DNA methylation, deamination, and translesion synthesis combine to generate footprint mutations in cancer driver genes in B-cell derived lymphomas and other cancers

Rogozin, Igor B., Roche-Lima, Abiel, Tyryshkin, Kathrin, Carrasquillo-Carrión, Kelvin, Lada, Artem G., Poliakov, Lennard Y., Schwartz, Elena, Saura, Andreu, Yurchenko, Vyacheslav, Cooper, David N., Panchenko, Anna R. and Pavlov, Youri I. 2021. DNA methylation, deamination, and translesion synthesis combine to generate footprint mutations in cancer driver genes in B-cell derived lymphomas and other cancers. Frontiers in Genetics 12 , 671866. 10.3389/fgene.2021.671866

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Abstract

Cancer genomes harbor numerous genomic alterations and many cancers accumulate thousands of nucleotide sequence variations. A prominent fraction of these mutations arises as a consequence of the off-target activity of DNA/RNA editing cytosine deaminases followed by the replication/repair of edited sites by DNA polymerases (pol), as deduced from the analysis of the DNA sequence context of mutations in different tumor tissues. We have used the weight matrix (sequence profile) approach to analyze mutagenesis due to Activation Induced Deaminase (AID) and two error-prone DNA polymerases. Control experiments using shuffled weight matrices and somatic mutations in immunoglobulin genes confirmed the power of this method. Analysis of somatic mutations in various cancers suggested that AID and DNA polymerases η and θ contribute to mutagenesis in contexts that almost universally correlate with the context of mutations in A:T and G:C sites during the affinity maturation of immunoglobulin genes. Previously, we demonstrated that AID contributes to mutagenesis in (de)methylated genomic DNA in various cancers. Our current analysis of methylation data from malignant lymphomas suggests that driver genes are subject to different (de)methylation processes than non-driver genes and, in addition to AID, the activity of pols η and θ contributes to the establishment of methylation-dependent mutation profiles. This may reflect the functional importance of interplay between mutagenesis in cancer and (de)methylation processes in different groups of genes. The resulting changes in CpG methylation levels and chromatin modifications are likely to cause changes in the expression levels of driver genes that may affect cancer initiation and/or progression.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Medicine
Additional Information:	This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).
ISSN:	16648021
Date of First Compliant Deposit:	25 January 2022
Date of Acceptance:	21 April 2021
Last Modified:	17 May 2023 02:36
URI:	https://orca.cardiff.ac.uk/id/eprint/146896

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