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Shah SM, Demidova EV, Ringenbach S, Faezov B, Andrake M, Gandhi A, Mur P, Viana-Errasti J, Xiu J, Swensen J, Valle L, Dunbrack RL, Hall MJ, Arora S. Exploring Co-occurring POLE Exonuclease and Non-exonuclease Domain Mutations and Their Impact on Tumor Mutagenicity. CANCER RESEARCH COMMUNICATIONS 2024; 4:213-225. [PMID: 38282550 PMCID: PMC10812383 DOI: 10.1158/2767-9764.crc-23-0312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/05/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024]
Abstract
POLE driver mutations in the exonuclease domain (ExoD driver) are prevalent in several cancers, including colorectal cancer and endometrial cancer, leading to dramatically ultra-high tumor mutation burden (TMB). To understand whether POLE mutations that are not classified as drivers (POLE Variant) contribute to mutagenesis, we assessed TMB in 447 POLE-mutated colorectal cancers, endometrial cancers, and ovarian cancers classified as TMB-high ≥10 mutations/Mb (mut/Mb) or TMB-low <10 mut/Mb. TMB was significantly highest in tumors with "POLE ExoD driver plus POLE Variant" (colorectal cancer and endometrial cancer, P < 0.001; ovarian cancer, P < 0.05). TMB increased with additional POLE variants (P < 0.001), but plateaued at 2, suggesting an association between the presence of these variants and TMB. Integrated analysis of AlphaFold2 POLE models and quantitative stability estimates predicted the impact of multiple POLE variants on POLE functionality. The prevalence of immunogenic neoepitopes was notably higher in the "POLE ExoD driver plus POLE Variant" tumors. Overall, this study reveals a novel correlation between POLE variants in POLE ExoD-driven tumors, and ultra-high TMB. Currently, only select pathogenic ExoD mutations with a reliable association with ultra-high TMB inform clinical practice. Thus, these findings are hypothesis-generating, require functional validation, and could potentially inform tumor classification, treatment responses, and clinical outcomes. SIGNIFICANCE Somatic POLE ExoD driver mutations cause proofreading deficiency that induces high TMB. This study suggests a novel modifier role for POLE variants in POLE ExoD-driven tumors, associated with ultra-high TMB. These data, in addition to future functional studies, may inform tumor classification, therapeutic response, and patient outcomes.
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Affiliation(s)
- Shreya M. Shah
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Science Scholars Program, Temple University, Philadelphia, Pennsylvania
| | - Elena V. Demidova
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
| | - Salena Ringenbach
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Lewis Katz School of Medicine, Temple University, Bethlehem, Pennsylvania
| | - Bulat Faezov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Mark Andrake
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Arjun Gandhi
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- University College Dublin School of Medicine and Medical Science, Dublin, Ireland
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Julen Viana-Errasti
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | | | | | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Roland L. Dunbrack
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Michael J. Hall
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Sanjeevani Arora
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
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Demidova EV, Serebriiskii IG, Vlasenkova R, Kelow S, Andrake MD, Hartman TR, Kent T, Virtucio J, Rosen GL, Pomerantz RT, Dunbrack RL, Golemis EA, Hall MJ, Chen DYT, Daly MB, Arora S. Correction: Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing. BMC Genomics 2023; 24:388. [PMID: 37430226 DOI: 10.1186/s12864-023-09486-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023] Open
Affiliation(s)
- Elena V Demidova
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
- Kazan Federal University, Kazan, 420008, Russia
| | - Ilya G Serebriiskii
- Kazan Federal University, Kazan, 420008, Russia
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Ramilia Vlasenkova
- Kazan Federal University, Kazan, 420008, Russia
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Simon Kelow
- Department of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mark D Andrake
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Tiffiney R Hartman
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
- Arcadia University, Glenside, PA, USA
| | - Tatiana Kent
- Department of Biochemistry & Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jeferson University, Philadelphia, PA, 19107, USA
| | - James Virtucio
- Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Department of Electrical and Computer Engineering, College of Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Gail L Rosen
- Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Department of Electrical and Computer Engineering, College of Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Richard T Pomerantz
- Department of Biochemistry & Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jeferson University, Philadelphia, PA, 19107, USA
| | - Roland L Dunbrack
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Erica A Golemis
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Michael J Hall
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
- Department of Clinical Genetics, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - David Y T Chen
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Mary B Daly
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA.
- Department of Clinical Genetics, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA.
| | - Sanjeevani Arora
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA.
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
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