DNA polymerase ε and δ variants drive mutagenesis in polypurine tracts in human tumors

Daria Ostroverkhova, Kathrin Tyryshkin, Annette K. Beach, Elizabeth A. Moore, Yosef Masoudi-Sobhanzadeh, Stephanie R. Barbari, Igor B. Rogozin, Konstantin V. Shaitan, Anna R. Panchenko, Polina V. Shcherbakova

Research output: Contribution to journalArticlepeer-review

Abstract

Alterations in the exonuclease domain of DNA polymerase ε cause ultramutated cancers. These cancers accumulate AGA>ATA transversions; however, their genomic features beyond the trinucleotide motifs are obscure. We analyze the extended DNA context of ultramutation using whole-exome sequencing data from 524 endometrial and 395 colorectal tumors. We find that G>T transversions in POLE-mutant tumors predominantly affect sequences containing at least six consecutive purines, with a striking preference for certain positions within polypurine tracts. Using this signature, we develop a machine-learning classifier to identify tumors with hitherto unknown POLE drivers and validate two drivers, POLE-E978G and POLE-S461L, by functional assays in yeast. Unlike other pathogenic variants, the E978G substitution affects the polymerase domain of Pol ε. We further show that tumors with POLD1 drivers share the extended signature of POLE ultramutation. These findings expand the understanding of ultramutation mechanisms and highlight peculiar mutagenic properties of polypurine tracts in the human genome.

Original languageEnglish (US)
Article number113655
JournalCell Reports
Volume43
Issue number1
DOIs
StatePublished - Jan 23 2024

Keywords

  • CP: Cancer
  • DNA polymerase delta
  • DNA polymerase epsilon
  • POLD1
  • POLE
  • VUS
  • colorectal cancer
  • endometrial cancer
  • mutation
  • polypurine tracts
  • tumor classification

ASJC Scopus subject areas

  • General Biochemistry, Genetics and Molecular Biology

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