Shared and specific competing endogenous RNAs network mining in four digestive system tumors
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Published on: November 30, 2016
Yulai Tang1,2,3, Aamir Fahira2, Siying Lin3
1Key Laboratory of Computer-Aided Drug Design of Dongguan City, The First Dongguan Affiliated Hospital, School of Pharmacy, Guangdong Medical University, Dongguan 523710, China.
Background:
Digestive system malignancies, including esophageal carcinoma (ESCA), stomach adenocarcinoma (STAD), liver hepatocellular carcinoma (LIHC), and colon adenocarcinoma (COAD), pose significant global health challenges. Identifying shared and distinct regulatory mechanisms across these cancers can lead to improved therapies. This study aims to construct and compare competing endogenous RNA (ceRNA) networks across ESCA, STAD, LIHC, and COAD to identify RNA biomarkers that could serve as precision therapeutic targets to enhance clinical outcomes and advance personalized cancer care.
Methods:
Clinical and transcriptomic data from The Cancer Genome Atlas (TCGA) were analyzed to predict differentially expressed RNAs using the edgeR package. The ceRNA networks were constructed using the miRcode and ENCORI databases. Functional enrichment analysis and prognostic RNA screening were performed with ConsensusPathDB and univariate Cox regression analysis.
Results:
we identified 6, 88, 55, and 41 RNA biomarkers in ESCA, STAD, LIHC, and COAD, respectively. Network analysis revealed shared and specific elements, with shared nodes enriched in cell cycle and mitotic processes. Several biomarkers, including HMGB3 and RGS16 (ESCA), COL4A1 and COL6A3 (STAD), CDCA5 and CDCA8 (LIHC), and LIMK1 and OSBPL3 (COAD), were consistent with prior studies, while novel biomarkers, such as C3P1 (ESCA), P2RY6 (STAD), and N4BP2L1 and PPP1R3B (LIHC), were discovered. Based on RNA correlation analysis, 1, 23, and 2 potential ceRNA regulatory axes were identified in STAD (PVT1/miR-490-3p/HMGA2), LIHC (DLX6-AS1/miR-139-5p/TOP2A, etc.), and COAD (STRCP1 & LINC00488/miR-142-3p/GAB1), respectively.
Conclusions:
This study advances the understanding of ceRNA networks in digestive cancers, highlighting RNA biomarkers with potential as therapeutic targets for personalized treatment strategies.
