Repair Enzyme Research Articles

Luteolin Alleviates Cadmium-Induced Kidney Injury by Inhibiting Oxidative DNA Damage and Repairing Autophagic Flux Blockade in Chickens.

Chickens are a major source of meat and eggs in human food and have significant economic value. Cadmium (Cd) is a common environmental pollutant that can contaminate feed and drinking water, leading to kidney injury in livestock and poultry, primarily by inducing the generation of free radicals. It is necessary to develop potential medicines to prevent and treat Cd-induced nephrotoxicity in poultry. Luteolin (Lut) is a natural flavonoid compound mainly extracted from peanut shells and has a variety of biological functions to defend against oxidative damage. In this study, we aimed to demonstrate whether Lut can alleviate kidney injury under Cd exposure and elucidate the underlying molecular mechanisms. Renal histopathology and cell morphology were observed. The indicators of renal function, oxidative stress, DNA damage and repair, NAD+ content, SIRT1 activity, and autophagy were analyzed. In vitro data showed that Cd exposure increased ROS levels and induced oxidative DNA damage and repair, as indicated by increased 8-OHdG content, increased γ-H2AX protein expression, and the over-activation of the DNA repair enzyme PARP-1. Cd exposure decreased NAD+ content and SIRT1 activity and increased LC3 II, ATG5, and particularly p62 protein expression. In addition, Cd-induced oxidative DNA damage resulted in PARP-1 over-activation, reduced SIRT1 activity, and autophagic flux blockade, as evidenced by reactive oxygen species scavenger NAC application. The inhibition of PARP-1 activation with the pharmacological inhibitor PJ34 restored NAD+ content and SIRT1 activity. The activation of SIRT1 with the pharmacological activator RSV reversed Cd-induced autophagic flux blockade and cell injury. In vivo data demonstrated that Cd treatment caused the microstructural disruption of renal tissues, reduced creatinine, and urea nitrogen clearance, raised MDA content, and decreased the activities or contents of antioxidants (GSH, T-SOD, CAT, and T-AOC). Cd treatment caused oxidative DNA damage and PARP-1 activation, decreased NAD+ content, decreased SIRT1 activity, and impaired autophagic flux. Notably, the dietary Lut supplement observably alleviated these alterations in chicken kidney tissues induced by Cd. In conclusion, the dietary Lut supplement alleviated Cd-induced chicken kidney injury through its potent antioxidant properties by relieving the oxidative DNA damage-activated PARP-1-mediated reduction in SIRT1 activity and repairing autophagic flux blockade.

Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach.

Base excision repair enzymes (BERs) detect and repair oxidative DNA damage with efficacy despite the small size of the defects and their often only minor structural impact. A charge transfer (CT) model for rapid scanning of DNA stretches has been evoked to explain the high detection rate in the face of numerous, small lesions. The viability of CT DNA defect detection is explored via hybrid QM/MM computational studies that leverage the accuracy of quantum mechanics (QM) for a region of interest and the descriptive power of molecularmechanics (MM) for the remainder of the system. We find that the presence of an oxidative lesion lowers theredox free energy of oxidation by approximately 1.0 eV regardless of DNA compaction (free DNA versus packed DNA in nucleosome core particles) and damage location indicating the high feasibility of a CT-based process for defect detection in DNA.

MTH1 inhibition synergizes with ROS-inducing agents to trigger cervical cancer cells undergoing parthanatos

Cervical cancer cells possess high levels of reactive oxygen species (ROS); thus, increasing oxidative stress above the toxicity threshold to induce cell death is a promising chemotherapeutic strategy. However, the underlying mechanisms of cell death are elusive, and efficacy and toxicity issues remain. Within DNA, 8-oxo-7,8-dihydroguanine (8-oxoG) is the most frequent base lesion repaired by 8-oxoguanine glycosylase 1 (OGG1)-initiated base excision repair. Cancer cells also express high levels of MutT homolog 1 (MTH1), which prevents DNA replication-induced incorporation of 8-oxoG into the genome by hydrolyzing 8-oxo-7,8-dihydro-2′-deoxyguanosine 5′-triphosphate (8-oxo-dGTP). Here, we revealed that ROS-inducing agents triggered cervical cancer to undergo parthanatos, which was mainly induced by massive DNA strand breaks resulting from overwhelming 8-oxoG excision by OGG1. Furthermore, the MTH1 inhibitor synergized with a relatively low dose of ROS-inducing agents by enhancing 8-oxoG loading in the DNA. In vivo, this drug combination suppressed the growth of tumor xenografts, and this inhibitory effect was significantly decreased in the absence of OGG1. Hence, the present study highlights the roles of base repair enzymes in cell death induction and suggests that the combination of lower doses of ROS-inducing agents with MTH1 inhibitors may be a more selective and safer strategy for cervical cancer chemotherapy.

Minocycline and photodynamic priming significantly improve chemotherapy efficacy in heterotypic spheroids of pancreatic ductal adenocarcinoma

The prognosis for patients with advanced-stage pancreatic ductal adenocarcinoma (PDAC) remains dismal. It is generally accepted that combination cancer therapies offer the most promise, such as Folforinox, despite their associated high toxicity. This study addresses the issue of chemoresistance by introducing a complementary dual priming approach to attenuate the DNA repair mechanism and to improve the efficacy of a type 1 topoisomerase (Top1) inhibitor. The result is a regimen that integrates drug-repurposing and nanotechnology using 3 clinically relevant FDA-approved agents (1) Top1 inhibitor (irinotecan) at subcytotoxic doses (2) benzoporphyrin derivative (BPD) as a photoactive molecule for photodynamic priming (PDP) to improve the delivery of irinotecan within the cancer cell and (3) minocycline priming (MNP) to modulate DNA repair enzyme Tdp1 (tyrosyl-DNA phosphodiesterase) activity. We demonstrate in heterotypic 3D cancer models that incorporate cancer cells and pancreatic cancer-associated fibroblasts that simultaneous targeting of Tdp1 and Top1 were significantly more effective by employing MNP and photoactivatable multi-inhibitor liposomes encapsulating BPD and irinotecan compared to monotherapies or a cocktail of dual or triple-agents. These data are encouraging and warrant further work in appropriate animal models to evolve improved therapeutic regimens.

RAS-RAF-miR-296-3p signaling axis increases Rad18 expression to augment radioresistance in pancreatic and thyroid cancers

Oncogenic RAS and RAF signaling has been implicated in contributing to radioresistance in pancreatic and thyroid cancers. In this study, we sought to better clarify molecular mechanisms contributing to this effect. We discovered that miRNA 296–3p (miR-296–3p) is significantly correlated with radiosensitivity in a panel of pancreatic cancer cells, and miR-296–3p is highly expressed in normal cells, but low in cancer cell lines. Elevated expression of miR-296–3p increases radiosensitization while decreasing the expression of the DNA repair enzyme RAD18 in both pancreatic and thyroid cancer cells. RAD18 is overexpressed in both pancreatic and thyroid tumors compared to matched normal controls, and high expression of RAD18 in tumors is associated with poor prognostic features. Modulating the expression of mutant KRAS in pancreatic cancer cells or mutant BRAF in thyroid cancer cells demonstrates a tight regulation of RAD18 expression in both cancer types. Depletion of RAD18 results in DNA damage and radiation-induced cell death. Importantly, RAD18 depletion in combination with radiotherapy results in marked and sustained tumor regression in KRAS mutant pancreatic cancer orthotopic tumors and BRAF mutant thyroid heterotopic tumors. Overall, our findings identify a novel coordinated RAS/RAF-miR-296-3p-RAD18 signaling network in pancreatic and thyroid cancer cells, which leads to enhanced radioresistance.

Discovery of Potent Isoindolinone Inhibitors that Target an Active Conformation of PARP1 Using DNA-Encoded Libraries.

Inhibition of poly (ADP-ribose) polymerase-1 (PARP1), a DNA repair enzyme, has proven to be a successful strategy for the treatment of various cancers. With the appropriate selection conditions and protein design, DNA-encoded library (DEL) technology provides a powerful avenue to identify small molecules with the desired mechanism of action towards a target of interest. However, DNA-binding proteins, such as PARP1, can be challenging targets for DEL screening due to non-specific protein-DNA interactions. To overcome this, we designed and screened a PARP1 catalytic domain construct without the autoinhibitory helical domain. This allowed us to interrogate an active, functionally-relevant form of the protein resulting in the discovery of novel isoindolinone PARP1 inhibitors with single-digit nanomolar potency. These inhibitors also demonstrated little to no PARP1-DNA trapping, a property that could be advantageous in the clinic.

Strategies of N-Glycosidic Bond Cleavage by DNA Repair Enzymes

Strategies of N-Glycosidic Bond Cleavage by DNA Repair Enzymes

Human and animal cells under influence of different lighting and stimulus

Circadian rhythms, are the basis of homeostasis of organisms like human and other mammals. Violation of circadian rhythms leads to the development of pathological conditions and severe course of preexisting pathologies. For example some work with B16-F1O cells (B16) has shown that molecules like opsins, Circadian Locomotor Output Cycles Kaput (CLOCK) and clock genes are changed after a white light pulse (WLP). Like this, melanopsin (OPN4) and rhodopsin (OPN2) through UVA irradiation induced B16 pigmentation. Thus, heat shock reduces secreted rhodopsin expression in normal Melan-a melanocytes, while the opposite effect is found in malignant B16 cells. In both cell lines UVA radiation increases the expression of melanopsin and melanin, interfering with several clock genes, and also increasing the DNA repair enzyme xeroderma pigmentosum, complementation group A (XPA). Furthermore, B16 are more responsive to UVA radiation when compared to normal cells. Thereby, opsins are involved in animal camouflage. And their functions in humans involve different wavelengths, for example in skin the keratinocyte differentiation by (410 nm) involved cone opsin (OPN1) and rhodopsin (OPN2), like this in epidermal keratinocytes irradiation by (447 nm) accelerates closure in wound-healing and violet light (415 nm) induced hyperpigmentation. Furthermore, in B16 cell culture certain wavelengths induce proliferation or inhibition like signs of apoptosis and necrosis. Finally understanding the response of opsins and clock genes to different wavelengths in the skin, we could attribute a therapeutic of photobiomodulation (PBM) to approach various dermatological conditions, such as psoriasis, atopic dermatitis, hair growth, wound healing and tissue regeneration.

Discovery of a potent inhibitor, D-132, targeting AsfvPolX, via protein-DNA complex‐guided pharmacophore screening and in vitro molecular characterizations

The heightened transmissibility and capacity of African swine fever virus (ASFV) induce fatal diseases in domestic pigs and wild boars, posing significant economic repercussions and global threats. Despite extensive research efforts, the development of potent vaccines or treatments for ASFV remains a persistent challenge. Recently, inhibiting the AsfvPolX, a key DNA repair enzyme, emerges as a feasible strategy to disrupt viral replication and control ASFV infections. In this study, a comprehensive approach involving pharmacophore-based inhibitor screening, coupled with biochemical and biophysical analyses, were implemented to identify, characterize, and validate potential inhibitors targeting AsfvPolX. The constructed pharmacophore model, Phar-PolX-S, demonstrated efficacy in identifying a potent inhibitor, D-132 (IC50 = 2.8 ± 0.2 µM), disrupting the formation of the AsfvPolX-DNA complex. Notably, D-132 exhibited strong binding to AsfvPolX (KD = 6.9 ± 2.2 µM) through a slow-on-fast-off binding mechanism. Employing molecular modeling, it was elucidated that D-132 predominantly binds in-between the palm and finger domains of AsfvPolX, with crucial residues (R42, N48, Q98, E100, F102, and F116) identified as hotspots for structure-based inhibitor optimization. Distinctively characterized by a 1,2,5,6-tetrathiocane with modifications at the 3 and 8 positions involving ethanesulfonates, D-132 holds considerable promise as a lead compound for the development of innovative agents to combat ASFV infections.

Dissecting gene expression networks in the developing hippocampus through the lens of NEIL3 depletion

Gene regulation in the hippocampus is fundamental for its development, synaptic plasticity, memory formation, and adaptability. Comparisons of gene expression among different developmental stages, distinct cell types, and specific experimental conditions have identified differentially expressed genes contributing to the organization and functionality of hippocampal circuits. The NEIL3 DNA glycosylase, one of the DNA repair enzymes, plays an important role in hippocampal maturation and neuron functionality by shaping transcription. While differential gene expression (DGE) analysis has identified key genes involved, broader gene expression patterns crucial for high-order hippocampal functions remain uncharted. By utilizing the weighted gene co-expression network analysis (WGCNA), we mapped gene expression networks in immature (p8-neonatal) and mature (3 m-adult) hippocampal circuits in wild-type and NEIL3-deficient mice. Our study unveiled intricate gene network structures underlying hippocampal maturation, delineated modules of co-expressed genes, and pinpointed highly interconnected hub genes specific to the maturity of hippocampal subregions. We investigated variations within distinct gene network modules following NEIL3 depletion, uncovering NEIL3-targeted hub genes that influence module connectivity and specificity. By integrating WGCNA with DGE, we delve deeper into the NEIL3-dependent molecular intricacies of hippocampal maturation. This study provides a comprehensive systems-level analysis for assessing the potential correlation between gene connectivity and functional connectivity within the hippocampal network, thus shaping hippocampal function throughout development.

Abstract 7131: Base excision repair regulation of replication stress induced poly(ADP-ribose) checkpoints

Abstract PARP-inhibitors (PARPi) have been developed to treat homology-directed repair deficient cancers such as BRCA1/2-defective breast and ovarian tumors. However, acquired resistance to PARPi is now common, suggesting the need to identify new protein targets. To that end, a missed opportunity is found in the PARP1/PARP2 activation mechanism in response to DNA damage and replication stress and the resulting protein complexes and enzymes that depend on and coordinate PARP-mediated DNA repair processes. We have found that PARP1/PARP2 activation, whether from acute DNA damage, from replication stress or both triggers a temporal and coordinated interplay of base excision repair and single-strand break repair (BER/SSBR) proteins and enzymes. In turn, the recruitment of these BER and SSBR proteins suppresses PARP1/PARP2 activation, thereby functioning as a network of PARP1/PARP2 regulators, modulating the PARP-mediated response to replication stress. To that end, we find that loss of expression of these key BER/SSBR proteins releases a break on replication-stress induced PARP1/PARP2 activation, triggering un-restrained PARP1/PARP2 activation and elevated levels of replication-dependent poly(ADP-ribose) (PAR). We next confirmed that the loss of these downstream BER enzymes render cancer cells responsive to PARPi’s when the BRCA1/2 pathways are restored. Further, we show that BER expression regulates the cellular response to inhibitors of the PAR degrading enzyme PARG, suggesting that XRCC1-dependent BER proteins regulate replication-stress dependent PAR accumulation. The increase in PAR due to PARG inhibition, that is further regulated by BER, drives a strong intra-S phase response, indicated by activation of ATR and CHK1 signaling. As the checkpoint governed by ATR and CHK1 functions as a protective mechanism, we show that PARG inhibition is synthetically lethal with ATR and CHK1 inhibition and this may be explained by our demonstration of PARGi-mediated trapping of essential BER proteins at the site of damage and PAR accumulation. Together, these studies reveal a significant role for BER/SSBR proteins in regulating replication stress induced PARylation and the resulting intra-S phase checkpoint. Citation Format: Md Ibrahim, Md Maruf Khan, Rasha Q. Al-Rahaleh, Jennifer Clark, Faisal Hayat, Qingming Fang, Christopher A. Koczor, Marie E. Migaud, Robert W. Sobol. Base excision repair regulation of replication stress induced poly(ADP-ribose) checkpoints [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7131.

Abstract 3113: Development of HTS enzymatic assays for WRN helicase and exonuclease functions

Abstract WRN, a double strand break repair enzyme with ATP-dependent DNA-helicase and 3’- >5’ exonuclease activities, is under intense focus as a therapeutic target because of its synthetic lethality in tumors with microsatellite instability. To accelerate discovery of WRN inhibitors, we developed and validated homogenous, fluorescence-based high throughput assays for WRN helicase and exonuclease enzymatic activities using the Transcreener HTS Assay platform, which relies on highly selective antibodies to detect nucleotides in a homogenous (mix-and-read) format with far red fluorescent readouts. We produced the WRN helicase domain (aa 500-946, N-terminal 6xHis) in BaV-infected insect cells and optimized detection of its dsDNA-dependent ATPase activity using the Transcreener ADP2 Assay in FP, TR-FRET, and FI detection modes. Optimal reaction conditions included 50 μM ATP (approximate Km) and saturating concentration (100 nM) of a 3’ flapped duplex DNA oligomer; these conditions yielded a good signal with 250 pM WRN, a kcat of 300 min−1, and a Z’ of 0.85. An IC50 of 35 nM was determined for the probe inhibitor NSC-617145, and a 1,280 compound pilot screen (Tocris 2.0 Micro) identified multiple hits that were confirmed in dose response experiments. We produced the WRN 3’-5’ exonuclease domain (aa 1-133-6xHis) in E. coli and used the Transcreener dAMP Exonuclease Assay to allow direct, FP-based detection of dAMP monomers released from a 52 bp dsDNA oligomer with a 5’ overhang. With saturating DNA present (1 μM), the assay produced a good signal with 1 nM enzyme; the Z’ value was 0.89. There are no published inhibitors for the WRN exonuclease, but suramin inhibited with an IC50 of approximately 100 nM. These assays allow sensitive, robust, quantitative detection of WRN ATPase and exonuclease activities using an extensively validated HTS platform; they should be valuable tools for screening and optimizing small molecules targeting specific WRN functions. Citation Format: Ha Pham, Mahbbat Ali, Anibal Ramos Martinez, Robert Lowery. Development of HTS enzymatic assays for WRN helicase and exonuclease functions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3113.

Abstract 3854: Revealing mismatch repair deficiency in Egyptian colorectal cancer patients using next generation sequencing a predictive biomarker for immunotherapy efficacy

Abstract Background: The mismatch repair (MMR) deficiency is a potential predictive biomarker for immunotherapy efficacy, particularly in colorectal cancer (CRC), where alterations in various DNA polymerases and MMR genes are prevalent. The accumulation of these genetic aberrations may cause a subsequent neoantigen formation. study aimed to identify the mutational profile of DNA polymerases and MMR genes in Egyptian CRC patients', providing insights into colorectal carcinogenesis and potential implications for immunotherapy. Material and Methods: Thirty-nine blood samples from Egyptian patients with CRC and twenty-four blood samples from healthy controls were collected. The libraries were prepared by Qiaseq UMI-based targeted panel and sequenced via an Ion proton sequencer. The detected genetic variants with an average coverage of 500x were annotated against Cosmic, dbSNP, and ClinVar databases using Ingenuity Variant analysis (IVA). Results: Our results revealed that the POLD1andPOLE genes (DNA polymerases) in the CRC patients, when compared with healthy controls, harbored 10 and 13 pathogenic variants (PVs), respectively. These PVs cause a loss of their functionality. The most frequently detected PVs and likely to be novel in the POLD1gene werec.44delC(31%)andc.3008delG(31%), while c.3510delA(18%)andc.2793delT(15%) were detected in the POLE gene. As per MMR genes, our study showed that the MLH1, MLH3, MSH2, MSH3, MSH6, PMS1,and PMS2 harbored 8, 13, 23, 19, 22, 23, and 7 PVs, respectively. The highly frequent PV in the MLH1wasc.469delT (26%), while the novel most frequently detected PV in the MLH3 wasc.1467delA (23%). Moreover, the PVs found highly frequent are c.2647delA (36%) in MSH2,c.1148delA (41%)in the MSH3, and c.2079delA (44%) in the MSH6. RegardingPMS1/2, the most frequently detected PV and likely to be novel was c.1647delA (44%) in PMS1, while c.869delT (13%) was the most prevalent PV in PMS2. Conclusion: Our results revealed the MMR mechanism deficiency in Egyptian CRC patients offering crucial insights into colorectal carcinogenesis and neoantigen formation. These insights are pivotal for developing ethnic-based personalized immunotherapy strategies in Egyptian CRC patients, shedding light on their role in CRC. Interestingly, we have identified novel variants in the DNA repair enzymes. However, further investigations and validations are required to corroborate these findings and explore their clinical significance in the personalized medicine. Citation Format: Amira Salah El-Din Youssef, Mohamed Ragab, Heba Aly Ateya, Mostafa Elberry, Nasra Fathy, Asmaa Elleithy, Abdel Rahman Zekri, Ola Sayed Ahmed, Auhood Nassar. Revealing mismatch repair deficiency in Egyptian colorectal cancer patients using next generation sequencing a predictive biomarker for immunotherapy efficacy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3854.

Abstract 992: The impact of tamoxifen on autophagic and epigenetic regulation in endometrial cancer

Abstract Background: Endometrial cancer, predominantly endometrioid adenocarcinoma, ranks as the fourth most common cancer in women globally, with an increasing incidence over the last two decades. Tamoxifen, well-known for its antiestrogenic characteristics in the treatment of breast cancer, paradoxically increases the risk of endometrial cancer. Understanding this dual role of tamoxifen is crucial for optimizing breast cancer therapy while mitigating endometrial cancer risk. This study aims to elucidate the molecular alterations induced by tamoxifen in endometrial thickening and its potential to induce cancer, particularly focusing on autophagy, epithelial-mesenchymal transition (EMT), and cancer stem-like cells (CSCs). Methods: In this study, female BALB/c mice were administered tamoxifen (20 mg/ml) orally for five consecutive days. We monitored changes in EMT markers, autophagy-related genes, and stem cell markers over 1 to 5 months. Furthermore, we investigated the epigenetic modulation of key genes involved in these processes. Results: Tamoxifen treatment led to altered expression of both epithelial and mesenchymal EMT markers, autophagy-related genes (p62, LC3B, Beclin-1, mTOR, ATG12, ATG16), and stem cell markers (Nanog, SOX2, ALDH1). Notably, we observed significant epigenetic changes, including increased methylation of E-cadherin and decreased methylation of Twist. Furthermore, we observed hypermethylation (a process often linked to the silencing of tumor-suppressing genes) in MGMT (Methylguanine methyltransferase), a DNA repair enzyme involved in chemoresistance, and DAPK (Death-associated protein kinase), a kinase associated with apoptosis, autophagy, and inflammation. We also observed hypermethylation in the CpG promoter regions of autophagy-related genes (Beclin-1 and LC3B) highlighting a potential mechanism for tamoxifen-induced tumorigenic changes. Conclusion: Our findings demonstrate tamoxifen's influence on cellular and molecular pathways, highlighting the complex interplay between drug treatment and cancer progression. The observed epigenetic changes provide insight into the mechanisms by which tamoxifen may contribute to endometrial cancer risk, suggesting potential targets for therapeutic intervention. Citation Format: Shilpa Thota, Rizwana Begum, Naveen Chintala, Abhishek Pandit, Biplov Sapkota, Joseph Francis. The impact of tamoxifen on autophagic and epigenetic regulation in endometrial cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 992.

Abstract 7595: PRMT5 inhibitor synergizes with PARP inhibitors in triple-negative breast cancer cells

Abstract Background: Treating triple-negative breast cancer (TNBC) patients, an aggressive subtype of breast cancer, is an ongoing clinical challenge. Small-molecule inhibitors targeting the poly ADP-ribose polymerase (PARP) DNA repair enzymes, have been approved for treating only a subset of TNBC patients with a specific genetic landscape (BRCA1 mutation). However, TNBC patients with wildtype BRCA1 (BRCA1WT) are still lacking targeted therapy and chemotherapy remains their main treatment strategy. High expression of protein arginine methyltransferase 5 (PRMT5) is linked to poor prognosis in breast cancer and PRMT5 alone or via its interacting proteins plays an oncogenic role in breast cancer. Recent evidence suggests that PRMT5 is a key player in regulating the repair of DNA double strand breaks (DSBs) either through homologous recombination (HR) or non-homologous end joining (NHEJ) depending on the PRMT5 expression level within the cell. This dependency of cancer cells on PRMT5 expression levels in deciding the repair pathway of choice can be exploited for developing therapies. We hypothesize that in BRCA1 wildtype TNBC cells, inhibiting PRMT5 activity will force the cells to rely on NHEJ rather than HR to repair DNA DSBs, and introducing PARP inhibitors in this setting will inactivate NHEJ as well, causing synthetic lethality and cell death. In this study, we evaluated the pre-clinical benefit of combining PARP inhibitors with a PRMT5 inhibitor in TNBC cells. Methods: Human TNBC cell lines with wildtype BRCA1 (MDA-MB-468, HCC1806) and mutant BRCA1 (MDA-MB-436, SUM149-PT) were treated with varying doses of two PARP inhibitors (Olaparib, Talazoparib) and a PRMT5 inhibitor (GSK3326595) as single agents or in combination. MTT-based cell viability assay was used to determine cytotoxicity of the treatments. mRNA expression was determined by RT-qPCR after drug treatment. Results and Conclusion: We report that PRMT5 inhibition synergizes with both Olaparib and Talazoparib, to potentiate cell death in two BRCA1WT but not in BRCA1mut TNBC cell lines. Furthermore, we show that inhibiting PRMT5 in BRCA1WT cells upregulates the mRNA expression of RAD50, a DNA damage sensing gene in the HR pathway. Our ongoing study is to delineate the molecular mechanism of action for the observed synergy and whether PRMT5 inhibition can overcome resistance to PARP inhibitors. Through this study, we will identify a novel treatment strategy for the majority of TNBC patients (BRCA1WT) who currently lack targeted therapies. Citation Format: Samyuktha Suresh, Lisa A. McPherson, James M. Ford. PRMT5 inhibitor synergizes with PARP inhibitors in triple-negative breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7595.

Abstract 3757: The development of MAGMAS as a potential therapeutic target in temozolomide-resistant glioma

Abstract Glioblastoma (GBM) is one of the most aggressive types of brain cancer and remains a significant challenge for drug development in oncology today. Temozolomide (TMZ) is the standard of care for GBM, and resistance to this drug is modulated partly by the DNA repair enzyme O6-methylguanine-DNA methyltransferase (MGMT). Clinical studies demonstrated that low MGMT expression in GBM enhances sensitivity to TMZ and prolongs survival for patients. However, recent clinical studies indicate MGMT is a discordant biomarker since the predictive value of MGMT methylation is relatively low and there is a lack of modalities to inhibit MGMT expression. Furthermore, glioma stem cells (GSC) are another contributing factor for resistance due to tumor heterogeneity, self-renewal capacity and activation of DNA repair responses to overcome the effect of radiation and TMZ treatment. These resistance mechanisms contribute to tumor recurrence and present major impediments for the development of effective treatments. MAGMAS, 13.8 kDa mitochondria protein, is a translocase of the inner mitochondrial membrane and regulates oxidative phosphorylation. Specifically, MAGMAS regulates the ATP stimulatory activity of DNAJC19 on mtHSP70 that drives the movement of peptides through the TIM23 complex into the mitochondrial matrix. Recent evidence suggests that MAGMAS can regulate oxidative phosphorylation via interactions with the respiratory complexes present in the inner mitochondrial membrane. Previously, our lab has shown MAGMAS overexpression in malignant glioma tissues of patients and murine intracranial xenografts. Additionally, pharmacological inhibition of MAGMAS with the small molecule BT9 promoted cytotoxicity and impaired respiratory functions in malignant glioma cells demonstrating that MAGMAS is a promising potential target for GBM patients. However, further studies are needed to investigate the role of MAGMAS across the spectrum from initial tumorigenesis to disease progression and to further determine how MAGMAS is implicated during the development of treatment resistance. This study is designed to investigate the role of MAGMAS in GSCs and their contribution to TMZ resistance. We observed temozolomide-resistant (TR) U251-TR and D54 MG-TR GBM cell lines expressed significantly higher levels of MAGMAS and several stem cell markers than their drug-sensitive (S) parental cell lines. Therefore, we hypothesized that silencing MAGMAS re-sensitizes TR GBM cell lines to TMZ. We found that MAGMAS knockdown in D54-MG and U251 S/TR cells in the presence of escalating TMZ concentrations, caused enhanced sensitivity to TMZ. Consistent with these results, inhibition of MAGMAS with the novel BT9 inhibitor enhances the TMZ sensitivity in the TMZ-resistant cell lines. Additional studies of patient-derived cell lines are being utilized further to validate MAGMAS as it is an attractive target in TMZ-resistant GBM patients. Citation Format: Jennifer D. Tran, Javier J. Lepe, Maria C. Kenney, Bhaskar C. Das, Daniela A. Bota. The development of MAGMAS as a potential therapeutic target in temozolomide-resistant glioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3757.

Abstract 960: Improved cfDNA methylation profiling through correction of misrepaired jagged-ends

Abstract Background: Profiling cfDNA methylation enables early cancer detection and classification, but challenges arise from "jagged ends" (JEs) for ~90% of cfDNA molecules, as well as for FFPE samples and partially degraded genomic DNA. Repair of these jagged ends introduces erroneous methylation signals, especially in shorter cfDNA fragments enriched for tumor derived molecules. Separately, DNA conversions during 5mC profiling hamper accurate simultaneous ctDNA genotyping of somatic mutations. To meet these needs, we developed a method preserving double-stranded cfDNA molecules without error-prone end-repair at jagged ends. This enables superior methylation profiling including hemimethylation detection, and simultaneous ctDNA SNV genotyping. Methods: We present JEEPERS (Jagged-End Error Polishing of Enzymatically misRepaired Sequences), a novel method for correcting errors in double-stranded library preparation for methylation profiling. JEEPERS detects and quantifies enzymatic repair errors at JEs, correcting them in silico. Leveraging duplex UMIs, it utilizes complementary strands and sibling reads from cfDNA families without jagged ends. The method exploits the 5' to 3' polarity of ER-associated errors and JE length profiles for correction. JEEPERS introduces anchor CpGs for precise correction of rare signals and enables accurate SNV calling at non CpG sites, addressing the challenge of differentiating true SNVs from conversion artifacts leading to C>T/G>A changes in sequencing data. Results: Analyzing 248 cfDNA samples (139 NSCLC patients, 109 healthy controls) by methylation profiling (EM-Seq) and ctDNA mutation genotyping (CAPP-Seq), JEEPERS correction efficiently addressed distortions, even at low tumor concentrations. Limiting dilution experiments demonstrated JEEPERS achieving a LOD95 of ~0.2% with 95% specificity (n=300). Despite ~50% lower molecular depth, JEEPERS-corrected cfDNA EM-Seq enabled accurate simultaneous methylation profiling and ctDNA genotyping, correlating strongly with CAPP-Seq genotypes (R=0.998, n=30). As expected, mutant ctDNA molecules were shorter than wild-type in both CAPP-Seq and EM-Seq data. cfDNA methylation patterns varied by oncogene vs. tumor suppressor status; EGFR mutants showed increased methylation (p<0.01), while TP53 mutants had lower methylation levels (p<0.05). Conclusions: Our method effectively corrects cfDNA methylation data, even at low tumor concentration, ensuring enhanced methylation signal accuracy and proficient SNV calling capabilities. This integrated approach offers a powerful means for investigating the link between SNVs and DNA methylation, significantly enhancing the accuracy of cancer detection using cfDNA, especially for early-stage tumors. This paves the way for a deeper understanding of the molecular mechanisms driving cancer initiation and progression. Citation Format: Rui Wang, Emily G. Hamilton, Diego Almanza, Angela Hui, Maximilian Diehn, Ash A. Alizadeh. Improved cfDNA methylation profiling through correction of misrepaired jagged-ends [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 960.

Genomic Diversity in the Endosymbiotic Bacteria of Human Head Lice.

Insects have repeatedly forged symbioses with heritable microbes, gaining novel traits. For the microbe, the transition to symbioses can lead to the degeneration of the symbiont's genome through transmission bottlenecks, isolation, and the loss of DNA repair enzymes. However, some insect-microbial symbioses have persisted for millions of years, suggesting that natural selection slows genetic drift and maintains functional consistency between symbiont populations. By sampling in multiple countries, we examine genomic diversity within a symbiont species, a heritable symbiotic bacterium found only in human head lice. We find that human head louse symbionts contain genetic diversity that appears to have arisen contemporaneously with the appearance of anatomically modern humans within Africa and/or during the colonization of Eurasia by humans. We predict that the observed genetic diversity underlies functional differences in extant symbiont lineages, through the inactivation of genes involved in symbiont membrane construction. Furthermore, we find evidence of additional gene losses prior to the appearance of modern humans, also impacting the symbiont membrane. From this, we conclude that symbiont genome degeneration is proceeding, via gene inactivation and subsequent loss, in human head louse symbionts, while genomic diversity is maintained. Collectively, our results provide a look into the genomic diversity within a single symbiont species and highlight the shared evolutionary history of humans, lice, and bacteria.

Imaging multiple DNA repair enzymes in living cells based on framework nucleic acid fluorescence nanoprobe

DNA repair enzymes play pivotal roles in DNA damage repair. Imaging multiple DNA repair enzymes in living cells is significant for DNA damage repair-related biological study and disease diagnosis. Here, we constructed a framework nucleic acids (FNAs) fluorescent nanoprobe for imaging multiple DNA repair enzymes in living cells. Uracil DNA glycosylase (UDG) and human apurinic/apyrimidinic endonuclease 1 (APE1) were used as the target analytes. Two double-stranded DNA probes (dsDNA1 and dsDNA2) were designed. dsDNA1 contained four uracil (U) bases for UDG recognition and was labeled with black hole quencher2 (BHQ2) /cyanine5 (Cy5). dsDNA2 contained one apurinic/apyrimidinic (AP) site for APE1 recognition and was labeled with black hole quencher1 (BHQ1) /fluorophore carboxyfluorescein (FAM). To obtain the FNAs fluorescent nanoprobe, dsDNA1 and dsDNA2 were attached to two vertices of a DNA tetrahedron (a type of FNAs). Under the action of UDG and APE1, dsDNA1 and dsDNA2 were both dissociated, generating fluorescence of Cy5 and FAM. Among them, Cy5 indicated the activity of UDG and FAM indicated the activity of APE1. This method had good sensitivity to UDG and APE1, and the detection limits were 0.0012 U/mL and 0.057 U/mL, respectively. This method also exhibited high selectivity for UDG and APE1. When the FNAs fluorescent nanoprobe was endocytosed, it had little toxicity to normal and cancer cells. Furthermore, this method successfully achieved multiple imaging UDG and APE1 in cancer cells. This study provides a novel strategy for imaging multiple DNA repair enzymes and holds great potential in biological applications and clinical diagnosis.

Understanding the unique mechanism of ferroptosis: a promising therapeutic target.

Ferroptosis is an iron-dependent form of regulated cell death and is characterized by high concentrations of intracellular lipid peroxide and a redox imbalance in the cells. Ferroptosis shows distinct morphological and biological features compared with other prominent mechanisms of programmed cell death. The distinct characteristics of ferroptosis include the dysfunction of the lipid peroxide repair enzyme glutathione peroxidase 4, the presence of ferrous iron overload, and the lipid peroxidation of polyunsaturated fatty acids. Several other metabolic pathways (including iron, lipid, and amino acid metabolism) and ferritinophagy, as well as transcription factors, can modulate ferroptosis. However, to date, the molecular mechanism of ferroptosis has not been elucidated. This review outlines the discovery, characterization, regulatory mechanisms, and crosstalk of ferroptosis. Further, we have noted the controversial elements in the ferroptosis-related mechanisms. Our inferences may provide a partial reference for developing strategies to regulate ferroptosis.