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Genome-wide profiling of the expression of exosomal circRNAs in patients with hepatic alveolar echinococcosis

ABSTRACT: Hepatic echinococcosis (HE) caused by Echinococcus spp. transmitted from carnivores is known as a severe zoonotic disease that formed into hepatic cystic echinococcosis (HCE) and hepatic alveolar echinococcosis (HAE). It continues to be a serious public health issue around the world. HAE is uncommon infection which is characterized by poor prognosis but it is the most life-threatening compare to HCE. Many cases of HAE are recognized at forward stages because clinical symptoms may remain silent in about 10 years of incubation period. Several pathological cases could be observed including septicemia, abscess, recurrent cholangitis, and portal hypertensive gastrointestinal bleeding in untreated people. It is provided that correlated factors includes CD44, Soluble ST2 (sST2), Plasma IL-23, IL-27, and IL-5 for metastasis and prognosis for patients with HAE were identified. However, data on metastatic and prognostic marker are still so poor. Recent studies have revealed that circRNAs are enriched and stable in exosomes. Exosomal circRNAs may be localized in platelet-derived extracellular vesicles, hepatic cells, and pancreatic cancer cells. Studies have suggested that it is possible that cells may transfer circRNAs by excreting them in exosomes. Whereas there are a lot of studies on cancer and other human diseases related exosomal circRNA, no studies on hepatic alveolar echinococcosis-related exosomal circRNAs in humans. Current study provides that exosomal circular RNAs from healthy humans and humans with hepatic alveolar echinococcal disease were detected and characterized using the RNA sequencing.

ORGANISM(S): Homo sapiens

PROVIDER: GSE183607 | GEO | 2022/09/01

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:Purpose. Simian virus 40 (SV40)-immortalized human corneal epithelial (HCE-T) cells have been widely used as an in vitro model of human corneal epithelial cells. To better understand the nature of this cell line, we assessed it for genomic aberrations and cellular heterogeneity. Methods. For the quantitative measurement of genomic aberrations, array based comparative genomic hybridization (CGH) analysis was performed. For identification of cellular heterogeneity, cell morphology, growth kinetics, trans-epithelial electrical resistance and transcriptional efficiency were analyzed. We also carried out real-time PCR and chromosomal fluorescent in situ hybridization (cFISH) against some gained or lost loci in order to assess genomic heterogeneity. To assess differences in the gene expression profiles between HCE-T cells and normal corneal epithelial cells, we collected expressed sequence tags (ESTs) for this cell line. Southern blotting and inverse PCR analyses were used to determine the genomic integration site of the SV40 large T antigen gene (LTAG). Results. Array CGH analysis indicated that the genomic content of HCE-T cells is different from the normal healthy genome. Our results from cellular functional assays, real-time PCR and cFISH strongly showed that HCE-T cells consist of a not insignificant number of heterogeneous cell populations. The genomic integration site of the SV40 large T antigen was at p22.1 of chromosome 9. Conclusions. Our results indicate that HCE-T cells have an altered genomic content and that they are composed of heterogeneous cell populations. This should be considered when conducting experiments or interpreting the results of studies which use this cell line. Keywords: comparative genomic hybridization Genomic DNAs from HCE-T cells, immortalized cell line of human corneal epithelial cells and normal female duploid cells were subjected to array CGH analysis to identify genomic alterations in the HCE-T cells. These DNAs were labeled with Cy5 and Cy3, respectively.

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Genome-wide profiling of the expression of exosomal circRNAs in patients with hepatic alveolar echinococcosis

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