Base Excision Repair Activity Research Articles

Multienzymatic Orthogonal Activation of DNA Codec Enables Tumor-Specific Imaging of Base Excision Repair Activity.

Accurate monitoring of base excision repair (BER) activity in cancer cells is critical for advancing the comprehension of DNA repair processes, gaining insights into cancer development, and guiding treatment strategies. However, current assay techniques for assessing BER activity in cancer cells face challenges due to the heterogeneous origins and diversity of BER enzymes. In this work, we present a highly reliable triple loop-interlocked DNA codec (GATED) that enables precise assessment of BER activity in cancer cells through signal amplification mediated by multienzyme orthogonal activation. The GATED device features a dumbbell-shaped DNA probe to encode two BER enzymes for BER-related signal conversion as well as two bound circular DNA to decode the apurinic/apyrimidinic sites for apurinic/apyrimidinic endonuclease 1 (APE1)-mediated signal amplification. Importantly, GATED is orthogonally activated by multiple target BER enzymes (i.e., uracil DNA glycosylase, thymine DNA glycosylase, and APE1), resulting in a unified fluorescent signal that significantly improves the detection specificity and sensitivity to BER enzymes. Additionally, we demonstrate that the GATED has exceptional biostability within complex biological systems, where it was successfully employed to monitor BER activity in cancer cells with high specificity and enabled cell-based high-throughput screening for BER inhibitors. The GATED provides a much-needed tool for the real-time monitoring of BER activity and the screening of BER inhibitors in cancer cells, potentially advancing both the investigation and clinical application of BER biology.

Abstract C028: Challenging PDAC adaptability: Uncovering therapeutic vulnerabilities in APE1 DNA repair mechanisms

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a therapeutically challenging malignancy notorious for its resilience to therapeutic strategies and ability to thrive under extreme conditions. The cancer's inherent ability to adaptively resist treatments underscores the need for novel and combinatorial therapeutic approaches. Our research focuses on elucidating the role of Apurinic-apyrimidinic endonuclease/Redox effector factor 1 (APE1/Ref-1), a critical multifunctional protein in PDAC pathobiology. APE1 serves two essential functions: as the principal endonuclease in the base excision repair (BER) pathway for DNA repair and as a redox regulator of transcription factors essential for cancer cell proliferation. While the therapeutic targeting of APE1’s redox function has been effective and continues to yield significant advances, the development of treatments aimed at its DNA repair function has proven more challenging with comparatively limited progress. Since standard PDAC treatment regimens involve DNA damaging agents potentially repaired via BER and APE1, we engineered three mutant cell lines with knock-in mutations resulting in a reduction of APE1’s BER activity while maintaining full redox activity. Biochemical evaluations confirmed the effects of the mutation, revealing a 30-fold reduction in DNA repair capacity. Surprisingly, with respect to growth and proliferation, the mutant and wild-type cell lines behaved similarly. Analyses of cytotoxic vulnerabilities revealed similar findings with the mutant lines exhibiting minimal phenotypic differences in sensitivity when challenged with cytotoxic and DNA damaging agents in proliferation-based assays. These findings led us to posit that the mutant cell lines were relying on compensatory DNA repair pathways which were providing sufficient compensation for the decrease in APE1 activity. We further hypothesized that the cell lines may still have hidden, long-term deficiencies in DNA damage processing which are not apparent during the initial stress response. Subsequent colony formation assays revealed that the mutant cell lines do exhibit poor long-term survival even after only short-term exposure to DNA damage. In vivo orthotopic mouse model experiments further corroborated these findings, showing a significant reduction in tumor size and decreased metastasis to the lungs and liver in mutant cell lines compared to wild-type controls. While APE1 is the primary endonuclease in the BER pathway, studies have demonstrated APE1-independent BER in rare, specific contexts. We are probing the hypothesis that these APE1-independent BER pathways function as the compensatory mechanism safeguarding these cells in short-term stress situations. Identifying and characterizing these backup pathways will not only offer a better understanding of APE1’s DNA repair capabilities within PDAC but will also provide a better understanding of how DNA repair mechanisms can be therapeutically targeted for novel therapeutic options or combinations. This opens the path to enhance standard of care treatments such as FOLFIRINOX. Citation Format: Eyram K Kpenu, Randall Wireman, Mahmut Mijiti, Silpa Gampala, Melissa L Fishel, Mark R Kelley. Challenging PDAC adaptability: Uncovering therapeutic vulnerabilities in APE1 DNA repair mechanisms [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr C028.

Effect of a personalized intensive dietary intervention on base excision repair (BER) in colorectal cancer patients: Results from a randomized controlled trial

DNA repair is essential to maintain genomic integrity and may affect colorectal cancer (CRC) patients’ risk of secondary cancers, treatment efficiency, and susceptibility to various comorbidities. Bioactive compounds identified in plant foods have the potential to modulate DNA repair mechanisms, but there is limited evidence of how dietary factors may affect DNA repair activity in CRC patients in remission after surgery. The aim of this study was to investigate the effect of a 6-month personalized intensive dietary intervention on DNA repair activity in post-surgery CRC patients (stage I-III). The present study included patients from the randomized controlled trial CRC-NORDIET, enrolled 2–9 months after surgery. The intervention group received an intensive dietary intervention emphasizing a prudent diet with specific plant-based foods suggested to dampen inflammation and oxidative stress, while the control group received only standard care advice. The comet-based in vitro repair assay was applied to assess DNA repair activity, specifically base excision repair (BER), in peripheral blood mononuclear cells (PBMCs). Statistical analyses were conducted using gamma generalized linear mixed models (Gamma GLMM). A total of 138 CRC patients were included, 72 from the intervention group and 66 from the control group. The BER activity in the intervention group did not change significantly compared to the control group. Our findings revealed a substantial range in both inter- and intra-individual levels of BER. In conclusion, the results do not support an effect of dietary intervention on BER activity in post-surgery CRC patients during a 6-month intervention period.

Optimizing the Comet Assay-Based In Vitro DNA Repair Assay for Placental Tissue: A Pilot Study with Pre-Eclamptic Patients.

The comet assay-based in vitro DNA repair assay has become a common tool for quantifying base excision repair (BER) activity in human lymphocytes or cultured cells. Here, we optimized the protocol for studying BER in human placental tissue because the placenta is a non-invasive tissue for biomonitoring of early-life exposures, and it can be used to investigate molecular mechanisms associated with prenatal disorders. The optimal protein concentration of placental protein extracts for optimal damage recognition and incision was 2 mg protein/mL. The addition of aphidicolin did not lead to reduced non-specific incisions and was, therefore, not included in the optimized protocol. The interval between sample collection and analysis did not affect BER activity up to 70 min. Finally, this optimized protocol was tested on pre-eclamptic (PE) placental tissues (n = 11) and significantly lower BER activity in PE placentas compared to controls (n = 9) was observed. This was paralleled by a significant reduction in the expression of BER-related genes and increased DNA oxidation in PE placentas. Our study indicates that BER activity can be determined in placentas, and lower activity is present in PE compared with healthy. These findings should be followed up in prospective clinical investigations to examine BER's role in the advancement of PE.

Oxidative DNA damage on the VEGF G-quadruplex forming promoter is repaired via long-patch BER.

In response to oxidative damage, base excision repair (BER) enzymes perturb the structural equilibrium of the VEGF promoter between B-form and G4 DNA conformations, resulting in epigenetic-like modifications of gene expression. However, the mechanistic details remain enigmatic, including the activity and coordination of BER enzymes on the damaged G4 promoter. To address this, we investigated the ability of each BER factor to conduct its repair activity on VEGF promoter G4 DNA substrates by employing pre-steady-state kinetics assays and in vitro coupled BER assays. OGG1 was able to initiate BER on double-stranded VEGF promoter G4 DNA substrates. Moreover, pre-steady-state kinetics revealed that compared to B-form DNA, APE1 repair activity on the G4 was decreased ~two-fold and is the result of slower product release as opposed to inefficient strand cleavage. Interestingly, Pol β performs multiple insertions on G4 substrates via strand displacement DNA synthesis in contrast to a single insertion on B-form DNA. The multiple insertions inhibit ligation of the Pol β products, and hence BER is not completed on the VEGF G4 promoter substrates through canonical short-patch BER. Instead, repair requires the long-patch BER flap-endonuclease activity of FEN1 in response to the multiple insertions by Pol β prior to ligation. Because the BER proteins and their repair activities are a key part of the VEGF transcriptional enhancement in response to oxidative DNA damage of the G4 VEGF promoter, the new insights reported here on BER activity in the context of this promoter are relevant toward understanding the mechanism of transcriptional regulation.

Chimeric d/l-DNA Probes of Base Excision Repair Enable Real-Time Monitoring of Thymine DNA Glycosylase Activity in Live Cells.

The base excision repair (BER) pathway is a frontline defender of genomic integrity and plays a central role in epigenetic regulation through its involvement in the erasure of 5-methylcytosine. This biological and clinical significance has led to a demand for analytical methods capable of monitoring BER activities, especially in living cells. Unfortunately, prevailing methods, which are primarily derived from nucleic acids, are mostly incompatible with intracellular use due to their susceptibility to nuclease degradation and other off-target interactions. These limitations preclude important biological studies of BER enzymes and many clinical applications. Herein, we report a straightforward approach for constructing biostable BER probes using a unique chimeric d/l-DNA architecture that exploits the bioorthogonal properties of mirror-image l-DNA. We show that chimeric BER probes have excellent stability within living cells, where they were successfully employed to monitor relative BER activity, evaluate the efficiency of small molecule BER inhibitors, and study enzyme mutants. Notably, we report the first example of a fluorescent probe for real-time monitoring of thymine DNA glycosylase (TDG)-mediated BER of 5-formylcytosine and 5-carboxylcytosine in living cells, providing a much-needed tool for studying DNA (de)methylation biology. Chimeric probes offer a robust and highly generalizable approach for real-time monitoring of BER activity in living cells, which should enable a broad spectrum of basic research and clinical applications.

Identification of PANoptosis-Based Prognostic Signature for Predicting Efficacy of Immunotherapy and Chemotherapy in Hepatocellular Carcinoma.

PANoptosis has been a research hotspot, but the role of PANoptosis in hepatocellular carcinoma (HCC) remains widely unknown. Drug resistance and low response rate are the main limitations of chemotherapy and immunotherapy in HCC. Thus, construction of a prognostic signature to predict prognosis and recognize ideal patients for corresponding chemotherapy and immunotherapy is necessary. The mRNA expression data of HCC patients was collected from TCGA database. Through LASSO and Cox regression, we developed a prognostic signature based on PANoptosis-related genes. KM analysis and ROC curve were implemented to evaluate the prognostic efficacy of this signature, and ICGC and GEO database were used as external validation cohorts. The immune cell infiltration, immune status, and IC50 of chemotherapeutic drugs were compared among different risk subgroups. The relationships between the signature and the efficacy of ICI therapy, sorafenib treatment, and transcatheter arterial chemoembolization (TACE) therapy were investigated. A 3-gene prognostic signature was constructed which divided the patients into low- and high-risk subgroups. Low-risk patients had better prognosis, and the risk score was proved to be an independent predictor of overall survival (OS), which had a well predictive effect. Patients in high-risk population had more immunosuppressive cells (Tregs, M0 macrophages, and MDSCs), higher TIDE score and TP53 mutation rate, and elevated activity of base excision repair (BER) pathways. Patients with low risk benefited more from ICI, TACE, and sorafenib therapy. The predictive value of the risk score was comparable with TIDE and MSI for OS under ICI therapy. The risk score could be a biomarker to predict the response to ICI, TACE, and sorafenib therapy. The novel signature based on PANoptosis is a promising biomarker to distinguish the prognosis predict the benefit of ICI, TACE, and sorafenib therapy, and forecast the response to them.

Abstract 2836: H2S donors as radiosensitizers for glioblastoma multiforme (GBM)

Abstract Glioblastoma multiforme (GBM) is an extremely aggressive CNS cancer in adults. Radiation is a cornerstone therapy but poses high risk of healthy tissue necrosis. Despite maximal treatment, GBM results in death within 15-21 months of diagnosis. These poor statistics suggest the need for a novel therapy. The use of radiosensitizing agents is a novel approach to minimizing radiation mediated healthy tissue necrosis by allowing use of lower doses to achieve comparable cytotoxic effects. Our lab has shown that sodium sulfide (Na2S), a hydrogen sulfide (H2S) donor, selectively kills GBM (T98G) cells while sparing normal human brain endothelial (hCMEC/D3) cells. Na2S also selectively radiosensitizes GBM cells and enhances cell killing with photon or proton radiation. We are currently exploring Diallyl Trisulfide (DATS), another H2S donor, as a radiosensitizing agent and have demonstrated that DATS can kill GBM cells. At a given dose of 2 Gy, radiation alone decreases T98G survival by 10%. With DATS, survival decreases by 70%, suggesting an additive effect. To determine if DATS increases DNA damage mediated cell death, T98G cells were treated with DATS, radiation, or combined DATS + radiation treatment and then analyzed for γH2AX foci, an indicator of double stand breaks (DSB). Our results show that compared to no treatment, DATS increased the number of γH2AX foci per cell by 1.5-fold, by 3-fold with radiation, and by 4-fold with combined DATS + radiation, an additive response. To elucidate the mechanism of increased DNA damage, a novel fluorescence multiplex host cell reactivation (FM-HCR) reporter system was used to assess repair activity of DSBs in live cells. T98G cells pre-treated with DATS were transfected with reporter plasmids containing site-specific lesions, mimicking radiation-like DNA damage. Repair resulted in expression of a fluorescent reporter protein, which was quantitated using flow cytometry. Our results show that DATS did not alter non-homologous end joining (NHEJ) or homologous repair (HR) activity of DSB. However, DATS did alter base excision repair (BER) activity by decreasing repair of abasic lesions and increasing repair 8oxoG lesions. We hypothesize that this attempted BER via simultaneous strand cleavage by AP endonuclease (Ape1) or glycosylase (Ogg1) may lead to build up of repair intermediates, threatening genomic stability and inducing DSB. Pursuing specific DNA repair biochemical assays is required to further understand this effect of DATS on DNA damage and repair inhibition. Citation Format: Morni Modi, Camila Weber, Qinqin Xu, Kuanling Chen, Ana Cheong, Zachery Nagel, Lynn Harrison. H2S donors as radiosensitizers for glioblastoma multiforme (GBM) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2836.

Assay conditions for estimating differences in base excision repair activity with Fpg-modified comet assay

DNA repair is an essential agent in cancer development, progression, prognosis, and response to therapy. We have adapted a cellular repair assay based on the formamidopyrimidine DNA glycosylase (Fpg)-modified comet assay to assess DNA repair kinetics. The removal of oxidized nucleobases over time (0–480 min) was analyzed in peripheral blood mononuclear cells (PBMCs) and 8 cell lines. DNA damage was induced by exposure to either Ro19-8022 plus visible light or potassium bromate (KBrO3). The initial amount of damage induced by Ro 19–8022 plus light varied between cell lines, and this was apparently associated with the rate of repair. However, the amount of DNA damage induced by KBrO3 varied less between cell types, so we used this agent to study the kinetics of DNA repair. We found an early phase of ca. 60 min with fast removal of Fpg-sensitive sites, followed by slower removal over the following 7 h. In conclusion, adjusting the initial damage at T0 to an equal level can be achieved by the use of KBrO3, which allows for accurate analysis of subsequent cellular DNA repair kinetics in the first hour after exposure.Graphical

Treatment of Human HeLa Cells with Black Raspberry Extracts Enhances the Removal of DNA Lesions by the Nucleotide Excision Repair Mechanism.

As demonstrated by us earlier and by other researchers, a diet containing freeze-dried black raspberries (BRB) inhibits DNA damage and carcinogenesis in animal models. We tested the hypothesis that the inhibition of DNA damage by BRB is due, in part, to the enhancement of DNA repair capacity evaluated in the human HeLa cell extract system, an established in vitro system for the assessment of cellular DNA repair activity. The pre-treatment of intact HeLa cells with BRB extracts (BRBE) enhances the nucleotide excision repair (NER) of a bulky deoxyguanosine adduct derived from the polycyclic aromatic carcinogen benzo[a]pyrene (BP-dG) by ~24%. The NER activity of an oxidatively-derived non-bulky DNA lesion, guanidinohydantoin (Gh), is also enhanced by ~24%, while its base excision repair activity is enhanced by only ~6%. Western Blot experiments indicate that the expression of selected, NER factors is also increased by BRBE treatment by ~73% (XPA), ~55% (XPB), while its effects on XPD was modest (<14%). These results demonstrate that BRBE significantly enhances the NER yields of a bulky and a non-bulky DNA lesion, and that this effect is correlated with an enhancement of expression of the critically important NER factor XPA and the helicase XPB, but not the helicase XPD.

Cysteine Oxidation to Sulfenic Acid in APE1 Aids G-Quadruplex Binding While Compromising DNA Repair.

Apurinic/apyrimidinic endonuclease-1 (APE1) is a base excision repair (BER) enzyme that is also engaged in transcriptional regulation. Previous work demonstrated that the enzymatic stalling of APE1 on a promoter G-quadruplex (G4) recruits transcription factors during oxidative stress for gene regulation. Also, during oxidative stress, cysteine (Cys) oxidation is a post-translational modification (PTM) that can change a protein's function. The current study provides a quantitative survey of cysteine oxidation to sulfenic acid in APE1 and how this PTM at specific cysteine residues affects the function of APE1 toward the NEIL3 gene promoter G4 bearing an abasic site. Of the seven cysteine residues in APE1, five (C65, C93, C208, C296, and C310) were prone to carbonate radical anion oxidation to yield sulfenic acids that were identified and quantified by mass spectrometry. Accordingly, five Cys-to-serine (Ser) mutants of APE1 were prepared and found to have attenuated levels of endonuclease activity, depending on the position, while KD values generally decreased for G4 binding, indicating greater affinity. These data support the concept that cysteine oxidation to sulfenic acid can result in modified APE1 that enhances G4 binding at the expense of endonuclease activity during oxidative stress. Cysteine oxidation to sulfenic acid residues should be considered as one of the factors that may trigger a switch from base excision repair activity to transcriptional modulation by APE1.

Abstract P1-16-07: A synthetic lethality treatment strategy for p53 mutant breast cancer

Abstract Breast carcinomas commonly carry mutations in the tumor suppressor p53, while therapeutic efforts to target mutant p53 were largely unfruitful. Here we report preclinical data supporting a novel combination therapy strategy for treatment of p53-mutant cancers. Genomic data revealed a high expression activity of Base-Excision Repair (BER) pathways in p53-mutant breast cancers. We designed a new methodology for testing BER in live cells. The BER studies revealed a significant dysregulation in BER-mediated repair in p53-mutant cancer cells. Taken advantage in the BER defect, we developed a novel treatment strategy that specifically targets p53-mt cancers. We found that treatment with deoxyuridine analogues induced accumulation of DNA damage selectively in p53-mutant cells. Further, inhibitors of poly (ADP-ribose) polymerase (PARPi) greatly enhanced this response and increased cell death, although PARPi as a single agent was not effective. In contrast, normal cells responded to PARPi with activation of the p53-p21 axis and cell cycle arrest. Inactivation of p53 in p53 wild-type cell lines conferred the p53-mutant phenotype. Preclinical breast cancer studies revealed that the combination of deoxyuridine analogue with PARPi was more effective in inhibition of tumor growth and metastases than either drug alone. This work illustrates a novel combination therapy strategy that may improve survival rates and outcomes for thousands of breast cancer patients. Citation Format: Andrei Bakin, Justin Zonneville, Moyi Wang, Mohammed Alruwaili, Kevin Eng, Renuka Iyer, Ben Park, Christos Fountzilas. A synthetic lethality treatment strategy for p53 mutant breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-16-07.

Signal-on/signal-off bead-based assays for the multiplexed monitoring of base excision repair activities by flow cytometry.

As the support of all living kingdoms' genetic information, the integrity of the DNA biomolecule must be preserved. To that goal, cells have evolved specific DNA repair pathways to thwart a large diversity of chemical substances and radiations that alter the DNA structure and lead to the development of pathologies such as cancers or neurodegenerative diseases. When dysregulated, activity rates of various actors of DNA repair can play a key role in carcinogenesis as well as in drugs resistance or hypersensitivity mechanisms. For the last 10years, new complementary treatments have aimed at targeting specific enzymes responsible for such resistances. It is therefore crucial for biomedical research and clinical diagnosis to develop fast and sensitive tools able to measure the activity rate of DNA repair enzymes. In this work, a new assay for measuring enzymatic activities using microbeacons (µBs) is expounded. µB refers to microsphere functionalized by hairpin-shaped nucleic acid probes containing a single site-specific lesion in the stem and modified with chromophores. Following the processing of the lesion by the targeted protein, µB is cleaved and either lights off (signal-off strategy) or on (signal-on), depending on the use of fluorescent or profluorescent probes, respectively. After an optimization phase of the assay, we reported the combined analysis of restriction enzyme, AP-endonuclease, and DNA N-glycosylase by real-time monitoring followed by a flow cytometry measurement. As proofs of concept, we demonstrated the potential of the biosensor for highlighting DNA repair inhibitors and discriminating cell lines from their enzymatic activities.

Fluorescence Imaging of Mitochondrial DNA Base Excision Repair Reveals Dynamics of Oxidative Stress Responses.

Mitochondrial function in cells declines with aging and with neurodegeneration, due in large part to accumulated mutations in mitochondrial DNA (mtDNA) that arise from deficient DNA repair. However, measuring this repair activity is challenging. We employ a molecular approach for visualizing mitochondrial base excision repair (BER) activity in situ by use of a fluorescent probe (UBER) that reacts rapidly with AP sites resulting from BER activity. Administering the probe to cultured cells revealed signals that were localized to mitochondria, enabling selective observation of mtDNA BER intermediates. The probe showed elevated DNA repair activity under oxidative stress, and responded to suppression of glycosylase activity. Furthermore, the probe illuminated the time lag between the initiation of oxidative stress and the initial step of BER. Absence of MTH1 in cells resulted in elevated demand for BER activity upon extended oxidative stress, while the absence of OGG1 activity limited glycosylation capacity.

Fluorescence Imaging of Mitochondrial DNA Base Excision Repair Reveals Dynamics of Oxidative Stress Responses

AbstractMitochondrial function in cells declines with aging and with neurodegeneration, due in large part to accumulated mutations in mitochondrial DNA (mtDNA) that arise from deficient DNA repair. However, measuring this repair activity is challenging. We employ a molecular approach for visualizing mitochondrial base excision repair (BER) activity in situ by use of a fluorescent probe (UBER) that reacts rapidly with AP sites resulting from BER activity. Administering the probe to cultured cells revealed signals that were localized to mitochondria, enabling selective observation of mtDNA BER intermediates. The probe showed elevated DNA repair activity under oxidative stress, and responded to suppression of glycosylase activity. Furthermore, the probe illuminated the time lag between the initiation of oxidative stress and the initial step of BER. Absence of MTH1 in cells resulted in elevated demand for BER activity upon extended oxidative stress, while the absence of OGG1 activity limited glycosylation capacity.

Versatile cell-based assay for measuring DNA alkylation damage and its repair

DNA alkylation damage induced by environmental carcinogens, chemotherapy drugs, or endogenous metabolites plays a central role in mutagenesis, carcinogenesis, and cancer therapy. Base excision repair (BER) is a conserved, front line DNA repair pathway that removes alkylation damage from DNA. The capacity of BER to repair DNA alkylation varies markedly between different cell types and tissues, which correlates with cancer risk and cellular responses to alkylation chemotherapy. The ability to measure cellular rates of alkylation damage repair by the BER pathway is critically important for better understanding of the fundamental processes involved in carcinogenesis, and also to advance development of new therapeutic strategies. Methods for assessing the rates of alkylation damage and repair, especially in human cells, are limited, prone to significant variability due to the unstable nature of some of the alkyl adducts, and often rely on indirect measurements of BER activity. Here, we report a highly reproducible and quantitative, cell-based assay, named alk-BER (alkylation Base Excision Repair) for measuring rates of BER following alkylation DNA damage. The alk-BER assay involves specific detection of methyl DNA adducts (7-methyl guanine and 3-methyl adenine) directly in genomic DNA. The assay has been developed and adapted to measure the activity of BER in fungal model systems and human cell lines. Considering the specificity and conserved nature of BER enzymes, the assay can be adapted to virtually any type of cultured cells. Alk-BER offers a cost efficient and reliable method that can effectively complement existing approaches to advance integrative research on mechanisms of alkylation DNA damage and repair.

Abstract 681: Prospective study for the identification of DNA repair radiotoxicity biomarkers in breast and prostate cancer patients: Cohort description and descriptive statistics

Abstract Introduction: Radiotherapy (RT) can induce with short-term (acute) and long term toxicity. Although acute toxicity is generally well tolerated, long term toxicity might be irreversible and progressive over time. RT induces damage in healthy tissue, triggers inflammation and bystander effects in non-irradiated cells. The toxicity is dependent on many variables and precise knowledge on the responsible mechanisms is still lacking. Purpose: DNA damage, DNA repair and inflammation are known to interplay. Because of the specific involvement of Base Excision Repair (BER) in Reactive Oxygen and Nitrogen species (RONs)-induced lesions and inflammation, we monitored BER activities in patients receiving radiotherapy to investigate glycosylase/AP endonucleases activities as potential biomarkers of radiotoxicity. First, impact of gender, age, concomitant treatment, body mass index (BMI), smoking and alcohol consumption, on basal repair levels, and radiation-induced repair activities were evaluated. Methods: About 220 patients suffering from non-metastatic breast or prostate cancer and treated by radiotherapy (RT) were enrolled by Institut de Cancérologie Lucien Neuwirth. 8 mL of blood was collected prior to RT, 24h after the first radiation dose and before the 6th radiation dose. We then used the Glyco-SPOT assay to quantify BER activities, and nucleases level in lysates prepared from the patients' lymphocytes. Patients were followed-up for at least 6 months. Clinical and toxicity data were collected. All adverse events (AE; acute, sub-acute and late) were scored according to Common Terminology Criteria for Adverse Events. Results: Due to differences in the BER profile between prostate and breast cancer patients, the two groups were analyzed separately. We provide a descriptive overview of recorded AE for each group, according to time period. Some significant specific changes in BER activities where associated with smoking, alcohol consumption, BMI, treatment type and age. Conclusion: Known risk factors significantly affected some BER activities. Males and females should be considered independently for radiotoxicity biomarkers identification using glycosylase/AP endonuclease/nucleases related biomarkers. The identification of possible confounding factors is a prerequisite to any selection of radiotoxicity biomarkers. Citation Format: Sylvie Sauvaigo, Giovanna Muggiolu, Sarah Libert, Elisabeth Daguenet, Claire Rodriguez-Lafrasse, Thierry Maillet, Nicolas Magné. Prospective study for the identification of DNA repair radiotoxicity biomarkers in breast and prostate cancer patients: Cohort description and descriptive statistics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 681.

Abstract 1180: A novel synthetic lethality treatment strategy for metastatic breast cancer

Abstract Breast carcinomas commonly carry mutations in the tumor suppressor p53, while therapeutic efforts to target mutant p53 were largely unfruitful. Here we present preclinical data supporting a novel combination therapy strategy for treatment of p53-deficient cancers. Genomic data revealed a high expression activity of Base-Excision Repair (BER) pathways in p53-deficient breast cancers. However, we found that BER-mediated repair was significantly dysregulated in p53-mutant cancer cells. Treatment with deoxyuridine analogues induced accumulation of DNA damage in p53-mutant cells and inhibitors of poly (ADP-ribose) polymerase (PARPi) greatly enhanced this response. In contrast, normal cells responded to PARPi with activation of the p53-p21 axis and cell cycle arrest. Inactivation of either p53 or p21/CDKN1A in p53 wild-type cells conferred the p53-mutant phenotype. Preclinical breast cancer studies revealed that the combination of deoxyuridine analogue with PARPi was more effective in inhibition of tumor growth and metastases than either drug alone. This work illustrates a novel combination therapy strategy that may improve survival rates and outcomes for thousands of breast cancer patients. Citation Format: Justin Zonneville, Moyi Wang, Mohammed Alruwaili, Kevin Eng, Thomas Melendy, Ben Ho Park, Renuka Iyer, Christos Fountzilas, Andrei V. Bakin. A novel synthetic lethality treatment strategy for metastatic breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1180.

Abstract 680: A DNA repair biomarker signature to predict radiotherapy side-effects in breast and prostate cancers

Abstract Introduction: About 50% of patients with solid tumors receive radiotherapy (RT) which induces cancer cells death through radiation-induced DNA damage. Five to 10% of these patients experience severe toxicity that can heavily impact their quality of life. The identification of predictive biomarkers to discriminate patients at high risk of developing radiotoxicity is needed to move towards a personalized treatment and to improve the management of these patients. Purpose: The aim of this clinical proof-of-concept was to identify blood radiotoxicity biomarkers based on a comprehensive analysis of several DNA repair activities. We relied on the hypothesis that DNA damage, DNA repair and inflammation are functionally associated and mutually supportive, and related to the appearance of side effects. Methods: 200 patients with either prostate or breast cancer who underwent RT were enrolled at the Lucien Neuwirth Cancer institute. Late radio-induced adverse events were recorded 6 months after the beginning of the treatment. Three blood samples per patient were collected before and early during the treatment course to monitor the ability of enzymes contained in lymphocytes to repair series of DNA lesions immobilized on biochip (Glyco-SPOT assay). We analyzed the association between the Base Excision Repair (BER), the primary pathway responsible for DNA repair during inflammation, and the appearance of severe late radiation-induced effects (3 in the female and 4 in the male cohort). Results: Late severe (Grade ≥3) and late moderate (Grade ≥2) radiation-induced events were recorded. Cutaneous, and gastro-intestinal and genitourinary adverse events, were considered respectively in breast cancer and prostate cancer patients. We observed some significantly lower BER activities in breast cancer patients who developed severe late events compared to those who did not. By contrast, it was the opposite in prostate cancer patients. In both cohort we defined a combination of biomarkers that predicted the appearance of severe late adverse events with 100% sensitivity and 100% negative predictive value using the blood sample taken after the first dose of RT. Conclusion: The risk of late radiotoxicity could be accurately predicted on the basis of combination of BER-related biomarkers. Interestingly, the biomarkers differed in breast and prostate cancer patients suggesting that beyond inflammation, hormone pathway regulation impacted the BER response to ionizing radiation, and the relationship with long-term severe side effects. These results require confirmation on a larger cohort. Citation Format: Giovanna Muggiolu, Libert Libert, Elisabeth Daguenet, Thierry Maillet, Claire Rodriguez-Lafrasse, Sylvie Sauvaigo, Nicolas Magné. A DNA repair biomarker signature to predict radiotherapy side-effects in breast and prostate cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 680.

Olaparib enhances curcumin-mediated apoptosis in oral cancer cells by inducing PARP trapping through modulation of BER and chromatin assembly

Apart from inducing catalytic inhibition of PARP-1, PARP inhibitors can also trap PARP proteins at the sites of DNA damage and forming toxic PARP-DNA complexes. These complexes obstruct the DNA repair process, resulting in cancer cell death. To study the detailed mechanism of anti-cancer action through PARP trapping, we have treated oral cancer cells (H-357) with curcumin (Cur), olaparib (Ola) and their combination (Cur + Ola). Cur + Ola treatment triggered the expressions of PARP-1 and adenomatous polyposis coli (APC) and down regulated other base excision repair (BER) proteins in the chromatin fraction but not in the nuclear fraction. Cur + Ola treatment inhibited PARylation, altered interaction of PARP-1 with representative BER proteins and arrested cells in S-phase. We have for the first time provided direct evidence and measured the cellular PARP-1 trapping potentiality of Ola in Cur pretreated H-357 cells. Unchanged cellular PARP-1 trapping, unaltered expression of BER proteins and BER activity were found in APC silenced H-357 cells, which further confirmed that the DNA damage/repair response was APC-dependent. Interestingly, complete abolishment of the chromatin remodeler ‘amplified in Liver Cancer 1’ (ALC1), decreased expression of Histone H3 and histone acetyltransferase (P300) was noted in chromatin of Cur + Ola treated cells. Their expressions remained unchanged in APC silenced cells. Cur + Ola also altered the interaction of ALC1 with BER proteins including APC. Thus, the present study reveals that Cur + Ola treatment increased oral cancer cell death not only through catalytic inhibition of PARP-1 but also predominantly through PARP-1 trapping and indirect inhibition of chromatin remodeling.