Abstract PR03: A novel deaminase independent function of APOBEC3A catalyzes widespread chromosomal instability to drive an aggressive metastatic phenotype in pancreatic cancer

Abstract

Abstract Introduction: Apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3A (A3A), is an endogenous deaminase acting upon gDNA at specific sequence motifs to create C>T edits and is upregulated in a number of cancers. Large-scale sequencing studies have demonstrated an enriched APOBEC mutational signature in a variety of solid tumors, indicating a strong mutagenic role of APOBEC in cancer. Although A3A has been found to be overexpressed and associated with poor overall survival in hPDACs (TCGA), a rather weak APOBEC mutational signature is present in hPDACs, leading us to the hypothesis that A3A may drive independent of its ability to create point mutations, an aggressive tumor burden in hPDAC. Here, we established a genetically engineered mouse model (GEMM) to unravel the novel function of A3A beyond its deaminase activity in PDAC. Methods: Unlike humans, mice have only one APOBEC3 isoform, lacking genomic DNA deaminase activity. Thus, to model A3A independent of its deaminase function in PDAC we generated a A3A (Exon1/2) transgenic mouse that we bred to a well-established GEMM of PDAC, yielding LSL-KrasG12D; p53fl/+; Pdx1-Cre; RosaLSL-YFP; hAPOBEC3A+/- (hA3A; PKCY) mice. hA3A;PKCY tumors were genotyped with Ilumina exome capture sequencing, whole-genome sequencing, and comparative RNAseq. In addition, PKCY tumors cells expressing deaminase deficient and competent A3A were analyzed for chromosomal instability (CIN) and metastatic capacity. Results: Although high expression of A3A was associated with significantly shorter survival in hPDACs (p=0.04; n=178 (TCGA)), levels of A3A did not correlate with the overall mutational rate. Interestingly, deaminase-deficient A3A mice (hA3A;PKCY) (n=29) expired significantly faster than PKCY (n=40) controls (p<0.0001). 62% of hA3A;PKCY mice developed macrometastatic disease compared to 38% in PKCY controls. While no difference in mutational burden was obvious, a significant increase in DNA damage, micronuclei, metaphases breaks, and anaphase bridges in deaminase-deficient A3A tumors was observed. WGS analysis revealed that hA3A;PKCY tumors harbored significantly more translocations, wide-scale deletions, and unique copy number alterations, suggesting that A3A independent of its deaminase function initiates CIN. Interestingly, a signature of deep deletions uniquely found in hA3A;PKCY tumors was also found in 6-9% of resected hPDACs, suggesting that A3A mediates a BRCAness phenotype defining tumor biology and a treatment-responsive subgroup of hPDACs. Conclusions: Our study suggests that A3A beyond deaminase function and creating point mutations may drive CIN and a more aggressive and metastatic phenotype in PDAC. As opposed to mutagenesis, we found that the more relevant and novel deaminase independent function of A3A is initiation of widespread CIN, SVs and copy number alterations. We unraveled an A3A-mediated BRCAness signature of deep deletion that could be used in PDAC patients to predict tumor biology, outcome, and therapeutic response. This abstract is also being presented as Poster A56. Citation Format: Sonja Maria Woermann, Robert Cowan, Susan M. Ross, Andrew D. Rhim. A novel deaminase independent function of APOBEC3A catalyzes widespread chromosomal instability to drive an aggressive metastatic phenotype in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr PR03.