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Quantification of ongoing APOBEC3A activity in tumor cells by monitoring RNA editing at hotspots.

  • Author(s): Jalili, Pégah
  • Bowen, Danae
  • Langenbucher, Adam
  • Park, Shinho
  • Aguirre, Kevin
  • Corcoran, Ryan B
  • Fleischman, Angela G
  • Lawrence, Michael S
  • Zou, Lee
  • Buisson, Rémi
  • et al.
Abstract

APOBEC3A is a cytidine deaminase driving mutagenesis, DNA replication stress and DNA damage in cancer cells. While the APOBEC3A-induced vulnerability of cancers offers an opportunity for therapy, APOBEC3A protein and mRNA are difficult to quantify in tumors due to their low abundance. Here, we describe a quantitative and sensitive assay to measure the ongoing activity of APOBEC3A in tumors. Using hotspot RNA mutations identified from APOBEC3A-positive tumors and droplet digital PCR, we develop an assay to quantify the RNA-editing activity of APOBEC3A. This assay is superior to APOBEC3A protein- and mRNA-based assays in predicting the activity of APOBEC3A on DNA. Importantly, we demonstrate that the RNA mutation-based APOBEC3A assay is applicable to clinical samples from cancer patients. Our study presents a strategy to follow the dysregulation of APOBEC3A in tumors, providing opportunities to investigate the role of APOBEC3A in tumor evolution and to target the APOBEC3A-induced vulnerability in therapy.

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