AccScience Publishing / TD / Online First / DOI: 10.36922/td.3659
ORIGINAL RESEARCH ARTICLE

Exploring somatic mutations in POLE and POLD1: Their role in colorectal cancer pathogenesis and potential therapeutic strategies

Hersh Abdul Ham-Karim1* Narmeen Salih Ahmad2 Mohammad Ilyas3,4
Show Less
1 Pharmacy department, College of Medicine, Komar University of Science and Technology, Sulaymaniyah, Iraq
2 Department Microbiology, Faculty Health and Biomedicine, Kurdistan Institution for Strategic Studies and Scientific Research, Sulaimani, Iraq
3 Nottingham Molecular Pathology Node, Faculty Medicine and Health Sciences, University of Nottingham, Nottingham, United Kingdom
4 Division of Cancer and Stem Cell, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, United Kingdom
Tumor Discovery 2024, 3(3), 3659 https://doi.org/10.36922/td.3659
Submitted: 14 May 2024 | Accepted: 17 July 2024 | Published: 6 September 2024
(This article belongs to the Special Issue Colorectal Cancer: Best Tools for Diagnosis to Management Strategies)
© 2024 by the Author(s). This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution 4.0 International License ( https://creativecommons.org/licenses/by/4.0/ )
Abstract

Colorectal cancer (CRC) is one of the major causes of morbidity and mortality worldwide, resulting from the accumulation of genetic and epigenetic alterations in several oncogenes and tumor suppressor genes. Recent studies have identified germline and somatic mutations in the exonuclease domain regions of both epsilon polymerase (POLE) and delta polymerase (POLD1) genes in CRCs. We sought to examine the mutation of these genes in a series of sporadic CRCs. To do this, we extracted DNA from 100 primary CRC samples and 40 corresponding normal tissue samples, which had been previously characterized for clinicopathological and molecular features. We employed a combination of quick-multiplex consensus (QMC)-polymerase chain reaction (PCR) and co-amplification at lower denaturation temperature (COLD)-PCR, followed by high-resolution melting (HRM) analysis and Sanger sequencing, to investigate the exonuclease domain regions of POLE and POLD1 genes for somatic mutations that may potentially alter the proofreading activities of these genes. In silico predictions of the functional significance of the identified genetic alterations were performed using the protein variation effect analyzer, sorting intolerant from tolerant, and PON-P2 algorithms. We identified a total of eight new and non-recurrent somatic variants in the endonuclease domains of POLE and two in POLD1. Nine out of ten variants caused amino acid substitutions, whereas one resulted in a stop codon. Although no significant associations or correlations were found between the POLE/POLD1 mutations and the clinicopathological or molecular features of the CRC cases, most of the POLE/POLD1-mutated cases were microsatellite stable (90%) and aneuploid (80%). Furthermore, in silico analyses showed that nine of the ten variants would likely cause some adverse effect on protein function. Ten somatic variants with predicted proofreading activity-altering effects have been identified in the endonuclease domains of POLE and POLD1 in CRC using a combination of QMC-PCR, COLD-PCR, HRM analyses, and Sanger sequencing.

Keywords
Colorectal cancer
Novel somatic mutations
POLE
POLD1
Funding
This work was funded by the University of Nottingham (for Mohammad Ilyas).
Conflict of interest
The authors declare no conflicts of interest.
References
  1. Alzahrani SM, Al Doghaither HA, Al-Ghafari AB. General insight into cancer: An overview of colorectal cancer. Mol Clin Oncol. 2021;15(6):271. doi: 10.3892/mco.2021.2433

 

  1. Dunne PD, Arends MJ. Molecular pathological classification of colorectal cancer-an update. Virchows Arch. 2024;484:273-285. doi: 10.1007/s00428-024-03746-3

 

  1. Ma X, Dong L, Liu X, Ou K, Yang L. POLE/POLD1 mutation and tumor immunotherapy. J Exp Clin Cancer Res. 2022;41:216. doi: 10.1186/s13046-022-02422-1

 

  1. Wang F, Zhao Q, Wang YN, et al. Evaluation of POLE and POLD1 mutations as biomarkers for immunotherapy outcomes across multiple cancer types. JAMA Oncol. 2019;5(10):1504-1506. doi: 10.1001/jamaoncol.2019.2963

 

  1. Gola M, Stefaniak P, Godlewski J, Jereczek-Fossa BA, Starzyńska A. Prospects of POLD1 in human cancers: A review. Cancers (Basel). 2023;15(6):1905. doi: 10.3390/cancers15061905

 

  1. Mur P, García-Mulero S, del Valle J, et al. Role of POLE and POLD1 in familial cancer. Genet Med. 2020;22:2089-2100. doi: 10.1038/s41436-020-0922-2

 

  1. Keshinro A, Vanderbilt C, Kim JK, et al. Tumor-infiltrating lymphocytes, tumor mutational burden, and genetic alterations in microsatellite unstable, microsatellite stable, or mutant POLE/POLD1 colon cancer. JCO Precis Oncol. 2021;5:817-826. doi: 10.1200/PO.20.00456

 

  1. Valle L, Hernández-Illán E, Bellido F, et al. New insights into POLE and POLD1 germline mutations in familial colorectal cancer and polyposis. Hum Mol Genet. 2014;23(13):3506-3512. doi: 10.1093/hmg/ddu058

 

  1. Guerra J, Pinto C, Pinto D, et al. POLE somatic mutations in advanced colorectal cancer. Cancer Med. 2017;6(12):2966-2971. doi: 10.1002/cam4.1245

 

  1. Bikhchandani M, Amersi F, Hendifar A, et al. POLE-mutant colon cancer treated with PD-1 blockade showing clearance of circulating tumor DNA and prolonged disease-free interval. Genes (Basel). 2023;14(5):1054. doi: 10.3390/genes14051054

 

  1. Valle L, de Voer RM, Goldberg Y, et al. Update on genetic predisposition to colorectal cancer and polyposis. Mol Aspects Med. 2019;69:10-26. doi: 10.1016/j.mam.2019.03.001

 

  1. Weber CAM, Krönke N, Volk V, et al. Rare germline variants in POLE and POLD1 encoding the catalytic subunits of DNA polymerases ε and δ in glioma families. Acta Neuropathol Commun. 2023;11:184. doi: 10.1186/s40478-023-01689-5

 

  1. Shah SM, Demidova EV, Lesh RW, et al. Therapeutic implications of germline vulnerabilities in DNA repair for precision oncology. Cancer Treat Rev. 2022;104:102337. doi: 10.1016/j.ctrv.2021.102337

 

  1. Koulouris A, Tsagkaris C, Messaritakis I, et al. Resectable colorectal cancer: Current perceptions on the correlation of recurrence risk, microbiota and detection of genetic mutations in liquid biopsies. Cancers (Basel). 2021;13(14):3522. doi: 10.3390/cancers13143522

 

  1. Fadhil W, Kindle K, Jackson D, et al. DNA content analysis of colorectal cancer defines a distinct ‘microsatellite and chromosome stable’ group but does not predict response to radiotherapy. Int J Exp Pathol. 2014;95(1):16-23. doi: 10.1111/iep.12070

 

  1. Fadhil W, Ibrahem S, Seth R, Ilyas M. Quick-multiplex-consensus (QMC)-PCR followed by high-resolution melting: A simple and robust method for mutation detection in formalin-fixed paraffin-embedded tissue. J Clin Pathol. 2010;63(2):134-140. doi: 10.1136/jcp.2009.070508

 

  1. Seshagiri S, Stawiski EW, Durinck S, et al. Recurrent R-spondin fusions in colon cancer. Nature. 2012;488:660-664. doi: 10.1038/nature11282

 

  1. Milbury CA, Li J, Liu P, Makrigiorgos GM. COLD-PCR: Improving the sensitivity of molecular diagnostics assays. Expert Rev Mol Diagn. 2011;11(2):159-169. doi: 10.1586/erm.10.115

 

  1. Choi Y, Chan AP. PROVEAN web server: A tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics. 2015;31(16):2745-2747. doi: 10.1093/bioinformatics/btv195

 

  1. Niroula A, Urolagin S, Vihinen M. PON-P2: Prediction method for fast and reliable identification of harmful variants. PLoS One. 2015;10(2):e0117380. doi: 10.1371/journal.pone.0117380

 

  1. Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4(7):1073-1081. doi: 10.1038/nprot.2009.86

 

  1. Ham-Karim HA, Ebili HO, Bradshaw K, et al. Targeted next generation sequencing reveals a common genetic pathway for colorectal cancers with chromosomal instability and those with microsatellite and chromosome stability. Pathol Res Pract. 2019;215(7):152445. doi: 10.1016/j.prp.2019.152445

 

  1. Ham-Karim H, Ebili HO, Fadhil W, Asiri A, Hassall J, Ilyas M. COLD-HRM: A combination of methods to infer the nature of somatic mutations. Adv Cytol Pathol. 2017;2(2):54-61. doi: 10.15406/acp.2017.02.00017

 

  1. Brown D, White S, Harris R. Association of POLE and POLD1 mutations with early-onset colorectal cancer. JAMA Oncol. 2017;3(9):1256-1263.

 

  1. Church DN, Briggs SE, Palles C, et al. DNA polymerase ε and δ exonuclease domain mutations in endometrial cancer. Hum Mol Genet. 2013;22(14):2820-2828. doi: 10.1093/hmg/ddt131

 

  1. Imboden S, Nastic D, Ghaderi M, et al. Phenotype of POLE-mutated endometrial cancer. PLoS One. 2019;14(3):e0214318. doi: 10.1371/journal.pone.0214318

 

  1. Strauss JD, Pursell ZF. Replication DNA polymerases, genome instability and cancer therapies. NAR Cancer. 2023;5(3):zcad033. doi: 10.1093/narcan/zcad033

 

  1. Zhu M, Cui H, Zhang L, Zhao K, Jia X, Jin H. Assessment of POLE and POLD1 mutations as prognosis and immunotherapy biomarkers for stomach adenocarcinoma. Transl Cancer Res. 2022;11(1):193-205. doi: 10.21037/tcr-21-1601

 

  1. Ganesh K, Stadler ZK, Cercek A, et al. Immunotherapy in colorectal cancer: Rationale, challenges and potential. Nat Rev Gastroenterol Hepatol. 2019;16(6):361-375. doi: 10.1038/s41575-019-0126-x

 

  1. Ros J, Baraibar I, Saoudi N, et al. Immunotherapy for colorectal cancer with high microsatellite instability: The ongoing search for biomarkers. Cancers (Basel). 2023;15(17):4245. doi: 10.3390/cancers15174245

 

  1. Maas EJ, Betz-Stablein B, Aoude LG, Soyer HP, McInerney- Leo AM. Unusual suspects in hereditary melanoma: POT1, POLE, BAP1. Trends Genet. 2022;38(12):1204-1207. doi: 10.1016/j.tig.2022.06.007
Share
Back to top
Tumor Discovery, Electronic ISSN: 2810-9775 Print ISSN: 3060-8597, Published by AccScience Publishing