Research Paper Volume 12, Issue 16 pp 16238—16254
Prognostic values of GPNMB identified by mining TCGA database and STAD microenvironment
- 1 Henan University, Kaifeng 475000, Henan, P.R. China
- 2 Department of General Surgery, Huaihe Hospital of Henan University, Kaifeng 475000, Henan, P.R. China
- 3 Department of Urology, Huaihe Hospital of Henan University, Kaifeng 475000, Henan, P.R. China
- 4 Department of Gastroenterology, Huaihe Hospital of Henan University, Kaifeng 475000, Henan, P.R. China
Received: February 28, 2020 Accepted: June 19, 2020 Published: August 21, 2020
https://doi.org/10.18632/aging.103646How to Cite
Copyright © 2020 Yao et al. This is an open-access article distributed under the terms of the Creative Commons Attribution (CC BY) 3.0 License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
The survival rate of stomach adenocarcinoma patients with immune and stromal scores and different clinicopathological features obtained from the TCGA datasets was systematically compared. A list of genes that are correlated with stomach adenocarcinoma microenvironment were extracted using the TCGA database to predict the prognosis and survival. In addition, the differentially expressed genes were extracted by comparing the immune and stromal scores of the groups. The protein-protein interaction network, and functional and pathway enrichment analyses of differentially expressed genes were performed. A total of 8 hub genes were selected from the differentially expressed genes to predict the overall survival and disease-free survival rates. GPNMB was selected from the hub genes based on the survival and prognosis analyses. A nomogram was built by including the potential risk factors based on multivariate Cox analysis. Cell function experiments and xenograft tumors were conducted in vivo to further verify the role of GPNMB in tumor progression. The predicted microRNA, miR-30b-3p, might act as upstream negative regulator and binding to 3’ UTR of GPNMB, confirming by fluorescent enzyme reporter gene experiment. In summary, immune-related scores are crucial factors in the malignant progression of stomach adenocarcinoma and GPNMB acts as a potentially useful prognostic factor for stratification and in developing the treatment strategy
Abbreviations
STAD: Stomach adenocarcinoma; TCGA: The Cancer Genome Atlas; GPNMB: Glycoprotein non-metastatic melanoma protein B; PCA: principal component analysis; ROC: receiver operating characteristic; DEGs: Differentially Expressed Genes; Pca: Prostate cancer; FDR: False Discovery Rate; TIMER: Tumor IMmune Estimation Resource.