Dataset Information

Utility of GDF-15 as a diagnostic biomarker in gastric cancer: an investigation combining GEO, TCGA and meta-analysis.

ABSTRACT: It was recently suggested that growth differentiation factor-15 (GDF-15) is associated with gastric cancer (GC) carcinogenesis. However, the diagnostic potential of GDF-15 for GC remains unclear. To address this issue, we obtained RNA sequencing and microarray data from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases, and searched PubMed, Google Scholar and Web of Science for relevant literature. We then used STATA to perform a meta-analysis. In total, reports of 253 GC patients and 112 healthy controls who contributed peripheral blood samples were taken from the four literature sources, while information on 754 GC tumor and 263 gastric normal tissues was drawn from TCGA and seven GEO datasets. The expression level of GDF-15 mRNA was significantly higher in tumor tissues than in normal tissues, with a standard mean difference (SMD) of 0.79% and a 95% confidence interval (95% CI) of 0.63-0.95. Consistently, the GDF-15 protein in blood was significantly increased in GC patients as compared to controls (SMD = 3.74, 95% CI = 1.81-5.68). In addition, based on information from TCGA and GEO datasets, the expression level of GDF-15 mRNA may be of use for the diagnosis of GC, with a combined sensitivity, specificity and odds ratio of 0.69 (95% CI = 0.58-0.79), 0.90 (95% CI = 0.84-0.93) and 6.32 (95% CI = 4.22-9.49), respectively. The summary receiver operating characteristic curve demonstrated that the area under the curve was 0.90 (95% CI = 0.87-0.93). The results suggest higher levels of GDF-15 may be associated with GC tumorigenesis and may have the potential to be a diagnostic biomarker of GC.

SUBMITTER: Liu JY

PROVIDER: S-EPMC6325603 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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Utility of GDF-15 as a diagnostic biomarker in gastric cancer: an investigation combining GEO, TCGA and meta-analysis.

Liu Jie-Yu JY Dong Xing-Xuan XX Lu Jia-Nan JN Zhang Yue Y Liu Kai-Fan KF Liu Ling-Feng LF E Qing-Zhi QZ Lu Xiao-Jing XJ Yin Jie-Yun JY Shen Yue-Ping YP

FEBS open bio 20181128 1

It was recently suggested that growth differentiation factor-15 (GDF-15) is associated with gastric cancer (GC) carcinogenesis. However, the diagnostic potential of GDF-15 for GC remains unclear. To address this issue, we obtained RNA sequencing and microarray data from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases, and searched PubMed, Google Scholar and Web of Science for relevant literature. We then used STATA to perform a meta-analysis. In total, reports of 2 ...[more]

PMID: 30652072

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Project description:Increasing evidence has demonstrated that microRNA (miR)‑133a‑3p is an important regulator of hepatocellular carcinoma (HCC). In the present study, the diagnostic role of miR‑133a‑3p in HCC, and the potential functional pathways, were both explored based on publicly available data. Eligible microarray datasets were collected from NCBI Gene Expression Omnibus (GEO) database and ArrayExpress database. The data related to HCC and matched adjacent normal tissues were also downloaded from The Cancer Genome Atlas (TCGA). Published studies reporting the association between miR‑133a‑3p expression and HCC were reviewed from multiple databases. By combining the data derived from three sources (GEO, TCGA and published studies), the authors analyzed the comprehensive relationship between miR‑133a‑3p expression and clinicopathological features of HCC. Eventually, putative targets of miR‑133a‑3p in HCC were selected for further bioinformatics prediction. A total of eight published microarray datasets were gathered, and the pooled results demonstrated that the expression of miR‑133a‑3p in the tumor group was lower than that in normal groups [standardized mean difference (SMD)=‑0.54; 95% confidence interval (CI), ‑0.74 to ‑0.35; P<0.001]. Consistently, the level of miR‑133a‑1 in HCC was reduced markedly compared to normal tissues (P<0.001) based on TCGA data, and the AUC value of low miR‑133a‑1 expression for HCC diagnosis was 0.670 (P<0.001). Furthermore, the combined SMD of all datasets (GEO, TCGA and literature) suggested that significant difference was observed between the HCC group and the normal control group, and lower miR‑133a‑3p expression in HCC group was noted (SMD=‑0.69; 95% CI, ‑1.10 to ‑0.29; P=0.001). In addition, the authors discovered five key genes of the calcium signaling pathway (NOS1, ADRA1A, ADRA1B, ADRA1D and TBXA2R) that may probably be targeted by miR‑133a‑3p in HCC. The study reveals that miR‑133a‑3p may function as a tumor suppressor in HCC. The prospective novel pathways and key genes of miR‑133a‑3p could offer potential biomarkers for HCC; however, the predictions require further confirmation.

Dataset Information

Utility of GDF-15 as a diagnostic biomarker in gastric cancer: an investigation combining GEO, TCGA and meta-analysis.

Publications

Utility of GDF-15 as a diagnostic biomarker in gastric cancer: an investigation combining GEO, TCGA and meta-analysis.

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