Based on the Cancer Genome Atlas Database Development of a prognostic model of RNA binding protein in stomach adenocarcinoma

Sayed Haidar Abbas Raza; Ruimin Zhong; Shen Xing; Xiaoting Yu; Liang Chengcheng; Linsen Zan; Nicola M Schreurs; Sameer D Pant; Hongtao Lei

doi:10.1016/j.compbiomed.2023.107307

Based on the Cancer Genome Atlas Database Development of a prognostic model of RNA binding protein in stomach adenocarcinoma

Comput Biol Med. 2023 Sep:164:107307. doi: 10.1016/j.compbiomed.2023.107307. Epub 2023 Jul 31.

Authors

Sayed Haidar Abbas Raza¹, Ruimin Zhong², Shen Xing³, Xiaoting Yu³, Liang Chengcheng⁴, Linsen Zan⁴, Nicola M Schreurs⁵, Sameer D Pant⁶, Hongtao Lei⁷

Affiliations

¹ Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, 512005, China.
² Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, 512005, China.
³ Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China.
⁴ College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
⁵ Animal Science, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand.
⁶ Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia.
⁷ Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China. Electronic address: hongtao@scau.edu.cn.

PMID: 37544249
DOI: 10.1016/j.compbiomed.2023.107307

Abstract

The purpose of this study was to identify potential RNA binding proteins associated with the survival of gastric adenocarcinoma, as well as the corresponding biological characteristics and signaling pathways of these RNA binding proteins. RNA sequencing and clinical data were obtained from the cancer genome map (N = 32, T = 375) and the comprehensive gene expression database (GSE84437, N = 433). The samples in The Cancer Genome Atlas were randomly divided into a development group and a test group. A total of 1495 RNA binding protein related genes were extracted. Using nonparametric tests to analyze the difference of RNA binding protein related genes, 296 differential RNA binding proteins were obtained, 166 were up-regulated and 130 were down regulated. Twenty prognosis-related RNA binding proteins were screened using Cox regression, including 14 high-risk genes (hazard ratio > 1.0) and 6 low-risk genes (hazard ratio < 1.0). Seven RNA binding protein related genes were screened from the final prognostic model and used to construct a new prognostic model. Using the development group and test group, the model was verified with survival analysis, receiver operating characteristics curves and prognosis analysis curves. A prediction nomogram was finally developed and showed good prediction performance.

Keywords: Gene expression omnibus (GEO); RNA binding protein (RBP); Stomach adenocarcinoma (STAD); The Cancer Genome Atlas (TCGA).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adenocarcinoma* / genetics
Humans
Prognosis
RNA-Binding Proteins / genetics
Stomach Neoplasms* / genetics

Substances

RNA-Binding Proteins