Shared and specific competing endogenous RNAs network mining in four digestive system tumors

• Published in: Computational and structural biotechnology journal 2024-12, Vol.23, p.4271-4287
• Main Authors: Tang, Yulai, Fahira, Aamir, Lin, Siying, Shao, Yiming, Huang, Zunnan
• Format: Article
• Language: English
• Subjects: Competing endogenous RNA; Cross-cancer analysis; Digestive system tumor; Prognosis
• ISSN: 2001-0370; 2001-0370
• DOI: 10.1016/j.csbj.2024.11.005

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. 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. 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. This study advances the understanding of ceRNA networks in digestive cancers, highlighting RNA biomarkers with potential as therapeutic targets for personalized treatment strategies. [Display omitted] •Distinct and shared differentially expressed lncRNAs, miRNAs, and mRNAs identified across four digestive cancers.•ceRNA networks revealed shared, semi-shared, and specific lncRNA-miRNA-mRNA interactions for ESCA, STAD, LIHC, and COAD.•Prognostic analysis identified key RNA nodes with significant prognostic value across ESCA, STAD, LIHC, and COAD.•Semi-shared ceRNA axes are more prevalent than shared or specific axes across digestive system tumors.•Potential biomarkers include N4BP2L1 and PPP1R3B in LIHC, P2RY6 in STAD, and C3P1 in ESCA suggest precision medicine avenues.