Mutagenic properties of APOBEC family protein in the human normal stomach organoid

Abstract

APOBEC family of proteins is presumed to generate single nucleotide variants (SNVs) in TCN context in various types of cancers beyond a notable role, the host defense mechanism. Among the 11 types of APOBEC family of proteins, APOBEC3A and APOBEC3B are presumed to be major mutagens. There have been only researches about APOBEC mediated mutations after overexpression of human APOBEC proteins in the non-human model system. In this study, changes in DNA and RNA induced by the APOBEC family of proteins were investigated through whole-genome and transcriptome sequencing analysis with organoids derived from normal human gastric stem cells that can overexpress APOBEC3A and APOBEC3B with doxycycline treatment. APOBEC3A showed strong mutagenicity on DNA regardless of TP53 gene knock-out, but APOBEC3B generated a few SNVs only after TP53 gene knock-out. Meanwhile, both APOBEC protein generated lots of RNA editing regardless of TP53 gene knock-out. Preferences on sequence contexts of APOBEC3A and APOBEC3B were different in DNA and RNA. d1c1 type deletion in DNA on TCW (W=A or T) context nearby T or A repeat sequences was increased as an expression level of APOBEC3A increased. Elevated expression of CDKN1A after overexpression of APOBEC proteins appears to induce cell cycle arrest at G1 phase. An increased expression level of DDB2 was only observed after APOBEC3A overexpression, but not genes related to base excision repair. In addition, upregulation of infection and inflammation related genes were observed. This study firstly revealed the context specificity of mutations in DNA and RNA by APOBEC3A and APOBEC3B and changes in the transcriptome of cells in normal human gastric cells.