Expression of the cancer-associatedDNA polymerase ε P286Rin fission yeast leads to translesion synthesis polymerase dependent hypermutation and defective DNA replication
Authors: Soriano Ignacio , Vazquez Enrique , De Leon Nagore , Bertrand Sibyl , Heitzer Ellen , Toumazou Sophia , Palles Claire , Pai Chen-Chen , Humphrey Timothy , Tomlinson Ian , Cotterill Sue , Kearsey Stephen E. 
Published: April 2021

Somatic mutations in the proofreading domain of the replicative DNA polymerase ε (POLE-exonuclease domain mutations,POLE-EDMs) are frequently found in colorectal and endometrial cancers and, occasionally, in other tumours. POLE-associated cancers typically display hypermutation, microsatellite stability and a unique mutational signature, with a predominance of C > A transversions in the context TCT. To understand better the contribution of hypermutagenesis to tumour development, we have modelled the most recurrentPOLE-EDM (POLE-P286R) inSchizosaccharomyces pombe. Whole-genome sequencing analysis revealed that the correspondingpol2-P287Rallele also has a strong mutator effect in vivo, with a high frequency of base substitutions and relatively few frameshift mutations. The mutations are equally distributed across different genomic regions, but they occur within an AT-rich context. The most abundant base-pair changes are TCT > TAT transversions and, in contrast to human mutations, TCG > TTG transitions are not elevated, likely due to the absence of cytosine methylation in fission yeast. Thepol2-P287Rvariant has an increased sensitivity to elevated dNTP levels and DNA damaging agents, and shows reduced viability on depletion of the Pfh1 helicase. In addition, S phase is aberrant and RPA foci are elevated, suggestive of persistent ssDNA or DNA damage, and thepol2-P287Rmutation is synthetically lethal withrad3inactivation, indicative of checkpoint activation. Significantly, deletion of genes encoding some translesion synthesis polymerases, most notably Pol κ, partially suppressespol2-P287Rhypermutation, indicating that polymerase switching contributes to this phenotype.

AUTHOR SUMMARY

Cancer is a genetic disease caused by mutations that lead to uncontrolled cell proliferation and other tumour properties. Defects in DNA repair or replication can lead to cancer development by increasing the likelihood that cancer-causing mutations will happen. Here we look at a pathogenic variant of a polymerase involved in genome replication (DNA polymerase ⍰⍰⍰POLE-P286R). This variant is associated with highly mutated cancer genomes. By introducing this mutation into the polymerase ⍰ gene of a model organism, fission yeast, we show that it causes a large increase in single base substitutions, scattered throughout the genome. The sequence context of mutations is similar in fission yeast and humans, suggesting that the yeast model is useful for understanding how POLE-P286R causes such a high mutation rate. Yeast POLE-P286R cells show slow chromosome replication, suggesting that the polymerase has difficulty in copying certain chromosomal regions. Yeast POLE-P286R cells become inviable when the concentration of dNTP building blocks for DNA synthesis is increased, probably because the mutation rate is pushed to an intolerable level. Interestingly, we find that specialised polymerases that are tolerant of DNA damage contribute to the high mutation rate caused by POLE-P286R. These findings have implications for the therapy of POLE-P286R tumours.