Genetic mechanism of β-alanine metabolic pathway affecting colorectal cancer prognosis

Abstract

Background: Colorectal cancer (CRC) is a common cause of cancer-related mortality and is mainly influenced by metabolic dysfunction. The β-alanine metabolic pathway plays an important role in altering the aggressiveness and metabolic characteristics of the cancer cells. This study aimed to investigate the genetic role of the β-alanine metabolic pathway in CRC patient survival.

Methods: Using a Cox regression model, we assessed the impact of 27 single-nucleotide polymorphisms (SNPs) from 31 genes in the β-alanine metabolic pathway on overall survival (OS) and progression-free survival (PFS) in 287 patients with CRC. Additional methods, including differential expression analysis, expression quantitative trait loci analysis, dual-luciferase reporter assay, and cell phenotype assay, were used to evaluate the genetic function of candidate SNPs in tumor progression.

Results: We identified that SNP rs2811182 A > G allele located in DPYD was significantly associated with poorer prognosis of CRC, with hazard ratio (HR) of 0.63 for OS [95% confidence interval (CI) = 0.45-0.88, P = 7.12 × 10^-3] and 0.68 for PFS (95% CI = 0.52-0.89, P = 5.01 × 10^-3). Mechanistically, the G allele of rs2811182 increased DPYD transcriptional activity and expression by mediating the binding affinity of the transcription factor POU1F1. Importantly, the overexpression of DPYD reduced the malignant cell phenotypes of proliferation, migration, and invasion.

Conclusions: This study indicates a pivotal genetic role for the β-alanine metabolic pathway, particularly rs2811182 in DPYD, in influencing CRC prognosis. These findings offer new perspectives for personalized treatment strategies and enhance our understanding of CRC pathogenesis.

Keywords: Beta-alanine metabolism; Colorectal cancer; Prognosis; Single-nucleotide polymorphisms.

Fig. 1

The flow chart of selecting SNPs in β-alanine metabolic pathway genes. DEGs, differentially expressed genes; MAF, minor allele frequency; HWE, HardyWeinberg Equilibrium; LD, linkage disequilibrium; SNP, single nucleotide polymorphism; OS, overall survival

Fig. 2

Kaplan–Meier curves of OS and PFS for rs2811182 in CRC patients. A-B Dominant model. C-D Additive model. Patients with incomplete genotype and endpoint information were excluded. Multivariate Cox regression analysis was used to calculate hazard ratios (HRs) and their 95% confidence intervals (CIs), as well as P values. OS, overall survival; PFS, progression-free survival

Fig. 3

Stratified analysis of the association between DPYD rs2811182 and clinical outcomes in CRC patients under the dominant genetic model. A Overall survival (OS); B Progression-free survival (PFS). CI: confidence interval; HR: hazard ratio. Pa: Adjusted for sex, age, smoking, drinking, and Dukes stage in the Cox regression model. Pb: P-value for heterogeneity

Fig. 4

Effect of rs2811182 allele on DPYD. A The eQTL analysis for the genetic effect of rs2811182 on DPYD expression in colorectal cancer according to the data from the TCGA database; B-C Luciferase activity was assessed 24 h after transfection of POU1 F1 siRNA or overexpression plasmids into DLD-1 and HCT116 cell lines; D-G RT-qPCR was employed to measure DPYD transcript levels following POU1 F1 knockdown (D-E) or overexpression (F-G)

Fig. 5

Expression pattern of DPYD in colorectal cancer (CRC) tissues. A Relative DPYD expression in unpaired CRC samples from the TCGA database. B–C Relative DPYD expression in paired CRC samples from the in-house dataset. D–E DPYD expression levels in CRC tissues from GEO datasets (D: GSE106582; E: GSE74602). Statistical comparisons were performed using unpaired or paired t tests, as appropriate. F–G Immunohistochemical analysis showing reduced DPYD protein levels in tumor tissues compared with adjacent normal tissues (magnification × 200)

Fig. 6

DPYD inhibited proliferation, migration and invasion of CRC cells. A-B Effect of DPYD overexpression on proliferation of CRC cells via CCK-8 assay. C-D Effect of DPYD overexpression on migration and invasion of CRC cells via colony formation assay. E–F Effect of DPYD overexpression on proliferation of CRC cells via transwell assay