The metabolism of ADP-ribose polymers (PAR) is involved in several cellular processes with a primary focus on maintaining genomic integrity. PAR metabolism following genotoxic stress is transient due to a close coordination between poly(ADP-ribose) polymerases (PARPs) which synthesize PAR and poly(ADP-ribose) glycohydrolase (PARG) which degrades PAR. PARP-1 inhibitors have emerged as promising anticancer therapeutics by increasing chemotherapy sensitivity and selectively target tumors harboring DNA repair defects. Several pharmaceutical companies have PARP-1 inhibitors in clinical trials for treatment of cancer. PARP-1 inhibitors are generally well tolerated, although they typically have poor selectivity among PARPs, and potentially other NAD binding enzymes. The promise of PARP-1 inhibitors as cancer therapeutics has led this dissertation research towards developing alternative tools and approaches to target PAR metabolism.One approach described is an evaluation of high-throughput PARP-1 screening assays as potential tools to discover new classes of PARP-1 inhibitors. These assays were compared to a widely used radiolabeling PARP-1 assay. They were found to offer several advantages that include simplicity, sensitivity, reproducibility, accuracy and eliminating the need for radioactive materials.The primary focus of this dissertation research was to develop PARG inhibitors as an alternative way of targeting PAR metabolism. Lack of viable genetically engineered animals, effective siRNA, and useful pharmacological 20 inhibitors has prevented PARG from being evaluated as a therapeutic target. This dissertation describes the first systematic approach, using Target related Affinity Profiling (TRAP) technology, for the discovery of PARG inhibitors. Identification of several hits led to the first detailed structural activity relationship (SAR) studies defining a pharmacophore for PARG inhibition. Interestingly, these molecules show varying degrees of PARP-1 inhibition, providing the first direct evidence for homology in the active sites of PARP-1 and PARG. Evaluation of a lead inhibitor has provided the first evidence for PARG inhibition in intact cells. Further optimization resulted in a cell permeable inhibitor with reduced toxicity and poor selectivity, providing evidence for a new class of inhibitors that disrupt PAR metabolism by inhibiting both enzymes. The use of dual PARG/PARP-1 inhibitors represents a new approach for therapeutic development of anticancer agents. Finally, directions aimed to overcome remaining challenges are discussed.

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The EWSR1-FLI1 t(11;22)(q24;q12) translocation is the pathognomonic genomic alteration in 85% of the Ewing Family of Tumors (EWFT) a malignancy of the bone and the surrounding tissue, predominantly affecting children and adolescents. This translocation results in the formation of a chimeric oncoprotein which acts as an aberrant transcription factor that is currently not pharmaceutically druggable, driving the need for more effective targeted therapies. The EWSR1-FLI1 translocation induces a variety of changes including dysregulation of the epigenome and altered gene expression to drive tumorigenesis, and consequently contributes to the hypersensitivity of EWFT to several classes of chemotherapeutics. We sought to exploit these intrinsic sensitivities by employing a matched pair of cell lines derived from the same patient with Ewing sarcoma prior to and following chemotherapy, a panel of Ewing sarcoma cell lines, and several patient-derived xenografts (PDX) collected at the time of relapse or autopsy, which led us to the development of two novel combination targeted therapies for EWFT. In our matched pair of EWFT cell lines, we found sensitivity to the Poly(ADP-ribose Polymerase (PARP) inhibitor olaparib was diminished following chemotherapy, despite a predicted sensitivity. In addition, we discovered increased expression of the antiapoptotic protein BCL-2 in the chemotherapy-resistant cells, conferring apoptotic resistance to olaparib. We found that EWS-FLI1 increases BCL-2 expression; however, inhibition of BCL-2 alone is insufficient to sensitize EWFT cells to olaparib, revealing a dual necessity for BCL-2 and BCL-XL (BCL2L1) in EWFT survival. These data reveal BCL-2 and BCL-XL act together to drive olaparib mediated apoptotic resistance in Ewing sarcoma and identify a novel, rational combination therapy using olaparib and the BCL-2/BCL-XL inhibitor navitoclax. In addition, using high throughput drug screening we have identified a novel epigenetic susceptibility in EWFT to GSK-J4 (GlaxoSmithKline), an inhibitor of lysine 27 of histone 3 (H3K27) demethylases: ubiquitously transcribed tetratricopeptide repeat, X chromosome (UTX) and Jumonji D3 (JMJD3). Treatment with GSK-J4 leads to a decrease in H3K27 acetylation (H3K27ac) and ultimately, the silencing of EWS-FLI1 gene targets. We sought to sensitize GSK-J4-mediated inhibition of EWS-FLI1 targets by blocking RNA polymerase II activity using the Cyclin Dependent Kinase 7 (CDK7) inhibitor THZ1. By targeting CDK7-mediated transcription we were able to sensitize EWFTs to H3K27 demethylase inhibition. We therefore propose co-targeting of H3K27 demethylases and CDK7 acts as a surrogate EWS-FLI1 inhibitor. Given the difficulties targeting EWS-FLI1, these strategies may present viable clinical therapies.

<p>Genomic imprinting marks a subset of autosomal loci expressed in parent of origin-dependent monoallelic expression in a non-Mendelian fashion. To restore totipotency and to reset the imprint according to the sex of the individual, the mark must be erased during germline development. The imprinted <i>Igf2-H19</i> loci located distally on chromosome 7 in mouse and 11p15.5 in human, share common regulatory elements that regulate differential expression. Where the <i>H19 </i>is silenced when paternally inherited, the <i>Igf2</i> is silenced when maternally inherited. </p><p>The differentially methylated 5'-flank of <i>H19</i> gene, termed imprinting control region (ICR), shown to display a unique chromatin organisation harbours hypersensitive sites in linker regions flanked by positioned nucleosomes on the maternal allele. This unique chromatin conformation functions as a methylation-sensitive and unidirectional chromatin insulator, which later was found to depend on the chromatin insulator protein CTCF. </p><p>The <i>H19</i> ICR exhibits default-silencing functions in promoter-proximal positions. The maximal distance between the <i>H19</i> ICR and the promoter of the reporter gene required for this effect was 1.2 ± 0.3kb which can be compared to the 1.9 kb distance between the endogenous <i>H19 </i>ICR and <i>H19</i> promoter. Results suggest that the <i>H19</i> ICR adopts a chromatin conformation that must be separated by a minimal distance from pivotal <i>cis</i>-regulatory elements to avoid adverse effects on neighbouring promoters. </p><p>Poly(ADP-ribosy)lation represents a novel post-translational epigenetic mark that segregates with exclusively the maternal derived <i>H19</i> ICR and associated with factors that interact with the CTCF target sites. CTCF is itself poly(ADP-ribosy)lated and the poly(ADP-ribose) polymerase inhibitor 3-aminobenzamide relieves the insulator function of the <i>H19</i> ICR. </p><p>Designed zinc finger proteins were applied to examine if epigenetic marks provided an obstacle for targeted activation and silencing. The zinc finger protein ZFP809 with activator/repressor domain able to efficiently activate/silence the <i>IGF2</i> target. Murine hybrid cell lines of human chromosome 11, demonstrated that the ZFP809 overcame the epigenetic marks that repressed maternal <i>IGF2</i> and paternal <i>H19</i> allele, respectively. Results suggested that imprinted genes are not normally exposed to strong <i>cis</i>-regulatory elements and that the designed ZFPs can be exploited to develop a therapeutic method for rectifying epigenetic lesions.</p>

Genomic imprinting marks a subset of autosomal loci expressed in parent of origin-dependent monoallelic expression in a non-Mendelian fashion. To restore totipotency and to reset the imprint according to the sex of the individual, the mark must be erased during germline development. The imprinted Igf2-H19 loci located distally on chromosome 7 in mouse and 11p15.5 in human, share common regulatory elements that regulate differential expression. Where the H19 is silenced when paternally inherited, the Igf2 is silenced when maternally inherited. The differentially methylated 5'-flank of H19 gene, termed imprinting control region (ICR), shown to display a unique chromatin organisation harbours hypersensitive sites in linker regions flanked by positioned nucleosomes on the maternal allele. This unique chromatin conformation functions as a methylation-sensitive and unidirectional chromatin insulator, which later was found to depend on the chromatin insulator protein CTCF. The H19 ICR exhibits default-silencing functions in promoter-proximal positions. The maximal distance between the H19 ICR and the promoter of the reporter gene required for this effect was 1.2 ± 0.3kb which can be compared to the 1.9 kb distance between the endogenous H19 ICR and H19 promoter. Results suggest that the H19 ICR adopts a chromatin conformation that must be separated by a minimal distance from pivotal cis-regulatory elements to avoid adverse effects on neighbouring promoters. Poly(ADP-ribosy)lation represents a novel post-translational epigenetic mark that segregates with exclusively the maternal derived H19 ICR and associated with factors that interact with the CTCF target sites. CTCF is itself poly(ADP-ribosy)lated and the poly(ADP-ribose) polymerase inhibitor 3-aminobenzamide relieves the insulator function of the H19 ICR. Designed zinc finger proteins were applied to examine if epigenetic marks provided an obstacle for targeted activation and silencing. The zinc finger protein ZFP809 with activator/repressor domain able to efficiently activate/silence the IGF2 target. Murine hybrid cell lines of human chromosome 11, demonstrated that the ZFP809 overcame the epigenetic marks that repressed maternal IGF2 and paternal H19 allele, respectively. Results suggested that imprinted genes are not normally exposed to strong cis-regulatory elements and that the designed ZFPs can be exploited to develop a therapeutic method for rectifying epigenetic lesions.

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Breast cancer is the main cause of cancer death in women. Improved treatments, prevention programs and earlier detection are reducing the rate of death; however, there is still a high percentage of mortality by this cancer. Identification of novel targets to predict response to specific treatments is a key goal for personalizing breast cancer therapy and to improve survival. Few years ago, PARP inhibitors appeared as a promising therapy, particularly in BRCA-mutated cancers. However, there was a clear need to conduct further preclinical and translational work to improve the rational development of PARP inhibition in breast cancer. In this work we described PARP1 expression in breast tumour samples and characterized the effects of its inhibition in preclinical models. We found that nuclear PARP1 protein overexpression was associated with malignant transformation and poor prognosis in breast cancer. PARP1 overexpression was more common in triple negative subtype, but was also detectable in small subsets of estrogen receptor positive and HER2 positive breast cancers. In preclinical models, PARP1 played distinct roles in different molecular subtypes of breast cancer. Moreover, we described that olaparib (novel PARP inhibitor) had antitumour effects in different breast cancer subtypes, and its combination with trastuzumab (anti-HER2 antibody) enhanced the antitumour effects of this therapy. / El càncer de mama és la principal causa de mort per càncer en dones. La millora dels tractaments i la detecció precoç estan reduint la taxa de mort, però segueix sent elevada. Identificar noves dianes per predir la resposta a tractaments és clau per millorar les teràpies contra aquest càncer i la supervivència. Els inhibidors de PARP van aparèixer com una teràpia prometedora, particularment en càncers BRCA-mutants, però, cal dur a terme més estudis preclínics i translacionals per fomentar un desenvolupament racional d’aquesta teràpia en càncer de mama. Aquest treball descriu l’expressió de PARP1 en mostres de tumors mamaris i caracteritza els efectes de la seva inhibició a models preclínics. Vam observar que la sobreexpressió nuclear de la proteïna PARP1 fou associada amb: la transformació maligna; mal pronòstic en càncer de mama; i fou més freqüent al subtipus triple-negatiu, però també es va detectar en un subgrup de càncers de mama receptors d’estrogen positius i HER2 positius. En models preclínics, PARP1 va exercir rols diferents als diferents subtipus de càncer de mama. Per altra banda, vam descriure que olaparib (inhibidor de PARP) té efectes antitumorals en els diversos subtipus, i combinat amb trastuzumab (anticòs anti-HER2) potencia els efectes antitumorals d’aquesta teràpia.

Ewing Sarcoma (ES) is an aggressive pediatric solid tumor. Even though overall-survival for localized patients is approximately 70%, the overall-survival for high risk ES patients has not improved in the last 20 years. Therefore, there is a need for exploration of new therapeutic agents in ES. Recent evidence has demonstrated that ES cells behave like BRCA-deficient tumor types which renders them sensitive to PARP inhibitors in vitro and in vivo. However, a phase II study of the efficacy of single-agent PARP inhibition in patients with relapsed ES did not significantly improve outcome. As single-agent therapy is rarely expected to result in significant clinical responses, in this study, we plan to validate potential targeted combination therapies with PARP inhibitors in ES. Since ES appears to demonstrated BRCA-deficient biology with impaired homologous recombination, cells are expected to be sensitive to both PARP inhibitors and ATR inhibitors, drugs which have a role in regulating DNA damage and impairing homologous recombination. In breast cancer and ovarian cell lines with genetic BRCA-deficiency, PARP and ATR inhibitors have synergistic activity. We hypothesize that these inhibitors will also have synergistic anti-Ewing activity. Furthermore, we recognize that ES cells demonstrate remarkably quiet genomes suggesting that there is minimal ongoing DNA-damage when cells are growing unperturbed. Therefore, we also plan to test the effect of adding low-dose genotoxic chemotherapy to induce additional sensitivity to the combination of PARP and ATR inhibitors in ES. The specific aims of this study were to explore the possible anti-tumor effect of PARP inhibitors combined with ATR inhibitors in ES cell lines, and to explore whether low dose genotoxic chemotherapy with SN38 can potentiate the anti-tumor effect of combined PARP and ATR inhibition in ES cell lines. We studied the anti-Ewing Sarcoma effect of the combination of a PARP inhibitor, AZD2281, and an ATR inhibitor, AZD6738, across a range of doses with and without low doses of a DNA damaging agent, SN38 (irinotecan metabolite), in two ES cell lines. We analyzed synergy by determining the Combination Index (CI) and Fractional Inhibition (FA) of each combination. We found that the ATR inhibitor, AZD6738, was synergistic across large range of concentrations when combined with the PARP inhibitor, AZD2281, in ES cell lines. We also found that treatment of cells with low doses of SN38 increases ES cell sensitivity to treatment with the PARP inhibitor and ATR inhibitor combination. This study provides preclinical support for additional studies exploring these combinations in ES. Given the low number of pediatric patients with ES compared to adult cancer patients, there will be limited attempts in combining these agents in clinical trials. Therefore, the development of an in vivo trial testing the safety and efficacy of this combination in ES mouse models is proposed. / 2020-07-03T00:00:00Z

O câncer é a principal causa de morte nos paises economicamente desenvolvidos e a segunda em paises em desenvolvimento, resultado, em parte, da grande falta de especificidade dos tratamentos atualmente disponíveis. Por outro lado, uma aplicação clínica muito específica, denominada letalidade sintética, foi recentemente proposta. Nesta abordagem terapêutica os inibidores de poli(ADP-ribose) polimerases (PARP), também conhecidos como PARPis, mostraram-se capazes de induzir a morte celular seletiva em células tumorais com defeitos em BRCA1 e BRCA2 (ambas envolvidas no reparo de quebras duplas - DSBR). Assim, a excitante possibilidade de eliminar as células cancerígenas de maneira seletiva fez com que os PARPis passassem de interessantes ferramentas moleculares às mais promissoras drogas anticâncer da atualidade. Contudo, os mecanismos básicos envolvidos na citotoxicidade dos PARPis continuam pouco conhecidos e suas aplicações restritas a um pequeno grupo de cânceres. Por este motivo, neste trabalho, a citotoxicidade do Olaparib (um inibidor de PARP) foi investigada em um painel de linhagens de câncer colorretal (CRC). Os resultados demonstraram que o Olaparib é uma droga de ação lenta, cuja citotoxicidade pode ser modulada por defeitos genéticos em MLH1 (envolvido no reparo de bases mal-emparelhadas) e no supressor tumoral PTEN. Por outro lado, observou-se que o fenótipo MSI (Instabilidade de microssatélites) e os defeitos genéticos em p53 não influenciaram a citotoxicidade do Olaparib. Além disso, linhagens com resistência adquirida a Oxaliplatina (Oxp) e a 5-Fluorouracil (5- Fu) não apresentaram efeito refratário ao Olaparib, enquanto que linhagens com resistência adquirida a SN-38 (metabólito ativo do Irinotecano) apresentaram um forte efeito refratário. Finalmente, as associações de Oxp ou 5-Fu com Olaparib foram capazes de sensibilizar células com resistência relativa e adquirida. Juntos, estes resultados sugerem uma série de novas possibilidades para o emprego de inibidores de PARP no tratamento de CRC. / Cancer is the main cause of death in developed countries and the second in lessdeveloped countries, that results in part from the low specific treatments available. However, a very specific therapeutic approach, called synthetic lethality, was recently proposed. The best documented synthetic lethal interaction was reported between poly(ADP-ribose) polymerases inhibitors (PARPis) and defects in BRCA1 and BRCA2 (both involved in double-strand break repair - DSBR), which may induce selective cancer cells death. Therefore, the exciting possibility to selectively kill cancer cells has been moving PARPis from interesting molecular tools to the forefront of cancer therapy research. However, the basic mechanisms involved in PARPis cytotoxicity are still poorly studied and its clinical applications are restricted to a small number of malignances. Herein, the Olaparib (PARPi) cytotoxicity was investigated in a colorectal cancer (CRC) cell line panel. The results demonstrated that Olaparib is a slow action drug, which may have its effects increased in cells with MLH1 (involved in mismatch repair) and PTEN (tumor supressor) defects. On the other hand, neither the MSI (microsatellite instability) phenotype nor the p53 defects were observed to influence on Olaparib cytotoxicity. Further, neither Oxp nor 5-Fu resistant cell lines presented cross-resistance to Olaparib, whereas a pronounced cross-resistance was observed for SN-38 (Irinotecan metabolite) resistant cell line. Finally, Olaparib associations with Oxaliplatin or 5-Fluorouracil were shown to sensitize cells with both relative and acquired resistances. Together, these results suggest a series of new possible uses for PARP inhibitors in CRC treatment.

O câncer é a principal causa de morte nos paises economicamente desenvolvidos e a segunda em paises em desenvolvimento, resultado, em parte, da grande falta de especificidade dos tratamentos atualmente disponíveis. Por outro lado, uma aplicação clínica muito específica, denominada letalidade sintética, foi recentemente proposta. Nesta abordagem terapêutica os inibidores de poli(ADP-ribose) polimerases (PARP), também conhecidos como PARPis, mostraram-se capazes de induzir a morte celular seletiva em células tumorais com defeitos em BRCA1 e BRCA2 (ambas envolvidas no reparo de quebras duplas - DSBR). Assim, a excitante possibilidade de eliminar as células cancerígenas de maneira seletiva fez com que os PARPis passassem de interessantes ferramentas moleculares às mais promissoras drogas anticâncer da atualidade. Contudo, os mecanismos básicos envolvidos na citotoxicidade dos PARPis continuam pouco conhecidos e suas aplicações restritas a um pequeno grupo de cânceres. Por este motivo, neste trabalho, a citotoxicidade do Olaparib (um inibidor de PARP) foi investigada em um painel de linhagens de câncer colorretal (CRC). Os resultados demonstraram que o Olaparib é uma droga de ação lenta, cuja citotoxicidade pode ser modulada por defeitos genéticos em MLH1 (envolvido no reparo de bases mal-emparelhadas) e no supressor tumoral PTEN. Por outro lado, observou-se que o fenótipo MSI (Instabilidade de microssatélites) e os defeitos genéticos em p53 não influenciaram a citotoxicidade do Olaparib. Além disso, linhagens com resistência adquirida a Oxaliplatina (Oxp) e a 5-Fluorouracil (5- Fu) não apresentaram efeito refratário ao Olaparib, enquanto que linhagens com resistência adquirida a SN-38 (metabólito ativo do Irinotecano) apresentaram um forte efeito refratário. Finalmente, as associações de Oxp ou 5-Fu com Olaparib foram capazes de sensibilizar células com resistência relativa e adquirida. Juntos, estes resultados sugerem uma série de novas possibilidades para o emprego de inibidores de PARP no tratamento de CRC. / Cancer is the main cause of death in developed countries and the second in lessdeveloped countries, that results in part from the low specific treatments available. However, a very specific therapeutic approach, called synthetic lethality, was recently proposed. The best documented synthetic lethal interaction was reported between poly(ADP-ribose) polymerases inhibitors (PARPis) and defects in BRCA1 and BRCA2 (both involved in double-strand break repair - DSBR), which may induce selective cancer cells death. Therefore, the exciting possibility to selectively kill cancer cells has been moving PARPis from interesting molecular tools to the forefront of cancer therapy research. However, the basic mechanisms involved in PARPis cytotoxicity are still poorly studied and its clinical applications are restricted to a small number of malignances. Herein, the Olaparib (PARPi) cytotoxicity was investigated in a colorectal cancer (CRC) cell line panel. The results demonstrated that Olaparib is a slow action drug, which may have its effects increased in cells with MLH1 (involved in mismatch repair) and PTEN (tumor supressor) defects. On the other hand, neither the MSI (microsatellite instability) phenotype nor the p53 defects were observed to influence on Olaparib cytotoxicity. Further, neither Oxp nor 5-Fu resistant cell lines presented cross-resistance to Olaparib, whereas a pronounced cross-resistance was observed for SN-38 (Irinotecan metabolite) resistant cell line. Finally, Olaparib associations with Oxaliplatin or 5-Fluorouracil were shown to sensitize cells with both relative and acquired resistances. Together, these results suggest a series of new possible uses for PARP inhibitors in CRC treatment.