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

Pégah Jalili; Danae Bowen; Adam Langenbucher; Shinho Park; Kevin Aguirre; Ryan B Corcoran; Angela G Fleischman; Michael S Lawrence; Lee Zou; Rémi Buisson

doi:10.1038/s41467-020-16802-8

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

Nat Commun. 2020 Jun 12;11(1):2971. doi: 10.1038/s41467-020-16802-8.

Authors

Pégah Jalili¹, Danae Bowen¹, Adam Langenbucher², Shinho Park¹, Kevin Aguirre¹, Ryan B Corcoran², Angela G Fleischman³, Michael S Lawrence^{4

5

6}, Lee Zou^{7

8}, Rémi Buisson^{9

10}

Affiliations

¹ Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA.
² Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA.
³ Department of Medicine, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA.
⁴ Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA. mslawrence@mgh.harvard.edu.
⁵ Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. mslawrence@mgh.harvard.edu.
⁶ Broad Institute of Harvard and MIT, Cambridge, MA, USA. mslawrence@mgh.harvard.edu.
⁷ Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA. zou.lee@mgh.harvard.edu.
⁸ Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. zou.lee@mgh.harvard.edu.
⁹ Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA. rbuisson@uci.edu.
¹⁰ Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA. rbuisson@uci.edu.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Cell Line
Cell Line, Tumor
Cytidine Deaminase / genetics*
Cytidine Deaminase / metabolism
Enzyme Assays / methods
Exome Sequencing / methods
Gene Expression Regulation, Neoplastic*
HEK293 Cells
Humans
Mutation*
Neoplasms / genetics*
Neoplasms / metabolism
Neoplasms / pathology
Proteins / genetics*
Proteins / metabolism
RNA Editing*
RNA Interference

Substances

Proteins
APOBEC3A protein, human
Cytidine Deaminase

Abstract

Publication types

MeSH terms

Substances

Grants and funding