N-terminal domain of tyrosyl-DNA phosphodiesterase I regulates topoisomerase I-induced toxicity in cells

Tyrosyl-DNA phosphodiesterase I (Tdp1) hydrolyzes phosphodiester-linked adducts from both ends of DNA. This includes the topoisomerase I (TOP1)-DNA covalent reaction intermediate that is the target of the camptothecin class of chemotherapeutics. Tdp1 two-step catalysis is centered on the formation of a Tdp1-DNA covalent complex (Tdp1cc) using two catalytic histidines. Here, we examined the role of the understudied, structurally undefined, and poorly conserved N-terminal domain (NTD) of Tdp1 in context of full-length protein in its ability to remove TOP1cc in cells. Using toxic Tdp1 mutants, we observed that the NTD is critical for Tdp1's ability to remove TOP1-DNA adducts in yeast. Full-length and N-terminal truncated Tdp1 mutants showed similar expression levels and cellular distribution yet an inversed TOP1-dependent toxicity. Single turnover catalysis was significantly different between full-length and truncated catalytic mutants but not wild-type enzyme, suggesting that Tdp1 mutants depend on the NTD for catalysis. These observations suggest that the NTD plays a critical role in the regulation of Tdp1 activity and interaction with protein-DNA adducts such as TOP1cc in cells. We propose that the NTD is a regulatory domain and coordinates stabilization of the DNA-adducted end within the catalytic pocket to access the phosphodiester linkage for hydrolysis.

Abstract A47: BMI1 constitutes a novel therapeutic vulnerability in fusion-positive rhabdomyosarcoma

Background: Despite intense efforts within pediatric oncology, novel, effective therapy for alveolar rhabdomyosarcoma, known as fusion-positive rhabdomyosarcoma (FP RMS) given the PAX-FOXO1 fusions characteristic of the disease, remains unrealized. Like many pediatric tumors, FP RMS displays a quiet genomic landscape, when focusing on the coding genome. However, the epigenome plays key roles in shaping tumor aggression, and previous studies have demonstrated that FP RMS is specifically enriched for methylation of Polycomb target genes, suggesting that Polycomb complexes may be deregulated and could constitute novel therapeutic targets. We hypothesized that BMI1, a key member of the Polycomb family and a tractable therapeutic target, represents a novel therapeutic vulnerability in FP RMS.

Methods: We analyzed RNA and protein expression in FP RMS cell lines, patient-derived xenografts (PDXs), and human tumor specimens. We used genetic and pharmacologic approaches to manipulate BMI1 in FP RMS cells and measured effects on proliferation, cell cycle, apoptosis, and signal transduction. To examine the effect of in vivo inhibition of BMI1, we utilized xenograft models of FP RMS.

Results: We examined RNA-Seq tumor datasets and tumor microarrays and demonstrated that BMI1 is robustly expressed in FP RMS tumors, PDXs, and cell line models. Next, in 2 cell line models, we depleted BMI-1 using shRNAs and siRNAs, and found that this led to striking (~70%) decreases in cell growth secondary to both G1/S phase arrest and apoptosis. Given these findings, we asked whether small-molecule inhibitors of BMI-1 mediated similar effects. We treated 4 independent FP RMS cell line models with both PTC-209 (first-generation inhibitor) and PTC-028 (orally available second-generation inhibitor with higher potency). Both compounds inhibited BMI-1 function and greatly reduced cell proliferation in FP rhabdomyosarcoma cell line models. Similar to genetically mediated depletion, pharmacologic inhibition of BMI1 led to G1/S phase arrest and apoptosis, as demonstrated by Annexin V staining and PARP cleavage. Finally, in a xenograft model of an aggressive FP RMS, PTC-028 treatment decreased tumor growth (p=0.0005) and significantly prolonged survival by 17 days (p=0.0002). Importantly, treatment was well tolerated without evidence of toxicity or weight loss.

Conclusions: BMI1 is robustly expressed in FP RMS and both genetic and pharmacologic inhibition of BMI1 lead to striking decreases in cell proliferation, with concomitant cell cycle arrest and apoptosis. BMI1 inhibition significantly decreases tumor growth, prolongs survival, and is well tolerated. Currently, we are further investigating combining BMI1 inhibition with standard chemotherapy and novel agents, as well as defining molecular mechanisms by which BMI1 exerts molecular functions in FP RMS. Targeting BMI-1 could provide a novel therapeutic option for patients with FP RMS, with potential broader implications for additional aggressive sarcomas.

Citation Format: Cara E. Shields, Selma M. Cuya, Sarah Chappell, Komal Rathi, Shiv Patel, Sindhu Potlapalli, Robert W. Schnepp. BMI1 constitutes a novel therapeutic vulnerability in fusion-positive rhabdomyosarcoma [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A47.

LIN28B promotes neuroblastoma metastasis and regulates PDZ binding kinase

Neuroblastoma is an aggressive pediatric malignancy of the neural crest with suboptimal cure rates and a striking predilection for widespread metastases, underscoring the need to identify novel therapeutic vulnerabilities. We recently identified the RNA binding protein LIN28B as a driver in high-risk neuroblastoma and demonstrated it promotes oncogenic cell proliferation by coordinating a RAN-Aurora kinase A network. Here, we demonstrate that LIN28B influences another key hallmark of cancer, metastatic dissemination. Using a murine xenograft model of neuroblastoma dissemination, we show that LIN28B promotes metastasis. We demonstrate that this is in part due to the effects of LIN28B on self-renewal and migration, providing an understanding of how LIN28B shapes the metastatic phenotype. Our studies reveal that the let-7 family, which LIN28B inhibits, decreases self-renewal and migration. Next, we identify PDZ Binding Kinase (PBK) as a novel LIN28B target. PBK is a serine/threonine kinase that promotes the proliferation and self-renewal of neural stem cells and serves as an oncogenic driver in multiple aggressive malignancies. We demonstrate that PBK is both a novel direct target of let-7i and that MYCN regulates PBK expression, thus elucidating two oncogenic drivers that converge on PBK. Functionally, PBK promotes self-renewal and migration, phenocopying LIN28B. Taken together, our findings define a role for LIN28B in neuroblastoma metastasis and define the targetable kinase PBK as a potential novel vulnerability in metastatic neuroblastoma.

Abstract 3838: Targeting epigenetic regulator BMI-1 in alveolar rhabdomyosarcoma

Background: Rhabdomyosarcoma (RMS) is an extremely aggressive soft tissue sarcoma which affects mainly children. There are two subtypes: alveolar rhabdomyosarcoma (ARMS) and embryonal rhabdomyosarcoma (ERMS). ARMS is characterized by PAX-FOXO1 fusion proteins, whereas subsets of ERMS harbor alterations within RAS and TP53 pathways. Currently, the outcomes for ARMS (especially when metastatic) remain dismal, thus underscoring the urgent need to identify novel targets for this cancer. The genomic landscape of many pediatric cancers, including ARMS, is relatively sparse. This led us to ask whether key epigenetic factors are driving tumor aggressiveness and could constitute novel approaches for treating ARMS. Notably, the epigenetic complexes PRC1 and PRC2 are overexpressed in a variety of sarcomas and are associated with worse overall survival. We took a hypothesis-based approach and focused on PRC1. We discovered that B lymphoma Mo-MLV insertion region 1 (BMI-1), a protein member of PRC1, is overexpressed in ARMS cells. BMI-1 is a known oncogene in other cancers, but its potential oncogenic role in ARMS and other pediatric malignancies has not yet been interrogated; thus we aim to study it within this context.

Methods: To analyze the function of BMI-1 in ARMS, we depleted the protein in ARMS cell line models by both shRNA/siRNA knockdown and measured expression, cell proliferation and apoptosis. We utilized two small molecule inhibitors, PTC-209 and PTC-028, to obtain IC50s in these cell lines, then determined effects on cell proliferation and apoptosis.

Results: We examined RNA-Seq tumor datasets and determined that BMI1 is robustly expressed in ARMS tumors. Additionally, we confirmed that BMI-1 is also overexpressed in ARMS cell lines at the levels of RNA and protein. Next, we depleted BMI-1 using multiple shRNAs and siRNAS and found that this led to striking (~70%) decreases in cell growth. We also observed increased levels of apoptosis within knockdown cells. Given these results, we asked whether small molecule inhibitors of BMI-1 mediated similar phenotypes, and so we used the inhibitors PTC-209 and PTC-028. PTC-209 is a first-generation BMI-1 inhibitor, while PTC-028 is a second-generation orally available inhibitor with higher potency. Both compounds inhibited BMI-1 function and greatly reduced cell proliferation in ARMS cell lines within the nanomolar range; however, as expected, PTC-028 showed a more pronounced effect compared to PTC-209.

Conclusions: BMI1 supports proliferation and survival in cell line models of ARMS. Both chemical and pharmacologic inhibition of BMI1 led to striking decreases in cell proliferation. Currently, we are further investigating the molecular impact of BMI1 inhibition, with plans to investigate its effectiveness within an in vivo ARMS model. Targeting BMI-1 pharmacologically could provide a novel therapeutic option for patients with ARMS and may apply more broadly to other sarcomas.

Citation Format: Cara E. Shields, Selma M. Cuya, Sarah K. Chappell, Komal Rathi, Shiv Patel, Sindhu Potlapalli, Robert W. Schnepp. Targeting epigenetic regulator BMI-1 in alveolar rhabdomyosarcoma [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 3838.

Abstract 3668: A LIN28B-PBK Axis promotes neuroblastoma dissemination and aggression

LIN28B is an RNA binding protein that plays key roles in normal development and, when deregulated, oncogenesis; mechanistically, it blocks the processing of the let-7 family of tumor suppressors and binds mRNAs directly. We previously demonstrated that LIN28B induces neuroblastoma proliferation, in part by regulating the expression of RAN GTPase and Aurora kinase A (AURKA). However, given the widespread metastases seen within neuroblastoma, we speculated that LIN28B might also influence neuroblastoma dissemination. We used gain and loss of function approaches to genetically manipulate transcripts of interest in neuroblastoma cells and measured effects on self-renewal, invasion, and downstream signaling. To examine the impact of LIN28B on dissemination, we generated GFP-luciferase expressing neuroblastoma cell line models in which LIN28B levels were manipulated, injected these lines into the tail veins of NSG mice, and tracked dissemination using an IVIS Spectrum system. Results show that depletion of LIN28B significantly delayed the onset of tumor metastasis, reduced tumor burden, and extended mouse survival (104 days versus 50 days, p<0.0001) compared to control cells. While LIN28B did not impact anoikis resistance, it did increase both tumorsphere number and size, linking self-renewal to metastatic dissemination. Additionally, LIN28B promoted cellular invasion. These effects were largely opposed by let-7. We next sought to understand how LIN28B promotes aggression and metastasis, specifically focusing on novel networks that are currently therapeutically targetable. Given our discovery of AURKA as a novel LIN28B target, we speculated that LIN28B might promote the expression of additional oncogenic kinases, perhaps revealing novel therapeutic possibilities to target the LIN28B network. We evaluated the TARGET dataset of neuroblastoma tumors and, focusing on the top 10 kinases most significantly and positively correlated with high LIN28B expression, nominated PBK for further study (4/10 of top correlated kinases). PBK (PDZ-binding kinase) is a Ser/Thr protein kinase expressed in normal embryonic tissues and various tumor types that plays a role in both mitosis and metastasis. Depletion of PBK mimicked the effects of LIN28B depletion, with respect to self-renewal and invasion. Depletion of LIN28B and overexpression of let-7 both reduced PBK protein expression, suggesting that PBK is a direct or indirect let-7 target. Taken together, our findings suggest that LIN28B/let-7 shapes neuroblastoma aggression, in part through influencing PBK, a kinase not previously implicated in the pathogenesis of neuroblastoma or other aggressive pediatric solid tumors. Current studies are further dissecting the functional and molecular relationships among LIN28B, let-7, and PBK in neuroblastoma.

Citation Format: Dongdong Chen, Julie Cox, Jayabhargav Annam, Melanie Weingart, Grace Essien, Komal Rathi, Priya Khurana, Selma M. Cuya, Robert W. Schnepp. A LIN28B-PBK Axis promotes neuroblastoma dissemination and aggression [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 3668.

Dysregulated human Tyrosyl-DNA phosphodiesterase I acts as cellular toxin

Tyrosyl-DNA phosphodiesterase I (TDP1) hydrolyzes the drug-stabilized 3’phospho-tyrosyl bond formed between DNA topoisomerase I (TOPO1) and DNA. TDP1-mediated hydrolysis uses a nucleophilic histidine (His^nuc) and a general acid/base histidine (His^gab). A Tdp1His^gab to Arg mutant identified in patients with the autosomal recessive neurodegenerative disease SCAN1 causes stabilization of the TDP1-DNA intermediate. Based on our previously reported His^gab-substitutions inducing yeast toxicity (Gajewski et al. J. Mol. Biol. 415, 741-758, 2012), we propose that converting TDP1 into a cellular poison by stabilizing the covalent enzyme-DNA intermediate is a novel therapeutic strategy for cancer treatment. Here, we analyzed the toxic effects of two TDP1 catalytic mutants in HEK293 cells. Expression of human Tdp1His^nucAla and Tdp1His^gabAsn mutants results in stabilization of the covalent TDP1-DNA intermediate and induces cytotoxicity. Moreover, these mutants display reduced in vitro catalytic activity compared to wild type. Co-treatment of Tdp1^mutant with topotecan shows more than additive cytotoxicity. Overall, these results support the hypothesis that stabilization of the TDP1-DNA covalent intermediate is a potential anti-cancer therapeutic strategy.

Abstract 501: Tyrosyl-DNA phosphodiesterase I cellular function dependent on its N-terminal residues

Tyrosyl-DNA phosphodiesterase I (Tdp1) is a highly conserved eukaryotic DNA repair enzyme that catalyzes the resolution of 3’ and 5’ phospho-DNA adducts. Tdp1 has been implicated in the repair of DNA topoisomerase I (Top1)-DNA covalent complexes reversibly stabilized by FDA approved camptothecins (CPTs) derivatives topotecan and irinotecan. Tdp1 activity relies on two catalytic histidines that function as a nucleophile and an acid-base residue. A mutation of the acid-base His to Arg (H493R) in human Tdp1 is associated with the rare recessive ataxia SCAN1. We defined alternative substitution of either catalytic histidine that induce cytotoxicity, reduce catalytic activity and enhances the requisite Tdp1-DNA covalent adduct lifetime in the cell. The phenotypes of the catalytic mutants provide excellent tools to study Tdp1 cellular function. Biochemical studies revealed that Tdp1 catalysis in vitro is independent of the N-terminal domain. Among Tdp1 proteins, the N-terminal domain is poorly conserved in sequence and size (79aa for yeast and 148aa for human Tdp1). Conversely, the N-terminal domain regulates the in vitro activity of these Tdp1 mutants. Additionally, we investigated the role of the N-terminal domain for Tdp1 activity in the yeast and human cell models. Expression of N-terminal truncated proteins showed similar cellular distribution as the full-length proteins. However, these N-terminal truncated Tdp1 mutants did not display the toxicity that was observed with the full-length Tdp1 mutant proteins. Our data suggests that the N-terminal domain is required to resolve protein-DNA covalent complexes, such as Top1. Indeed, preliminary results suggest that this domain is also critical to process Top2-DNA covalent complexes, but only in the presences of etoposide. We are currently investigating other protein-DNA adducts that are resolved by Tdp1. These results suggests that the N-terminal domain is a critical determinate of Tdp1 cellular function. However, further studies are necessary to ensure that these constructs are properly distributed and retain their catalytic activity. Additionally, the N-terminal domain of human Tdp1 is post-translational modified, while our preliminary results suggest that this domain is important for protein-protein interaction and Tdp1 recruitment to its substrates. Understanding Tdp1 substrate and protein-interactions are important in the development of Tdp1 as therapeutic target. This work is in part supported by the ADDA, UAB Cancer Comprehensive Center (P30CA013148), ACS-IRG-60-001-53, DOD OCRP (W81XWH-15-1-0198).

Citation Format: Selma M. Cuya, Robert C.A.M. Van Waardenburg. Tyrosyl-DNA phosphodiesterase I cellular function dependent on its N-terminal residues [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 501. doi:10.1158/1538-7445.AM2017-501

DNA topoisomerase-targeting chemotherapeutics: what's new?

To resolve the topological problems that threaten the function and structural integrity of nuclear and mitochondrial genomes and RNA molecules, human cells encode six different DNA topoisomerases including type IB enzymes (TOP1 and TOP1mt), type IIA enzymes (TOP2α and TOP2β) and type IA enzymes (TOP3α and TOP3β). DNA entanglements and the supercoiling of DNA molecules are regulated by topoisomerases through the introduction of transient enzyme-linked DNA breaks. The covalent topoisomerase-DNA complexes are the cellular targets of a diverse group of cancer chemotherapeutics, which reversibly stabilize these reaction intermediates. Here we review the structure-function and catalytic mechanisms of each family of eukaryotic DNA topoisomerases and the topoisomerase-targeting agents currently approved for patient therapy or in clinical trials, and highlight novel developments and challenges in the clinical development of these agents.

Abstract 2761: Cellular consequences of human tyrosyl-DNA phosphodiesterase I dysregulation

Tyrosyl-DNA phosphodiesterase I (Tdp1) is a highly conserved eukaryotic DNA repair enzyme that catalyzes the resolution of 3’ and 5’ phospho-DNA adducts. Tdp1 has been implicated in the repair of DNA topoisomerase I (Topo1)-DNA covalent complexes reversibly stabilized by camptothecins (CPTs) such as the FDA approved CPT derivatives topotecan and irinotecan. Tdp1 utilizes a two-step catalytic cycle that centers on the formation of an obligatory Tdp1-DNA covalent complex (Tdp1-cc) through its nucleophilic histidine (Hisnuc), resulting in dissociation of the adduct, while its general acid/base histidine (Hisgab) mediates Tdp1 dissociation. A Tdp1Hisgab to Arg (H493R) mutant stabilizes the Tdp1-cc and is associated with autosomal recessive ataxia SCAN1. Alternative substitutions of Hisgab or substitutions of the Hisnuc transforms yeast Tdp1 into a potent toxin via stabilization of Tdp1-cc. We propose that stabilization of this Tdp1-DNA covalent complex is a potential novel therapeutic anti-cancer strategy. As proof-of-concept, we analyzed two catalytic Hisgab (H493R or H493N) mutants and one Hisnuc (H263A) mutant of hTdp1 in HEK293 cells. Doxycycline-induced expression of Tdp1H263A, Tdp1H493R, and Tdp1H493N mutant enzymes induced Tdp1-dependent cytotoxicity without additional genotoxic stress. Utilizing two different immuno-assays, we validated that the observed Tdp1-dependent toxicity correlates with stabilization of their enzyme-DNA covalent complex. Moreover, all of these Tdp1 catalytic mutants show reduced catalytic activity compared to wild type hTdp1, but they do not all show a stabilized Tdp1-cc in this in vitro assay. This indicates a significant difference between in vitro Tdp1 activity and cellular Tdp1 activity, which is most likely due to the difference in substrate; a small oligonucleotide with a 3’phospho-tyrosyl modification versus covalent complex of full length Topo1 with genomic DNA. However, these results confirm our previous yeast studies: Stabilization of the Tdp1-cc converts a DNA repair enzyme into a cellular toxin, which constitutes a potential novel therapeutic strategy to treat cancer. In addition, we are comparing schedule dependent ‘drug’-combinations of our toxic Tdp1 mutant expression with topotecan, etoposide (targets Topo2-cc) and cisplatin to evaluate the potential therapeutic value of this novel Tdp1 targeted strategy.

This work is in part supported by the ADDA, UAB ACS-IRG, and DOD OCRP WX81WH-15-1-0198.

Citation Format: Selma M. Cuya, Kellie M. Regal, Robert C.A.M. Van Waardenburg. Cellular consequences of human tyrosyl-DNA phosphodiesterase I dysregulation. [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 2761.

Abstract 3628: Tyrosyl-DNA phosphodiesterase I as a therapeutic target: lessons from yeast functional studies

Tyrosyl-DNA phosphodiesterase I (Tdp1) resolves various 3′phospho-adducts within DNA breaks induced by numerous chemotherapeutics. This includes Tdp1 ability to repair DNA topoisomerase I (Topo1)-DNA covalent complexes reversibly stabilized by camptothecins (CPTs) such as the FDA approved CPT derivatives topotecan and irinotecan. Tdp1 uses a two-step catalytic cycle that requires the formation of a Tdp1-DNA covalent intermediate through its nucleophilic histidine (Hisnuc) resulting in dissociation of the adduct, while the general acid/base histidine (Hisgab) mediates Tdp1 dissociation. A Tdp1Hisgab to Arg mutant stabilizes the Tdp1-DNA intermediate and is associated with autosomal recessive ataxia SCAN1. Alternative substitutions of Hisgab transforms yeast Tdp1 into a potent Topo1-depended toxin via stabilization of enzyme-DNA intermediates. We propose that stabilization of the Tdp1-DNA complex is a potential novel therapeutic anti-cancer strategy. As proof-of-concept, we analyzed two different catalytic human Tdp1 mutants in HEK293 cells without additional stress. Expression of hTdp1HisnucAla and hTdp1HisgabAsn mutants induced cytotoxicity, which correlates with stabilization of their enzyme-DNA intermediates. Serendipitously, we discovered that Tdp1's N-terminal residues are critical for Tdp1HisnucAla catalytic activity but not for wild type Tdp1. In addition, analyzing the effect of the N-terminal domain of other Tdp1 catalytic mutants revealed that these residues influence the formation of covalent Tdp1-DNA intermediates in vitro, which is conserved from yeast to human. To better understand the interaction between Tdp1 and its substrates, we examined the cellular role of the poorly conserved N-terminal domain (∼80aa yTdp1 and 140aa hTdp1). This domain is not essential for catalytic activity per se, however, we observed that it is critical for Tdp1 cellular function in yeast and human cells. Comparison of the full-length and N-terminal truncated Tdp1 mutants showed similar cellular distribution, but a converse toxicity. This suggests that the N-terminal domain is a critical determinant of Tdp1 cellular function and this function is conserved from yeast to human. Thus, understanding the mechanism of interaction between Tdp1 and Topo1-DNA intermediate is important for the development of Tdp1 as a therapeutic target. Overall, these results support our concept that stabilization of Tdp1-DNA covalent intermediates converting this DNA repair enzyme into a cellular toxin is a potential novel anti-cancer therapeutic strategy, which is different from the intuitive strategy of inhibiting (preventing) Tdp1 catalytic activity.

This work is in part supported by the ADDA.

Citation Format: Selma M. Cuya, Ashley C. Conoway, Robert C.A.M. van Waardenburg. Tyrosyl-DNA phosphodiesterase I as a therapeutic target: lessons from yeast functional studies. [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 3628. doi:10.1158/1538-7445.AM2015-3628

Tyrosyl-DNA phosphodiesterase I catalytic mutants reveal an alternative nucleophile that can catalyze substrate cleavage

Tyrosyl-DNA phosphodiesterase I (Tdp1) catalyzes the repair of 3'-DNA adducts, such as the 3'-phosphotyrosyl linkage of DNA topoisomerase I to DNA. Tdp1 contains two conserved catalytic histidines: a nucleophilic His (His(nuc)) that attacks DNA adducts to form a covalent 3'-phosphohistidyl intermediate and a general acid/base His (His(gab)), which resolves the Tdp1-DNA linkage. A His(nuc) to Ala mutant protein is reportedly inactive, whereas the autosomal recessive neurodegenerative disease SCAN1 has been attributed to the enhanced stability of the Tdp1-DNA intermediate induced by mutation of His(gab) to Arg. However, here we report that expression of the yeast His(nuc)Ala (H182A) mutant actually induced topoisomerase I-dependent cytotoxicity and further enhanced the cytotoxicity of Tdp1 His(gab) mutants, including H432N and the SCAN1-related H432R. Moreover, the His(nuc)Ala mutant was catalytically active in vitro, albeit at levels 85-fold less than that observed with wild type Tdp1. In contrast, the His(nuc)Phe mutant was catalytically inactive and suppressed His(gab) mutant-induced toxicity. These data suggest that the activity of another nucleophile when His(nuc) is replaced with residues containing a small side chain (Ala, Asn, and Gln), but not with a bulky side chain. Indeed, genetic, biochemical, and mass spectrometry analyses show that a highly conserved His, immediately N-terminal to His(nuc), can act as a nucleophile to catalyze the formation of a covalent Tdp1-DNA intermediate. These findings suggest that the flexibility of Tdp1 active site residues may impair the resolution of mutant Tdp1 covalent phosphohistidyl intermediates and provide the rationale for developing chemotherapeutics that stabilize the covalent Tdp1-DNA intermediate.

Abstract 3327: N-terminal domain of Tyrosyl-DNA phosphodiesterase I (Tdp1) is critical for its cellular function

Tyrosyl-DNA phosphodiesterase I (Tdp1) is a highly conserved eukaryotic DNA repair enzyme that catalyzes the resolution of 3’ and 5’ phospho-DNA adducts. Tdp1 has been implicated in the repair of DNA topoisomerase I (Top1)-DNA covalent complexes reversibly stabilized by camptothecins (CPTs) such as the FDA approved CPT derivatives topotecan and irinotecan. Tdp1 contains two HKD-motifs that provide two catalytic histidines that function as a nucleophile and an acid-base residue. A mutation of the acid-base His to Arg (H493R) in human Tdp1 is associated with the rare recessive ataxia SCAN1. hTdp1H493R and the analogous yeast mutant (Tdp1H432R) enhances cell sensitivity to CPT. In addition, the toxicity induced by this mutant is caused by the formation of a more stable Tdp1-DNA covalent intermediate, a rare characteristic for a DNA repair enzyme. However, this His to Arg substitution induces a minor toxic phenotype compared to other substitutions, such as the His432 to Asn substitution, which induces a Top1 dependent cellular lethality. A band depletion assay suggests that in vivo/cell Tdp1His432Asn remains in complex with Top1 on the DNA, which was not observed in a biochemical in vitro assay.

Biochemical studies revealed that Tdp1 catalysis is independent of the N-terminal domain. Among Tdp1 proteins, the N-terminal domain is poorly conserved in sequence and size (∼80aa for yeast and 140aa for human Tdp1).

We investigated the role of the N-terminal domain for Tdp1 activity in the cell. The N-terminal truncated proteins showed similar cellular distribution as the full-length proteins. Interestingly, the N-terminal truncated proteins did not display the toxicity that was observed with the full-length Tdp1 mutant proteins. This suggests that the N-terminal domain is a critical determinate of Tdp1 cellular function.

Preliminary results from our human cell line model shows similar results implying that the function of the N-terminal domain is conserved among Tdp1 proteins although it is poorly conserved. Further studies are necessary to ensure that these constructs are properly distributed. Moreover, the N-terminal domain of hTdp1 is post-translational modified, while our preliminary results suggest that this domain is important for protein-protein interaction and Tdp1 recruitment to its substrates. Understanding Tdp1 substrate and protein-interactions are important in the development of Tdp1 as therapeutic target.

This work is in part supported by the ADDA.

Citation Format: Selma M. Cuya, Keith C. Wanzeck, Evan Q. Comeaux, Robert C. van Waardenburg. N-terminal domain of Tyrosyl-DNA phosphodiesterase I (Tdp1) is critical for its cellular function. [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 3327. doi:10.1158/1538-7445.AM2013-3327