Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Small RNA sequencing in cells and exosomes identifies eQTLs and 14q32 as a region of active export

ABSTRACT: Exosomes are small extracellular vesicles that carry heterogeneous cargo, including RNA, between cells. Increasing evidence suggests that exosomes are important mediators of intercellular communication and biomarkers of disease. Despite this, the variability of exosomal RNA between individuals has not been well quantified. To assess this variability, we sequenced the small RNA of cells and exosomes from a 17-member family. Across individuals, we show that selective export of miRNAs occurs not only at the level of specific transcripts, but that a cluster of 74 mature miRNAs on chromosome 14q32 is massively exported in exosomes while mostly absent from cells. We also observe more inter-individual variability between exosomal samples than between cellular ones and identify four miRNA expression quantitative trait loci (eQTLs) shared between cells and exosomes. Our findings indicate that genomically co-located miRNAs can be exported together and highlight the variability in exosomal miRNA levels between individuals as relevant for exosome use as diagnostics.

ORGANISM(S): Homo sapiens

PROVIDER: GSE74759 | GEO | 2017/03/08

SECONDARY ACCESSION(S): PRJNA301431

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Deregulated Expression of the 14q32 miRNA Cluster in Clear Cell Renal Cell Carcinomas

Project description:Clear cell renal cell carcinomas (ccRCC) are characterized by arm-wide chromosomal alterations. Loss at 14q is associated with disease aggressiveness in ccRCC, which responds poorly to chemotherapeutics. The 14q locus contains one of the largest miRNA clusters in the human genome; however, little is known about the contribution of these miRNAs to ccRCC pathogenesis. In this regard, we investigated the expression pattern of selected miRNAs at the 14q32 locus in TCGA kidney tumors and in ccRCC cell lines. We validated that the miRNA cluster is downregulated in ccRCC (and cell lines) as well as in papillary kidney tumors relative to normal kidney tissues and primary renal proximal tubule epithelial (RPTEC) cells. We demonstrated that agents modulating expression of DNMT1 (e.g., 5-Aza-deoxycytidine) could modulate miRNA expression in ccRCC cell lines. Lysophosphatidic acid (LPA, a Lysophospholipid mediator elevated in ccRCC) not only increased labile iron content but also modulated expression of 14q32 miRNAs. Through an overexpression approach targeting a subset of 14q32 miRNAs (specifically at subcluster A: miR-431, miR-432, miR-127, and miR-433) in 769-P cells, we uncovered changes in cellular viability and claudin-1, a tight junction marker. A global proteomic approach was implemented using these miRNA overexpressing cell lines which uncovered ATXN2 as a highly downregulated target, which has a role in chronic kidney disease pathogenesis. Collectively, these findings support a contribution of miRNAs at 14q32 in ccRCC pathogenesis.

2023-05-10 | PXD036428 | Pride

The RNA binding protein SYNCRIP is a component of the hepatocyte exosomal machinery controlling microRNAs sorting

Project description:Despite clear evidence that exosomal microRNAs (miRNAs) are able to modulate the cellular microenvironment and that exosomal RNA cargo selection is often deregulated in pathological conditions, the mechanisms controlling specific RNA sorting into extracellular vescicles are still poorly understood. We identified here the RNA binding protein SYNCRIP (Synaptotagmin-binding Cytoplasmic RNA-Interacting Protein, also known as hnRNP-Q or NSAP1) as a component of the hepatocyte exosomal miRNA sorting machinery. SYNCRIP was found to bind directly a subset of miRNAs enriched in exosomes, sharing a common extra-seed sequence that we named hEXO motif. In vivo knock-down of SYNCRIP impaired microRNA sorting in exosomes and the hEXO motif was proven to play a role in the regulation of miRNA localization, as its embedment into a poorly exported miRNA enhanced its loading into exosomes. These results provide a new insight in the mechanisms of miRNA exosomal sorting process, that ca be exploited to further understand the role of these extracellular vescicles in cell-to-cell communications and the control of tissue micoenvironments.

2016-09-02 | E-MTAB-4502 | biostudies-arrayexpress

RNA-seq of non coding RNA from serum exosomes of GC patients and healthy individuals

Project description:The dysregulation of exosomal microRNAs (miRNAs) play a crucial role in the development and progression of cancer. Differentially expressed miRNAs were identified in serum exosomes of GC patients and healthy individuals using next-generation sequencing and bioinformatics.

2023-11-01 | E-MTAB-12763 | biostudies-arrayexpress

Modulation of gene expression after inducing expression of 14q32 miRNAs by CRISPR activation technology in lung adenocarcinoma

Project description:Most lung adenocarcinoma deaths are related to metastases, indicating the necessity of detecting and inhibiting tumor cell dissemination. We have identified that overexpression of miRNAs located on 14q32 was associated with metastasis in lung adenocarcinoma patients. For functional analysis, we utilized CRISPR activation technology to increase levels of miRNAs clustered on 14q32 in a coordinated manner, and the results showed that 14q32 miRNA overexpression promoted tumor cell migratory and invasive properties. Whole transcriptome microarray analysis of the miRNA-overexpressing cells was performed to define the underlying molecular mechanisms. Microarray analysis was used to investigate the gene expression changes underlying the tumor cell migratory and invasive properties induced by 14q32 miRNAs in lung adenocarcinoma.

2018-03-12 | GSE99050 | GEO

A set of circulating microRNAs belonging to the 14q32 chromosomic locus identifies two different subgroups of individuals with recent onset Stage 3 type 1 diabetes [second cohort, untargeted]

Project description:Circulating microRNAs are linked to the onset and progression of type 1 diabetes mellitus (T1DM), making them potential biomarkers for the disease. In this study, we employ a multiplatform sequencing approach to analyze circulating microRNAs in an extended cohort of individuals with T1DM from the INNODIA consortium. Our findings reveal that a set of microRNAs located within the T1DM susceptibility chromosomal locus 14q32 distinguishes two subgroups of individuals. To validate our results, we conduct additional analyses on a second cohort of T1DM individuals, confirming the identification of these subgroups, which we have named Cluster A and Cluster B. Remarkably, Cluster B T1DM individuals, who exhibit increased expression of a set of 14q32 miRNAs, show better glycaemic control and display a different blood immunomics profile. Our findings suggest that this set of circulating microRNAs can identify two different T1DM subgroups with distinct blood immunomics at baseline and clinical outcomes during follow-up.

2024-05-03 | GSE265981 | GEO

A set of circulating microRNAs belonging to the 14q32 chromosomic locus identifies two different subgroups of individuals with recent onset Stage 3 type 1 diabetes [first cohort, untargeted]

2024-05-03 | GSE265980 | GEO

A set of circulating microRNAs belonging to the 14q32 chromosomic locus identifies two different subgroups of individuals with recent onset Stage 3 type 1 diabetes [first cohort, targeted]

2024-05-03 | GSE265976 | GEO

Profile analysis of endogenous and exosomal microRNAs in human colon cancer cell lines-1

Project description:MicroRNAs (miRNAs) are intrinsic regulators in the various cellular processes, and their abnormalities are considered to be involved in the onset of human disorders, including cancer. Circulating miRNA is focused as new cancer biomarker however it is regarded that circulating RNA are released not only from tumor but also by various pathways. Recently, exosomes, small membrane vesicles, have been a major interest in cancer research field, because of their unique biological properties. Exosomes are secreted from various cells and the components (Lipids, mRNAs, miRNAs and proteins) reflect origin of the cells secreting them. Identification of exosomal miRNAs from cancer cells is expected to provide useful biomarkers of cancer. To identify specific exosomal miRNAs as candidate biomarkers for colorectal cancer, we compared exosomal miRNA profiles of 5 colon cancer cell lines with that of normal colon-derived epithelial cells, and isolated a subset of miRNAs as commonly-secreted miRNAs from colon cancer cells Endogenously expression of microRNAs were analyzed by Agilent Human miRNA V3 Microarray (G4470C) using total RNAs of human colon-derived FHC cells and human colon cancer cell lines (HCT116 cells and SW480 cells) at two independent experiments. Exosomal microRNAs were analyzed by microRNA microarray using total RNAs of exosomes from conditioned media of FHC cells, HCT116 cells, and SW480 cells at three independent experiments.As negative control of exosomal microRNAs in conditioned media, FBS-exosomal microRNAs were analyzed at four independent experiments. Exosomes were prepared by step-wise ultra-centrifugation methods. RNA was prepared by Trizol or Trizol-LS reagent (Invitrogen) and RNeasy mini spin column (Qiagen).

2014-04-01 | E-GEOD-39814 | biostudies-arrayexpress

Keratinocyte-derived circulating exosomal miRNAs as a novel biomarker of disease severity in psoriasis

Project description:To reveal the relationship between circulating exosomal miRNAs and the disease severity of psoriasis, we performed next-generation sequencing from plasma exosomes of patients with high psoriasis area and severity index (PASI) score (>10) and low PASI score (<5). We identified 19 differentially expressed exosomal miRNAs that were significantly different between the groups. We validated the top three up-and down-regulated exosomal miRNAs using quantitative real-time PCR.

2024-03-13 | GSE215124 | GEO

The miRNAs in plasma exosomes may serve as markers for segmental vitiligo

Project description:More and more studies have showed that plasma exosomal miRNAs are biomarkers for disease. The aim of the study were to investigate the miRNA profiling in plasma exosomes of patients with segmental vitiligo (SV) and to find biomarkers in plasma exosomes for patients with SV. Plasma exosomes and exosomal RNA of 7 SV patients and 8 health persons were purified by exoRNeasy Serum/Plasma Maxi Kit. The miRNA profiles of the 15 samples were sequenced using HiSeq 2500 (Illumina) and analyzed by Reads Per Million (RPM) values and edgeR algorithm. Some differently expressed miRNAs in plasma exosomes and skin tissues of the two sets were validated by qRT–PCR.A total of 85 miRNAs in plasma exosomes showed differential expression between SV patients and health persons, with a |log2（Fold Change）|≥1 and P-value < 0.05. Several miRNAs were confirmed by qRT–PCR and showed similar expression patterns between plasma exosomes and skin tissues. Our study depict the miRNAs expression profiles in plasma exosomes of SV patients and suggest that several miRNAs in plasma exosomes may serve as biomarkers for SV.

2022-03-24 | GSE198956 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data