Value of brain-expressed X-linked family genes in the diagnosis and prognosis prediction of pan-cancer
10.3760/cma.j.cn115355-20220704-00420
- VernacularTitle:脑表达X连锁家族基因在泛癌诊断和预后预测中的价值
- Author:
Min YANG
1
;
Jiaxin FAN
;
Lin CHEN
;
Jiansheng GUO
Author Information
1. 山西医科大学第一临床医学院，太原 030001
- Keywords:
Genes, X-linked;
Pan-cancer;
Brain-expressed X-linked;
Biomarkers;
Prognosis;
Tumor microenvironment
- From:
Cancer Research and Clinic
2023;35(4):291-298
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To investigate the differential expression of brain-expressed X-linked (BEX) family genes in pan-cancer and its value in diagnosis and prognosis of pan-cancer.Methods:RNA sequencing (RNA-seq) data, survival data, immune subtypes, the stem cell scores based on RNA and DNA methylation of 33 different tumors from The Cancer Genome Atlas (TCGA) database were downloaded from the online database of University of California, Santa Cruz (UCSC Xena) on April 10, 2022. The limma package of R software (V.4.2.0) was used to analyze the expression of BEX family genes in the TCGA database. The differential expression of BEX family genes in pan-cancer tissues and normal tissues was compared by using Wilcox test. Pan-cancer patients were divided into high expression group and low expression group according to the median expression level of BEX family genes; Kaplan-Meier survival analysis was used to evaluate the relationship between the expression of BEX family genes and the overall survival (OS) of patients; Cox proportional risk model was used to analyze the effect of the expression of BEX family genes on OS in pan-cancer patients and then the forest map was drawn. The correlation of the expression of BEX family genes with tumor microenviroment and tumor stem cells in pan-cancer patients was analyzed based on the correlation index Cor value. Spearman correlation analysis was used to analyze the correlation between the expression of BEX family genes and tumor microenviroment and cancer stem cell index in gastric cancer tissues. The RNA-seq of different tumor cell lines and drug sensitivity data download from the CellMiner database were used to analyze the correlation between the expression of BEX family genes and drug sensitivity. The correlation of pan-cancer and gastric cancer immune subtypes with the expression of BEX family genes was analyzed by using Kruskal test.Results:BEX3 was highly expressed in pan-cancer tissues in TCGA database, BEX2 and BEX4 were moderately expressed in pan-cancer tissues, and BEX1 and BEX5 were relatively low expressed in pan-cancer tissues. The expressions of BEX2, BEX3 and BEX4 were the highest in cholangiocarcinoma, the expression of BEX5 was the highest in endometrial neoplasms, and the expression of BEX1 was the highest in invasive breast cancer. Compared with normal tissue samples, the expressions of BEX family genes were up-regulated or down-regulated in various cancers (all P < 0.05). Survival analysis showed that the expressions of BEX family genes were associated with the OS of various cancers. Some tumor patients with high expressions of BEX1, BEX3, BEX4 and BEX5 had better OS compared with those with low expressions, and the differences were statistically significant (all P < 0.05). Other patients with high expression of BEX family genes had worse OS compared with those with low expressions, and the differences were statistically significant (all P < 0.05). Cox regression analysis showed that the high expression of BEX1 for stomach neoplasms; the high expression of BEX2 for acute myeloid leukemia, thymoma and endometrial neoplasms; the expression high of BEX3 for squamous cell carcinoma of head and neck,sarcoma, stomach neoplasms and endometrial neoplasms; the high expression of BEX4 for rectal adenocarcinoma, stomach neoplasms and endometrial neoplasms; the high expression of BEX5 for renal suspicious cell carcinoma and thymoma were risk factors for OS (all P < 0.05).The expression of BEX family genes was negatively correlated with the stromal score of most cancers (all P < 0.05), and positively correlated with the stem cell score (all P < 0.05). The expression of BEX family genes was negatively correlated with cancer stem cell index of gastric cancer ( P < 0.05), and was positively correlated with matrix score and estimated total score (all P < 0.05). Among different tumor cell lines in CellMiner database, BEX family genes were closely related to drug resistance of vemurafenib (Cor = -0.368, P = 0.004), Kahalide f (Cor = -0.391, P = 0.002), O-6-benzylguanine (Cor = -0.375, P = 0.003) and other drugs. All genes in the BEX family were related to the immune subtypes of pan-cancer and were highly expressed in C5 subtype (all P < 0.05).For gastric cancer, all genes showed high expression in the C3 subtype (all P < 0.05), except BEX5 ( P = 0.24). Conclusions:The expression of BEX family genes is closely related to the prognosis of pan-cancer patients, and has an impact on the tumor microenvironment, cancer stem cells and drug sensitivity. BEX family genes may be potential biomarkers for diagnosis and prognosis of pan-cancer.
