LAUSR

APOBEC3‐related somatic mutations are predominant in biliary tract cancers (BTCs). We aimed to elucidate the roles of APOBEC3A/3B functional polymorphisms and their influencing factors on the development of cholangiocarcinoma (CCA) and gallbladder cancer (GBC). Polymorphisms at the promoter regions of APOBEC3A and APOBEC3B were genotyped in 3231 participants using quantitative PCR. Dual‐luciferase reporter assay was applied to investigate the promoter activity. The difference in gene accessibility between CCA cells and GBC cells was analyzed through single‐cell transposase accessible chromatin sequencing. The effect of APOBEC3A on apoptosis was examined by cytometry. It is found that rs2267401‐G at the APOBEC3B promoter decreases CCA risk (age‐, gender‐adjusted odds ratio [AOR], 0.69; 95% confidence interval [CI], 0.51‐0.94) but increases GBC risk (AOR, 2.04; 95% CI, 1.35‐3.10). rs2267401‐G confers a decreased APOBEC3B promoter activity in CCA cells but an increased activity in GBC cells, possibly because the transcriptional repressor TFAP2A is over‐expressed in CCA. Tumor necrosis factor‐α (TNF‐α) increases the level of APOBEC3B via inhibiting TFAP2A expression rather than directly increasing the accessibility of APOBEC3B promoter. APOBEC3A promoter rs12157810‐C decreased the risks of CCA and GBC, with an AOR (95% CI) of 0.80 (0.66‐0.97) and 0.75 (0.59‐0.95), respectively. rs12157810‐C upregulated the promoter activity in both CCA and GBC cells. TNF‐α upregulated the activity of the APOBEC3A promoter with rs12157810‐C via increasing the accessibility of Ets‐1 p68. APOBEC3A overexpression attenuates cancer evolution by causing apoptosis, in contrast to APOBEC3B. The heterogeneity in the transcriptional regulation of APOBEC3B affects the evolutionary potential of cancer cells in the inflammatory microenvironment.