Dataset Information

The Somatic Mutation Landscape and RNA Prognostic Markers in Stomach Adenocarcinoma.

ABSTRACT: Purpose:Stomach cancer is one of the highest incidence and mortality malignancies worldwide. Our study aimed to illustrate the somatic mutation landscape and identify molecular markers of stomach cancer. Materials and Methods:By integrated analysis of sequencing data and clinical data of stomach adenocarcinoma (STAD) from The Cancer Genome Atlas (TCGA) database, we identified several susceptibility genes and novel molecular markers and validated their potential function by the starBase website. Further, we validated the clinical value of two candidate lncRNAs in collected STAD samples by RT-qPCR. Results:We illustrated the distributions of mutation frequencies and types to get the top 20 high-mutation frequency genes in STAD. We also found 2127 mRNAs, 129 miRNAs, and 170 lncRNAs that were differentially expressed. We identified four lncRNA-miRNA-mRNA ceRNAs (PVT1, MAGI2-AS3, MIR17HG, KCNQ1OT1). Besides, 27 mRNAs (PDE4C, ID1, AQP3, VCAN, FAP, NOX4, ANGPT2, SERPINE1, SPARC, PDGFRB, FN1, MFAP2, CSMD2, INHBA, COL10A1, MATN3, P4HA3, ADAMTS12, DGKI, OLFML2B, TMEM200A, FNDC1, CTHRC1, CHST1, F5, COL5A2, TUBB3) and two lncRNAs (MIR4458HG, LINC01235) showed a significant prognostic value, and their prognostic values were validated by the starBase website. What's more, the clinical values of MIR4458HG and LINC01235 were also demonstrated in collected STAD samples. Conclusion:We constructed the lncRNA ceRNA networks and identified 20 high-mutation frequency genes and 29 prognostic markers (27 mRNAs and two lncRNAs).

SUBMITTER: Zhang X

PROVIDER: S-EPMC7414981 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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The Somatic Mutation Landscape and RNA Prognostic Markers in Stomach Adenocarcinoma.

Zhang Xiulei X Zheng Peiming P Li Zhen Z Gao Shanjun S Liu Guangzhi G

OncoTargets and therapy 20200804

<h4>Purpose</h4>Stomach cancer is one of the highest incidence and mortality malignancies worldwide. Our study aimed to illustrate the somatic mutation landscape and identify molecular markers of stomach cancer.<h4>Materials and methods</h4>By integrated analysis of sequencing data and clinical data of stomach adenocarcinoma (STAD) from The Cancer Genome Atlas (TCGA) database, we identified several susceptibility genes and novel molecular markers and validated their potential function by the sta ...[more]

PMID: 32801780

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Project description:BackgroundLong noncoding RNA-based prognostic biomarkers have demonstrated great potential in the diagnosis and prognosis of cancer patients. However, systematic assessment of a multiple lncRNA-composed prognostic risk model is lacking in stomach adenocarcinoma (STAD). This study is aimed at constructing a lncRNA-based prognostic risk model for STAD patients.MethodsRNA sequencing data and clinical information of STAD patients were retrieved from The Cancer Genome Atlas (TCGA) database. Differentially expressed lncRNAs (DElncRNAs) were identified using the R software. Univariate and multivariate Cox regression analyses were performed to construct a prognostic risk model. The survival analysis, C-index, and receiver operating characteristic (ROC) curve were employed to assess the sensitivity and specificity of the model. The results were verified using the GEPIA online tool and our clinical samples. Pearson correlation coefficient analysis, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were performed to indicate the potential biological functions of the selected lncRNA.ResultsA total of 1917 DElncRNAs were identified from 343 cases of STAD tissues and 30 cases of noncancerous tissues. According to univariate and multivariable Cox regression analyses, four DElncRNAs (AC129507.1, LINC02407, AL022316.1, and AP000695.2) were selected to establish a prognostic risk model. There was a significant difference in the overall survival between high-risk patients and low-risk patients based on this risk model. The C-index of the model was 0.652. The area under the curve (AUC) for the ROC curve was 0.769. GEPIA results confirmed the expression and prognostic significance of AP000695.2 in STAD. Our clinical data confirmed that upregulated expression of AP000695.2 was correlated with the T stage, distant metastasis, and TNM stage in STAD. GO and KEGG analyses demonstrated that AP000695.2 was closely related to the tumorigenesis process.ConclusionsIn this study, we constructed a lncRNA-based prognostic risk model for STAD patients. Our study will provide novel insight into the diagnosis and prognosis of STAD patients.

Dataset Information

The Somatic Mutation Landscape and RNA Prognostic Markers in Stomach Adenocarcinoma.

Publications

The Somatic Mutation Landscape and RNA Prognostic Markers in Stomach Adenocarcinoma.

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