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ORIGINAL RESEARCH article

Front. Genet.
Sec. Cancer Genetics and Oncogenomics
Volume 15 - 2024 | doi: 10.3389/fgene.2024.1418818

Construction of prognostic model via WGCNA combined LASSO algorithm for stomach adenocarcinoma patient

Provisionally accepted
Zi-Duo Huang Zi-Duo Huang 1Wen-Hua Ran Wen-Hua Ran 1Guo-zhu Wang Guo-zhu Wang 2*
  • 1 Qianjiang Central Hospital of Chongqing, Chongqing, China
  • 2 Nanjing First Hospital, Nanjing Medical University, Nanjing, China

The final, formatted version of the article will be published soon.

    Objective: This study aimed to identify prognostic signatures to predict the prognosis of patients with stomach adenocarcinoma (STAD), which is necessary to improve poor prognosis and offer possible treatment strategies for STAD patients.The overlapping genes between the key model genes that were screened by the Weighted Gene Co-expression Network Analysis (WGCNA) and differential expression genes (DEGs) whose expression was different with significance between normal and tumor tissue were extracted to serve as co-expression genes. Then, those genes were performed enrichment analysis. Furthermore, the Least Absolute Shrinkage and Selection Operator regression (LASSO) was performed to screen the 2 hub genes among overlapping genes. Lastly, we constructed a model to explore the influence of polygenic risk scores on the survival probability of patients with STAD, and interaction effect analysis and mediating analysis were also performed.The DEGs included 2899 upregulated genes and 2896 downregulated genes. After crossing the DEGs and light-yellow module genes that were obtained by WGCNA a total of 39 overlapping genes were extracted. The gene enrichment analysis revealed that these genes were enriched in the prion diseases, biosynthesis of unsaturated fatty acids, RNA metabolic process, hydrolase activity, etc. PIP5K1P1, PTTG3P, and SNORD15B were determined by LASSO-cox. The prognostic prediction of the 3 genes model was established. The Cox regression analysis showed that the comprehensive risk score for 3 genes was an independent prognosis factor. Conclusion: PIP5K1P1, PTTG3P, and SNORD15B are related to the prognosis and overall survival of patients. The 3 genes risk model constructed has an independent prognosis predictive ability for STAD.

    Keywords: Stomach adenocarcinoma, Prognostic signature, WGCNA, LASSO, Mediating analysis

    Received: 17 Apr 2024; Accepted: 24 Jul 2024.

    Copyright: © 2024 Huang, Ran and Wang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Guo-zhu Wang, Nanjing First Hospital, Nanjing Medical University, Nanjing, China

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.