs could also enable RNA-mediated intercellular communication in Drosophila.

ORGANISM(S): Homo sapiens Drosophila melanogaster

PROVIDER: GSE76173 | GEO | 2016/06/15

SECONDARY ACCESSION(S): PRJNA306512

REPOSITORIES: GEO

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Comparative transcriptomic analysis of human and Drosophila extracellular vesicles reveals extensive conservation

Project description:Extracellular vesicles (EVs) are membrane-enclosed nanoparticles containing specific repertoires of genetic material. In mammals, EVs can mediate the horizontal transfer of various cargos and signaling molecules, notably miRNA and mRNA species. Whether this form of intercellular communication prevails in other metazoans remains unclear. Here, we report the first parallel comparative morphologic and transcriptomic characterization of EVs from Drosophila and human cellular models. Electronic microscopy revealed that Drosophila, like human cells release exosome-like EVs with diameter ranging from 30 to 200 nm, which contain complex populations of transcripts. RNA-seq identified abundant ribosomal RNA pseudogenes and retrotransposons in human and Drosophila EVs. Vault RNAs and Y RNAs abounded in human samples, whereas small nucleolar RNAs involved in pseudouridylation were most prevalent in Drosophila EVs. Numerous mRNAs were identified, largely consisting of exonic sequences displaying full-length read coverage and enriched for translation and electronic transport chain functions. By analogy with human systems, these extensive similarities suggest that EVs could also enable RNA-mediated intercellular communication in Drosophila. We performed RNA-seq on extracellular vesicles purified from of human and Drosophila cell line cultures. S2R+ and D17 Drosophila EVs were analyzed, along with human A431 and HepG2 EVs. No ribosomal RNA depletion or polyA selection was performed on EV samples. For comparative analyses, we also analyzed total cellular RNA from Drosophila D17 and human HepG2. Ribodepletion was performed on cellular samples.

2016-06-15 | E-GEOD-76173 | biostudies-arrayexpress

Exploring extracellular vesicles of probiotic yeast Saccharomyces boulardii CNCM I-745 as carriers of biologically active molecules transferred to human intestinal cells

Project description:Extracellular vesicles (EVs) are nanoparticles containing various bioactive cargos, e.g., proteins, RNAs, and lipids, that are released into the environment by all cell types. They are involved in, amongst others, intercellular communication. This article presents studies on EVs produced by the probiotic yeast Saccharomyces boulardii CNCM I-745. The size distribution and concentration of EVs in the liquid culture of yeast were estimated. Moreover, the vesicles of S. boulardii were tested for their cytotoxicity against three model human intestinal cell lines. This study did not show any significant negative effect of yeast EVs on these cells under tested conditions. In addition, EVs of S. boulardii were verified for their ability to internalize in vitro with human cells and transfer their cargo. The yeast vesicles were loaded with doxorubicin, an anticancer agent, and added to the cellular cultures. Subsequently, microscopic observations revealed that these EVs transferred the chemotherapeutic to human intestinal cell lines. A cytotoxicity test confirmed the activity of the transferred doxorubicin. Detailed information about the proteins present in EVs might be important in terms of exploring yeast EVs as carriers of active molecules. Thus, proteomic analysis of the EV content was also conducted within the present study, and it allowed to identify 541 proteins after matching to the Saccharomyces Genome Database (SGD). Altogether, this study provides strong evidence that the EVs of the probiotic CNCM I-745 strain could be considered a drug delivery system.

2023-06-29 | PXD042660 | Pride

Jurkat cell exosomes bound by CD47, CD63 and MHC1 harbor different RNA content

Project description:Extracellular vesicles (EVs) mediate cell-cell communication including the intercellular transfer of RNAs, which alter gene expression in target cells. However, heterogeneity in the size, density, and composition of EVs has limited progress towards defining their physiological functions and utility as disease-specific biomarkers. CD63 and MHC-1 are widely used as markers to purify EVs. CD47 is also present on EVs and alters their effects on target cells, suggesting that specific surface markers define functionally distinct EVs. This hypothesis was addressed by comparing the properties of Jurkat T cell EVs captured using CD47, CD63, and MHC-1 antibodies. These EV subsets have similar sizes but divergent RNA contents.

2018-03-13 | GSE103493 | GEO

Jurkat cell exosomes bound by either CD47 or CD63 harbor different RNA content

Project description:xtracellular vesicles (EVs) mediate cell-cell communication including the intercellular transfer of RNAs, which alter gene expression in target cells. However, heterogeneity in the size, density, and composition of EVs has limited progress towards defining their physiological functions and utility as disease-specific biomarkers. CD63 and MHC-1 are widely used as markers to purify EVs. CD47 is also present on EVs and alters their effects on target cells, suggesting that specific surface markers define functionally distinct EVs. This hypothesis was addressed by comparing the properties of Jurkat T cell EVs captured using CD47, CD63, and MHC-1 antibodies. These EV subsets have similar sizes but divergent RNA contents.

2018-08-03 | GSE103310 | GEO

Expression profiling in exosomal miRNAs of human bone marrow stromal cells derived from myelodysplastic syndrome patients

Project description:Myelodysplastic syndromes (MDS) constitute a heterogeneous group of clonal hematological disorders characterized by the presence of peripheral cytopenias and an increased risk of transformation into acute myeloblastic leukemia (AML). These hematological disorders are complex and their origin in a clonal hematopoietic stem cell disorder is accepted. In the last few years, the importance of the bone marrow (BM) microenvironment has been highlighted. Bone marrow stromal cells (BMSCs) are a non-hematopoietic BM cell population considered to be the osteoblastic progenitors and a key component of the hematopoietic microenvironment. As usual, it was considered that intercellular communication could be achieved by direct cell-to-cell contact or the exchange of soluble factors and intercellular adhesion molecule. Recently, a new mechanism of intercellular communication based on the secretion of extracellular esicles (EVs) has been described. Such a mechanism modifies the functional properties of recipient cells by the transfer of bioactive molecules such as mRNA, proteins and micro-RNAs, among others. BMSCs play an important role in bone marrow environment. Recent evidences suggest that EVs act as a mediator of cell-cell interaction in hematologic neoplasms. To clarify the possible association between the cargo of BMSC-EVs and disease severity, we performed miRNA profiling in BMSC-EVs derived from MDS patients.

2019-06-26 | GSE133276 | GEO

The effect of colorectal cancer (CRC) organoid-derived extracellular vesicles on the expression profile of fibroblasts

Project description:Extracellular vesicles (EV) are membrane-surrounded vesicles secreted by cells that carry biologically important molecules to the target cells. EVs form a heterogenous group and they represent a novel way of intercellular communication. To study the importance of colorectal cancer (CRC)-derived EVs on stromal fibroblasts, we applied CRC patient-derived 3D organoid cultures and commercially available human colon fibroblasts. We studied the gene expression changes in fibroblasts in the presence and absence pf CRC-derived EVs.

2019-02-25 | GSE114979 | GEO

Sequential phosphoproteomics and N-glycoproteomics of plasma-derived extracellular vesicles

Project description:Extracellular vesicles (EVs) are increasingly recognized as important cargos for intercellular communication and promising sources for less invasive biomarker discovery. As the state of protein post-translational modifications (PTMs) such as phosphorylation and glycosylation can be a key determinant of cellular physiology such as early stage cancer, comprehensive characterization of protein PTMs in EVs are highly valuable, but significant challenges remain. Recently we demonstrated the feasibility to isolate and identify phosphoproteins and glycoproteins in EVs from human plasma as potential markers to differentiate disease from healthy states. We identified close to 10,000 unique phosphopeptides and 1,500 unique glycopeptides in EVs isolated from small volumes of plasma samples. Using label-free quantitative phospho- and glyco-proteomics, we identified a number of phosphoproteins and glycoproteins in plasma EVs that are significantly higher in patients diagnosed with breast cancer. Here we present an updated workflow to sequentially isolate phosphopeptides and N-glycopeptides, enabling multiple PTM analyses with the same clinical samples and presenting intriguing functional molecules for further validation.

2019-09-25 | PXD013893 | Pride

Characterization and Small RNA Content of Extracellular Vesicles in Follicular Fluid of Developing Bovine Antral Follicles

Project description:Exosomes and microvesicles (i.e., extracellular vesicles; EVs) have been identified within ovarian follicular fluid, and recent evidence suggests that EVs are able to elicit profound effects on ovarian cell function. While existence of miRNA within EVs has been reported, it remains unknown if EV size and concentration as well as their cargos (i.e., proteins and RNA) change during antral follicle growth. Extracellular vesicles isolated from follicular fluid of small, medium and large bovine follicles were similar in size, while concentration of EVs decreased progressively as follicle size increased. Electron microscopy indicated a highly purified population of the lipid bilayer enclosed vesicles that were enriched in exosome biomarkers including CD81 and Alix. Small RNA sequencing identified a large number of known and novel miRNAs that changed in the EVs of different size follicles. Ingenuity Pathway Analysis (IPA) indicated that miRNA abundant in small follicle EV preparations were associated with cell proliferation pathways, while those miRNA abundant in large follicle preparations were related to inflammatory response pathways. These studies are the first to demonstrate that EVs change in their levels and makeup during antral follicle development and point to the potential for a unique vesicle-mediated cell-to-cell communication network within the ovarian follicle. Examination of small RNA population in bovine follicular fluid extracellular vesicles isolated from antral follicles

2016-02-09 | E-GEOD-74879 | biostudies-arrayexpress

MicroRNA and protein cargos of human limbal epithelial cell-derived exosomes and their regulatory roles in limbal stromal cells of diabetic and non-diabetic cornea

Project description:Epithelial and stromal/mesenchymal limbal stem cells contribute to corneal homeostasis and cell renewal. Extracellular vesicles (EVs), including exosomes (Exos), can be paracrine mediators of intercellular communication. Previously, we described cargos and regulatory roles of limbal stromal cell (LSC)-derived Exos in non-diabetic (N) and diabetic (DM) limbal epithelial cells (LEC). Presently, we quantify the miRNA and proteome profiles of human LEC-derived Exos and their regulatory roles in N- and DM-LSC. We revealed some miRNA and protein differences in DM vs. N-LEC-derived Exos' cargos including proteins involved in Exo biogenesis and packaging that may affect Exo production and ultimately cellular crosstalk and corneal function. Treatment by N-Exos, but not by DM-Exos enhanced wound healing in cultured N-LSC and increased proliferation rate in N and DM LSCs vs. corresponding untreated (control) cells. N-Exos treated LSC reduced keratocyte markers ALDH3A1 and lumican, and increased MSC markers CD73, CD90 and CD105 vs. control LSC. These being opposite to the changes quantified in wounded LSCs. Overall, N-LEC Exos have a more pronounced effect on LSC wound healing, proliferation, and stem cell marker expression than DM-LEC Exos. This suggests that regulatory miRNA and protein cargo differences in DM- vs. N-LEC-derived Exos could contribute to the disease state.

2023-09-29 | GSE243345 | GEO

Extracellular Vesicles Originate from the Conceptus and Uterus During Early Pregnancy in Sheep

Project description:The present studies tested the hypothesis that the elongating ovine conceptus and uterus produces EVs with the potential to mediate conceptus-maternal communication during early pregnancy. In Study One, EVs were purified from uterine luminal fluid (ULF) of day 14 cyclic sheep. The EVs were fluorescently labeled with PKH67 dye and infused into the uterine lumen of pregnant sheep for 6 days using an osmotic pump. On day 14, labeled EVs were observed in the conceptus trophectoderm and uterine epithelia, but not in the uterine stroma or myometrium. In Study Two, day 14 conceptuses were cultured ex vivo for 24 hours and found to release EVs into the culture medium. Isolated EVs from conceptuses were fluorescently labeled with PKH67 and infused into the uterine lumen of cyclic sheep for 6 days using an osmotic pump. On day 14, labeled EVs were observed in the uterine epithelia, but not in the uterine stroma or myometrium. No evidence of EV escape from the uterine lumen was observed by analysis of the ovary and other maternal tissues. Proteomics analysis of the day 14 conceptus-derived EVs identified 231 proteins that were enriched for extracellular space and several protein classes including proteases, protease inhibitors, chaperones and chaperonins. RNA-sequencing of day 14 conceptus-derived EVs detected expression of 512 mRNAs. The top expressed genes were overrepresented in ribosomal functions and components. These studies support the ideas that EVs emanate from both the conceptus trophectoderm and uterine epithelia and are involved in intercellular communication during the establishment of pregnancy. Transcriptional profiles from day 14 conceptus extracellular vesicles isolated from 24 hour conceptus-conditioned culture media (n=3) were generated by sequencing on the Illumina HiSeq 2500 platform.

2015-12-16 | E-GEOD-76035 | biostudies-arrayexpress

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