Polymerase Proofreading Research Articles

High predictability for identifying Lynch syndrome via microsatellite instability testing or immunohistochemistry in all Lynch-associated tumor types.

Lynch syndrome is an inherited cancer-prone syndrome identified in ~3% of all colorectal cancer (CRC) patients and ~2% of all endometrial cancer (EC) patients (1-3). It is defined by identification of a germline mutation in one of the DNA mismatch repair (MMR) genes ( MSH2, MLH1, MSH6, PMS2, EPCAM ) whose proteins function to maintain replication fidelity of DNA prior to mitosis, and sets it apart from other hereditary non-polyposis colorectal cancer (HNPCC) syndromes such as Familial Colorectal Cancer Type X and Polymerase Proofreading Polyposis syndrome (3).

Mutational signatures of early-onset colorectal cancer.

e15113 Background: Despite a reduction of Colorectal Cancer (CRC) incidence in western countries in the past decades, Early-Onset CRCs (EO-CRC, patients diagnosed with CRC ≤ 40 years old) incidence has increased. Although frequently occurring in the context of familial syndromes, EO-CRCs are mainly sporadic cases and phenotipically enriched for distal localisation and advanced stage at diagnosis. Whether EO-sporadic CRCs pathogenesis differs from that of normal-onset (NO) CRC and how this might impact incidence rates is currently unknown. This had prompted us to ask if, at the genetic level, “traces” of peculiar pathogenic processes could be identified in EO-specific (or -enriched) genetic signatures (GS). Methods: The mutational signatures of 424 TCGA CRC patient samples (19 EO and 405 ≥ 50 years at diagnosis) were analyzed and the similarity between each mutational profile and COSMIC GS was calculated using Bioconductor R package Mutational Patterns (doi: 10.1186/s13073-018-0539-0). Unsupervised hierarchical clustering of the samples according to similarity to GS was performed in single cohort and pooled analysis. Association between age and individual GS was assessed through grouped and linear correlation analysis. Results: EO-CRC patients were grouped in three main clusters: Cluster1 exposing a major similarity with GS10 (associated with defects in polymerase proofreading activity), Cluster2 showing stronger similarities with GS6 (associated with mismatch repair deficiency), and GS1 (associated with 5-MeC deamination) and Cluster3 presenting similarity with multiple GSs, such as 3 (associated with homologous recombination deficiency) and 5 (pathogenesis unknown). Overall this clustering was maintained when EO-CRC samples were pooled with NO CRC. Grouped and correlation analysis revealed no significant association between age and individual GSs, including GS1 (associated with age). Conclusions: These preliminary analyses show that the relative contribution of known GS is similar in EO and NO cohorts of patients. Possible enrichment for EO-CRC in specific signature clusters will be analysed on a wider sample series.

Development of an MSI-positive colon tumor with aberrant DNA methylation in a PPAP patient

Polymerase proofreading-associated polyposis (PPAP) is a disease caused by germline variations in the POLE and POLD1 genes that encode catalytic subunits of DNA polymerases. Studies of cancer genomes have identified somatic mutations in these genes, suggesting the importance of polymerase proofreading of DNA replication in suppressing tumorigenesis. Here, we identified a germline frameshift variation in the POLE gene (c.4191_4192delCT, p.Tyr1398*) in a case with multiple adenomatous polyps and three synchronous colon cancers. Interestingly, one of the colon cancers showed microsatellite instability-high (MSI-H) and another microsatellite stable. Immunohistochemical staining revealed that the MSI-H tumor cells lost the expression of MLH1 protein. Whole genome sequencing of the MSI-H tumor did not find pathogenic somatic mutations in mismatch repair genes but found frameshift mutations in the TET genes that catalyze 5-methylcytosine hydroxylation. Bisulfite sequencing of the tumor corroborated an increase in the number of hypermethylated regions including the MLH1 promoter. These data indicate that PPAP patients might develop MSI-positive tumors through epigenetic silencing of MLH1. These findings will contribute to comprehensive understanding of the molecular basis of tumors that involve deficiency of proofreading activity of DNA polymerases.

DNA Rereplication Is Susceptible to Nucleotide-Level Mutagenesis.

The sources of genome instability, a hallmark of cancer, remain incompletely understood. One potential source is DNA rereplication, which arises when the mechanisms that prevent the reinitiation of replication origins within a single cell cycle are compromised. Using the budding yeast Saccharomyces cerevisiae, we previously showed that DNA rereplication is extremely potent at inducing gross chromosomal alterations and that this arises in part because of the susceptibility of rereplication forks to break. Here, we examine the ability of DNA rereplication to induce nucleotide-level mutations. During normal replication these mutations are restricted by three overlapping error-avoidance mechanisms: the nucleotide selectivity of replicative polymerases, their proofreading activity, and mismatch repair. Using lys2InsEA14 , a frameshift reporter that is poorly proofread, we show that rereplication induces up to a 30× higher rate of frameshift mutations and that this mutagenesis is due to passage of the rereplication fork, not secondary to rereplication fork breakage. Rereplication can also induce comparable rates of frameshift and base-substitution mutations in a more general mutagenesis reporter CAN1, when the proofreading activity of DNA polymerase ε is inactivated. Finally, we show that the rereplication-induced mutagenesis of both lys2InsEA14 and CAN1 disappears in the absence of mismatch repair. These results suggest that mismatch repair is attenuated during rereplication, although at most sequences DNA polymerase proofreading provides enough error correction to mitigate the mutagenic consequences. Thus, rereplication can facilitate nucleotide-level mutagenesis in addition to inducing gross chromosomal alterations, broadening its potential role in genome instability.

Defining the impact of mutation accumulation on replicative lifespan in yeast using cancer-associated mutator phenotypes

Mutations accumulate within somatic cells and have been proposed to contribute to aging. It is unclear what level of mutation burden may be required to consistently reduce cellular lifespan. Human cancers driven by a mutator phenotype represent an intriguing model to test this hypothesis, since they carry the highest mutation burdens of any human cell. However, it remains technically challenging to measure the replicative lifespan of individual mammalian cells. Here, we modeled the consequences of cancer-related mutator phenotypes on lifespan using yeast defective for mismatch repair (MMR) and/or leading strand (Polε) or lagging strand (Polδ) DNA polymerase proofreading. Only haploid mutator cells with significant lifetime mutation accumulation (MA) exhibited shorter lifespans. Diploid strains, derived by mating haploids of various genotypes, carried variable numbers of fixed mutations and a range of mutator phenotypes. Some diploid strains with fewer than two mutations per megabase displayed a 25% decrease in lifespan, suggesting that moderate numbers of random heterozygous mutations can increase mortality rate. As mutation rates and burdens climbed, lifespan steadily eroded. Strong diploid mutator phenotypes produced a form of genetic anticipation with regard to aging, where the longer a lineage persisted, the shorter lived cells became. Using MA lines, we established a relationship between mutation burden and lifespan, as well as population doubling time. Our observations define a threshold of random mutation burden that consistently decreases cellular longevity in diploid yeast cells. Many human cancers carry comparable mutation burdens, suggesting that while cancers appear immortal, individual cancer cells may suffer diminished lifespan due to accrued mutation burden.

The role of inherited genetic variants in colorectal polyposis syndromes.

Colorectal carcinoma (CRC) is the third most common cancer in men and the second most common cancer in women across the world. Most CRCs occur sporadically, but in 15-35% of cases, hereditary factors are important. Some patients with an inherited predisposition to CRC will be diagnosed with a "genetic polyposis syndrome" such as familial adenomatous polyposis (FAP), MUTYH-associated polyposis (MAP), polymerase proofreading associated polyposis (PPAP), NTHL1-associated polyposis, MSH3-associated polyposis or a hamartomatous polyposis syndrome. Individuals with ≥10 colorectal polyps have traditionally been referred for genetic diagnostic testing to identify APC and MUTYH mutations which cause FAP and MAP respectively. Mutations are found in most patients with >100 adenomas but in only a minority of those with 10-100 adenomas. The reasons that diagnostic laboratories are not identifying pathogenic variants include mutations occurring outside of the open reading frames of genes, individuals exhibiting generalized mosaicism and the involvement of additional genes. It is important to identify patients with an inherited polyposis syndrome, and to define the mutations causing their polyposis, so that the individuals and their relatives can be managed appropriately.

Distinct mutational signatures characterize concurrent loss of polymerase proofreading and mismatch repair

Fidelity of DNA replication is maintained using polymerase proofreading and the mismatch repair pathway. Tumors with loss of function of either mechanism have elevated mutation rates with characteristic mutational signatures. Here we report that tumors with concurrent loss of both polymerase proofreading and mismatch repair function have mutational patterns that are not a simple sum of the signatures of the individual alterations, but correspond to distinct, previously unexplained signatures: COSMIC database signatures 14 and 20. We then demonstrate that in all five cases in which the chronological order of events could be determined, polymerase epsilon proofreading alterations precede the defect in mismatch repair. Overall, we illustrate that multiple distinct mutational signatures can result from different combinations of a smaller number of mutational processes (of either damage or repair), which can influence the interpretation and discovery of mutational signatures.

The Drift in Molecular Testing for Influenza: Mutations Affecting Assay Performance.

Influenza is associated with rapid evolution due to lack of RNA polymerase proofreading, immunogenic selection, and frequent rearrangement of gene segments. Evolutionary changes affecting the performance of diagnostic testing have long been recognized. Hence, it is not surprising that such challenges apply to nucleic acid amplification tests, even though they are designed to target highly conserved regions. Initially, case reports involved single isolates of A(H1N1)pdm09. Over the past 4 years, subtype H3N2 viruses evolved to viral clades with mutations in the WHO-recommended target region, such that almost all isolates worldwide have significantly reduced sensitivities with many commercial reverse transcription-PCR tests.

Multisubunit DNA-Dependent RNA Polymerases from Vaccinia Virus and Other Nucleocytoplasmic Large-DNA Viruses: Impressions from the Age of Structure.

The past 17 years have been marked by a revolution in our understanding of cellular multisubunit DNA-dependent RNA polymerases (MSDDRPs) at the structural level. A parallel development over the past 15 years has been the emerging story of the giant viruses, which encode MSDDRPs. Here we link the two in an attempt to understand the specialization of multisubunit RNA polymerases in the domain of life encompassing the large nucleocytoplasmic DNA viruses (NCLDV), a superclade that includes the giant viruses and the biochemically well-characterized poxvirus vaccinia virus. The first half of this review surveys the recently determined structural biology of cellular RNA polymerases for a microbiology readership. The second half discusses a reannotation of MSDDRP subunits from NCLDV families and the apparent specialization of these enzymes by virus family and by subunit with regard to subunit or domain loss, subunit dissociability, endogenous control of polymerase arrest, and the elimination/customization of regulatory interactions that would confer higher-order cellular control. Some themes are apparent in linking subunit function to structure in the viral world: as with cellular RNA polymerases I and III and unlike cellular RNA polymerase II, the viral enzymes seem to opt for speed and processivity and seem to have eliminated domains associated with higher-order regulation. The adoption/loss of viral RNA polymerase proofreading functions may have played a part in matching intrinsic mutability to genome size.

DNA replication and mismatch repair safeguard against metabolic imbalances.

During DNA replication, the major DNA replicative polymerases Polδ and Pole introduce noncomplementary nucleotides approximately once in every 100,000 polymerization events. Proofreading properties of these polymerases improve their fidelity by 10- to 100-fold, and postreplicative DNA mismatch repair (MMR), which acts as a spell checker to remove mismatches that escape polymerase proofreading, improves this fidelity even further, resulting in mutation rates as low as 2 × 10−10 substitutions per base per cell division (1). Mutations in genes encoding MMR proteins and DNA polymerase proofreading activities are linked to elevated mutation rates and diseases such as cancer, and these rates are synergistically increased in double mutants (2, 3). In PNAS, Schmidt et al. (4) describe work in which they screened for defects in genome stability in genetic backgrounds where processes that limit mutagenesis were compromised. Their work provides new insights for how cellular metabolism and nucleotide pool homeostasis interact to avoid mutation and maintain genome stability. They also provide evidence that DNA polymerase fidelity and MMR functions are sufficiently robust to compensate at least partially for defects in cellular metabolism (Fig. 1). Fig. 1. Removing the buffering capabilities of DNA replication and DNA MMR uncovers new factors that contribute to nucleotide pool homeostasis. Multiple mechanisms contribute to the overall fidelity of DNA replication. For example, each of the four mechanisms outlined in this figure can compensate for defects in the others. ( i ) A homeostasis mechanism responds to cellular metabolism to regulate the biosynthesis of dNTP and dNTP precursors to maintain a balanced concentration of dNTPs. ( ii ) DNA polymerase proofreading activities: During eukaryotic DNA replication, the major replicative polymerases Pole and Polδ both contain proofreading activities that enable them to excise misincorporation errors. However, Polα, which initiates DNA synthesis at origins and at Okazaki fragments, does not contain such a function. … [↵][1]1To whom correspondence should be addressed. Email: eea3{at}cornell.edu. [1]: #xref-corresp-1-1

Alterations in cellular metabolism triggered by URA7 or GLN3 inactivation cause imbalanced dNTP pools and increased mutagenesis

Eukaryotic DNA replication fidelity relies on the concerted action of DNA polymerase nucleotide selectivity, proofreading activity, and DNA mismatch repair (MMR). Nucleotide selectivity and proofreading are affected by the balance and concentration of deoxyribonucleotide (dNTP) pools, which are strictly regulated by ribonucleotide reductase (RNR). Mutations preventing DNA polymerase proofreading activity or MMR function cause mutator phenotypes and consequently increased cancer susceptibility. To identify genes not previously linked to high-fidelity DNA replication, we conducted a genome-wide screen in Saccharomyces cerevisiae using DNA polymerase active-site mutants as a "sensitized mutator background." Among the genes identified in our screen, three metabolism-related genes (GLN3, URA7, and SHM2) have not been previously associated to the suppression of mutations. Loss of either the transcription factor Gln3 or inactivation of the CTP synthetase Ura7 both resulted in the activation of the DNA damage response and imbalanced dNTP pools. Importantly, these dNTP imbalances are strongly mutagenic in genetic backgrounds where DNA polymerase function or MMR activity is partially compromised. Previous reports have shown that dNTP pool imbalances can be caused by mutations altering the allosteric regulation of enzymes involved in dNTP biosynthesis (e.g., RNR or dCMP deaminase). Here, we provide evidence that mutations affecting genes involved in RNR substrate production can cause dNTP imbalances, which cannot be compensated by RNR or other enzymatic activities. Moreover, Gln3 inactivation links nutrient deprivation to increased mutagenesis. Our results suggest that similar genetic interactions could drive mutator phenotypes in cancer cells.

Polymerase proofreading domain mutations: New opportunities for immunotherapy in hypermutated colorectal cancer beyond MMR deficiency.

Immune checkpoint inhibition is a new therapeutic strategy that has shown promising efficacy in many cancer types. Significant activity associated with mismatch repair (MMR) deficiency has been observed in hypermutated, microsatellite unstable (MSI) metastatic colorectal cancer (CRC). Beyond deficient-MMR tumors, somatic or germline DNA polymerase D1 (POLD1) or DNA polymerase E (POLE) alterations cause a hypermutated phenotype in CRC. This recently identified and rare subgroup of proficient-MMR tumors may also benefit from immunotherapy. In this review, we provide a comprehensive overview of recent data on CRC tumors harboring POLD1 or POLE mutations, with a focus on their molecular, histological, and clinical features. We also examine the evidence supporting the development of immune checkpoint inhibitors in this specific subgroup of CRC patients.

Abstract IA02: The discovery of the hereditary colorectal cancer genes: A historical perspective

Abstract IA02: The discovery of the hereditary colorectal cancer genes: A historical perspective

Abstract IA08: Polyposis beyond FAP (and APC)

Abstract Familial adenomatous polyposis (FAP) is the most common high-penetrant Mendelian syndrome predisposing to adenomatous polyposis. FAP is caused by monoallelic germline mutations in the gene APC, and shows autosomal dominant inheritance. A somatic mutation in the remaining wild type APC allele results in loss of APC activity, which is one of the initiating events of adenoma development. The high proliferation rate in the colorectum increases the chance that an intestinal epithelium cell obtains this somatic second hit, which explains why FAP patients usually develop hundreds to thousands of adenomatous polyps and, if untreated, inevitably develop colorectal cancer (CRC). Nevertheless, the majority of polyposis patients and families are not explained by mutations in APC. Since the discovery of FAP in 1991, several additional polyposis syndromes have been discovered, usually associated with lower number of polyps and somewhat less elevated risk of CRC. Many of the genes underlying these syndromes play a role in DNA repair and have a wider tumor spectrum. As becomes apparent from the somatic mutation profiles in tumors of these polyposis patients, these DNA repair deficiencies cause increased somatic mutation rates that affect proliferating tissues like the colon, and accelerate the formation of polyps and carcinomas. As an example, polymerase proofreading associated polyposis (PPAP) is a recently discovered autosomal dominant syndrome caused by mutations in the exonuclease domains of the polymerase genes POLE and POLD1. In addition, mutations in the base excision repair genes MUTYH and NTHL1, and the mismatch repair gene MSH3 underlie autosomal recessive polyposis syndromes. Notably, the incidences of these syndromes, particularly those recently discovered, are low. The question therefore arises how many more genes in which mutations cause high-penetrant polyposis still await their discovery. Here, I will present the latest findings on NTHL1-associated polyposis, it's expected incidence and its phenotypic characteristics. Furthermore, I will discuss the possible role of other DNA glycosylase genes of the base excision repair pathway in the development of polyposis and colorectal cancer. Citation Format: Roland P. Kuiper. Polyposis beyond FAP (and APC). [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr IA08.

Familial Polyposis Syndromes

Although sporadic polyps in the gastrointestinal tract are common with increasing age, the finding of a large number of polyps raises suspicion for a hereditary polyposis syndrome associated with a germline genetic mutation. Because many of these hereditary polyposis syndromes also confer an increased risk of gastrointestinal and extraintestincal cancers, implicated in approximately 1% of all colorectal cancers, recognition of these syndromes is critical to offer preventive screening measures. A key distinguishing feature is polyp histologic type, ranging from adenomatous, to serrated, to hamartomatous. A clinical diagnosis can be confirmed by genetic testing for a germline mutation in known cancer susceptibility genes, although in many polyposis families, a genetic etiology has not yet been identified. This review covers familial adenomatous polyposis, MUTYH-associated polyposis, polyposis associated with polymerase proofreading, juvenile polyposis syndrome, PTEN hamartoma tumor syndromes, hereditary mixed polyposis syndrome, and serrated polyposis. The figures shows the spectrum of histologic types and genetic etiologies of hereditary polyposis syndromes. Tables list polyposis syndromes, American College of Gastroenterology surveillance guidelines for hereditary polyposis syndromes, diagnostic criteria for juvenile polyposis syndrome, diagnostic criteria for PTEN hamartoma tumor syndrome, and World Health Organization diagnostic criteria for serrated polyposis syndrome. This review contains 1 highly rendered figure, 5 tables, and 172 references Key words: Familial adenomatous polyposis; Polyposis syndromes; Gastrointestinal polyps; Hereditary polyposis syndromes

A panoply of errors: polymerase proofreading domain mutations in cancer.

Although it has long been recognized that the exonucleolytic proofreading activity intrinsic to the replicative DNA polymerases Pol δ and Pol ε is essential for faithful replication of DNA, evidence that defective DNA polymerase proofreading contributes to human malignancy has been limited. However, recent studies have shown that germline mutations in the proofreading domains of Pol δ and Pol ε predispose to cancer, and that somatic Pol ε proofreading domain mutations occur in multiple sporadic tumours, where they underlie a phenotype of 'ultramutation' and favourable prognosis. In this Review, we summarize the current understanding of the mechanisms and consequences of polymerase proofreading domain mutations in human malignancies, and highlight the potential utility of these variants as novel cancer biomarkers and therapeutic targets.

GE-09 * COMBINED HEREDITARY AND SOMATIC MUTATIONS OF REPLICATION ERROR REPAIR GENES RESULT IN RAPID ONSET OF ULTRA-HYPERMUTATED MALIGNANT BRAIN TUMORS IN CHILDREN

BACKGROUND: Biallelic Mismatch Repair Deficiency (bMMRD) Syndrome is a childhood cancer predisposition syndrome with a wide tumor spectrum where malignant brain tumors predominate. Mismatch repair and DNA polymerase proofreading are two components necessary to repair DNA replication − associated mutations. The consequences of disruption to both repair components in humans are not well studied. Furthermore, it is unknown how defects in DNA repair processes cause and perpetuate childhood CNS tumorigenesis. METHODS: We analyzed17 bMMRD cancers using genome, exome sequencing and microarrays. Additionally, we sequenced non-neoplastic tissues from patients and compared the mutational landscape of bMMRD tumors to a reference data set of all childhood and adult cancers. RESULTS: BMMRD malignant brain tumors harbored massive numbers of substitution mutations (>250/Mb), which was greater than all childhood and most adult cancers (>7,000 analyzed). These cancers lacked copy number alterations (p < 0.01) and microsatellite instability as seen in sporadic glioblastoma and adult deficient MMR cancers respectively. These mutation signatures and numbers are unique and diagnostic of childhood germ-line bMMRD (P < 10−13). Strikingly, all ultra-hypermutated bMMRD cancers acquired early and conserved somatic mutations in DNA polymerases ɛ or δ. Polymerase driver mutations resulted in a unique mutation signature reflective of the repair processes and unique to MMRD/polymerase mutant cancers. Sequential tumor biopsy analysis revealed that MMR mutations and combined MMRD/polymerase mutations add a log-scale increment to cancer mutation load. BMMRD/polymerase mutant cancers rapidly amass mutations (∼600 mutations/cell division), reaching a threshold of ∼20,000 exonic mutations in <6 months. CONCLUSIONS/SIGNIFICANCE: Early-onset brain tumors from bMMRD patients offer an unobstructed view of mutation types and secondary pathways that drive carcinogenesis. We suggest a new mechanism of cancer progression where mutations develop in a rapid burst after ablation of replication repair. The high mutation load and threshold may be this cancer's Achilles' heel, exploitable for diagnosis and therapeutic intervention.

Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers.

DNA replication-associated mutations are repaired by two components: polymerase proofreading and mismatch repair. The mutation consequences of disruption to both repair components in humans are not well studied. We sequenced cancer genomes from children with inherited biallelic mismatch repair deficiency (bMMRD). High-grade bMMRD brain tumors exhibited massive numbers of substitution mutations (>250/Mb), which was greater than all childhood and most cancers (>7,000 analyzed). All ultra-hypermutated bMMRD cancers acquired early somatic driver mutations in DNA polymerase ɛ or δ. The ensuing mutation signatures and numbers are unique and diagnostic of childhood germ-line bMMRD (P < 10(-13)). Sequential tumor biopsy analysis revealed that bMMRD/polymerase-mutant cancers rapidly amass an excess of simultaneous mutations (∼600 mutations/cell division), reaching but not exceeding ∼20,000 exonic mutations in <6 months. This implies a threshold compatible with cancer-cell survival. We suggest a new mechanism of cancer progression in which mutations develop in a rapid burst after ablation of replication repair.

Lynch syndrome and Lynch syndrome mimics: The growing complex landscape of hereditary colon cancer.

Hereditary non-polyposis colorectal cancer (HNPCC) was previously synonymous with Lynch syndrome; however, identification of the role of germline mutations in the DNA mismatch repair (MMR) genes has made it possible to differentiate Lynch syndrome from other conditions associated with familial colorectal cancer (CRC). Broadly, HNPCC may be dichotomized into conditions that demonstrate defective DNA MMR and microsatellite instability (MSI) vs those conditions that demonstrate intact DNA MMR. Conditions characterized by MMR deficient CRCs include Lynch syndrome (germline MMR mutation), Lynch-like syndrome (biallelic somatic MMR mutations), constitutional MMR deficiency syndrome (biallelic germline MMR mutations), and sporadic MSI CRC (somatic biallelic methylation of MLH1). HNPCC conditions with intact DNA MMR associated with familial CRC include polymerase proofreading associated polyposis and familial colorectal cancer type X. Although next generation sequencing technologies have elucidated the genetic cause for some HNPCC conditions, others remain genetically undefined. Differentiating between Lynch syndrome and the other HNPCC disorders has profound implications for cancer risk assessment and surveillance of affected patients and their at-risk relatives. Clinical suspicion coupled with molecular tumor analysis and testing for germline mutations can help differentiate the clinical mimicry within HNPCC and facilitate diagnosis and management.

DNA Replication Error-Induced Extinction of Diploid Yeast

Genetic defects in DNA polymerase accuracy, proofreading, or mismatch repair (MMR) induce mutator phenotypes that accelerate adaptation of microbes and tumor cells. Certain combinations of mutator alleles synergistically increase mutation rates to levels that drive extinction of haploid cells. The maximum tolerated mutation rate of diploid cells is unknown. Here, we define the threshold for replication error-induced extinction (EEX) of diploid Saccharomyces cerevisiae. Double-mutant pol3 alleles that carry mutations for defective DNA polymerase-δ proofreading (pol3-01) and accuracy (pol3-L612M or pol3-L612G) induce strong mutator phenotypes in heterozygous diploids (POL3/pol3-01,L612M or POL3/pol3-01,L612G). Both pol3-01,L612M and pol3-01,L612G alleles are lethal in the homozygous state; cells with pol3-01,L612M divide up to 10 times before arresting at random stages in the cell cycle. Antimutator eex mutations in the pol3 alleles suppress this lethality (pol3-01,L612M,eex or pol3-01,L612G,eex). MMR defects synergize with pol3-01,L612M,eex and pol3-01,L612G,eex alleles, increasing mutation rates and impairing growth. Conversely, inactivation of the Dun1 S-phase checkpoint kinase suppresses strong pol3-01,L612M,eex and pol3-01,L612G,eex mutator phenotypes as well as the lethal pol3-01,L612M phenotype. Our results reveal that the lethal error threshold in diploids is 10 times higher than in haploids and likely determined by homozygous inactivation of essential genes. Pronounced loss of fitness occurs at mutation rates well below the lethal threshold, suggesting that mutator-driven cancers may be susceptible to drugs that exacerbate replication errors.