<i>POLE</i> variant phenotypic classification to enable identification of patients with colorectal cancer (CRC) who may benefit from immune checkpoint inhibition (ICI).
Authors: Rachel Beth Keller, Zoe Fleischmann, Smruthy Sivakumar, Radwa Sharaf, Tyler Janovitz, Alexa B. Schrock, Hanna Tukachinsky, Lei Zhong, Douglas A. Mata, Lyle Lopez, Ethan Sokol, Garrett M. Frampton, Douglas I. Lin, Geoffrey R. Oxnard, Erik A. Williams, Julia A. Elvin, Brennan J. Decker
Journal: Journal of Clinical Oncology (2024)

194 Background: Pathogenic POLE (p POLE) variants interfere with the exonuclease activity of POLε during DNA replication, resulting in somatic ultramutation and conferring susceptibility to ICI. Historical classification of p POLE relies on localization to the exonuclease domain (ED). We present the landscape of p POLE variants in CRC according to a proposed phenotypic classification model. Methods: Comprehensive genomic profiling was performed on tissue (TBx) and liquid (LBx) biopsies during the course of clinical care. A POLE-specific variant classification model including tumor mutational burden (TMB), mutational signatures, and germline frequency was used to differentiate p POLE from benign POLE (b POLE) variants. Results: POLE variant status was evaluated in 455,965 TBx and 41,804 LBx pan-tumor. POLE alterations, including p POLE and variants of unknown significance, were detected in 3.9% of samples with 7,404 discrete alleles observed. After applying the classification model, 30 variants were classified as p POLE, representing 3.6% (751/20,601) of observed POLE variants. All p POLE were localized to the ED and a majority were missense substitutions (29/30). There were an additional 620 ED variants categorized as b POLE. CRC had the second highest prevalence of p POLE variants (0.5%, 302/60,547). p POLE variants were associated with ultramutation in CRC where the median tissue TMB was 183.0 mut/Mb, 1-2 orders of magnitude higher than for CRC harboring b POLE variants (7.8 mut/Mb) or without POLE variants (3.5 mut/Mb). 32.2% of p POLE CRC also had evidence of high microsatellite instability (MSI-H). Combined p POLE + MSI-H was associated with markedly elevated TMB compared to either signature alone (344.4 versus 53.1 and 151.3 mut/Mb for b POLE + MSI-H and p POLE + MS-Stable, respectively). A small minority of CRC tumors with p POLE variants (7/298, 2.3%) had low TMB (&lt;10 mut/Mb). However, this was associated with a low p POLE variant allele frequency (VAF; median 2.8% versus 24.0% for tumors w/ TMB ≥10, p &lt; .0001) pointing to low tumor purity and likely an underestimation of TMB. While targetable alterations (e.g., homologous recombination repair [HR] gene variants) were enriched in p POLE tumors, these tumors had a low rate of HR deficiency (HRD) as determined by a computational algorithm (HRDsig), suggesting these are likely incidental monoallelic variants. Conclusions: A POLE phenotype-specific classification model identified p POLE variants associated with ultramutation in CRC. Co-occurrence of p POLE and MSI-H in CRC is common and has a synergistic effect leading to even higher TMB. We hypothesize that p POLE detection predicts ultramutation and response to ICI even when TMB is under-detected due to low tumor purity. Caution is advised for therapy selection based on co-alterations in the setting of p POLE due to an abundance of incidental variants.