Sequencing of serum exosomal circRNAs in colorectal cancer
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE149200 | GEO | 2020/05/15
REPOSITORIES: GEO
Similar Datasets
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.
2021-06-08 | GSE173719 | GEO
Project description:Background: Osteoporosis is one of the most common chronic diseases around the world, especially in postmenopausal women. Circular RNAs (circRNAs) are emerging as important regulators in human disease. The aim of the present study was to analyze circRNA expression profiles in osteoporosis and to explore the clinical significance. Methods: The serum samples were collected from osteoporosis patients and healthy people. The circRNA array was performed to screen for differentially expressed circRNAs. The mRNA expression levels of target genes were analyzed by quantitative real-time PCR (qRT-PCR). Results: Hsa_circ_0006859 was identified as one of the most upregulated circRNAs in the microarray analysis. Hsa_circ_0006859 in exosome was upregulated in osteoporosis patients compared with healthy controls. Hsa_circ_0006859 could differentiate osteopenia or osteoporosis patients from healthy controls with high sensitivity and specificity. Conclusion: Exosomal hsa_circ_0006859 is a potential biomarker for postmenopausal osteoporosis.
2020-11-13 | GSE161361 | GEO
Project description:Exosomal circRNA sequencing was used to identify differentially expressed circRNAs between LAA stroke and normal controls. From a further validation stage, the results were validated using RT-qPCR.
2022-02-02 | GSE190869 | GEO
Project description:Background: Circular RNA (circRNA) has been reported to be involved in the pathogenesis of cardiovascular disease (CVD), however, it is unclear whether circRNA carried by exosomes (exos) can be used as biomarkers for chronic coronary syndrome (CCS). This study aimed to investigate the expression pattern of exosomal circRNAs in the plasma of CCS patients, and to screen exo-circRNAs that can act as biomarkers for the diagnosis of CCS. Methods: High-throughput sequencing technology was carried out in the plasma exosomal RNA of 15 CCS patients and 15 non-cardiac chest pain patients (NCCP, control group) (sequencing cohort) to screen for differentially expressed circRNAs. Selected differentially expressed exo-circRNAs were further verified by real time polymerase chain reaction (RT-PCR) in a small-sample cohort (derivation cohort) and a large-sample cohort (validation cohort). Receiver operating characteristic (ROC) curve analysis was performed to evaluate the diagnostic value of exo-circRNAs for CCS patients. Results: By high-throughput sequencing of circRNAs in 15 CCS patients and 15 NCCP patients, 276 circRNAs differentially expressed in plasma exosomes of CCS patients were screened by using |log2(Fold change) |>1 and q-value<0.001, and 103 were up-regulated and 173 were down-regulated. Among the 103 up-regulated circRNAs, 5 circRNAs with high expression levels and significantly increased in plasma exosomes of CCS patients were selected for validation. Twice RT-PCR validation demonstrated that exo-hsa_circ_0075269 and exo-hsa_circ_0000284 were significantly up-regulated in patients with CCS (P<0.001). Circulating exo-hsa_circ_0075269 and exo-hsa_circ_0000284 yielded the area under the curve (AUC) values of 0.761 (P<0.001, 95%CI=0.669, 0.852) and 0.623 (P=0.015, 95%CI=0.522, 0.724) for CCS, respectively by ROC curve analysis. Moreover, AUC of hsa_circ_0075269 combined with hsa_circ_0000284 for diagnosing CCS was 0.741 (P<0.001, 95%CI=0.667, 0.850). Conclusion: The expression profile of circRNA in plasma exosomes of patients with CCS was significantly different from that of the control group. Plasma exo-hsa_circ_0075269 and exo-hsa_circ_0000284 have the potential to be new biomarkers for CCS diagnosis.
2023-11-09 | GSE237983 | GEO
Project description:Circular RNA (circRNA) is a kind of transcripts characterized by originating from the back-splicing of pre-mRNA. CircRNAs have higher stability than liner transcripts and are more resistant to RNase R due to their loop structure, which makes circRNAs potential diagnostic markers and therapeutic targets for cancer . The biological functions of circRNAs are widely involved in the proliferation, metastasis, apoptosis, and autophagy of various cancers via multiple ways. To further investage the role of circRNA in CRC, a circRNA micoarray was performed.
2021-04-17 | GSE172229 | GEO
Project description: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.
2022-09-01 | GSE183607 | GEO
Project description:Sequencing of serum exosomal circRNAs in colorectal cancer
| PRJNA627650 | ENA
Project description:we used microarray technology to construct a comparative circRNA profiling of exosomes isolated from cell supernatant of high glucose stimulated human proximal tubular epithelial cell line (HK-2 cells) and nomal controls, aimed to explore gene expression and the underlying molecular mechanism of exosomal circRNAs in DN development.
2023-12-13 | GSE207495 | GEO
Project description:Circular RNAs (circRNAs), formed by the atypical head-to-tail splicing of exons, have re-emerged as a potentially interesting RNA species given recent reports of a surprising diversity and abundance of circRNA in organisms ranging from worm to human. Here, using deep RNA sequencing, we profiled different RNA species in mouse and observed that circRNAs are significantly enriched in neural tissue, relative to other tissues. Using PacBio sequencing, we determined, for the first time, the circular structure of this population of circRNAs as well as their full-length sequences. We discovered that a disproportionate fraction of the brain circRNA population is derived from host genes that code for synaptic proteins. Moreover, based on the separate profiling of the RNAs localized in neuronal cell bodies and neuropil (enriched in axons and dendrites), we found that, on average, circular RNAs are more enriched in the neuropil than their host gene mRNA isoforms. Using high resolution in situ hybridization we, for the first time, directly visualized circRNA punctae in the dendrites of neurons. The host gene origin and location of the circRNA in neurons suggest the possibility that circRNAs might participate in the regulation of synaptic function and plasticity. Consistent with this idea, we observed via profiling at different developmental stages, that the abundance of many circular RNAs changes abruptly at a time corresponding to synaptogenesis. In addition, following a homeostatic downscaling of neuronal activity many circRNAs exhibit significant up or down-regulation. These data indicate that brain circRNAs are positioned to respond to and regulate synaptic function. Circular RNA profiling in 13 different samples in mice and four samples in rat, using Illumina sequencing
2015-02-25 | E-GEOD-61991 | biostudies-arrayexpress
Project description:Circular RNAs (circRNAs) are a large class of animal RNAs. To investigate possible circRNA functions, it is important to understand circRNA biogenesis. Besides human Alu repeats, sequence features that promote exon circularization are largely unknown. We experimentally identified new circRNAs in C. elegans. Reverse complementary sequences between introns bracketing circRNAs were significantly enriched compared to linear controls. By scoring the presence of reverse complementary sequences in human introns we predicted and experimentally validated novel circRNAs. We show that introns bracketing circRNAs are highly enriched in RNA editing or hyper-editing events. Knockdown of the double-strand RNA editing ADAR1 enzyme significantly and specifically up-regulated circRNA expression. Together, our data support a model of animal circRNA biogenesis in which competing RNA:RNA interactions of introns form larger structures which promote circularization of embedded exons, while ADAR1 antagonizes circRNA expression by melting stems within these interactions. Thus, we assign a new function to ADAR1. Examination of 12 samples in different stages of C.elegans development.
2015-01-06 | E-GEOD-63823 | biostudies-arrayexpress