A recurrent cancer-associated substitution in DNA polymerase ε produces a hyperactive enzyme

Xing, Xuanxuan; Kane, Daniel P.; Bulock, Chelsea R.; Moore, Elizabeth A.; Sharma, Sushma; Chabes, Andrei; Shcherbakova, Polina V.

doi:10.1038/s41467-018-08145-2

Cited by 67 publications

(114 citation statements)

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“…However, V411 is far away from exonuclease active site may function by affecting the positions of other residues adjacent to the active site [9]. In yeast, POLE mutants with a weak exonuclease activity have more C>T and less C>A mutations than mutants with no exonuclease activity [7]. We therefore speculate that the proportionally reduced C>A and increased C>T mutation loads in V411 may arise due to stronger exonuclease activity, as the mutation is distal from that site.…”

Section: Discussionmentioning

confidence: 92%

“…V411L and P286R are the two most frequent POLE mutants and they are located far away from each other in the exonuclease domain, thus conferring different functions [37]. Structural and molecular dynamics simulation studies in S. cerevisiae have revealed that P301R (P286R in Human) substitution prevents proper positioning of ssDNA in the exonuclease active site of Pol ε, resulting in promoting the extension of mismatched primer termini [7,8]. However, V411 is far away from exonuclease active site may function by affecting the positions of other residues adjacent to the active site [9].…”

Section: Discussionmentioning

confidence: 99%

“…Several driver mutations have been identified in the POLE exonuclease domain (codons 268-471) [6], the most frequent being P286R and V411L [2]. The crystal structure of the yeast orthologue has shown that P301R (P286R in Human) could change the exonuclease domain, with R301 pointing towards the exonuclease site, leading to polymerase hyperactivity and increased capacity to extend mismatches by interfering with DNA binding to the exonuclease site [7,8]. By contrast, residue V411 lies a distance away from the binding site and does not interact with the DNA sequence directly [9].…”

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confidence: 99%

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Mutational processes of distinct POLE exonuclease domain mutants drive an enrichment of a specific TP53 mutation in colorectal cancer

Barbour

Poulos

et al. 2020

PLoS Genet

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Cancer genomes with mutations in the exonuclease domain of Polymerase Epsilon (POLE) present with an extraordinarily high somatic mutation burden. In vitro studies have shown that distinct POLE mutants exhibit different polymerase activity. Yet, genome-wide mutation patterns and driver mutation formation arising from different POLE mutants remains unclear. Here, we curated somatic mutation calls from 7,345 colorectal cancer samples from published studies and publicly available databases. These include 44 POLE mutant samples including 9 with whole genome sequencing data available. The POLE mutant samples were categorized based on the specific POLE mutation present. Mutation spectrum, associations of somatic mutations with epigenomics features and co-occurrence with specific driver mutations were examined across different POLE mutants. We found that different POLE mutants exhibit distinct mutation spectrum with significantly higher relative frequency of C>T mutations in POLE V411L mutants. Our analysis showed that this increase frequency in C>T mutations is not dependent on DNA methylation and not associated with other genomic features and is thus specifically due to DNA sequence context alone. Notably, we found strong association of the TP53 R213* mutation specifically with POLE P286R mutants. This truncation mutation occurs within the TT[C>T]GA context. For C>T mutations, this sequence context is significantly more likely to be mutated in POLE P286R mutants compared with other POLE exonuclease domain mutants. This study refines our understanding of DNA polymerase fidelity and underscores genome-wide mutation spectrum and specific cancer driver mutation formation observed in POLE mutant cancers.

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Section: Discussionmentioning

confidence: 92%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Mutational processes of distinct POLE exonuclease domain mutants drive an enrichment of a specific TP53 mutation in colorectal cancer

Barbour

Poulos

et al. 2020

PLoS Genet

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“…Haploid yeast deficient in MMR and harboring pol3-D520V are not viable (41); therefore, we assessed the epistatic relationship between pol3-D520V and MMR deficiency in diploid strains, which can tolerate a higher level of mutagenesis. We used the MSH6 deletion to inactivate MMR as the Msh6-dependent pathway is primarily responsible for the repair of single-base mismatches (42), which is the predominant type of replication errors generated by exonucleasedeficient Polδ and Pole (43)(44)(45). Diploids homozygous for both pol3-D520V and msh6 mutations showed a strong synergistic increase in mutation rate as compared with the single pol3-D520V and msh6 mutants (SI Appendix, Table S2).…”

Section: Polδ Proofreads Errors Made By Pole But Pole Does Not Proofmentioning

confidence: 99%

DNA polymerase δ proofreads errors made by DNA polymerase ε

Bulock

Xing

Shcherbakova

2020

Proc. Natl. Acad. Sci. U.S.A.

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During eukaryotic replication, DNA polymerases e (Pole) and δ (Polδ) synthesize the leading and lagging strands, respectively. In a long-known contradiction to this model, defects in the fidelity of Pole have a much weaker impact on mutagenesis than analogous Polδ defects. It has been previously proposed that Polδ contributes more to mutation avoidance because it proofreads mismatches created by Pole in addition to its own errors. However, direct evidence for this model was missing. We show that, in yeast, the mutation rate increases synergistically when a Pole nucleotide selectivity defect is combined with a Polδ proofreading defect, demonstrating extrinsic proofreading of Pole errors by Polδ. In contrast, combining Polδ nucleotide selectivity and Pole proofreading defects produces no synergy, indicating that Pole cannot correct errors made by Polδ. We further show that Polδ can remove errors made by exonuclease-deficient Pole in vitro. These findings illustrate the complexity of the one-strand-one-polymerase model where synthesis appears to be largely divided, but Polδ proofreading operates on both strands.DNA replication | extrinsic proofreading | DNA polymerase δ |

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“…POLE mutants with a weak exonuclease activity have more C>T and less C>A 280 mutations than mutants with no exonuclease activity (Xing et al, 2019). We therefore 281 speculate that the proportionally reduced C>A and increased C>T mutation loads in 282 V411 may arise due to stronger exonuclease activity, as the mutation is distal from 283 that site.…”

mentioning

confidence: 95%

Mutational processes of distinct POLE exonuclease domain mutants drive an enrichment of a specific TP53 mutation in colorectal cancer

Barbour

Poulos

et al. 2019

Preprint

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20Cancer genomes with mutations in the exonuclease domain of Polymerase Epsilon 21 (POLE) present with an extraordinarily high somatic mutation burden. In vitro studies 22 have shown that distinct POLE mutants exhibit different polymerase activity and yet, 23 how these POLE mutants generate mutations across cancer genomes and influence 24 driver events remains poorly understood. Here we analyzed 7,345 colorectal cancer 25 samples, including nine whole genome sequenced samples harboring POLE mutations. 26 Our analysis identified differential mutation spectra across the mutants including 27 methylation-independent enrichment of C>T mutations in POLE V411L. In contrast, 28 analysis of other genomic regions showed similar mutation profiles across the 29 different POLE mutants. Notably, we found that POLE mutants with the TP53 R213* 30 mutation, caused by a TT[C>T]GA substitution, have significantly higher relative 31 frequency of this mutational context compared with samples without this mutation. 32This finding demonstrates that variations in underlying mutation spectra can increase 33 the likelihood of specific driver mutation formation. 34 Introduction 35POLE encodes the catalytic subunit of DNA Polymerase Epsilon, which is responsible 36 for DNA fidelity during the process of eukaryotic nuclear genome replication (Jansen 37 et al., 2016). Functional POLE mutations have been identified in less than 1% of all 38 cancer genomes but these genomes are characterized by exceptionally high tumor 39 mutation burden (Campbell et al., 2017). Somatic mutations of POLE exonuclease 40 domain are frequently enriched in brain, uterine and colorectal cancer, and patients 41 with POLE dysfunction usually have significantly better prognosis and require less 42 intensive treatment (Cancer Genome Atlas Research et al., 2013). 43The POLE mutational process shapes the cancer genome into a unique mutational 44 signature with high proportions of C>A mutations at TCT contexts, C>T mutations at 45 TCG contexts and T>G mutations at TTT contexts, which is known as COSMIC 46 signature 10 (Alexandrov et al., 2013a). Several driver mutations have been identified 47 in the POLE exonuclease domain (codons 268-471) (Church et al., 2013), the most 48 frequent being P286R and V411L (Campbell et al., 2017). Residue P286 is located in 49 the DNA binding pocket which is adjacent to the exonuclease active site. A change of 50 this amino acid has been predicted to affect the structure of the DNA binding pocket 51 and cause polymerase hyperactivity (Xing et al., 2019). By contrast, residue V411 lies 52 a distance away from the binding site and does not interact with the DNA sequence 53 directly (Briggs and Tomlinson, 2013). Data showing the mutation spectrum of 54 individual POLE mutants supports differences in the way mutants generate somatic 55 mutations (Shinbrot et al., 2014) but these differences have not yet been quantified. 56 Mutations are distributed unevenly across the cancer genome and mutation rates 57 across genomic regions are hi...

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A recurrent cancer-associated substitution in DNA polymerase ε produces a hyperactive enzyme

Cited by 67 publications

References 54 publications

Mutational processes of distinct POLE exonuclease domain mutants drive an enrichment of a specific TP53 mutation in colorectal cancer

Mutational processes of distinct POLE exonuclease domain mutants drive an enrichment of a specific TP53 mutation in colorectal cancer

DNA polymerase δ proofreads errors made by DNA polymerase ε

Mutational processes of distinct POLE exonuclease domain mutants drive an enrichment of a specific TP53 mutation in colorectal cancer

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