Tumor mutation burden in colorectal cancers with POLE exonuclease and non-exonuclease domain variants.

Authors

null

Salena Ringenbach

Temple University Lewis Katz School of Medicine, Philadelphia, PA;

Salena Ringenbach , Shreya M. Shah , Elena Demidova , Bulat Faezov , Mark D. Andrake , Pilar Mur , Joanne Xiu , Wolfgang Michael Korn , Sanjay Goel , Heinz-Josef Lenz , John Marshall , Anthony Frank Shields , Matthew James Oberley , David Spetzler , Laura Valle , Roland Dunbrack Jr., Michael J. Hall , Sanjeevani Arora

Organizations

Temple University Lewis Katz School of Medicine, Philadelphia, PA; , Fox Chase Cancer Center, Philadelphia, PA; , Catalan Institute of Oncology, IDIBELL, L'hospitalet De Llobregat, Spain; , Caris Life Sciences, Phoenix, AZ; , Rutgers Cancer Institute of New Jersey, New Brunswick, NJ; , Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA; , Lombardi Cancer Center, Georgetown University, Washington, DC; , Barbara Ann Karmanos Cancer Institute, Detroit, MI;

Research Funding

Other
DOD W81XWH-18-1-0148, U.S. National Institutes of Health, CEP Award from the Yale Head and Neck Cancer SPORE

Background: Driver mutations in the exonuclease domain (ExoD) of DNA polymerase epsilon (POLE) have been associated with high tumor mutation burden (TMB). High TMB is an important marker for immunotherapy, and thus understanding the mechanisms that lead to high TMB is an area of active investigation. Many tumors with POLE ExoD driver mutations have additional POLE variants of uncertain significance (VUS). Some of these VUS lie within the ExoD, while most lie outside the ExoD. This study investigates the role of such POLE VUS on TMB and POLE functionality of ExoD-mutated tumors. Methods: Retrospective colorectal cancer (CRC) genomic profiles from Caris Life Sciences (n=1,870) were separated into groups based on the presence of POLE ExoD mutations and the TMB status. Groups were defined as: ‘TMB-high (TMB-H) POLE ExoD driver without additional POLE VUS’, ‘TMB-H POLE ExoD driver plus POLE VUS’, and ‘TMB-low (TMB-L) POLE variant(s) without ExoD driver’. An additional group with ‘TMB-H POLE variant(s) without ExoD driver’ was identified as potentially novel drivers for future study. The microsatellite instability status (MSI or MSS) was also considered. The level of TMB, the presence of polymerase proofreading-associated mutational signatures and POLE stability/functionality analyzed using AlphaFold2 models and Rosetta Molecular Modeling Suite, were evaluated. Results:POLE variants were identified in 4.9% of the CRCs studied (92/1870). In all, 52.2% (48/92) of those tumors were TMB-H, and 38.0% (35/92) of them contained POLE ExoD drivers. The highest median TMB (mTMB) was found in the ‘TMB-H POLE ExoD driver plus POLE VUS’ group, and this was significantly different from the ‘TMB-H POLE ExoD driver without additional POLE VUS’ and the ‘TMB-L POLE variant without ExoD driver’ group, even when MSI tumors were excluded (p<0.001, Mann-Whitney). These results were validated in TCGA CRC tumors and in other tumor types. Within the ‘TMB-H POLE ExoD driver plus POLE VUS’ group, the mTMB increased with the number of accumulated POLE VUS (p<0.001, Mann Whitney). The nucleotide sequence context of 77.8% of the POLE VUS matched mutational spectra associated with POLE ExoD defects, suggesting that most of the POLE VUS are secondary to the ExoD driver mutation. Finally, the majority of POLE VUS within ‘TMB-H POLE ExoD driver plus POLE VUS’ group have a predicted effect on POLE stability and/or function. Conclusions: Our results suggest that the presence of secondary POLE non-driver variants increase TMB in POLE ExoD-mutated tumors. Although still preliminary, these data could impact prognosis and response to immune checkpoint inhibitors in patients.

CohortPatients (n)mTMB (range), mut/MbMSSMSI<50 years>50 yearsFemaleMale
POLE ExoD driver TMB-H11115 (61-216)11056110
POLE ExoD driver plus POLE VUS TMB-H24264.5 (114-414)2131410618
POLE variants TMB-L446.5 (3-14)4407372321
POLE variantsTMB-H1348 (19-461)3107649

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Abstract Details

Meeting

2023 ASCO Gastrointestinal Cancers Symposium

Session Type

Poster Session

Session Title

Poster Session C: Cancers of the Colon, Rectum, and Anus

Track

Colorectal Cancer,Anal Cancer

Sub Track

Tumor Biology, Biomarkers, and Pathology

Citation

J Clin Oncol 41, 2023 (suppl 4; abstr 224)

DOI

10.1200/JCO.2023.41.4_suppl.224

Abstract #

224

Poster Bd #

M6

Abstract Disclosures

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