Examining exosomes from blood taken from gastric cancer samples
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ABSTRACT:
PROVIDER: PRJNA694314 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13515338_1.fastq.gz | Fastqsanger.gz | |||
| SRR13515338_2.fastq.gz | Fastqsanger.gz | |||
| SRR13515339_1.fastq.gz | Fastqsanger.gz | |||
| SRR13515339_2.fastq.gz | Fastqsanger.gz | |||
| SRR13515340_1.fastq.gz | Fastqsanger.gz |
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Project description:Examining exosomes from blood taken from gastric cancer samples
2022-09-15 | GSE165394 | GEO
Project description:Aim: EBV encode at least 44 miRNAs involved in immune regulation and disease progression. Exosomes can be used as carriers of EBV-miRNA-BART intercellular transmission and affect the biological behavior of cells. We characterized exosomes and established a co-culture experiment of exosomes to explore the mechanism of miR-BART1-3p transmission through the exosome pathway and its influence on tumor cell proliferation and invasion. Materials and methods: Exosomes of EBV-positive and EBV-negative gastric cancer cells were characterized by transmission electron microscopy, Nanosight and western blotting, and miRNA expression profiles in exosomes were sequenced with high throughput. Exosomes with high or low expression of miR-BART1-3p were co-cultured with AGS cells to study the effects on proliferation, invasion and migration of gastric cancer cells. The target genes of EBV-miR-BART1-3p were screened and predicted by PITA, miRanda, RNAhybrid, virBase and Diana-Tarbase v.8 databases, and the expression of the target genes after co-culture was detected by qPCR. Results：The exosomes secreted by EBV positive and negative gastric cancer cells range in diameter from 30 nm to 150nm and express the exosomal signature proteins CD63 and CD81. High throughput sequencing showed that exosomes expressed some human miRNAs, among which has-miR-23b-3p, has-miR-320a-3p and has-miR-4521 were highly expressed in AGS-exo. has-miR-21-5p, has-miR-148a-3p and has-miR-7-5p were highly expressed in SNU-719-exo. All EBV miRNAs were expressed in SNU-719 cells and their exosomes, among which EBV- miR-Bart1-5p, EBV- miR-bart22 and EBV- miR-bart16 were the highest in SNU-719 cells. EBV-miR-BART1-5p, EBV-miR-BART10-3p and EBV-miR-BART16 were the highest in SNU-719-exo. After miR-BART1-3p silencing in gastric cancer cells, the proliferation, healing, migration and invasion of tumor cells were significantly improved. Laser confocal microscopy showed that exosomes could carry miRNA into recipient cells. After co-culture with miR-BART1-3p silenced exosomes, the proliferation, healing, migration and invasion of gastric cancer cells were significantly improved. The target gene of miR-BART1-3p was FMA168A, MACC1, CPEB3, ANKRD28 and USP37 after screening by targeted database. CPEB3 was not expressed in all exosome co-cultured cells, while ANKRD28, USP37, MACC1 and FAM168A were all expressed to varying degrees. USP37 and MACC1 are down-regulated after up-regulation of miR-BART1-3p, which may be the key target genes for miR-BART1-3p to regulate the proliferation of gastric cancer cells through exosomes. Conclusions: miR-BART1-3p can affect the growth of tumor cells through exosome pathway. The proliferation, healing, migration and invasion of gastric cancer cells were significantly improved after co-culture with exosomes of miR-BART1-3p silenced expression. USP37 and MACC1 may be potential target genes of miR-BART1-3p in regulating cell proliferation.
2023-03-13 | GSE227017 | GEO
Project description:The sensitivity and specificity of traditional non-invasive diagnostic markers for gastric cancer are insufficient. Long-chain noncoding RNAs (lncRNAs) in circulating exosomes are a new class of promising cancer biomarkers. However, the expression profile of long-chain noncoding RNAs (lncRNAs) in exosomes derived from gastric high-grade intraepithelial neoplasia (GHGIN) has not been reported.The aim of this study was to investigate the expression profile of long non-coding RNAs (lncRNAs) in the plasma exosomes of patients with gastric high-grade intraepithelial neoplasia. Peripheral blood samples were collected from five patients with GHGIN and five healthy donors, and the exosomes were isolated. We used high-throughput sequencing to detect differently expressed lncRNAs (DE lncRNAs) in these individuals. Real-time quantitative polymerase chain reaction (RT-qPCR) assay was performed to verify the sequencing results. The potential roles of the DE lncRNAs in GHGIN were speculated by performing Gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) analysis. We constructed a lncRNAs–miRNA–mRNA network diagram and performed association analyses to explore the underlying molecular mechanisms. A total of 25145 lncRNAs were identified in all samples; 83 lncRNAs that showed significant differential expression were further screened, including 76 up‐regulated and 7 down‐regulated lncRNAs. RT-qPCR further confirmed these results. GO and KEGG analyses predicted that these lncRNAs played important roles in protein and macromolecule glycosylation, regulation of protein ubiquitination, and renin-angiotensin system and MAPK signaling pathways. We further constructed a lncRNA–miRNA–mRNA interaction network. This study may help in discovering new molecular changes, enrich the expression profile of lncRNAs in human GHGIN, and help us better understand the molecular mechanisms of GHGIN and gastric cancer.
2020-06-29 | GSE153413 | GEO
Project description:Exosomes from the culture media (CM) of four GC cells (GCCs) and human gastric epithelial cells were isolated. Exosomal RNA was extracted, and circRNA microarray assay was performed to identify GC-specific exosomal circRNAs. A total of 58 exosomal circRNAs were expressed at considerable higher levels in GCCs than those in normal controls.The expression level of several top upregulated circRNAs were detected using qRT-PCR in both GC cells and clinical specimens of GC patients. More interesting, besides the high expression in GC cell derived exosomes, hsa_circ_0015286 was the uniquely upregulated circRNA in the plasma exosomes and tissues of GC patients..The result suggested that exosomal hsa_circ_0015286 may be a potential noninvasive biomarker for the diagnosis and prognosis monitoring of GC.
2022-05-12 | GSE202538 | GEO
Project description:To investigate the role of Fusobacterium nucleatum (Fn) in the development of gastric cancer, we extracted exosomes from the culture supernatant of MKN-28 cells treated with Fn or PBS, co-cultured them with AGS cells, and analyzed their miRNA-seq data for gene expression profiling.
2023-06-07 | GSE213833 | GEO
Project description:To investigate the role of Fusobacterium nucleatum (Fn) in the development of gastric cancer, we extracted exosomes from the culture supernatant of MKN-28 cells treated with Fn or PBS, co-cultured them with AGS cells, and analyzed their RNA-seq data for gene expression profiling.
2023-06-07 | GSE214817 | GEO
Project description:Exosomes from the culture media (CM) of four GC cells (GCCs) and human gastric epithelial cells were isolated. Exosomal RNA was extracted, and lncRNA microarray assay was performed to identify GC-specific exosomal lncRNAs. A total of 199 exosomal lncRNAs were expressed at considerable higher levels in GCCs than those in normal controls, among which the top 10 upregulated lncRNAs were selected for further validation. qRT-PCR revealed that lnc-SLC2A12-10:1 was remarkably upregulated in exosomes derived from patients with GC and GCCs. The expression levels of the candidate exosomal lncRNAs lnc-SLC2A12-10:1 were validated in 120 subjects via quantitative reverse transcription PCR (qRT-PCR).The result suggested that exosomal lnc-SLC2A12-10:1 may be a potential noninvasive biomarker for the diagnosis and prognosis monitoring of GC.
2020-06-04 | GSE148334 | GEO
Project description:Clinical management of metastatic gastric cancer (mGC) remains a major challenge due to a lack of specific biomarkers and effective therapeutic targets. Recently, accumulating evidence has suggested that exosomes play an essential role in cancer metastasis and can be an excellent reservoir of novel biomarkers and candidate therapeutic targets for cancer. Therefore, in this study, we aimed to reveal the proteomic profile of mGC-derived exosomes.Exosomes were isolated from pooled serum samples of 20 mGC patients and 40 healthy controls (HCs) by ultracentrifugation. Next, quantitative proteomic analyses were applied to analyze the protein profiles of the exosomes, and bioinformatic analyses were conducted on the proteomic data. Finally, the expression of exosomal protein candidates was selectively validated in individual subjects by western blot analysis. We isolated exosomes from serum samples. The size of the serum derived exosomes ranged from 30 to 150 nm in diameter. The exosomal markers CD9 and CD81 were observed in the serum exosomes. However, the exosomal negative marker calnexin, an endoplasmic reticulum protein, was not detected in exosomes. Overall, 443 exosomal proteins, including 110 differentially expressed proteins (DEPs) were identified by quantitative proteomics analyses. The bioinformatics analyses indicated that the upregulated proteins were enriched in the process of protein metabolic, whereas the downregulated proteins were largely involved in cell-cell adhesion organization. Surprisingly, ten highly vital proteins (UBA52, PSMA1, PSMA5, PSMB6, PSMA7, PSMA4, PSMA3, PSMB1, PSMA6, and FGA) were filtered from DEPs, most of which are proteasome subunits. Moreover, the validation data confirmed that PSMA3 and PSMA6 was explicitly enriched in the serum derived exosomes from patients with mGC. The present study provided a comprehensive description of the serum exosome proteome of mGC patients, which could be an excellent resource for further studies of mGC.
2020-06-29 | PXD019387 | Pride
Project description:Purpose: The purpose of this study was to detect the expression profiles of circRNAs, lncRNAs and mRNAs in umbilical cord blood (UCB) exosomes from BPD infants. Methods:Microarray analysis was performed to compare the RNA profiles of UCB-derived exosomes from preterm newborn with and without BPD. Then, circRNA/lncRNA-miRNA-mRNA co-expression networks were built to determine their associations with BPD.Results:A total of 317 circRNAs, 104 lncRNAs, 135 mRNAs showed significant differential expression in UCB-derived exosomes from BPD preterm infants compared with the NBPD group. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted for examining differentially expressed exosomal circRNAs, lncRNAs and mRNAs. Our results showed the GO terms and KEGG pathways mostly involving differentially expressed exosomal RNAs were closely associated with endothelial or epithelial cell development. In addition, two networks were identified, including circRNA-circ_0086018/miR-762/MEN1 and lncRNA-BASP1-AS1/miR-20a-5p/DNAJC22 networks, which may take part in BPD.
2022-08-31 | GSE190215 | GEO
Project description:microRNA profiles of Exosomes from Pooled NPC Patients serum comparing Control Exosomes from Healthy donors serum Two-condition experiment, Exosomes from Pooled Healthy donors serum vs. Exosomes from Pooled NPC Patients serum. Biological replicates: 1 Exosomes from Pooled Healthy donors serum, 1 Exosomes from Pooled NPC Patients serum,
2014-05-06 | E-GEOD-57319 | biostudies-arrayexpress