CYP4B1 is a prognostic biomarker and potential therapeutic target in lung adenocarcinoma

Abstract

CYP4B1 belongs to the mammalian CYP4 enzyme family and is predominantly expressed in the lungs of humans. It is responsible for the oxidative metabolism of a wide range of endogenous compounds and xenobiotics. In this study, using data from The Cancer Genome Atlas (TCGA) project and the Gene Expression Omnibus (GEO) database, a secondary analysis was performed to explore the expression profile of CYP4B1, as well as its prognostic value in patients with lung adenocarcinoma (LUAD). Based on the obtained results, a significantly decreased CYP4B1 expression was discovered in patients with LUAD when compared with their normal counterparts (p<0.05), and was linked to age younger than 65 years (p = 0.0041), history of pharmaceutical (p = 0.0127) and radiation (p = 0.0340) therapy, mutations in KRAS/EGFR/ALK (p = 0.0239), and living status of dead (p = 0.0026). Survival analysis indicated that the low CYP4B1 expression was an independent prognostic indicator of shorter survival in terms of overall survival (OS) and recurrence-free survival (RFS) in patients with LUAD. The copy number alterations (CNAs) and sites of cg23440155 and cg23414387 hypermethylation might contribute to the decreased CYP4B1 expression. Gene set enrichment analysis (GSEA) suggested that CYP4B1 might act as an oncogene in LUAD by preventing biological metabolism pathways of exogenous and endogenous compounds and enhancing DNA replication and cell cycle activities. In conclusion, CYP4B1 expression may serve as a valuable independent prognostic biomarker and a potential therapeutic target in patients with LUAD.

Fig 1. CYP4B1 mRNA expression profiles in patients with LUAD from TCGA and GEO dataset cohorts.

(A–D) CYP4B1 mRNA expression in LUAD tissues and normal controls from a TCGA cohort (A), GSE30219 cohort (B), GSE31210 cohort (C) and GSE32863 cohort (D). (E) ROC curves showing the diagnostic value of CYP4B1 in LUAD (red curve, data from TCGA cohort; purple curve, data from GSE30219 cohort; blue curve, data from GSE32863 cohort; green curve, data from GSE31210 cohort). ****p<0.0001. LUAD, lung adenocarcinoma; TCGA, The Cancer Genome Atlas; GEO, Gene Expression Omnibus; ROC, receiver operating characteristic.

Fig 2. Low CYP4B1 expression was associated with unfavorable survival in patients with LUAD.

(A–C) Kaplan-Meier curves of OS in patients with LUAD from a TCGA cohort (A), GSE30219 cohort (B) and GSE31210 cohort (C). (D-F) Kaplan-Meier curves of RFS in patients with LUAD from a TCGA cohort (D), GSE30219 cohort (E) and GSE31210 cohort (F). LUAD, lung adenocarcinoma; OS, overall survival; TCGA, The Cancer Genome Atlas; RFS, recurrence-free survival.

Fig 3. Forest plots of Cox regression analysis.

(A) Forest plots showing univariate and multivariate analysis of OS in patients with LUAD. (B) Forest plots showing univariate and multivariate analysis of RFS in patients with LUAD. *p<0.05. OS, overall survival; LUAD, lung adenocarcinoma; RFS, recurrence-free survival.

Fig 4. CYP4B1 expression was modulated by its gene alterations and DNA methylation in LUAD.

(A) Genetic alterations of CYP4B1 in LUAD. (B) Heatmap of CYP4B1 expression, DNA copy number alterations (gistic2 linear and gistic2 thresholded), and DNA methylation (Methylation 450k). (C) CYP4B1 expression correlates with its linear copy number values by linear regression analysis. (D) DNA methylation level of cg23440155 and cg23414387 sites is significantly upregulated in LUAD tissues when compared with adjacent normal tissues. (E) CYP4B1 expression correlates with cg23440155 and cg23414387 methylation levels by a linear regression analysis. LUAD, lung adenocarcinoma.

Fig 5. Differentially expressed genes correlated with CYP4B1 in LUAD.

(A) Volcano plot showing differentially expressed genes significantly associated with CYP4B1 (FDR<0.05; |Pearson’s r|>0.2). (B, C) Heatmaps showing the top 50 significant genes positively and negatively correlated with CYP4B1 in LUAD. (D-F) The top three significant genes demonstrating positive co-expression with CYP4B1 in LUAD. (D) Pearson correlation of CYP4B1 expression with PEBP4, C16orf89, and SFTPD. (E) The mRNA expression profiles of PEBP4, C16orf89, and SFTPD in LUAD tissues when compared with normal lung tissues. (F) Survival analysis of PEBP4, C16orf89, and SFTPD in LUAD. FDR, false discovery rate; LUAD, lung adenocarcinoma.

Fig 6. Gene ontology and GSEA analysis categorized by the KEGG pathway of the genes co-expressed with CYP4B1 in TCGA-LUAD.

GSEA, Gene set enrichment analysis; KEGG, Kyoto Encyclopedia of Genes and Genomes; TCGA, The Cancer Genome Atlas; LUAD, lung adenocarcinoma.