Differential effects on tumor progression by APOBEC3A, APOBEC3B, and APOBEC3H Haplotype I in a breast cancer mouse xenograft model

The APOBEC3 (A3) family of cytidine deaminases induce somatic mutations that are highly prevalent in cancers, but the functional consequences are largely unknown. To determine functional consequences we exposed MCF7 tumorigenic breast epithelial cells to APOBEC3A, APOBEC3B or APOBEC3H Haplotype I. Comparative analysis between cells pre and post -APOBEC3 exposure revealed fewer deamination-dependent ?H2AX foci post-APOBEC3 exposure, despite maintaining A3 protein expression. In a mouse xenograft model, high expressing, but not low expressing APOBEC3A-exposed cells caused increased tumor progression. In contrast, high expressing, but not low expressing APOBEC3B-exposed cells decreased tumor size. APOBEC3H Haplotype I-exposed cells stochastically increased tumor progression independent of expression levels. Consistent with tumor data, RNA-seq showed upregulation of tumor enhancing pathways only in cells that enhanced tumor progressiongrowth. The results indicate that in a breast cancer xenograft model, APOBEC3A and APOBEC3H Haplotype I are more likely to contribute to enhanced tumor progression than APOBEC3B. Overall design: MCF7 cells were engineered to express doxycycline inducible APOBEC3A, APOBEC3B, or APOBEC3H Haplotype I (APOBEC3H). Cells were (Induced, I) or were not exposed (Uninduced, U) to doxycycline for 3 weeks in soft agar. Cells were then isolated, RNA extracted and sequenced. Isogenic cells lines were compared in Induced (I) versus Uninduced (U) pairs as follows: APOBEC3A_I4 vs APOBEC3A_U1 (APOBEC3A low expression), APOBEC3A_I5 vs APOBEC3A_U6 (APOBEC3A high expression), APOBEC3B_I2 vs APOBEC3B_U1 (APOBEC3B high expression), APOBEC3B_I5 vs APOBEC3B_U2 (APOBEC3B low expression), APOBEC3H_I4 vs APOBEC3H_U1 (APOBEC3H High 1), APOBEC3H_I1 vs APOBEC3H_U2 (APOBEC3H High 2)