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Development of lncRNAs expression signatures in exosomes derived from different gastric cancer cells

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE148334 | GEO | 2020/06/04

REPOSITORIES: GEO

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Project description:Purpose: This study aimed to explore the differential expression profiles of exosomal lncRNAs and evaluated their potential utility in the accurate diagnosis of LAA stroke. Methods: LncRNA profiles of exosomes in large artery atherosclerosis stroke and controls were generated by high-throughput sequencing. The sequence reads that passed quality filters were analyzed at the transcript isoform level with Hisat2, Trapnell, STAR. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: A total of 1020 differentially expressed lncRNAs were identified in LAA stroke patients. GO and KEGG pathway analyses indicated that their target genes are involved in atherosclerosis-related pathways, including inflammation, cell adhesion, and cell migration. 8 exosomal lncRNAs were confirmed with qRT–PCR.The result showed that the expression trend of differential expressed lncRNAs in validation was consistent with RNA-seq.Conclusion: Our study showed the differential expression of lncRNAs in plasma exosomes and presented related diagnostic potential for LAA stroke for the first time. The results suggested that exosomal lncRNA could be potential diagnostic tools in LAA stroke. Circular RNAs (circRNAs), novel endogenous noncoding RNAs, play diverse roles in ischemic stroke. Recently, the abundance and stability of circRNAs in exosomes have been identified. However, a comprehensive analysis of exosomal circRNAs in large artery atherosclerotic (LAA) stroke has not yet been reported. We performed RNA sequencing (RNA-Seq) to comprehensively identify differentially expressed exosomal circRNAs in five paired LAA and normal controls. RNA-Seq identified a total of 462 circRNAs in peripheral exosomes; there were 25 differentially expressed circRNAs among them. Additionally, circRNA competing endogenous RNA (ceRNA) network and translatable analysis revealed the potential functions of the exosomal circRNAs in LAA progression. Two ceRNA pathways involving 5 circRNAs, 2 miRNAs, and 3 mRNAs were confirmed by qRT-PCR. In the validation cohort, receiver operating characteristic (ROC) curve analysis identified two circRNAs as possible novel biomarkers, and a logistic model combining two and four circRNAs increased the area under the curve compared with the individual circRNAs.

Project description:Background:Exosomes are extracellular vesicles secreted by a variety of cells and are widely distributed in human body fluids. Exosomal long non-coding RNA (lncRNA) is a by-product of gene transcription and is involved in the regulation of cancer cell growth and migration. Numerous studies have identified aberrant lncRNA levels in pancreatic cancer (PC), but studies on exosomal lncRNA expression in pancreatic ductal adenocarcinoma (PDAC) plasma are relatively few and remain largely unknown. Methods:We studied the expression of exosomal lncRNAs and mRNAs in the plasma of 5 PDAC patients and 5 healthy human subjects using high-throughput sequencing. Results:A total of 43715 exosomal lncRNAs were found to be expressed in PDAC and healthy human plasma, of which 5851 were up-regulated, and 1055 were down-regulated in all 5 PDAC plasma (≥2.0-fold change, P<0.05). The expression of eight significantly expressed genes (ABCD4, RP11-77P6.2, FLVCR1-AS1, HMBOX1, TUBA1C, RP11-115C21.2, PRKG1-AS1, and MTATP6P1) were selected to be measured in 5 patients using database and real-time quantitative reverse transcription PCR (qRT-PCR), and the data were consistent with those obtained from high-throughput sequencing. Analysis of their nearby coding genes (mRNAs) showed that the principal functions of most genes were to regulate cell metabolism process, apoptosis, protein binding and receptor binding. The main regulatory pathways included the ErbB signaling pathway, which regulates cell proliferation and differentiation, and the tumour pathway. Analysis of the co-expressed gene regulatory network identified key lncRNA-mRNA pairs that may play an important role in the pathogenesis of PDAC. Conclusions: Expression differences in exosomal lncRNAs exist between PDAC and healthy human plasma, so the expression profile of exosomal lncRNAs could explain the onset and development of PDAC and could also serve as a candidate biomarker for the diagnosis of PDAC and a potential therapeutic target.

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Development of lncRNAs expression signatures in exosomes derived from different gastric cancer cells

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