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Collateral genomic damage due to aberrant RNA editing activity in cancer

Tasakis, Rafail Nikolaos

[thumbnail of TasakisRN_2021_Dissertation.pdf] PDF, English
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Abstract

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.

Document type: Dissertation
Supervisor: Papavasiliou, Prof. Dr. Nina
Place of Publication: Heidelberg
Date of thesis defense: 16 November 2021
Date Deposited: 02 Dec 2021 13:55
Date: 2022
Faculties / Institutes: The Faculty of Bio Sciences > Dean's Office of the Faculty of Bio Sciences
Service facilities > German Cancer Research Center (DKFZ)
DDC-classification: 500 Natural sciences and mathematics
570 Life sciences
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