POLE-mutant Tumors: Mechanisms of Genomic Instability and Discovery of New Driver Alleles

Amino acid substitutions in the exonuclease domain of DNA polymerase ε (POLE) cause cancers with extremely high mutation burdens. POLE-mutant status is associated with improved patient outcomes due to high neoantigen production and an enhanced anti-tumor immune response. The ability to recognize driver variants is critical for designing personalized treatment strategies. Mechanisms of ultramutation that defines good prognosis are also of high interest. The long-term goals of our research are to understand the mechanisms of POLE-linked ultramutation and improve the detection of functionally significant variants in patients. Our laboratory experimentally validated 15 of 17 currently known POLE drivers. We also deciphered the mechanisms through which amino acid changes at the protein-DNA interface in the exonuclease domain cause ultramutation. However, much remains to be explored in this relatively young field. Mechanisms remain unclear for other categories of POLE driver mutations, which include a highly prevalent pathogenic variant V411L. Further, we recently discovered that changes in the DNA polymerase domain of POLE can also drive ultramutation in tumors, constituting another poorly understood group of drivers. There is a paucity of experimental models for assessing the consequences of variants in the context of human cells and proteins. Methods to determine POLE status unambiguously in the clinical setting are also lacking. The proposed research will fill these gaps. We will use novel genetic, biochemical, and computational tools and a broad arsenal of experimental models, including “humanized” yeast, POLE-mutant human cells, knock-in mouse lines, and clinical samples to facilitate this research. In Aim 1, we will develop new, improved approaches to identify POLE tumors and disambiguate variants of unknown significance. In Aim 2, we will characterize novel drivers affecting the DNA polymerase domain of POLE. In Aim 3, we will define the mechanism of tumorigenesis for the highly recurrent V411L variant. This research will advance the mechanistic understanding of POLE-driven tumorigenesis and help address current clinical needs. Project Number: 1R01CA300960-01A1 | Fiscal Year: 2026 | NIH Institute/Center: National Cancer Institute (NCI) | Principal Investigator: Polina Shcherbakova | Institution: UNIVERSITY OF NEBRASKA MEDICAL CENTER, OMAHA, NE | Award Amount: $584,852 | Activity Code: R01 | Study Section: Biochemical and Cellular Oncogenesis Study Section[BCO] View on NIH RePORTER: https://reporter.nih.gov/project-details/11297188