Collateral genomic damage due to aberrant RNA editing activity in cancer

RNA editing is an epitranscriptomic modification of rising prominence in health and disease. It is catalyzed by enzymes from the families of 'Adenosine Deaminases Acting on RNA’ (ADAR) or ‘Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like’ (APOBEC). Multiple RNA editing deaminases, however, not only can they edit RNA, but also mutate DNA. ADARs particularly, are naturally capable of editing dsRNA co-transcriptionally, as well as mutating DNA in DNA/RNA hybrids. Although, the mutagenic role of ADARs is well-studied in vitro, its relevance with in vivo models has yet to be explored. DNA/RNA hybrids (or R-loops) form co-transcriptionally in the human genome between the nascent RNA and the template DNA strand, and I hypothesized that ADARs can access them to mutate the DNA strand in the hybrid, after losing touch with the nascent RNA-target. Here, I focus on ADAR1, which is overexpressed in Multiple Myeloma (MM) leading to aberrant editing activity and poor disease outcomes. RNA-seq and Whole-Exome Sequencing (WES) matched datasets from 23 MM patients pre- and post-relapse revealed acquisition of unique mutations post-relapse, enriched in the vicinity of RNA editing events pre-relapse. For proof-of-concept experiments in cell lines, I employed site-directed mRNA editing tools to target ADARs to specific transcripts, and evaluated whether ADAR-mediated DNA mutation was generated in their cognate genes. I found that ADARs may mutate genomic DNA in a rate of 1 in 25 000. Last, I explored the evolutionary impact of mutagenesis mediated by RNA editing enzymes (ADARs and APOBECs) in single-stranded RNA viral genomes from SARS-CoV-2 and showed that RNA editing enzymes may drive genome evolution by gradually accumulating co-occurring mutations, which similarly in cancer biology would translate to clonal expansion for tumor adaptation. Overall, my findings, suggest that DNA mutations may arise as collateral genomic damage by RNA editing deaminases, the initial job of which was to edit the cognate transcript in situ

Acute expression of human APOBEC3B in mice results in RNA editing and lethality

Abstract Background RNA editing has been described as promoting genetic heterogeneity, leading to the development of multiple disorders, including cancer. The cytosine deaminase APOBEC3B is implicated in tumor evolution through DNA mutation, but whether it also functions as an RNA editing enzyme has not been studied. Results Here, we engineer a novel doxycycline-inducible mouse model of human APOBEC3B-overexpression to understand the impact of this enzyme in tissue homeostasis and address a potential role in C-to-U RNA editing. Elevated and sustained levels of APOBEC3B lead to rapid alteration of cellular fitness, major organ dysfunction, and ultimately lethality in mice. Importantly, RNA-sequencing of mouse tissues expressing high levels of APOBEC3B identifies frequent UCC-to-UUC RNA editing events that are not evident in the corresponding genomic DNA. Conclusions This work identifies, for the first time, a new deaminase-dependent function for APOBEC3B in RNA editing and presents a preclinical tool to help understand the emerging role of APOBEC3B as a driver of carcinogenesis

Additional file 1 of Acute expression of human APOBEC3B in mice results in RNA editing and lethality

Additional file 1. Supplementary figures

ADAR1-mediated RNA editing promotes B cell lymphomagenesis

Summary: Diffuse large B cell lymphoma (DLBCL) is one of the most common types of aggressive lymphoid malignancies. Here, we explore the contribution of RNA editing to DLBCL pathogenesis. We observed that DNA mutations and RNA editing events are often mutually exclusive, suggesting that tumors can modulate pathway outcomes by altering sequences at either the genomic or the transcriptomic level. RNA editing targets transcripts within known disease-driving pathways such as apoptosis, p53 and NF-κB signaling, as well as the RIG-I-like pathway. In this context, we show that ADAR1-mediated editing within MAVS transcript positively correlates with MAVS protein expression levels, associating with increased interferon/NF-κB signaling and T cell exhaustion. Finally, using targeted RNA base editing tools to restore editing within MAVS 3′UTR in ADAR1-deficient cells, we demonstrate that editing is likely to be causal to an increase in downstream signaling in the absence of activation by canonical nucleic acid receptor sensing