Dataset Information

Expression Analysis of the Circular RNA Molecules in the Human Retinal Cells Treated with Homocysteine.

ABSTRACT: PURPOSE:To characterize the global profile of circular RNAs (circRNAs) and their differential expression levels in homocysteine (Hcy)-treated ARPE-19 cells, a line of human retinal pigment epithelial (RPE) cells. MATERIALS AND METHODS:We treated ARPE-19 cells with and without Hcy to investigate the influence of Hcy on circRNA expression levels using dedicated human circRNA microarrays. RESULTS:A total of 12,233 circRNAs were identified out of them 54 were differentially expressed (17 were down-regulated, and 37 were up-regulated) with a fold change >2.0 (p < 0.05) in Hcy-treated versus untreated cells. CONCLUSIONS:To our knowledge, this is the first report profiling circRNAs in human RPE cells post-Hcy treatment mimicking hyperhomocysteinemic (HHcy) conditions that negatively affect retinal biology and vision. These findings are of potential clinical significance as they will help understand Hcy metabolism and HHcy-mediated diseases and identify potential diagnostic and therapeutic targets for eye diseases that are caused by elevated Hcy concentrations.

SUBMITTER: Singh M

PROVIDER: S-EPMC6709669 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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Expression Analysis of the Circular RNA Molecules in the Human Retinal Cells Treated with Homocysteine.

Singh Mahavir M George Akash K AK Homme Rubens Petit RP Majumder Avisek A Laha Anwesha A Sandhu Harpal S HS Tyagi Suresh C SC

Current eye research 20181205 3

<h4>Purpose</h4>To characterize the global profile of circular RNAs (circRNAs) and their differential expression levels in homocysteine (Hcy)-treated ARPE-19 cells, a line of human retinal pigment epithelial (RPE) cells.<h4>Materials and methods</h4>We treated ARPE-19 cells with and without Hcy to investigate the influence of Hcy on circRNA expression levels using dedicated human circRNA microarrays.<h4>Results</h4>A total of 12,233 circRNAs were identified out of them 54 were differentially exp ...[more]

PMID: 30369271

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Project description:BackgroundCervical cancer is one of the most common cancers in women worldwide. Malignant tumors develop resistance mechanisms and are less sensitive to or do not respond to irradiation. With the development of high-throughput sequencing technologies, circular RNA (circRNA) has been identified in an increasing number of diseases, especially cancers. It has been reported that circRNA can compete with microRNAs (miRNAs) to change the stability or translation of target RNAs, thus regulating gene expression at the transcriptional level. However, the role of circRNAs in cervical cancer and the radioresistance mechanisms of HeLa cells are unknown. The objective of this study is to investigate the role of circRNAs in radioresistance in HeLa cells.MethodsHigh-throughput sequencing and bioinformatics analysis of irradiated and sham-irradiated HeLa cells. The reliability of high-throughput RNA sequencing was validated using quantitative real-time polymerase chain reaction. The most significant circRNA functions and pathways were selected by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. A circRNA-miRNA-target gene interaction network was used to find circRNAs associated with radioresistance. Moreover, a protein-protein interaction network was constructed to identify radioresistance-related hub proteins.ResultsHigh-throughput sequencing allowed the identification of 16,893 circRNAs involved in the response of HeLa cells to radiation. Compared with the control group, there were 153 differentially expressed circRNAs, of which 76 were up-regulated and 77 were down-regulated. GO covered three domains: biological process (BP), cellular component (CC) and molecular function (MF). The terms assigned to the BP domain were peptidyl-tyrosine dephosphorylation and regulation of cell migration. The identified CC terms were cell-cell adherens junction, nucleoplasm and cytosol, and the identified MF terms were protein binding and protein tyrosine phosphatase activity. The top five KEGG pathways were MAPK signaling pathway, endocytosis, axon guidance, neurotrophin signaling pathway, and SNARE interactions in vesicular transport. The protein-protein interaction analysis indicated that 19 proteins might be hub proteins.ConclusionsCircRNAs may play a major role in the response to radiation. These findings may improve our understanding of the role of circRNAs in radioresistance in HeLa cells and allow the development of novel therapeutic approaches.

Project description:BackgroundArteriosclerosis obliterans (ASO) is the leading cause of nontraumatic lower-extremity amputations. Multiple researches have suggested that circular RNAs (circRNAs) played vital regulatory functions in cancer and cardiovascular disease. Nevertheless, the underlying effect and pathological mechanism of circRNAs in the formation and progression of ASO are still indistinct.Methods and resultsThis study used microarray analysis to investigate the expression portrait of circRNAs in normal lower extremity arteries and ASO arteries. Bioinformatics analysis was conducted using the KEGG database to study the enrichment of differentially expressed circRNAs (DE circRNAs) and predict their functions. The accuracy of microarray assay was verified by evaluating expression of the top 5 upregulated and 5 downregulated circRNAs (raw density of normal group ≥200) using RT-qPCR. A circRNA-miRNA-mRNA interaction network was further predicted using software. Compared to the normal lower extremity group, the ASO arteries with HE and EVG staining presented hyperplastic fibrous membrane and luminal stenosis. A total of 12,735 circRNAs were identified, including 1196 DE circRNAs with 276 upregulated and 920 downregulated in ASO group based on |log2(FC)| > 1 and padj < 0.05. Among selected 10 circRNAs, RT-qPCR confirmed that hsa_circ_0003266, hsa_circ_0118936 and hsa_circ_0067161 were upregulated while hsa_circ_0091934 and hsa_circ_0092022 were downregulated in ASO group (p < 0.05). GO analysis presented that the DE circRNAs were primarily enriched in protein binding, intracellular part and organelle organization. KEGG pathway analysis indicated that MAPK signaling pathway, human T-cell leukemia virus 1 infection, proteoglycans in cancer were associated with the DE circRNAs. The circRNA-miRNA-mRNA interactive network revealed that both mRNAs and miRNAs linked to circRNAs played an indispensable role in ASO.ConclusionThis study described the expression portrait of circRNAs in human ASO arteries, and revealed the molecular background for further investigations of the circRNA regulatory mechanism in the formation and progression of ASO.

Dataset Information

Expression Analysis of the Circular RNA Molecules in the Human Retinal Cells Treated with Homocysteine.

Publications

Expression Analysis of the Circular RNA Molecules in the Human Retinal Cells Treated with Homocysteine.

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