Modeling Allosteric Mechanisms of Eukaryotic Type II Topoisomerases

Type II topoisomerases (TopoIIs) are ubiquitous enzymes that are involved in crucial nuclear processes such as genome organization, chromosome segregation, and other DNA metabolic processes. These enzymes function as large, homodimeric complexes that undergo a complex cycle of binding and hydrolysis of two ATP molecules in their ATPase domains, which regulates the capture and passage of one DNA double-helix through a second, cleaved DNA molecule. This process requires the transmission of information about the state of the bound nucleotide over vast ranges in the TopoII complex. How this information is transmitted at the molecular level to regulate TopoII functions and how protein substitutions disrupt these mechanisms remains largely unknown. Here, we employed extensive microsecond scale molecular dynamics simulations of the yeast TopoII enzyme in multiple nucleotide-bound states and with amino acid substitutions near both the N- and C-terminals of the complex. Simulation results indicate that the ATPase domains are remarkably flexible on the sub-microsecond timescale and that these dynamics are modulated by the identity of the bound nucleotides and both local and distant amino acid substitutions. Network analyses point towards specific allosteric networks that transmit information about the hydrolysis cycle throughout the complex, which include residues in both the protein and the bound DNA molecule. Amino acid substitutions weaken many of these pathways. Together, our results provide molecular-level details on how the TopoII catalytic cycle is controlled through nucleotide binding and hydrolysis and how mutations may disrupt this process.

RAD54L2 counters TOP2-DNA adducts to promote genome stability

The catalytic cycle of topoisomerase 2 (TOP2) enzymes proceeds via a transient DNA double-strand break (DSB) intermediate termed the TOP2 cleavage complex (TOP2cc), in which the TOP2 protein is covalently bound to DNA. Anticancer agents such as etoposide operate by stabilizing TOP2ccs, ultimately generating genotoxic TOP2-DNA protein cross-links that require processing and repair. Here, we identify RAD54 like 2 (RAD54L2) as a factor promoting TOP2cc resolution. We demonstrate that RAD54L2 acts through a novel mechanism together with zinc finger protein associated with tyrosyl-DNA phosphodiesterase 2 (TDP2) and TOP2 (ZATT/ZNF451) and independent of TDP2. Our work suggests a model wherein RAD54L2 recognizes sumoylated TOP2 and, using its ATPase activity, promotes TOP2cc resolution and prevents DSB exposure. These findings suggest RAD54L2-mediated TOP2cc resolution as a potential mechanism for cancer therapy resistance and highlight RAD54L2 as an attractive candidate for drug discovery.

Naturally mutagenic sequence diversity in a human type II topoisomerase

Type II topoisomerases transiently cleave duplex DNA as part of a strand passage mechanism that helps control chromosomal organization and superstructure. Aberrant DNA cleavage can result in genomic instability, and how topoisomerase activity is controlled to prevent unwanted breaks is poorly understood. Using a genetic screen, we identified mutations in the beta isoform of human topoisomerase II (hTOP2β) that render the enzyme hypersensitive to the chemotherapeutic agent etoposide. Several of these variants were unexpectedly found to display hypercleavage behavior in vitro and to be capable of inducing cell lethality in a DNA repair-deficient background; surprisingly, a subset of these mutations were also observed in TOP2B sequences from cancer genome databases. Using molecular dynamics simulations and computational network analyses, we found that many of the mutations obtained from the screen map to interfacial points between structurally coupled elements, and that dynamical modeling could be used to identify other damage-inducing TOP2B alleles present in cancer genome databases. This work establishes that there is an innate link between DNA cleavage predisposition and sensitivity to topoisomerase II poisons, and that certain sequence variants of human type II topoisomerases found in cancer cells can act as DNA-damaging agents. Our findings underscore the potential for hTOP2β to function as a clastogen capable of generating DNA damage that may promote or support cellular transformation.

Using energy to go downhill - a genoprotective role for ATPase activity in DNA topoisomerase II

Type II topoisomerases effect topological changes in DNA by cutting a single duplex, passing a second duplex through the break, and resealing the broken strand in an ATP-coupled reaction. Curiously, most type II topoisomerases (topos II, IV, and VI) catalyze DNA transformations that are energetically favorable, such as the removal of superhelical strain; why ATP is required for such reactions is unknown. Here, using human topoisomerase II β (hTOP2β) as a model, we show that the ATPase domains of the enzyme are not required for DNA strand passage, but that their loss leads to increased DNA nicking and double strand break formation by the enzyme. The unstructured C-terminal domains (CTDs) of hTOP2β strongly potentiate strand passage activity in the absence of the ATPase regions, as do cleavage-prone mutations that confer hypersensitivity to the chemotherapeutic agent etoposide. The presence of either the CTD or the mutations lead ATPase-less enzymes to promote even greater levels of DNA cleava in ge vitro , as well as in vivo . By contrast, the aberrant cleavage phenotypes of these topo II variants is significantly repressed when the ATPase domains are restored. Our findings are consistent with the proposal that type II topoisomerases acquired an ATPase function to maintain high levels of catalytic activity while minimizing inappropriate DNA damage.

Requirements for MRN endonuclease processing of topoisomerase II-mediated DNA damage in mammalian cells

During a normal topoisomerase II (TOP2) reaction, the enzyme forms a covalent enzyme DNA intermediate consisting of a 5′ phosphotyrosyl linkage between the enzyme and DNA. While the enzyme typically rejoins the transient breakage after strand passage, a variety of conditions including drugs targeting TOP2 can inhibit DNA resealing, leading to enzyme-mediated DNA damage. A critical aspect of the repair of TOP2-mediated damage is the removal of the TOP2 protein covalently bound to DNA. While proteolysis plays a role in repairing this damage, nucleolytic enzymes must remove the phosphotyrosyl-linked peptide bound to DNA. The MRN complex has been shown to participate in the removal of TOP2 protein from DNA following cellular treatment with TOP2 poisons. In this report we used an optimized ICE (In vivo Complex of Enzyme) assay to measure covalent TOP2/DNA complexes. In agreement with previous independent reports, we find that the absence or inhibition of the MRE11 endonuclease results in elevated levels of both TOP2α and TOP2β covalent complexes. We also examined levels of TOP2 covalent complexes in cells treated with the proteasome inhibitor MG132. Although MRE11 inhibition plus MG132 was not synergistic in etoposide-treated cells, ectopic overexpression of MRE11 resulted in removal of TOP2 even in the presence of MG132. We also found that VCP/p97 inhibition led to elevated TOP2 covalent complexes and prevented the removal of TOP2 covalent complexes by MRE11 overexpression. Our results demonstrate the existence of multiple pathways for proteolytic processing of TOP2 prior to nucleolytic processing, and that MRE11 can process TOP2 covalent complexes even when the proteasome is inhibited. The interactions between VCP/p97 and proteolytic processing of TOP2 covalent complexes merit additional investigation.

SUMO: A Swiss Army Knife for Eukaryotic Topoisomerases

Topoisomerases play crucial roles in DNA metabolism that include replication, transcription, recombination, and chromatin structure by manipulating DNA structures arising in double-stranded DNA. These proteins play key enzymatic roles in a variety of cellular processes and are also likely to play structural roles. Topoisomerases allow topological transformations by introducing transient breaks in DNA by a transesterification reaction between a tyrosine residue of the enzyme and DNA. The cleavage reaction leads to a unique enzyme intermediate that allows cutting DNA while minimizing the potential for damage-induced genetic changes. Nonetheless, topoisomerase-mediated cleavage has the potential for inducing genome instability if the enzyme-mediated DNA resealing is impaired. Regulation of topoisomerase functions is accomplished by post-translational modifications including phosphorylation, polyADP-ribosylation, ubiquitylation, and SUMOylation. These modifications modulate enzyme activity and likely play key roles in determining sites of enzyme action and enzyme stability. Topoisomerase-mediated DNA cleavage and rejoining are affected by a variety of conditions including the action of small molecules, topoisomerase mutations, and DNA structural forms which permit the conversion of the short-lived cleavage intermediate to persistent topoisomerase DNA-protein crosslink (TOP-DPC). Recognition and processing of TOP-DPCs utilizes many of the same post-translational modifications that regulate enzyme activity. This review focuses on SUMOylation of topoisomerases, which has been demonstrated to be a key modification of both type I and type II topoisomerases. Special emphasis is placed on recent studies that indicate how SUMOylation regulates topoisomerase function in unperturbed cells and the unique roles that SUMOylation plays in repairing damage arising from topoisomerase malfunction.

Recurrent mutations in topoisomerase IIα cause a previously undescribed mutator phenotype in human cancers

Topoisomerases nick and reseal DNA to relieve torsional stress associated with transcription and replication and to resolve structures such as knots and catenanes. Stabilization of the yeast Top2 cleavage intermediates is mutagenic in yeast, but whether this extends to higher eukaryotes is less clear. Chemotherapeutic topoisomerase poisons also elevate cleavage, resulting in mutagenesis. Here, we describe p.K743N mutations in human topoisomerase hTOP2α and link them to a previously undescribed mutator phenotype in cancer. Overexpression of the orthologous mutant protein in yeast generated a characteristic pattern of 2- to 4-base pair (bp) duplications resembling those in tumors with p.K743N. Using mutant strains and biochemical analysis, we determined the genetic requirements of this mutagenic process and showed that it results from trapping of the mutant yeast yTop2 cleavage complex. In addition to 2- to 4-bp duplications, hTOP2α p.K743N is also associated with deletions that are absent in yeast. We call the combined pattern of duplications and deletions ID_TOP2α. All seven tumors carrying the hTOP2α p.K743N mutation showed ID_TOP2α, while it was absent from all other tumors examined (n = 12,269). Each tumor with the ID_TOP2α signature had indels in several known cancer genes, which included frameshift mutations in tumor suppressors PTEN and TP53 and an activating insertion in BRAF. Sequence motifs found at ID_TOP2α mutations were present at 80% of indels in cancer-driver genes, suggesting that ID_TOP2α mutagenesis may contribute to tumorigenesis. The results reported here shed further light on the role of topoisomerase II in genome instability.

Topoisomerase Assays

Topoisomerases are enzymes that play essential roles in DNA replication, transcription, chromosome segregation, and recombination. All cells have two major forms of DNA topoisomerases: type I enzymes, which make single-stranded cuts in DNA, and type II enzymes, which cut and decatenate double-stranded DNA. DNA topoisomerases are important targets of approved and experimental anti-cancer agents. Provided in this article are protocols to assess activities of topoisomerases and their inhibitors. Included are an assay for topoisomerase I activity based on relaxation of supercoiled DNA; an assay for topoisomerase II based on the decatenation of double-stranded DNA; and approaches for enriching and quantifying DNA-protein covalent complexes formed as obligatory intermediates in the reactions of type I and II topoisomerases with DNA; and assays for measuring DNA cleavage in vitro. Topoisomerases are not the only proteins that form covalent adducts with DNA in living cells, and the approaches described here are likely to find use in characterizing other protein-DNA adducts and exploring their utility as targets for therapy. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Assay of topoisomerase I activity Basic Protocol 2: Assay of topoisomerase II activity Basic Protocol 3: In vivo determination of topoisomerase covalent complexes using the in vivo complex of enzyme (ICE) assay Support Protocol 1: Preparation of mouse tissue for determination of topoisomerase covalent complexes using the ICE assay Support Protocol 2: Using recombinant topoisomerase standard for absolute quantification of cellular TOP2CC Basic Protocol 4: Quantification of topoisomerase-DNA covalent complexes by RADAR/ELISA: The rapid approach to DNA adduct recovery (RADAR) combined with the enzyme-linked immunosorbent assay (ELISA) Basic Protocol 5: Analysis of protein-DNA covalent complexes by RADAR/Western Support Protocol 3: Adduct-Seq to characterize adducted DNA Support Protocol 4: Nuclear fractionation and RNase treatment to reduce sample complexity Basic Protocol 6: Determination of DNA cleavage by purified topoisomerase I Basic Protocol 7: Determination of inhibitor effects on DNA cleavage by topoisomerase II using a plasmid linearization assay Alternate Protocol: Gel electrophoresis determination of topoisomerase II cleavage.

A conserved SUMO pathway repairs topoisomerase DNA-protein cross-links by engaging ubiquitin-mediated proteasomal degradation

Topoisomerases form transient covalent DNA cleavage complexes to perform their reactions. Topoisomerase I cleavage complexes (TOP1ccs) are trapped by camptothecin and TOP2ccs by etoposide. Proteolysis of the trapped topoisomerase DNA-protein cross-links (TOP-DPCs) is a key step for some pathways to repair these lesions. We describe a pathway that features a prominent role of the small ubiquitin-like modifier (SUMO) modification for both TOP1- and TOP2-DPC repair. Both undergo rapid and sequential SUMO-2/3 and SUMO-1 modifications in human cells. The SUMO ligase PIAS4 is required for these modifications. RNF4, a SUMO-targeted ubiquitin ligase (STUbL), then ubiquitylates the TOP-DPCs for their subsequent degradation by the proteasome. This pathway is conserved in yeast with Siz1 and Slx5-Slx8, the orthologs of human PIAS4 and RNF4.

Kinetic Study of DNA Topoisomerases by Supercoiling-Dependent Fluorescence Quenching

DNA topoisomerases are essential enzymes for all living organisms and important targets for anticancer drugs and antibiotics. Although DNA topoisomerases have been studied extensively, steady-state kinetics has not been systematically investigated because of the lack of an appropriate assay. Previously, we demonstrated that newly synthesized, fluorescently labeled plasmids pAB1_FL905 and pAB1_FL924 can be used to study DNA topoisomerase-catalyzed reactions by fluorescence resonance energy transfer (FRET) or supercoiling-dependent fluorescence quenching (SDFQ). With the FRET or SDFQ method, we performed steady-state kinetic studies for six different DNA topoisomerases including two type IA enzymes (Escherichia coli and Mycobacterium smegmatis DNA topoisomerase I), two type IB enzymes (human and variola DNA topoisomerase I), and two type IIA enzymes (E. coli DNA gyrase and human DNA topoisomerase IIα). Our results show that all DNA topoisomerases follow the classical Michaelis-Menten kinetics and have unique steady-state kinetic parameters, K _M, V _max, and k _cat. We found that k _cat for all topoisomerases are rather low and that such low values may stem from the tight binding of topoisomerases to DNA. Additionally, we confirmed that novobiocin is a competitive inhibitor for adenosine 5'-triphosphate binding to E. coli DNA gyrase, demonstrating the utility of our assay for studying topoisomerase inhibitors.

A complex suite of loci and elements in eukaryotic type II topoisomerases determine selective sensitivity to distinct poisoning agents

Type II topoisomerases catalyze essential DNA transactions and are proven drug targets. Drug discrimination by prokaryotic and eukaryotic topoisomerases is vital to therapeutic utility, but is poorly understood. We developed a next-generation sequencing (NGS) approach to identify drug-resistance mutations in eukaryotic topoisomerases. We show that alterations conferring resistance to poisons of human and yeast topoisomerase II derive from a rich mutational 'landscape' of amino acid substitutions broadly distributed throughout the entire enzyme. Both general and discriminatory drug-resistant behaviors are found to arise from different point mutations found at the same amino acid position and to occur far outside known drug-binding sites. Studies of selected resistant enzymes confirm the NGS data and further show that the anti-cancer quinolone vosaroxin acts solely as an intercalating poison, and that the antibacterial ciprofloxacin can poison yeast topoisomerase II. The innate drug-sensitivity of the DNA binding and cleavage region of human and yeast topoisomerases (particularly hTOP2β) is additionally revealed to be significantly regulated by the enzymes' adenosine triphosphatase regions. Collectively, these studies highlight the utility of using NGS-based methods to rapidly map drug resistance landscapes and reveal that the nucleotide turnover elements of type II topoisomerases impact drug specificity.

DNA Damage by an essential enzyme: A delicate balance act on the tightrope

DNA topoisomerases are essential for DNA metabolic processes such as replication and transcription. Since DNA is double stranded, the unwinding needed for these processes results in DNA supercoiling and catenation of replicated molecules. Changing the topology of DNA molecules to relieve supercoiling or resolve catenanes requires that DNA be transiently cut. While topoisomerases carry out these processes in ways that minimize the likelihood of genome instability, there are several ways that topoisomerases may fail. Topoisomerases can be induced to fail by therapeutic small molecules such as by fluoroquinolones that target bacterial topoisomerases, or a variety of anti-cancer agents that target the eukaryotic enzymes. Increasingly, there have been a large number of agents and processes, including natural products and their metabolites, DNA damage, and the intrinsic properties of the enzymes that can lead to long-lasting DNA breaks that subsequently lead to genome instability, cancer, and other diseases. Understanding the processes that can interfere with topoisomerases and how cells respond when topoisomerases fail will be important in minimizing the consequences when enzymes need to transiently interfere with DNA integrity.

Abstract 4724: Regulation of DNA cleavage by the amino and carboxyl domains of human Top2α

DNA topoisomerases are involved in processing DNA structures such as knots and supercoils formed during cellular processes. hTop2α functions by creating transient DNA double-strand breaks, through which a second DNA molecule can be passed. DNA breakage by hTop2α involves formation of a transient covalent DNA-protein intermediate that can be stabilized by small molecules like etoposide and doxorubicin. Therefore, these agents convert Top2 into a DNA damaging agent. The overall architecture of type II topoisomerases has been defined by a combination of biochemical and structural studies. The homodimeric eukaryotic Top2 includes an N-terminal domain that includes an ATP dependent dimerization and ATPase activity, a domain that connects the ATPase domain to the catalytic core, termed the transducer domain, a central breakage/reunion core that carries out metal ion dependent formation of the protein/DNA covalent complex and a C-terminal domain that includes a second dimerization domain. Since drug resistance to Top2 targeting drugs can occur by mutations that greatly reduce enzyme activity, they are of limited usefulness in understanding detailed mechanisms of drug action. We carried out a large-scale screen to identify etoposide hypersensitive mutations in hTop2α. We developed novel approaches to target small regions of the hTop2α coding sequence. As anticipated, we identified several domains of hTop2α that were hotspots for changes leading to etoposide hypersensitivity. These regions included the N-terminal region of the protein (transducer and ATPase domain), the breakage/reunion catalytic core of the enzyme, and C-terminal dimerization domains. For example, we identified a prominent class of mutations including Asp374Gly, Asp374Glu, Asn445Asp, Val415Leu and Thr377Ile in the transducer domain, which confer hypersensitivity to etoposide. We purified and characterized the Asp374Gly mutant protein. In addition to an increased in vitro sensitivity to etoposide, Top2α (Asp374Gly) had a decreased requirement for ATP compared to the wild-type enzyme. The decreased requirement for ATP is unexpected and may suggest an alteration in the communication between the ATPase domain and the catalytic core. In addition, we also isolated etoposide hypersensitive alleles close to the C-terminal dimerization domain. These mutations included Asp1130Asn, Ala1052Gly and Gln1109Lys. Our results suggest at least two distinct controlling modules for Top2 cleavage: the ATPase/transducer module, and the C-terminal dimerization domain. Our results provide additional insight into how etoposide inhibits Top2α and may suggest new domains of the protein suitable for drug targeting.

Citation Format: Abhishek Dilip Deshpande, Matthew A. Gilbertson, Hannah N. Miles, Karin C. Nitiss, John L. Nitiss. Regulation of DNA cleavage by the amino and carboxyl domains of human Top2α [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4724.

Abstract 1742: Modulation of genotoxic DNA damage by the ATPase domain of type II topoisomerases

Type II topoisomerases play key roles in transcription, replication and chromosome segregation. These enzymes modulate DNA structure by generating transient DNA breaks where the protein is covalently bound to DNA. Anti-cancer drugs targeting topoisomerase II (Top2) inhibit the religation of enzyme-induced breaks, and exert their anti-cancer effects through the generation of enzyme mediated DNA damage. In addition to small molecule inhibitors, it has been suggested that aberrant DNA structures or DNA lesions may also lead to Top2/DNA lesions. A mammalian Top2 isoform, Top2β has been suggested to play a key role in hormone-mediated transcription, and in carrying out this function, generates potentially oncogenic DNA damage. We have assessed the generation of potentially oncogenic DNA damage by Top2β in model organisms, and using the purified protein. We found that ectopic expression of Top2β is poorly tolerated in repair deficient yeast strains, while expression of the mammalian Top2α isoform lacks this property. We measured the induction of homologous recombination by Top2β in yeast and found that ectopic expression of the enzyme led to elevated levels of recombination. Recently, a de novo mutation in Top2β was reported in a patient with severe developmental delay resulting from an His63Tyr substitution in Top2β 1. We found that Top2β (His63Tyr) could not complement a defect in yeast Top2, but encoded an enzyme that was catalytically active, and induced elevated levels of recombination. Because of the inferred location of His63 in the ATPase domain of Top2β, and proximity to the ATP binding site of the enzyme, we hypothesized that the mutant protein was partially defective in ATP regulated DNA cleavage. To further explore how ATP regulates Top2β cleavage, we examined the effects of expressing a Top2β variant completely lacking the N-terminal ATPase domain of Top2β. While this mutant did not complement yeast top2 mutants, we found that it s expression induced 10-20 fold higher levels of recombination than cells expressing wild type Top2β. This result indicates that an ATP deficient variant of Top2β induces very high levels of DNA damage. We suggest that regulation of the ATPase activity of Top2β may be critical for maintaining genome stability, and may be responsible for induction of DNA damage during hormone-mediated transcription.

1. C.W. Lam et al., Global developmental delay and intellectual disability associated with a de novo TOP2B mutation. Clinica Chimica Acta 469:63-68, 2017.

Citation Format: Amanda M. Johnson, Lokha Ranjani A. Boopathy, Raveena Gupta, Hannah N. Miles, Matthew Gilbertson, Karin C. Nitiss, John L. Nitiss. Modulation of genotoxic DNA damage by the ATPase domain of type II topoisomerases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1742.

Abstract 4727: Role of SUMOylating enzymes in repair of Topoisomerase II mediated DNA damage

Topoisomerase 2 (Top2) enzymes regulate DNA topology for efficient DNA replication and transcription by introducing transient double strand breaks (DSBs) in the DNA. To generate the DSBs, Top2 forms a covalent intermediate with the DNA termed as the Top2 DNA covalent complex (Top2cc). Top2 is a target of clinically used anticancer agents such as etoposide and doxorubicin. Mammalian cells have two Top2 isozymes, Top2α and Top2β. Top2α is primarily expressed in proliferating cells and essential for cell division. Top2β is expressed in all cells and has been shown to play key roles in transcription. Top2 targeting agents generate anticancer activity by trapping both Top2αcc and Top2βcc. Factors that affect repair of Top2cc are likely to be a key determinant of the clinical efficacy of Top2 targeting agents. Identifying factors that play a role in repair of Top2cc offers a potential strategy for increasing clinical efficacy of Top2 targeting agents. Previous work has demonstrated that an important pathway for removal of trapped Top2 from DNA is initiated through proteolytic degradation of Top2 by the proteasome. Other proteases may also participate in degradation of the protein covalently bound to DNA. Proteasomal inhibition increased Top2cc, especially Top2β, and enhanced the cytotoxicity of Top2 targeting drugs. To study steps involved in proteasomal degradation of Top2cc, we developed a method to purify genomic DNA under conditions that preserve proteins covalently bound to DNA. Levels of trapped topoisomerases can be measured using Top2 isoform specific antibodies. Alternately, after micrococcal nuclease degradation of DNA, the proteins covalently bound to DNA can be characterized for post-translational modifications (PTMs) using antibodies specific for the modifying agents. Etoposide treatment induced SUMOylation of both Top2α and Top2β covalently bound to DNA. Blocking SUMOylation of Top2 by siRNA knockdown of the SUMO E2 conjugating enzyme UBC9 increased levels of both Top2α and Top2β covalent complexes, indicating that SUMOylation is likely involved in the repair of both Top2α and Top2β covalent complexes. We have extended this approach to identify SUMO ligases that directly act on Top2 isoforms. We found that depletion of the SUMO E3 PIAS4 resulted in elevated levels of Top2αcc with minimal effect on levels of Top2βcc. This result suggest that PIAS4 participates in a repair pathway that is specific for repairing Top2α covalent complexes. We have constructed PIAS4 knockouts using CRISPR/Cas9 and are currently examining the roles of other SUMO E3 ligases that may participate in the repair of Top2 damage. Our current results suggest that some pathways for repair of Top2 covalent complexes are likely isoform specific. This allows targeting of specific Top2 isoforms without the need to identify agents that discriminate between Top2 isoforms, and may help alleviate some of the undesirable side effects of Top2 targeting agents.

Citation Format: Bhargavi Ramesh, Yilun Sun, John L. Nitiss, Jay Anand, Karin C. Nitiss. Role of SUMOylating enzymes in repair of Topoisomerase II mediated DNA damage [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4727.

Abstract 4853: Regulation of proteolytic repair of Top2 covalent complexes

DNA topoisomerases (topos) play an essential role in nuclear processes such as replication, transcription, and chromosome segregation. These enzymes regulate DNA topology by introducing transient breaks in DNA with formation of transient protein/DNA covalent complexes. These complexes can be trapped by aberrant DNA structures, and are also the basis for anti-cancer drugs that target topos. Since topos can be trapped on DNA, leading to strand breaks with protein adducts at the site of the breaks, cells require DNA repair pathways to process protein adducts. We have examined the repair of the type II topos (Top2) in yeast and mammalian cells. We developed a sensitive assay to detect ubiquitylation and other post-translational modifications (PTMs) of Top2 trapped on DNA in S. cerevisiae and have shown that the proteasome plays a key role in repair of Top2 damage induced by the anti-cancer drug etoposide. We demonstrated that sumoylation of Top2 is induced by etoposide, and that deletion of the SUMO ligase Siz2 prevents etoposide induced sumoylation. Deletion of either of the genes encoding the ubiquitin ligase Slx5/Slx8 led to decreased ubiquitylation of trapped Top2. The mammalian ortholog of Slx5/Slx8 is Rnf4, and it too plays a role in ubiquitylation and degradation of Top2 trapped by etoposide. A human cell line completely lacking Rnf4 is defective in ubiquitylation of Top2β, one of the two mammalian Top2 isoforms. Interestingly, repair of the Top2α isoform is unaffected in an Rnf4 knockout cell line. Proteolysis of trapped Top2 is also subject to negative regulation. The UBA domain protein UBAP2L, (also termed NICE4) is amplified in various cancers. Knockout of the UBAP2L increases proteolysis of trapped Top2. Levels of trapped Top2α and Top2β are decreased in the absence of UBAP2L, and the level of trapped Top2 returns to the wild type level when MG132 is added, indicating UBAP2L regulates the proteasome mediated degradation of Top2. UBAP2L physically interacts with Top2β as determined by co-immunoprecipitation, and the interaction is not seen in Rnf4 knockout cells. Finally, knockout of UBAP2L confers high level resistance to etoposide. Our results provide insights to the response of cancer cells to Top2 targeting agents.

Citation Format: Yilun Sun, Karin C. Nitiss, John L. Nitiss. Regulation of proteolytic repair of Top2 covalent complexes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4853.

Effects of an unusual poison identify a lifespan role for Topoisomerase 2 in Saccharomyces cerevisiae

A progressive loss of genome maintenance has been implicated as both a cause and consequence of aging. Here we present evidence supporting the hypothesis that an age-associated decay in genome maintenance promotes aging in Saccharomyces cerevisiae (yeast) due to an inability to sense or repair DNA damage by topoisomerase 2 (yTop2). We describe the characterization of LS1, identified in a high throughput screen for small molecules that shorten the replicative lifespan of yeast. LS1 accelerates aging without affecting proliferative growth or viability. Genetic and biochemical criteria reveal LS1 to be a weak Top2 poison. Top2 poisons induce the accumulation of covalent Top2-linked DNA double strand breaks that, if left unrepaired, lead to genome instability and death. LS1 is toxic to cells deficient in homologous recombination, suggesting that the damage it induces is normally mitigated by genome maintenance systems. The essential roles of yTop2 in proliferating cells may come with a fitness trade-off in older cells that are less able to sense or repair yTop2-mediated DNA damage. Consistent with this idea, cells live longer when yTop2 expression levels are reduced. These results identify intrinsic yTop2-mediated DNA damage as a potentially manageable cause of aging.

TDP1 is required for efficient non-homologous end joining in human cells

Tyrosyl-DNA phosphodiesterase 1 (TDP1) can remove a wide variety of 3' and 5' terminal DNA adducts. Genetic studies in yeast identified TDP1 as a regulator of non-homologous end joining (NHEJ) fidelity in the repair of double-strand breaks (DSBs) lacking terminal adducts. In this communication, we show that TDP1 plays an important role in joining cohesive DSBs in human cells. To investigate the role of TDP1 in NHEJ in live human cells we used CRISPR/cas9 to produce TDP1-knockout (TDP1-KO) HEK-293 cells. As expected, human TDP1-KO cells were highly sensitive to topoisomerase poisons and ionizing radiation. Using a chromosomally-integrated NHEJ reporter substrate to compare end joining between wild type and TDP1-KO cells, we found that TDP1-KO cells have a 5-fold reduced ability to repair I-SceI-generated DSBs. Extracts prepared from TDP1-KO cells had reduced NHEJ activity in vitro, as compared to extracts from wild type cells. Analysis of end-joining junctions showed that TDP1 deficiency reduced end-joining fidelity, with a significant increase in insertion events, similar to previous observations in yeast. It has been reported that phosphorylation of TDP1 serine 81 (TDP1-S81) by ATM and DNA-PK stabilizes TDP1 and recruits TDP1 to sites of DNA damage. We found that end joining in TDP1-KO cells was partially restored by the non-phosphorylatable mutant TDP1-S81A, but not by the phosphomimetic TDP1-S81E. We previously reported that TDP1 physically interacted with XLF. In this study, we found that XLF binding by TDP1 was reduced 2-fold by the S81A mutation, and 10-fold by the S81E phosphomimetic mutation. Our results demonstrate a novel role for TDP1 in NHEJ in human cells. We hypothesize that TDP1 participation in human NHEJ is mediated by interaction with XLF, and that TDP1-XLF interactions and subsequent NHEJ events are regulated by phosphorylation of TDP1-S81.

Abstract 3580: Topoisomerase II mediated DNA damage generates unique classes of genome rearrangements

Topoisomerase 2 (Top2) is the target of active anti-cancer agents such as etoposide and doxorubicin. These drugs interfere with the Top2 catalytic cycle and lead to trapping of the enzyme as a covalent protein: DNA complex. This trapped covalent complex is a unique DNA lesion that includes DNA strand breaks and covalent protein adducts at the site of the breaks. While Top2 mediated DNA damage is the major mechanism for tumor cell killing, it is also responsible for drug-induced translocations that can lead to secondary malignancies. We have developed several novel systems for assessing Top2-mediated genome instability using yeast as a model system. We developed repair proficient yeast strains that accumulate high levels of etoposide and other Top2 targeting drugs. We selected for loss-of-function mutations in the yeast CAN1 gene that arise following etoposide treatment, and examined the induced mutations by DNA sequencing. We identified a unique spectrum of mutations generated by etoposide in yeast. One novel class of mutational events induced by etoposide is relatively large deletions (>300 bp) and tandem duplications. Most of these etoposide-induced events are flanked by 4-8 nucleotide direct repeats. To further characterize the mechanism of Top2 induced genome instability, we took advantage of a novel Top2 allele isolated in our laboratory. This Top2 allele, termed top2AR, exhibits elevated levels of drug independent DNA cleavage in vitro, and inviability when combined with yeast mutants defective in DNA double strand break repair. We found a similar spectrum of large deletions and tandem duplications flanked by 4-8 nucleotide direct repeats. Interestingly, we also found that the recovery of large deletions and insertions was enhanced in yeast cells lacking Tdp1, a gene that participates in the repair of protein:DNA covalent complexes. Our results illustrate a novel type of genome rearrangement that is mediated by covalent Top2 DNA damage. It is noteworthy that the deletions and insertions flanked by short direct repeats have not been previously observed with other classes of DNA damaging agents. We suggest that the unique properties of these lesions may also contribute to oncogenic translocations induced by etoposide and other Top2 targeting drugs. We are currently using next-generation sequencing of etoposide treated yeast cells and cells carrying the top2AR allele to obtain a more complete picture of the types of alterations induced by Top2 mediated DNA damage.

Citation Format: Matthew Gilbertson, Radhika Patel, Karin C. Nitiss, John L. Nitiss. Topoisomerase II mediated DNA damage generates unique classes of genome rearrangements. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3580.

Abstract 1658: Proteolytic processing pathways for topoisomerase covalent complexes

DNA topoisomerase II (Top2) is the target of several important anti-cancer agents, including doxorubicin and etoposide. Clinically active Top2 agents, termed Top2 poisons, act by blocking the enzyme reaction at a step where the protein is covalently bound to DNA. This leads to the accumulation of Top2/DNA complexes that act as DNA damaging agents that can trigger cell death. Surviving Top2-induced damage likely requires the repair of the enzyme induced damage and has been hypothesized to include pathways that proteolyze the protein bound to DNA followed by nucleolytic removal of the remaining peptide that is bound to DNA by a phosphotyrosyl linkage. This model of repair suggests that inhibition of proteolysis would lead to elevated levels of intact Top2/DNA complexes, and increased sensitivity to Top2 poisons such as etoposide. We have tested this model using the proteasome inhibitor carfilzomib in a pediatric rhabdomyosarcoma cell line (Rh30). We found that carfilzomib enhanced cell killing by etoposide, and that co-treatment of Rh30 cells with carfilzomib led to increases in both Top2 alpha and Top2 beta covalent complexes. These results suggest that proteasomal degradation of both Top2 isoforms is important for repairing DNA damage arising from etoposide. We are also interested in identifying the determinants of Top2 degradation following treatment with etoposide, especially proteins that recognize the trapped enzyme as DNA damage. We used a yeast genetic model system to address this question. We showed that the proteasome inhibitor MG132 greatly enhanced the sensitivity of yeast cells to etoposide, and that co-treatment of MG132 and etoposide led to elevated levels of Top2/DNA complexes compared to etoposide alone. We found that deletion of the human RNF4 homolog Slx5/Slx8 (a SUMO dependent ubiquitin ligase) also leads to an increase in Top2 covalent complexes induced by etoposide. We found that deletion of the genes encoding either Slx5 or Slx8 along with the repair protein Tdp1 led to much higher levels of cell killing compared to single deletions. These results suggest that there are at least two independent pathways for repairing Top2 damage, one dependent on Slx5/Slx8 dependent protein degradation and a second pathway dependent on nucleolytic removal of Top2. We suggest that Slx5/Slx8 plays a role in targeting Top2 for degradation following etoposide treatment. Our results also provide a rationale for the combination of a proteasome inhibitor with etoposide as an approach of increasing the efficacy of etoposide.

Citation Format: Yilun Sun, Karin C. Nitiss, John L. Nitiss. Proteolytic processing pathways for topoisomerase covalent complexes. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1658. doi:10.1158/1538-7445.AM2015-1658

TDP1 promotes assembly of non-homologous end joining protein complexes on DNA

The repair of DNA double-strand breaks (DSB) is central to the maintenance of genomic integrity. In tumor cells, the ability to repair DSBs predicts response to radiation and many cytotoxic anti-cancer drugs. DSB repair pathways include homologous recombination and non-homologous end joining (NHEJ). NHEJ is a template-independent mechanism, yet many NHEJ repair products carry limited genetic changes, which suggests that NHEJ includes mechanisms to minimize error. Proteins required for mammalian NHEJ include Ku70/80, the DNA-dependent protein kinase (DNA-PKcs), XLF/Cernunnos and the XRCC4:DNA ligase IV complex. NHEJ also utilizes accessory proteins that include DNA polymerases, nucleases, and other end-processing factors. In yeast, mutations of tyrosyl-DNA phosphodiesterase (TDP1) reduced NHEJ fidelity. TDP1 plays an important role in repair of topoisomerase-mediated DNA damage and 3'-blocking DNA lesions, and mutation of the human TDP1 gene results in an inherited human neuropathy termed SCAN1. We found that human TDP1 stimulated DNA binding by XLF and physically interacted with XLF to form TDP1:XLF:DNA complexes. TDP1:XLF interactions preferentially stimulated TDP1 activity on dsDNA as compared to ssDNA. TDP1 also promoted DNA binding by Ku70/80 and stimulated DNA-PK activity. Because Ku70/80 and XLF are the first factors recruited to the DSB at the onset of NHEJ, our data suggest a role for TDP1 during the early stages of mammalian NHEJ.

Twisting and ironing: doxorubicin cardiotoxicity by mitochondrial DNA damage

Anthracyclines are active clinical agents that have multiple mechanisms of cytotoxicity. Cardiotoxicity by anthracyclines limits the therapeutic potential of these agents, but mechanisms leading to cardiotoxicity remain controversial. Transgenic mice that lack mitochondrial topoisomerase I are hypersensitive to doxorubicin cardiotoxicity, providing support for cardiotoxicity arising from damage of mitochondrial DNA.

Aberrant topoisomerase-1 DNA lesions are pathogenic in neurodegenerative genome instability syndromes

DNA damage is considered to be a prime factor in several spinocerebellar neurodegenerative diseases; however, the DNA lesions underpinning disease etiology are unknown. We observed the endogenous accumulation of pathogenic topoisomerase-1 (Top1)-DNA cleavage complexes (Top1ccs) in murine models of ataxia telangiectasia and spinocerebellar ataxia with axonal neuropathy 1. We found that the defective DNA damage response factors in these two diseases cooperatively modulated Top1cc turnover in a non-epistatic and ATM kinase-independent manner. Furthermore, coincident neural inactivation of ATM and DNA single-strand break repair factors, including tyrosyl-DNA phosphodiesterase-1 or XRCC1, resulted in increased Top1cc formation and excessive DNA damage and neurodevelopmental defects. Notably, direct Top1 poisoning to elevate Top1cc levels phenocopied the neuropathology of the mouse models described above. Our results identify a critical endogenous pathogenic lesion associated with neurodegenerative syndromes arising from DNA repair deficiency, indicating that genome integrity is important for preventing disease in the nervous system.

Proteolytic degradation of topoisomerase II (Top2) enables the processing of Top2·DNA and Top2·RNA covalent complexes by tyrosyl-DNA-phosphodiesterase 2 (TDP2)

Eukaryotic type II topoisomerases (Top2α and Top2β) are homodimeric enzymes; they are essential for altering DNA topology by the formation of normally transient double strand DNA cleavage. Anticancer drugs (etoposide, doxorubicin, and mitoxantrone) and also Top2 oxidation and DNA helical alterations cause potentially irreversible Top2·DNA cleavage complexes (Top2cc), leading to Top2-linked DNA breaks. Top2cc are the therapeutic mechanism for killing cancer cells. Yet Top2cc can also generate recombination, translocations, and apoptosis in normal cells. The Top2 protein-DNA covalent complexes are excised (in part) by tyrosyl-DNA-phosphodiesterase 2 (TDP2/TTRAP/EAP2/VPg unlinkase). In this study, we show that irreversible Top2cc induced in suicidal substrates are not processed by TDP2 unless they first undergo proteolytic processing or denaturation. We also demonstrate that TDP2 is most efficient when the DNA attached to the tyrosyl is in a single-stranded configuration and that TDP2 can efficiently remove a tyrosine linked to a single misincorporated ribonucleotide or to polyribonucleotides, which expands the TDP2 catalytic profile with RNA substrates. The 1.6-Å resolution crystal structure of TDP2 bound to a substrate bearing a 5'-ribonucleotide defines a mechanism through which RNA can be accommodated in the TDP2 active site, albeit in a strained conformation.

Abstract 4480: New approaches to changing an enzyme into a cytotoxic agent: A novel way to stimulate DNA cleavage by topoisomerase II

Topoisomerase poisons are important anti-cancer drugs, and include agents such as etoposide and doxorubicin that target eukaryotic topoisomerase II. Most topoisomerase II poisons act as interstitial inhibitors. This mode of inhibition depends on the coordination of the enzyme and DNA substrate to form a drug binding site. While recent structural studies have localized topoisomerase II poisons to the drug/DNA interface, our understanding of the mechanism of enzyme inhibition remains incomplete. We have combined genetic, biochemical, and structural approaches to identify regions of topoisomerase II that are important for drug action and identified sites near the active site tyrosine that contribute to drug sensitivity. Interestingly, we also identified amino acids near the C-terminal dimerization domain that also control DNA cleavage. Mutations in the C-terminal dimerization domain exhibit several unique characteristics. Importantly, we identified two mutants in the dimerization domain of yeast Top2 that could not be viably expressed in yeast mutants defective in double strand break repair. Expression of these mutants in repair proficient strains led to elevated rates of homologous recombination, suggesting that these mutant proteins are able to generate DNA damage even in the absence of topoisomerase II targeting agents. We purified the mutant proteins and demonstrated that they possess elevated levels of drug independent DNA cleavage, compared to wild type proteins. Elevated cleavage was only seen in the presence of ATP, indicating that the mutant proteins are likely defective in DNA religation at a specific step in the catalytic cycle, and that the C-terminal dimerization and DNA religation occurs by a coordinated process. Finally, we have also shown that homologous mutations in human topoisomerase II alpha generate effects similar to those described for the yeast protein. Taken together, these results suggest that it may be possible to identify potent allosteric inhibitors of topoisomerase II directed against the C-terminal catalytic domain of the protein. These hypothetical inhibitors may have unique therapeutic potential, especially because they represent an approach for isoform specific topoisomerase poisons.

Citation Format: Anna Rogojina, Karin C. Nitiss, John L. Nitiss. New approaches to changing an enzyme into a cytotoxic agent: A novel way to stimulate DNA cleavage by topoisomerase II. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4480. doi:10.1158/1538-7445.AM2013-4480

The anticancer multi-kinase inhibitor dovitinib also targets topoisomerase I and topoisomerase II

Dovitinib (TKI258/CHIR258) is a multi-kinase inhibitor in phase III development for the treatment of several cancers. Dovitinib is a benzimidazole-quinolinone compound that structurally resembles the bisbenzimidazole minor groove binding dye Hoechst 33258. Dovitinib bound to DNA as shown by its ability to increase the DNA melting temperature and by increases in its fluorescence spectrum that occurred upon the addition of DNA. Molecular modeling studies of the docking of dovitinib into an X-ray structure of a Hoechst 33258-DNA complex showed that dovitinib could reasonably be accommodated in the DNA minor groove. Because DNA binders are often topoisomerase I (EC 5.99.1.2) and topoisomerase II (EC 5.99.1.3) inhibitors, the ability of dovitinib to inhibit these DNA processing enzymes was also investigated. Dovitinib inhibited the catalytic decatenation activity of topoisomerase IIα. It also inhibited the DNA-independent ATPase activity of yeast topoisomerase II which suggested that it interacted with the ATP binding site. Using isolated human topoisomerase IIα, dovitinib stabilized the enzyme-cleavage complex and acted as a topoisomerase IIα poison. Dovitinib was also found to be a cellular topoisomerase II poison in human leukemia K562 cells and induced double-strand DNA breaks in K562 cells as evidenced by increased phosphorylation of H2AX. Finally, dovitinib inhibited the topoisomerase I-catalyzed relaxation of plasmid DNA and acted as a cellular topoisomerase I poison. In conclusion, the cell growth inhibitory activity and the anticancer activity of dovitinib may result not only from its ability to inhibit multiple kinases, but also, in part, from its ability to target topoisomerase I and topoisomerase II.

Topoisomerase assays

Topoisomerases are nuclear enzymes that play essential roles in DNA replication, transcription, chromosome segregation, and recombination. All cells have two major forms of topoisomerases: type I enzymes, which make single-stranded cuts in DNA, and type II enzymes, which cut and pass double-stranded DNA. DNA topoisomerases are important targets of approved and experimental anti-cancer agents. The protocols described in this unit are for assays used to assess new chemical entities for their ability to inhibit both forms of DNA topoisomerase. Included are an in vitro assay for topoisomerase I activity based on relaxation of supercoiled DNA, and an assay for topoisomerase II based on the decatenation of double-stranded DNA. The preparation of mammalian cell extracts for assaying topoisomerase activity is described, along with a protocol for an ICE assay to examine topoisomerase covalent complexes in vivo, and an assay for measuring DNA cleavage in vitro.

Abstract 3889: Direct evidence that the MRN complex is required for a pathway that processes Top2 covalent complexes

Drugs targeting topoisomerase II (Top2) such as etoposide or doxorubicin generate enzyme mediated DNA damage. During the normal Top2 reaction, the enzyme forms a covalent enzyme DNA intermediate consisting of a 5’ phosphotyrosyl linkage between the enzyme and DNA. Many compounds that generate Top2 mediated damage inhibit the enzyme-catalyzed religation step leading to DNA breaks. Therefore an important aspect of the repair of Top2 mediated damage includes removal of the protein covalently bound to DNA. One way of eliminating that protein is by proteolysis. Liu and colleagues have clearly demonstrated that proteolysis plays a role in repairing Top2 beta damage1 and it is likely that proteolysis is also important for repairing Top2 alpha mediated damage. Proteolysis cannot remove all of the peptide bound to DNA; therefore nucleolytic enzymes are also needed for repairing Top2 damage. Since the MRN complex is required for nucleolytic removal of the meiotic Top2-like protein Spo11, it has been hypothesized that the MRN complex also participates in removal of Top2 protein from DNA following cellular treatment with Top2 poisons. However, there is no direct evidence for processing of Top2 mediated damage by the MRN complex. We have used the ICE assay to directly measure Top2 covalent complexes in mammalian cells treated with Top2 poisons such as etoposide. The ICE assay uses CSCl centrifugation to isolate protein:DNA covalent complexes. We have combined this assay with siRNA knockdowns to assess whether specific protein complexes are required for processing Top2 covalent complexes. Since this assay depends on recognition of Top2 epitopes by monoclonal antibodies directed towards Top2 isoforms, we have examined levels of Top2 complexes in cells treated with the proteasome inhibitor, MG132. In cells treated with siRNA directed against Mre11, we observed an increase in Top2:DNA covalent complexes following treatment with either etoposide or mAMSA. These results provide direct evidence that the MRN complex is required for at least one pathway for removal of Top2 covalent complexes. It is likely that this MRN dependent pathway is capable of removing Top2 bound to DNA without proteolytic processing of the covalent complex. We are currently using this approach to assess other recently described processing pathways including pathways requiring CtiP and pathways requiring Tdp2.

(1) Mao, Y.; Desai, S. D.; Ting, C. Y.; Hwang, J.; Liu, L. F. J Biol Chem 2001, 276, 40652.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3889. doi:10.1158/1538-7445.AM2011-3889

Abstract 2527: Amonafide and its metabolite N-acetyl amonafide are Top2 poisons with differing biochemical properties

Naphthalimides derivatives have been extensively studied as anti-cancer agents. Amonafide (5-amino-2-[2-(dimethylamino)ethyl]-1H-benzo[de]isoquinoline-1,3(2H)-dione) showed clinical activity especially in some groups of AML patients. Amonafide has been shown to target topoisomerase II (Top2), and to stabilize Top2 covalent complexes. Therefore, the agent is a Top2 poison, however, the compound shows some unusual properties. Unlike most Top2 poisons, the action of amonafide against Top2 is largely ATP independent; In addition, amonafide leads to cleavage of DNA at a very restricted set of sites compared to other Top2 poisons such as mitoxantrone or etoposide. These findings have led to suggestions that amonafide may target Top2 in an unconventional way. Another obstacle to the clinical use of amonafide is variable drug metabolism. Felder and colleagues showed that amonafide is metabolized by N-acetyl transferase 2 (NAT2) to form N-acetyl amonafide (NAA). Toxicity of amonafide regimens is associated with higher levels of NAT2 activity 2. The mechanism of NAA toxicity has not been reported. We have used the ICE assay developed by Muller and colleagues to assess Top2 covalent complex levels in cells treated with either amonafide or NAA. We found that amonafide induces Top2 mediated DNA cleavage, and that covalent complexes formed by both Top2 alpha and Top2 beta were seen. Interestingly, NAA induced higher levels of Top2 covalent complexes than the parent compound. In addition, the level of Top2 covalent complexes increased with increasing NAA dose, whereas a plateau in the level of Top2 covalent complexes was seen with amonafide at relatively low doses. We are currently comparing the action of amonafide and NAA against purified human topoisomerases. We suggest that NAA is a Top2 poison, and a plausible hypothesis is that NAA may act more like a conventional Top2 poison, while amonafide may show a better therapeutic index because it has more limited potential for forming Top2 covalent complexes. These results may be useful in the further development of amonafide derivatives with a favorable therapeutic profile.

(1) Felder, T. B.; McLean, M. A.; Vestal, M. L.; Lu, K.; Farquhar, D.; Legha, S. S.; Shah, R.; Newman, R. A. Drug Metab Dispos 1987, 15, 773.

(2) Ratain, M. J.; Rosner, G.; Allen, S. L.; Costanza, M.; Van Echo, D. A.; Henderson, I. C.; Schilsky, R. L. J Clin Oncol 1995, 13, 741.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2527. doi:10.1158/1538-7445.AM2011-2527

End-processing during non-homologous end-joining: a role for exonuclease 1

Non-homologous end-joining (NHEJ) is a critical error-prone pathway of double strand break repair. We recently showed that tyrosyl DNA phosphodiesterase 1 (Tdp1) regulates the accuracy of NHEJ repair junction formation in yeast. We assessed the role of other enzymes in the accuracy of junction formation using a plasmid repair assay. We found that exonuclease 1 (Exo1) is important in assuring accurate junction formation during NHEJ. Like tdp1Δ mutants, exo1Δ yeast cells repairing plasmids with 5′-extensions can produce repair junctions with templated insertions. We also found that exo1Δ mutants have a reduced median size of deletions when joining DNA with blunt ends. Surprisingly, exo1Δ pol4Δ mutants repair blunt ends with a very low frequency of deletions. This result suggests that there are multiple pathways that process blunt ends prior to end-joining. We propose that Exo1 acts at a late stage in end-processing during NHEJ. Exo1 can reverse nucleotide additions occurring due to polymerization, and may also be important for processing ends to expose microhomologies needed for NHEJ. We propose that accurate joining is controlled at two steps, a first step that blocks modification of DNA ends, which requires Tdp1, and a second step that occurs after synapsis that requires Exo1.

Abstract 3500: Nucleolytic processing of Topoisomerase 2 covalent complexes

The generation of elevated levels of enzyme: DNA covalent complexes is the key event in cell killing by many drugs targeting DNA topoisomerases. These agents, termed topoisomerase poisons generate protein linked DNA strand that block transcription and replication, leading to cell death. A critical step in the repair of topoisomerase mediated DNA damage is the removal of protein that is covalently attached to DNA. Several specialized repair enzymes, including Tdp1 (tyrosyl DNA phosphodiesterase I) and TTRAP (TRAF and TNF receptor-associated protein) can hydrolyze phosphotyrosyl: DNA linkages. We previously reported that yeast Tdp1 could hydrolyze 5′ as well as 3′ phosphotyrosyl linkages. Human Tdp1 can also hydrolyze 5′ phosphotyrosyl linkages, although the efficiency of the reaction with the human enzyme is much less than that seen with the yeast enzyme. Interestingly, the human enzyme processes adducts bearing a seven amino acid peptide linked to an oligonucleotide with greater efficiency than a 5′ biotin linked oligonucleotide, suggesting that the nature of the adduct at DNA ends influences Tdp1 reaction kinetics. We also used substrates derived from Top2 trapped covalent complexes to assess the ability of other DNA repair enzymes to remove peptides covalently bound to DNA. We found that the heterodimeric nuclease Slx1/Slx4 is able to remove Top2 peptides that are covalently bound to DNA. This result is consistent with our genetic data from yeast that a mutation in the subunit that includes the nuclease (Slx1) is hypersensitive to Top2 poisons, but not sensitive to other DNA damaging agents. Our results indicate that there are multiple pathways for repairing Top2 covalent complexes and suggest that the Slx1/Slx4 dependent pathway may be particularly relevant to repairing topoisomerase mediated damage at replication forks.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3500.

Abstract CN08-02: Repair of topoisomerase II mediated DNA damage: A potential mechanism for targeting specific Top2 isoforms

DNA topoisomerases are ubiquitous enzymes that change a property of DNA structure that is termed DNA topology (1). During the processes of DNA replication, transcription, nucleosomes assembly, and chromosome condensation, the double stranded structure of DNA imposes restraints that can lead to overwinding or underwinding of DNA. DNA topoisomerases overcome these constraints by making transient breaks in DNA using a unique mechanism that entails the creation of an enzyme:DNA covalent intermediate. Drugs targeting these enzymes exploit this enzymatic mechanism and increase the level of enzyme covalently bound to DNA. The generation of elevated levels of enzyme:DNA covalent complexes is the key event in cell killing by drugs targeting DNA topoisomerases. Drugs that lead to elevated cleavage are termed topoisomerase poisons (2,3). Protein linked DNA strand breaks are rapidly induced by topoisomerase poisons, and enzyme mediated DNA damage effectively blocks transcription and replication.

Mammalian cells encode two type II topoisomerases that function in distinct biological processes. Top2α is the main isoform involved in DNA replication and chromosome separation, and is required for the viability of all dividing cells (4). While mouse knockouts of Top2β are inviable due to neuromuscular defects (5), viable Top2β- cells can be recovered, and show no effects on replication or cell viability. The two isoforms show similar biochemical properties, and both isozymes are inhibited by most Top2 poisons. Since Top2α is expressed in dividing cells, it has been broadly assumed that the most important target for anti-cancer drugs is Top2α, and the relevance of Top2β to anti-cancer drug action remains an open question (6). However, recent results suggest that Top2β may be a contributor to some of the deleterious effects of drugs that target Top2 enzymes. Treatment regimens that include Top2 poisons, especially etoposide and teniposide, have been shown to cause translocations that can lead to secondary acute myeloid leukemia and other malignancies (7). A novel insight into secondary malignancies induced by Top2 targeting drugs has come from studies using a transgenic mouse model that carried skin specific knockout of Top2β. While etoposide applied to skin can generate melanomas, in skin lacking Top2β, the frequency of etoposide induced tumors was substantially reduced (8). An intriguing hypothesis is that targeting Top2β in non-dividing cells may lead to non-lethal DNA damage that results in oncogenic translocations.

Top2β may also play an important role in anthracycline-induced cardiomyopathy. Anthracyclines affect cells by a variety of mechanisms including acting as Top2 poisons, but also by the generation of free radicals. Bisdioxopiperazines are effective cardioprotectants and the major mechanism had been proposed to be due to chelation of iron that participates in free radical formation. Anthracyclines induce DNA damage signals that are blocked by bisdioxopiperazines. The DNA damage signal induced by anthracyclines is attenuated in MEFs derived from Top2β-null mice compared with MEFs that express Top2β (9). Since bisdioxopiperazines can lead to targeted degradation of Top2β, an important part of the cardioprotective mechanism may be the selective elimination of Top2β, thereby reducing the effects of drug induced DNA damage.

While specific targeting of Top2α may be an effective therapeutic strategy that eliminates some of the toxicity due to targeting both isoforms of Top2, it is less clear how this can be accomplished. While a Top2α specific drug has been recently described (10), the high degree of homology between the two enzymes suggests that it may be difficult to devise a potent and specific inhibitor of Top2α. A second approach may be to enhance specific targeting of Top2α by inhibiting repair of Top2α but not Top2α mediated DNA damage. Is this possible?

Repair of Top2 mediated damage requires recognition of a trapped Top2 complex, removal of the protein that is covalently bound to DNA, and repair of the DNA strand breaks. There are two mechanisms that have been described for initiating repair of Top2 DNA damage. In the first mechanism, covalently bound Top2 is targeted for degradation by the proteasome. Liu and colleagues showed that treatment with Top2 poisons led to a rapid depletion of Top2β (11). Degradation of Top2β could be prevented by inhibitors of transcription, but not by replication inhibitors. Subsequent work has shown that in some cell lines, the α isoform is also degraded in a proteasome dependent fashion. These results suggest that there may be differential recognition of trapped Top2α and Top2β. There is little information concerning effectors of repair after proteolytic degradation of Top2, but if the recognition mechanisms differ, then subsequent repair steps may in part by separate pathways.

An important pathway for removing protein DNA adducts is to excise the “adduct” by nucleolytic digestion of DNA that is covalently bound to the protein. A nucleolytic step is required even if the Top2 complex is partially degraded by proteolysis, since a protease cannot hydrolyze the phosphotyrosyl linkage of the protein bound to DNA. Until recently, there has been little direct information about nucleolytic removal of Top2 covalently bound to DNA. Recent results have implicated CtIP, a nuclease associated with the MRN complex as one protein that may participate in removal of trapped Top2 DNA covalent complexes (6). Other nucleases in yeast may also play important roles in processing Top2 covalent complexes including the structure specific nuclease Slx1/Slx4 and the excision repair nuclease Rad2 (XPG in mammalian cells). Deciphering the pathways involved in repairing Top2α and Top2β complexes will require additional information about genes that function in the repair of Top2 mediated damage, and the development of assays that can assess isoform specific repair pathways.

We have identified a large number of genes in yeast that are required for the repair of Top2 mediated DNA damage. These include genes required for double strand break repair, checkpoint surveillance of DNA damage, and many unanticipated genes. Importantly, several genes encoding nucleases and genes encoding proteins that participate in proteolytic degradation pathways confer high levels of sensitivity to etoposide when mutated. These genes represent a useful starting point for defining pathways that are required for repairing Top2 mediated damage in mammalian cells.

Keeney and colleagues developed a novel assay in yeast to identify potential nucleolytic processing pathways of a Top2 related protein that initiates meiotic recombination (12). We have applied the Keeney assay to identify whether direct nucleolytic processing of Top2α or Top2β occurs in mammalian cells. Our initial results suggest that nucleolytic processing of both Top2 and Top2 occur even in the absence of proteolysis. Interestingly, the products of the processing reactions suggest that there may be important differences in processing of the two isoforms.

DNA topoisomerase II has been a known important target of anti-cancer drugs for more than 25 years. He results described above provide unexpected aspects of reducing side effects of Top2 targeting drugs, and perhaps increasing their clinical efficacy. Substantial efforts will be required both in rational drug discovery, and in the understanding of the cellular responses to Top2 targeting to maximize the clinical usefulness of Top2 targeting agents.

Citation Information: Mol Cancer Ther 2009;8(12 Suppl):CN08-02.

DNA topoisomerase II and its growing repertoire of biological functions

DNA topoisomerases are enzymes that disentangle the topological problems that arise in double-stranded DNA. Many of these can be solved by the generation of either single or double strand breaks. However, where there is a clear requirement to alter DNA topology by introducing transient double strand breaks, only DNA topoisomerase II (TOP2) can carry out this reaction. Extensive biochemical and structural studies have provided detailed models of how TOP2 alters DNA structure, and recent molecular studies have greatly expanded knowledge of the biological contexts in which TOP2 functions, such as DNA replication, transcription and chromosome segregation -- processes that are essential for preventing tumorigenesis.

Targeting DNA topoisomerase II in cancer chemotherapy

Recent molecular studies have expanded the biological contexts in which topoisomerase II (TOP2) has crucial functions, including DNA replication, transcription and chromosome segregation. Although the biological functions of TOP2 are important for ensuring genomic integrity, the ability to interfere with TOP2 and generate enzyme-mediated DNA damage is an effective strategy for cancer chemotherapy. The molecular tools that have allowed an understanding of the biological functions of TOP2 are also being applied to understanding the details of drug action. These studies promise refined targeting of TOP2 as an effective anticancer strategy.

Isolation and characterization of mAMSA-hypersensitive mutants. Cytotoxicity of Top2 covalent complexes containing DNA single strand breaks

Topoisomerase II (Top2) is the primary target for active anti-cancer agents. We developed an efficient approach for identifying hypersensitive Top2 mutants and isolated a panel of mutants in yeast Top2 conferring hypersensitivity to the intercalator N-[4-(9-acridinylamino)-3-methoxyphenyl]methanesulphonanilide (mAMSA). Some mutants conferred hypersensitivity to etoposide as well as mAMSA, whereas other mutants exhibited hypersensitivity only to mAMSA. Two mutants in Top2, changing Pro(473) to Leu and Gly(737) to Val, conferred extraordinary hypersensitivity to mAMSA and were chosen for further characterization. The mutant proteins were purified, and their biochemical activities were assessed. Both mutants encode enzymes that are hypersensitive to inhibition by mAMSA and other intercalating agents and exhibited elevated levels of mAMSA-induced Top2:DNA covalent complexes. While Gly(737) --> Val Top2p generated elevated levels of Top2-mediated double strand breaks in vitro, the Pro(473) --> Leu mutant protein showed only a modest increase in Top2-mediated double strand breaks but much higher levels of Top2-mediated single strand breaks. In addition, the Pro(473) --> Leu mutant protein also generated high levels of mAMSA-stabilized covalent complexes in the absence of ATP. We tested the role of single strand cleavage in cell killing with alleles of Top2 that could generate single strand breaks, but not double strand breaks. Expression in yeast of a Pro(473) --> Leu mutant that could only generate single strand breaks conferred hypersensitivity to mAMSA. These results indicate that generation of single strand breaks by Top2-targeting agents can be an important component of cell killing by Top2-targeting drugs.

Enhancing drug accumulation in Saccharomyces cerevisiae by repression of pleiotropic drug resistance genes with chimeric transcription repressors

Yeast is a powerful model system for studying the action of small-molecule therapeutics. An important limitation has been low efficacy of many small molecules in yeast due to limited intracellular accumulation. We used the DNA binding domain of the pleiotropic drug resistance regulator pleiotropic drug resistance 1 (Pdr1) fused in-frame to transcription repressors to repress Pdr1-regulated genes. Expression of these chimeric regulators conferred dominant enhancement of sensitivity to a different class of compounds and led to greatly diminished levels of Pdr1p-regulated transcripts, including the yeast p-glycoprotein homolog Pdr5. Enhanced sensitivity was seen for a wide range of small molecules. Biochemical measurements demonstrated enhanced accumulation of rhodamine in yeast cells expressing the chimeric repressors. These repressors of Pdr1p-regulated transcripts can be introduced into large collections of strains such as the Saccharomyces cerevisiae deletion set and enhance the utility of yeast for studying drug action and for mechanism-based drug discovery.

Assessing sensitivity to antibacterial topoisomerase II inhibitors

Both prokaryotes and eukaryotes have two major classes of topoisomerases that make transient single- or double-strand cuts in DNA. While these enzymes play critical roles in cellular processes, they are also important targets of therapeutic agents. This unit describes assays to use in characterizing topoisomerase II-targeting agents in vitro and in bacterial cells. It provides protocols for characterizing the action of small molecules against bacterial type II topoisomerases in vitro and the in vivo effects of putative topoisomerase II-targeting antibiotics, as well as for measuring trapped enzyme/DNA covalent complexes, the major cytotoxic lesion induced by fluoroquinolones.

Mutation of a Conserved Active Site Residue Converts Tyrosyl-DNA Phosphodiesterase I into a DNA Topoisomerase I-dependent Poison

Tyrosyl-DNA phosphodiesterase 1 (Tdp1) catalyzes the resolution of 3' and 5' phospho-DNA adducts. A defective mutant, associated with the recessive neurodegenerative disease SCAN1, accumulates Tdp1-DNA complexes in vitro. To assess the conservation of enzyme architecture, a 2.0 A crystal structure of yeast Tdp1 was determined that is very similar to human Tdp1. Poorly conserved regions of primary structure are peripheral to an essentially identical catalytic core. Enzyme mechanism was also conserved, because the yeast SCAN1 mutant (H(432)R) enhanced cell sensitivity to the DNA topoisomerase I (Top1) poison camptothecin. A more severe Top1-dependent lethality of Tdp1H(432)N was drug-independent, coinciding with increased covalent Top1-DNA and Tdp1-DNA complex formation in vivo. However, both H(432) mutants were recessive to wild-type Tdp1. Thus, yeast H(432) acts in the general acid/base catalytic mechanism of Tdp1 to resolve 3' phosphotyrosyl and 3' phosphoamide linkages. However, the distinct pattern of mutant Tdp1 activity evident in yeast cells, suggests a more severe defect in Tdp1H(432)N-catalyzed resolution of 3' phospho-adducts.

Roles of nonhomologous end-joining pathways in surviving topoisomerase II-mediated DNA damage

Topoisomerase II is a target for clinically active anticancer drugs. Drugs targeting these enzymes act by preventing the religation of enzyme-DNA covalent complexes leading to protein-DNA adducts that include single- and double-strand breaks. In mammalian cells, nonhomologous repair pathways are critical for repairing topoisomerase II-mediated DNA damage. Because topoisomerase II-targeting agents, such as etoposide, can also induce chromosomal translocations that can lead to secondary malignancies, understanding nonhomologous repair of topoisomerase II-mediated DNA damage may help to define strategies that limit this critical side effect on an important class of anticancer agents. Using Saccharomyces cerevisiae as a model eukaryote, we have determined the contribution of genes required for nonhomologous end-joining (NHEJ) for repairing DNA damage arising from treatment with topoisomerase II poisons, such as etoposide and 4'-(9-acridinylamino)methanesulfon-m-anisidide (mAMSA). To increase cellular sensitivity to topoisomerase II poisons, we overexpressed either wild-type or drug-hypersensitive alleles of yeast topoisomerase II. Using this approach, we found that yku70 (hdf1), yku80 (hdf2), and other genes required for NHEJ were important for cell survival following exposure to etoposide. The clearest increase in sensitivity was observed with cells overexpressing an etoposide-hypersensitive allele of TOP2 (Ser740Trp). Hypersensitivity was also seen in some end-joining defective mutants exposed to the intercalating agent mAMSA, although the increase in sensitivity was less pronounced. To confirm that the increase in sensitivity was not solely due to the elevated expression of TOP2 or due to specific effects of the drug-hypersensitive TOP2 alleles, we also found that deletion of genes required for NHEJ increased the sensitivity of rad52 deletions to both etoposide and mAMSA. Taken together, these results show a clear role for NHEJ in the repair of DNA damage induced by topoisomerase II-targeting agents and suggest that this pathway may participate in translocations generated by drugs, such as etoposide.

Tyrosyl-DNA phosphodiesterase (Tdp1) participates in the repair of Top2-mediated DNA damage

Agents targeting topoisomerases are active against a wide range of human tumors. Stabilization of covalent complexes, converting topoisomerases into DNA-damaging agents, is an essential aspect of cell killing by these drugs. A unique aspect of the repair of topoisomerase-mediated DNA damage is the requirement for pathways that can remove protein covalently bound to DNA. Tyrosyl-DNA phosphodiesterase (Tdp1) is an enzyme that removes phosphotyrosyl moieties bound to the 3' end of DNA. Cells lacking Tdp1 are hypersensitive to camptothecin, consistent with a role for Tdp1 in processing 3' phosphotyrosyl protein-DNA covalent complexes. Because Top2p forms a 5' phosphotyrosyl linkage with DNA, previous work predicted that Tdp1p would not be active against lesions involving Top2p. We found that deletion of the TDP1 gene in yeast confers hypersensitivity to Top2 targeting agents. Combining tdp1 mutations with deletions of genes involved in nonhomologous end joining, excision repair, or postreplication repair enhanced sensitivity to Top2 targeting drugs over the level seen with single mutants, suggesting that Tdp1 may function in collaboration with multiple pathways involved in strand break repair. tdp1 mutations can sensitize yeast cells to drugs targeting Top2 even when TOP1 is deleted. Finally, bacterially expressed yeast Tdp1p is able to remove a peptide derived from yTop2 that is covalently bound to DNA by a 5' phosphotyrosyl linkage. Our results show that Tdp1 plays more general roles in DNA repair than repair of Top1 mediated DNA damage, and may participate in repairing many types of base damage to DNA.

Activation of the unfolded protein response is necessary and sufficient for reducing topoisomerase IIalpha protein levels and decreasing sensitivity to topoisomerase-targeted drugs

A wide range of chemotherapeutic agents has been identified that are active against solid tumors. However, resistance remains an important obstacle to the development of curative regimens. Whereas much attention has been paid to acquired drug resistance, a variety of physiological pathways also have been described that reduce the sensitivity of previously untreated tumors to cytotoxic antitumor agents. Treatment of cells with pharmacological agents that alter the environment of the endoplasmic reticulum (ER) and activate the unfolded protein response (UPR) can render cells resistant to topoisomerase II poisons. We describe experiments showing that activation of the mammalian ER stress response is both necessary and sufficient to decrease topoisomerase IIalpha protein levels and to render cells resistant to etoposide, a topoisomerase II-targeting drug. This is not caused by the elevated levels of BiP that are a hallmark of this response, because a cell line that has been engineered to overexpress BiP does not show increased resistance to etoposide. The UPR was shown to be required for altered drug sensitivity, because the BiP-overexpressing cell line, which is unable to activate the UPR, did not show decreased topoisomerase II levels or increased resistance to etoposide in response to stress conditions. The transient overexpression of an unfolded protein activated the UPR and led to the concomitant loss of topoisomerase IIalpha protein from the cells, demonstrating that UPR activation is sufficient for the changes in topoisomerase II levels that had been observed previously with pharmacological induction of the UPR.

Gimatecan (sigma-tau industrie farmaceutiche riunite/novartis)

Sigma-Tau Industrie Farmaceutiche Riunite SpA and Novartis AG are developing oral gimatecan, a camptothecin derivative, for the potential treatment of tumors, including glioblastoma.

A mutation in Escherichia coli DNA gyrase conferring quinolone resistance results in sensitivity to drugs targeting eukaryotic topoisomerase II

Fluoroquinolones are broad-spectrum antimicrobial agents that target type II topoisomerases. Many fluoroquinolones are highly specific for bacterial type II topoisomerases and act against both DNA gyrase and topoisomerase IV. In Escherichia coli, mutations causing quinolone resistance are often found in the gene that encodes the A subunit of DNA gyrase. One common site for resistance-conferring mutations alters Ser83, and mutations to Leu or Trp result in high levels of resistance to fluoroquinolones. In the present study we demonstrate that the mutation of Ser83 to Trp in DNA gyrase (Gyr(S83W)) also results in sensitivity to agents that are potent inhibitors of eukaryotic topoisomerase II but that are normally inactive against prokaryotic enzymes. Epipodophyllotoxins, such as etoposide, teniposide and amino-azatoxin, inhibited the DNA supercoiling activity of Gyr(S83W), and the enzyme caused elevated levels of DNA cleavage in the presence of these agents. The DNA sequence preference for Gyr(S83W)-induced cleavage sites in the presence of etoposide was similar to that seen with eukaryotic type II topoisomerases. Introduction of the Gyr(S83W) mutation in E. coli strain RFM443-242 by site-directed mutagenesis sensitized it to epipodophyllotoxins and amino-azatoxin. Our results demonstrate that sensitivity to agents that target topoisomerase II is conserved between prokaryotic and eukaryotic enzymes, suggesting that drug interaction domains are also well conserved and likely occur in domains important for the biochemical activities of the enzymes.

Stability of the topoisomerase II closed clamp conformation may influence DNA-stimulated ATP hydrolysis

Type II DNA topoisomerases catalyze changes in DNA topology and use nucleotide binding and hydrolysis to control conformational changes required for the enzyme reaction. We examined the ATP hydrolysis activity of a bisdioxopiperazine-resistant mutant of human topoisomerase II alpha with phenylalanine substituted for tyrosine at residue 50 in the ATP hydrolysis domain of the enzyme. This substitution reduced the DNA-dependent ATP hydrolysis activity of the mutant protein without affecting the relaxation activity of the enzyme. A similar but stronger effect was seen when the homologous mutation (Tyr28 --> Phe) was introduced in yeast Top2. The ATPase activities of human TOP2alpha(Tyr50 --> Phe) and yeast Top2(Tyr28 --> Phe) were resistant to both bisdioxopiperazines and the ATPase inhibitor sodium orthovanadate. Like bisdioxopiperazines, vanadate traps the enzyme in a salt-stable closed conformation termed the closed clamp, which can be detected in the presence of circular DNA substrates. Consistent with the vanadate-resistant ATPase activity, salt-stable closed clamps were not detected in reactions containing the yeast or human mutant protein, vanadate, and ATP. Similarly, ADP trapped wild-type topoisomerase II as a closed clamp, but could not trap either the human or yeast mutant enzymes. Our results demonstrate that bisdioxopiperazine-resistant mutants exhibit a difference in the stability of the closed clamp formed by the enzyme and that this difference in stability may lead to a loss of DNA-stimulated ATPase. We suggest that the DNA-stimulated ATPase of topoisomerase II is intimately connected with steps that occur while the N-terminal domain of the enzyme is dimerized.