Identification of Novel circRNA-Based ceRNA Network Involved in the Pathogenesis of Gastric Cancer
Objective. Evidence increasingly shows that circular RNAs (circRNAs) are closely associated with tumorigenesis and cancer progression. However, the roles of circRNAs and the underlying mechanism behind these circRNAs in gastric cancer (GC) remain to be elucidated. This study is aimed at conferring a...
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Wiley
2022-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2022/5281846 |
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| author | Dengfa Peng Li Feng Huqing Li |
| author_facet | Dengfa Peng Li Feng Huqing Li |
| author_sort | Dengfa Peng |
| collection | DOAJ |
| description | Objective. Evidence increasingly shows that circular RNAs (circRNAs) are closely associated with tumorigenesis and cancer progression. However, the roles of circRNAs and the underlying mechanism behind these circRNAs in gastric cancer (GC) remain to be elucidated. This study is aimed at conferring a better understanding of GC pathogenesis with a specific focus on circRNA-based ceRNA action. Methods. circRNA expression profiles were downloaded from two Gene Expression Omnibus (GEO) microarray datasets, GSE152309 and GSE121445. Expression profiles of miRNAs and mRNAs were collected from The Cancer Genome Atlas (TCGA) database. The ceRNA network was constructed based on circRNA-miRNA pairs and miRNA-mRNA pairs. Functional and pathway enrichment analyses were performed to evaluate functional pathways of differentially expressed mRNAs (DEmRNAs). The PPI network was constructed by mapping DEmRNAs into the STRING database to identify hub genes, and then the DEcircRNA-DEmiRNA-hub gene subnetwork was constructed. The expression levels of candidate differentially expressed circRNAs (DEcircRNAs) in cancerous and matched noncancerous gastric tissues surgically resected from 52 GC patients were determined by the RT-qPCR analysis. Results. Differential expression analysis with Venn diagram analysis showed 11 overlapped DEcircRNAs (7 upregulated circRNAs and 4 downregulated ones) between cancerous tissues and noncancerous gastric tissues. The DEcircRNA-DEmiRNA-DEmRNA network was constructed, consisting of 2 DEcircRNAs, 7 DEmiRNAs, and 104 DEmRNAs. GO and KEGG pathway analyses revealed that 104 DEmRNAs might be associated with GC development and progression. The PPI network was constructed, yielding 16 hub genes, TFDP1, KRAS, LMNB1, MET, MYBL2, CDC25A, E2F5, HMGA1, HMGA2, CBFB, CBX3, CDC7, IGF2BP3, KIF11, PDGFB, and SMC1A, which were all upregulated in GC tissues compared with adjacent tumor-free gastric tissues. Based on the above hub genes in GC, the DEcircRNA-DEmiRNA-hub gene subnetwork was reconstructed based on hsa_circ_0000384 and hsa_circ_0000043, including 22 pairs of the upcircRNA-downmiRNA-upmRNA network. The expression levels of hsa_circ_0000384 and hsa_circ_0000043 were remarkably higher in GC tissues than those in matched adjacent tumor-free gastric tissues (p<0.001), concurring with the bioinformatics results. Conclusion. Our study offers a better understanding of circRNA-related ceRNA regulatory mechanism in the pathogenesis of GC, highlighting two ceRNA networks based on hsa_circ_0000384 and hsa_circ_0000043. |
| format | Article |
| id | doaj-art-dbc81e982a0a4952a82b1ceaa535b536 |
| institution | OA Journals |
| issn | 2314-4378 |
| language | English |
| publishDate | 2022-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-dbc81e982a0a4952a82b1ceaa535b5362025-08-20T02:21:30ZengWileyInternational Journal of Genomics2314-43782022-01-01202210.1155/2022/5281846Identification of Novel circRNA-Based ceRNA Network Involved in the Pathogenesis of Gastric CancerDengfa Peng0Li Feng1Huqing Li2First Surgical DepartmentFirst Surgical DepartmentFirst Surgical DepartmentObjective. Evidence increasingly shows that circular RNAs (circRNAs) are closely associated with tumorigenesis and cancer progression. However, the roles of circRNAs and the underlying mechanism behind these circRNAs in gastric cancer (GC) remain to be elucidated. This study is aimed at conferring a better understanding of GC pathogenesis with a specific focus on circRNA-based ceRNA action. Methods. circRNA expression profiles were downloaded from two Gene Expression Omnibus (GEO) microarray datasets, GSE152309 and GSE121445. Expression profiles of miRNAs and mRNAs were collected from The Cancer Genome Atlas (TCGA) database. The ceRNA network was constructed based on circRNA-miRNA pairs and miRNA-mRNA pairs. Functional and pathway enrichment analyses were performed to evaluate functional pathways of differentially expressed mRNAs (DEmRNAs). The PPI network was constructed by mapping DEmRNAs into the STRING database to identify hub genes, and then the DEcircRNA-DEmiRNA-hub gene subnetwork was constructed. The expression levels of candidate differentially expressed circRNAs (DEcircRNAs) in cancerous and matched noncancerous gastric tissues surgically resected from 52 GC patients were determined by the RT-qPCR analysis. Results. Differential expression analysis with Venn diagram analysis showed 11 overlapped DEcircRNAs (7 upregulated circRNAs and 4 downregulated ones) between cancerous tissues and noncancerous gastric tissues. The DEcircRNA-DEmiRNA-DEmRNA network was constructed, consisting of 2 DEcircRNAs, 7 DEmiRNAs, and 104 DEmRNAs. GO and KEGG pathway analyses revealed that 104 DEmRNAs might be associated with GC development and progression. The PPI network was constructed, yielding 16 hub genes, TFDP1, KRAS, LMNB1, MET, MYBL2, CDC25A, E2F5, HMGA1, HMGA2, CBFB, CBX3, CDC7, IGF2BP3, KIF11, PDGFB, and SMC1A, which were all upregulated in GC tissues compared with adjacent tumor-free gastric tissues. Based on the above hub genes in GC, the DEcircRNA-DEmiRNA-hub gene subnetwork was reconstructed based on hsa_circ_0000384 and hsa_circ_0000043, including 22 pairs of the upcircRNA-downmiRNA-upmRNA network. The expression levels of hsa_circ_0000384 and hsa_circ_0000043 were remarkably higher in GC tissues than those in matched adjacent tumor-free gastric tissues (p<0.001), concurring with the bioinformatics results. Conclusion. Our study offers a better understanding of circRNA-related ceRNA regulatory mechanism in the pathogenesis of GC, highlighting two ceRNA networks based on hsa_circ_0000384 and hsa_circ_0000043.http://dx.doi.org/10.1155/2022/5281846 |
| spellingShingle | Dengfa Peng Li Feng Huqing Li Identification of Novel circRNA-Based ceRNA Network Involved in the Pathogenesis of Gastric Cancer International Journal of Genomics |
| title | Identification of Novel circRNA-Based ceRNA Network Involved in the Pathogenesis of Gastric Cancer |
| title_full | Identification of Novel circRNA-Based ceRNA Network Involved in the Pathogenesis of Gastric Cancer |
| title_fullStr | Identification of Novel circRNA-Based ceRNA Network Involved in the Pathogenesis of Gastric Cancer |
| title_full_unstemmed | Identification of Novel circRNA-Based ceRNA Network Involved in the Pathogenesis of Gastric Cancer |
| title_short | Identification of Novel circRNA-Based ceRNA Network Involved in the Pathogenesis of Gastric Cancer |
| title_sort | identification of novel circrna based cerna network involved in the pathogenesis of gastric cancer |
| url | http://dx.doi.org/10.1155/2022/5281846 |
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