BRCA1 Mutant Cells Research Articles

Single-Stranded DNA Gap Accumulation Is a Functional Biomarker for USP1 Inhibitor Sensitivity.

Recent studies suggest that PARP and POLQ inhibitors confer synthetic lethality in BRCA1-deficient tumors by accumulation of single-stranded DNA (ssDNA) gaps at replication forks. Loss of USP1, a deubiquitinating enzyme, is also synthetically lethal with BRCA1 deficiency, and USP1 inhibitors are now undergoing clinical development for these cancers. Herein, we show that USP1 inhibitors also promote the accumulation of ssDNA gaps during replication in BRCA1-deficient cells, and this phenotype correlates with drug sensitivity. USP1 inhibition increased monoubiquitinated proliferating cell nuclear antigen at replication forks, mediated by the ubiquitin ligase RAD18, and knockdown of RAD18 caused USP1 inhibitor resistance and suppression of ssDNA gaps. USP1 inhibition overcame PARP inhibitor resistance in a BRCA1-mutated xenograft model and induced ssDNA gaps. Furthermore, USP1 inhibition was synergistic with PARP and POLQ inhibition in BRCA1-mutant cells, with enhanced ssDNA gap accumulation. Finally, in patient-derived ovarian tumor organoids, sensitivity to USP1 inhibition alone or in combination correlated with the accumulation of ssDNA gaps. Assessment of ssDNA gaps in ovarian tumor organoids represents a rapid approach for predicting response to USP1 inhibition in ongoing clinical trials. Significance: USP1 inhibitors kill BRCA1-deficient cells and cause ssDNA gap accumulation, supporting the potential of using ssDNA gap detection as a functional biomarker for clinical trials on USP1 inhibitors.

Abstract IA009: Single strand DNA GAP accumulation as a functional biomarker for DNA Repair Inhibitors

Abstract Deficiency of homologous recombination (HR)-mediated DNA repair occurs through genetic or epigenetic inactivation of the BRCA1 and BRCA2 (BRCA1/2) genes. HR-deficiency also provides unique opportunities for targeted therapy, through the mechanism of synthetic lethality, as exemplified by the hypersensitivity of BRCA1/2-mutated tumors to PARP inhibitors (PARPi). To date, several PARP inhibitors have been approved for clinical use. The promising clinical response of patients with germline BRCA1/2-mutations prompted the use of PARPi for patients with somatic BRCA1/2 mutations as well. In addition, these results extended the use of PARPi for various types of ovarian, breast, pancreatic, and prostate tumors with HR defects. PARPi resistance is emerging as the major obstacle to clinical effectiveness in patients with HR-deficient tumors. PARPi resistance results from several independent mechanisms, leading to the restoration of Homologous Recombination and/or Replication Fork stabilization. The absence of alternative options for patients with tumors with innate or acquired resistance underlines the urgency to develop additional therapeutics. More recent studies have identified new synthetic lethal opportunities for BRCA1/2 deficient tumors. Knockout of the genes for POLQ (DNA polymerase theta) or for USP1 (Ubiquitin Specific Protease 1) results in killing of these tumors, and inhibitors of these enzymes are emerging as promising agents for HR-deficient tumors. POLQ and USP1 expression is particularly high in subtypes of breast and ovarian tumors with defects in HR. As a result, POLQi or USP1i in HR-deficient tumors induces cell death. POLQi or USP1i can synergize with PARPi in killing HR-deficient tumors or PARPi-resistant tumors. BRCA1/2 deficient tumors have an increase in single strand DNA gaps (ssGAPs) near replication forks. Treatment with PARPi results in an increase in the size and number for these ssGAPs, ultimately leading to DSBs and cell death. Interestingly, PARPi resistance results, at least in part, from the ability of resistant cells to close the ssGAPs through enhanced POLQ and USP1 activity, thereby providing a rationale for the combination of PARP1, POLQi, and USP1 in HR-deficient cancers. USP1 inhibition was synergistic with PARP and POLQ inhibition in BRCA1-mutant cells, with enhanced ssDNA gap accumulation. Moreover, this synergy was observed in a set of patient-derived ovarian cancer organoids (PDOs), thus confirming the sensitivity of BRCA1-deficient cells to inhibition by these agents. The accumulation of ssDNA gaps after treatment with a USP1i, PARP, or POLQi correlated with the sensitivity to these drugs in all models tested. Ovarian cancer PDOs provide a powerful tool for detecting drug synergy and for rapid in vitro sensitivity testing. The detection of ssDNA gap accumulation may be a useful predictive biomarker for response to DNA Repair inhibitors as monotherapy or in combination in ongoing clinical trials. Citation Format: Alan D. D'Andrea. Single strand DNA GAP accumulation as a functional biomarker for DNA Repair Inhibitors [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr IA009.

Examination of in vitro and in vivo antitumor activity of PARP1 selective inhibitor D0112-005.

e15115 Background: The approved PARP inhibitors have demonstrated efficacy in ovarian, breast, prostate, and pancreatic cancers, particularly in homologous recombination repair (HRR)-deficient tumors, including BRCA mutant tumors. The severe hematological toxicity of first-generation PARPi in combination with chemotherapy is due to the lack of selectivity for PARP2. So, we developed selective PARP1 inhibitor D0112-005 with the aim to improve safety and efficacy. Methods: The selectivity of D0112-005 on PARP1, PARP2 was measured by chemiluminescent assay kit and PARP trap™ assay kit. The anti-proliferative ability of D0112-005 was evaluated by CCK-8 in BRCA mutant cell lines. In vivo anti-tumor effect of D0112-005 was evaluated in MDA-MB-436 BRCA1 mutant xenograft model. The potential for hematologic toxicity was evaluated in rats for 28 days repeat-dose and dogs for 14 days repeat-dose. Results: D0112-005 is a highly potent and selective inhibitor of PARP1 with 2000-fold selectivity for PARP1 over PARP2 and PARP3. D0112-005 trapped PARP1-DNA with an EC50 value of 6.49 nM. In contrast, the EC50 of PARP2-DNA trapping was 430μM. These data demonstrate that D0112-005 is a potent and selective PARP1 trapper. D0112-005 showed high anti-proliferation activity against BRCA mutant MDA-MB-436 and HCC1395 cell lines, with IC50 values of 2.06 nM and 2.446 nM, respectively. In the MDA-MB-436 BRCA1m xenograft model, a dose-dependent anti-tumor effect was observed after 21 days administration, with TGIs of 38.77%, 106.7% and 111.73% at the dose of 0.1, 0.3 or 1 mg/kg once daily by oral, respectively. In the 1 mg/kg group, the anti-tumor efficacy was maintained after 14 days of drug withdrawal. D0112-005 showed well tolerance without bodyweight loss. In rat 28 days repeat dose study, D0112-005 100mg/kg had less changes on hematologic parameters compared with Olaparib. The main toxic reaction of D0112-005 (10mg/kg) was reversible thrombocytopenia in dog 14 days repeated toxicity study. Conclusions: D0112-005 potently and selectively inhibits PARP1 resulting in excellent anti-tumor activity in vivo and in vitro, which also good safety profile in the repeated toxicity study in rats and dogs.

Abstract PO3-13-07: MUC1-C INTEGRATES CHRONIC ACTIVATION OF INTERFERON PATHWAYS WITH CHROMATIN REMODELING IN TREATMENT RESISTANCE OF TRIPLE-NEGATIVE BREAST CANCER

Abstract Chronic inflammation is intimately linked to cancer progression and resistance to treatment. Triple-negative breast cancer (TNBC) is a recalcitrant malignancy largely unresponsive to cytotoxic, targeted and immunotherapeutic agents. The Mucin1 (MUC1) transmembrane heterodimeric protein, which is aberrantly expressed in TNBCs, evolved in mammals to provide protection of epithelia from the external environment. With loss of homeostasis, the (i) MUC1 N-terminal (MUC1-N) subunit is shed and released into serum as detected by the CA15-3 assay, and (ii) MUC1 C-terminal (MUC1-C) subunit is activated and thereby induces inflammatory, proliferative and remodeling signaling pathways associated with wound healing. However, prolonged MUC1-C activation in settings of chronic inflammation promotes cancer progression and treatment resistance. The SWI/SNF PBAF chromatin remodeling complex includes the polybromo-1 (PBRM1) subunit and drives DNA damage resistance and immune evasion in certain cancer cells through mechanisms that remain unclear. Recent studies in TNBCs have demonstrated that MUC1-C drives intrinsic activation of type II interferon (IFN) pathway that is linked to chronic inflammation and immune evasion. In extending this work, we have found that MUC1-C activates the type I IFN pathway, which contributes to genomic instability and DNA damage tolerance in TNBC cells. Importantly, our results further demonstrate that MUC1-C interacts with interferon regulatory factor 1 (IRF1) as a key regulatory node in integrating activation of the type I and II IFN pathways. Here, we report that MUC1-C is necessary for PBRM1 expression and that it forms a nuclear complex with PBRM1 in TNBC cells. Analysis of global transcriptional (RNA-seq) and chromatin accessibility (ATAC-seq) profiles further demonstrated that MUC1-C and PBRM1 drive STAT1 and IRF1 expression by increasing chromatin accessibility of promoter-like signatures (PLS) on their respective genes. We also found that MUC1-C, PBRM1, and IRF1 increase the expression and chromatin accessibility on PLSs of the (i) type II IFN pathway IDO1 and WARS genes and (ii) type I IFN pathway RIG-I, MDA5, cGAS, STING and ISG15 genes that collectively contribute to DNA damage resistance and immune evasion. In support of these results, targeting MUC1-C in wild-type BRCA1/2 TNBC cells enhanced carboplatin-induced DNA damage and loss of self- renewal capacity. In addition, MUC1-C was necessary for DNA damage resistance, self-renewal and tumorigenicity of olaparib-resistant BRCA1-mutant TNBC cells. Analysis of TNBC clinical samples corroborated that (i) MUC1 and PBRM1 are associated with decreased responsiveness to chemotherapy and (ii) MUC1-C expression is associated with the depletion of tumor-infiltrating lymphocytes. These findings demonstrate that MUC1-C activates PBRM1, and thereby chromatin remodeling of IFN-stimulated genes that promote chronic inflammation, DNA damage resistance, and immune evasion. These findings have identified MUC1-C as a potential target for the treatment of TNBC that have limited therapeutic options. To that end, the generation of MAb 3D1 against the MUC1-C extracellular domain provided an opportunity for the development of agents that target MUC1-C on the cancer cell surface. As one example, an allogeneic anti-MUC1-C CAR T cell using MAb 3D1 sequences is undergoing Phase I evaluation for the treatment of MUC1-C-expressing cancers (NCT05239143: P-MUC1C-ALLO1 Allogeneic CAR-T Cells in the Treatment of Subjects with Advanced or Metastatic Solid Tumors). In addition, anti-MUC1-C huMAb3D1-MMAE ADCs are under development by the NCI NExT Program for IND-enabling studies and performing early phase clinical trials in patients with TNBC. Citation Format: Nami Yamashita, Yoshihiro Morimoto, Atsushi Fushimi, Rehan Ahmad, Atrayee Bhattacharya, Yuka Inoue, Henry Withers, Geoffrey Shapiro, Tomoharu Yoshizumi, Takayuki Ueno, Shinji Ohno, Mark Long, Donald Kufe. MUC1-C INTEGRATES CHRONIC ACTIVATION OF INTERFERON PATHWAYS WITH CHROMATIN REMODELING IN TREATMENT RESISTANCE OF TRIPLE-NEGATIVE BREAST CANCER [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-13-07.

Abstract LB181: First disclosure of XRD-0394, a novel dual ATM/DNA-PK inhibitor, that potently radiosensitizes and potentiates PARP and topoisomerase inhibitors

Abstract A majority of cancer patients receive radiation therapy (RT) as part of their treatment regimens, whether using external beam therapy or locally-delivered radioisotopes. While often effective, RT may not be efficacious for some tumors while exerting significant short-term and long-term toxicities. Thus, enhancing therapeutic effectiveness of radiation therapy remains an important goal. ATM (ataxia-telangiectasia, mutated) and DNA-PKcs (deoxyribonucleic acid [DNA]-dependent protein kinase, catalytic subunit) are related protein kinases and both are critical regulators of cellular responses to ionizing radiation. We report here the identification and initial characterization of XRD-0394, a potent, specific dual inhibitor of both ATM and DNA-PKcs, whose chemical structure will be disclosed. A dual ATM/DNA-PK inhibitor has practical and theoretical advantages over compounds which inhibit just one of these kinases: 1) blunting both DNA damage response (DDR) pathways enhances radiation-induced tumor cell kill compared to single target inhibition; and 2) simultaneous inhibition of two DDR pathways should overcome intrinsic or acquired resistance of tumor cells to either target alone. Notably, transient inhibition of both kinases by XRD-0394 has little adverse effects on cells in the absence of irradiation. XRD-0394 is orally bioavailable, with excellent pharmacological profiles, demonstrating significant in vitro and in vivo sensitizing activity in combination with ionizing radiation and in combination with immunotherapy and radiation. In addition, a CRISPR screen identified alterations in the Fanconi A/BRCA pathway as an opportunity for synthetic lethality in tumor cells exposed to XRD-0394, an insight that was validated in multiple tumor cell types. In vitro studies demonstrated synergy of XRD-0394 in combination with PARP inhibitors, particularly in BRCA-mutant cells. XRD-0394 also potentiates the effectiveness of topoisomerase inhibitors in vitro. Single doses of XRD-0394 were well-tolerated in combination with palliative RT in subjects with advanced cancer in a Phase Ia clinical trial (NCT05002140). No DLTs were observed. At a dose of 160 mg, plasma concentrations were well above the preclinical target plasma level of 530 ng/mL (1 µM) for up to 15 h and inhibition of ATM kinase activity was demonstrated by inhibition of radiation-induced pKAP1 in tumor tissue. Importantly, this concentration of drug is sufficient to induce potent radiosensitization in numerous preclinical models. The median tmax (2.3 h) and mean terminal t½ (11.1 h) at the 160 mg dose in subjects support coadministration of XRD-0394 and RT within a clinically feasible time frame. These results provide a rationale for future clinical trials with XRD-0394 in combination with RT, RT and immunotherapy, PARP inhibitors and targeted delivery of topoisomerase inhibitors. Citation Format: Tona M. Gilmer, Chun-Hsiang Lai, Kexiao Guo, Katherine Deland, Kathleen A. Ashcraft, Amy E. Stewart, Yaode Wang, Jianmin Fu, Kris C. Wood, Deborah A. Smith, Jonathan T. Yang, Christopher T. Chen, Michael F. Gensheimer, Paul B. Romesser, Steven H. Lin, David G. Kirsch, Michael B. Kastan. First disclosure of XRD-0394, a novel dual ATM/DNA-PK inhibitor, that potently radiosensitizes and potentiates PARP and topoisomerase inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB181.

A Novel Inhibitor of Poly(ADP-Ribose) Polymerase-1 Inhibits Proliferation of a BRCA-Deficient Breast Cancer Cell Line via the DNA Damage-Activated cGAS-STING Pathway.

Loss-of-function mutations in the Breast Cancer Susceptibility Gene (BRCA1 and BRCA2) are often detected in patients with breast cancer. Poly(ADP-ribose) polymerase-1 (PARP1) plays a key role in the repair of DNA strand breaks, and PARP inhibitors have been shown to induce highly selective killing of BRCA1/2-deficient tumor cells, a mechanism termed synthetic lethality. In our previous study, a novel PARP1 inhibitor─(E)-2-(2,3-dibromo-4,5-dimethoxybenzylidene)-N-(4-fluorophenyl) hydrazine-1-carbothioamide (4F-DDC)─was synthesized, which significantly inhibited PARP1 activity with an IC50 value of 82 ± 9 nM. The current study aimed to explore the mechanism(s) underlying the antitumor activity of 4F-DDC under in vivo and in vitro conditions. 4F-DDC was found to selectively inhibit the proliferation of BRCA mutant cells, with highly potent effects on HCC-1937 (BRCA1-/-) cells. Furthermore, 4F-DDC was found to induce apoptosis and G2/M cell cycle arrest in HCC-1937 cells. Interestingly, immunofluorescence and Western blot results showed that 4F-DDC induced DNA double strand breaks and further activated the cGAS-STING pathway in HCC-1937 cells. In vivo analysis results revealed that 4F-DDC inhibited the growth of HCC-1937-derived tumor xenografts, possibly via the induction of DNA damage and activation of the cGAS-STING pathway. In summary, the current study provides a new perspective on the antitumor mechanism of PARP inhibitors and showcases the therapeutic potential of 4F-DDC in the treatment of breast cancer.

Abstract 4644: Single strand DNA GAP accumulation as a functional biomarker for USP1 inhibitor sensitivity in ovarian cancer patient-derived organoid models

Abstract Recent studies suggest that PARP inhibitors and POLQ inhibitors confer synthetic lethality in BRCA1-deficient tumors by accumulation of single-stranded DNA gaps (ssDNA gaps) at replication forks. Loss of USP1, a deubiquitinating enzyme, is also synthetic lethal with BRCA1 deficiency, and USP1 inhibitors are now undergoing clinical development for these cancers. Here, we show that USP1 inhibitors also promote the accumulation of ssDNA gaps during replication in BRCA1-deficient cells. USP1 inhibition increased monoubiquitinated PCNA at replication forks and resulted in accumulation of ssDNA gaps in BRCA1-deficient cancer cells. Knockdown of RAD18, the E3 ubiquitin ligase known to ubiquitinate PCNA, caused USP1 inhibitor resistance and suppression of ssDNA gaps. ssDNA gap accumulation induced by USP1 inhibition correlates with drug sensitivity of BRCA1-mutated cancer cells and overcomes PARP inhibitor resistance in cell line and xenograft models. Furthermore, USP1 inhibition was synergistic with PARP and POLQ inhibition in BRCA1-mutant cells, with enhanced ssDNA gap accumulation. A set of patient-derived ovarian cancer organoids (PDOs) were used to confirm the sensitivity of BRCA1-deficient cells to USP1 inhibition. Five PDOs were derived from patients with high grade-serous ovarian cancer (HGSOC). Among the five PDOs, two of them were from tumors harboring germline BRCA1 pathogenic mutations. BRCA1-mutant PDOs, but not BRCA1-WT PDOs, were sensitive to a USP1 inhibitor and to PARP inhibitor monotherapies. The accumulation of ssDNA gaps after treatment with a USP1 inhibitor or a PARP inhibitor correlated with the sensitivity to these drugs in all the models tested. Moreover, the combination of a PARP inhibitor and a USP1 inhibitor showed synergy in a BRCA1-WT model, which was resistant to both monotherapies. Interestingly, ssDNA gaps accumulated with the combination treatment and not with monotherapy in this model. Ovarian cancer PDOs therefore provide a powerful tool for rapid in vitro sensitivity testing. The detection of ssDNA gap accumulation may be a useful predictive biomarker for response to USP1 inhibition as monotherapy or in combination in ongoing clinical trials. Citation Format: Alexandre Andre B. A. Da Costa, Ozge Somuncu, Ramya Ravindranathan, Sirisha Mukkavalli, David Martigneti, Huy Nguyen, Yuqing Jiao, Benjamin Lamarre, Golbahar Sadatrezai, Lisa Moreau, Joyce Liu, Divya Iyer, Jean-Bernard Lazaro, Geoffrey Shapiro, Kalindi Parmar, Alan D. D'Andrea. Single strand DNA GAP accumulation as a functional biomarker for USP1 inhibitor sensitivity in ovarian cancer patient-derived organoid models [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 4644.

Abstract 3363: LIG1 inactivation selectively inhibits growth of BRCA1 mutant cells in vitro and in vivo

Abstract Women harboring a mutation in the BRCA1 gene have a >7X increased risk of developing breast cancer and >35X increased risk of developing ovarian cancer in their lifetime compared to women lacking such mutations. While PARP1/2 inhibitors are efficacious in the BRCA mutant setting, this efficacy is limited and resistance develops readily. Additional therapeutic targets beyond PARP1/2 are needed to treat cancer patients with BRCA mutations. We performed CRISPR screens in 11 BRCA1/2 wild-type and 2 BRCA1 mutant cancer cell lines to identify targets that are synthetic lethal with BRCA1 mutations. In addition to USP1, PARP1 and POLQ, we identified the DNA ligase gene LIG1 as a novel target that when knocked out kills BRCA1 mutant cells selectively. Internal analysis of BRCA mutations in breast and ovarian cancer cell lines in the Project Achilles database further validated the hyperdependence of BRCA1 mutant cells on LIG1. Single-gene perturbation of LIG1 using CRISPRn, CRISPRi, and RNAi confirm the lethal effect of LIG1 inactivation in BRCA1 mutant cell lines, but not BRCA1/2 wild-type cell lines. This loss of viability could be rescued by complementing with an exogenous wild-type LIG1 cDNA, demonstrating the on-target nature of the genetic tools. Using a degradable DNA Ligase I fusion protein, we demonstrate a strong correlation between DNA Ligase I protein level and viability in BRCA1 mutant cells. Enzymatically inactive DNA Ligase I mutant protein (LIG1K568A) was unable to rescue the loss of viability caused by endogenous LIG1 depletion supporting the tractability of this target from a small molecule inhibitor perspective. These data were reproduced in vivo using BRCA1 mutant MDA-MB-436 derived tumors, in which tumor growth was inhibited >80% upon loss of LIG1.Mechanistically, DNA ligase I plays a critical role in DNA replication and damage repair by sealing nicks in the phosphodiester backbone of DNA. When these nicks are not repaired, they are marked by the addition of PAR chains. Consistent with this mechanism, we demonstrated that inactivation of LIG1 leads to increased PARylation. The induction of PARylation was proportional to the level of inactivation of LIG1 protein, supporting a correlation between LIG1 activity and DNA nick repair. Together, these data support DNA ligase I as a synthetic lethal target in the context of BRCA1 mutations. Citation Format: Lauren Martires, Leanne G. Ahronian, Charlotte Pratt, Nikitha Das, Xiaobin Zhang, Douglas A. Whittington, Hongxiang Zhang, Binzhang Shen, Jon Come, Patrick McCarren, Mu-Sen Liu, Chengyin Min, Tianshu Feng, Haris Jahic, Eric Brophy, Daniel Aird, Jannik N. Andersen, Alan Huang, Fang Li, William D. Mallender, Hilary E. Nicholson. LIG1 inactivation selectively inhibits growth of BRCA1 mutant cells in vitro and in vivo [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 3363.

Abstract 7149: Discovery of a novel USP1 inhibitor: Targeted therapy for BRCA-mutated and PARPi-resistant cancers

Abstract Harnessing synthetic lethality offers an innovative approach to targeted cancer treatment. USP1, a specific deubiquitinating enzyme, has gained attention as a potential synthetic lethality target for BRCA-mutated cancers. At AIGEN Sciences, Inc., we've integrated the advanced capabilities of our human-in-the-loop (HITL) AI drug discovery platform, AIGEN ChemTailor. This cutting-edge platform thrives on continuous learning enhanced by expert feedback, refining our approach to drug discovery. Using AIGEN ChemTailor, we synthesized a specific USP1 inhibitor. Its inhibitory capabilities were validated through the Ubiquitin-rhodamine 110 assay. Notably, our inhibitor presented remarkable anti-proliferative effects on BRCA1 mutant cells (MDA-MB-436) while showing no activity against BRCA wild-type cells (HCC1954), highlighting its specificity. The efficacy of our inhibitor was enhanced when combined with PARP inhibitors, such as olaparib or AZD5305, especially in UWB1.289 cells. Impressively, the USP1 inhibitor also effectively targeted PARPi-resistant cell lines, including A2780-ola, UWB1.289-nir, HCC38-ola, MDA-MB-468-ola, U251MG-ola, and OVCAR8-ola. Clonogenic assays with MDA-MB-436 and MCF-10A emphasized our inhibitor's selectivity towards BRCA mutant phenotypes. Subsequent studies demonstrated the compound's mechanism: inducing replication stress by impairing of DNA synthesis and activating DNA damage pathways via ATR signaling. Preclinical mouse studies highlighted favorable pharmacokinetics and involved the assessment of anti-tumor effects in animal models. In summation, our USP1 inhibitor, developed using AIGEN ChemTailor and advanced molecular modeling techniques, stands out as a potent therapeutic against BRCA-mutated cancers and PARP inhibitor-resistant strains. Citation Format: Jihye Kim, Sunkyu Kim, Sejeong Park, Sanghoon Lee, Kiwoong Yoo, Ho-Jeong Lee, Jaewoo Kang, Kwang-Ok Lee. Discovery of a novel USP1 inhibitor: Targeted therapy for BRCA-mutated and PARPi-resistant cancers [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 7149.

Abstract 2013: Extracellular vesicles transfer miR-181a to confer PARP inhibitor resistance and induce STING degradation in BRCA-mutated triple-negative breast and ovarian cancers cells

Abstract Background: Patients with BRCA-mutated breast cancer (BC), including triple-negative BC (TNBC), and ovarian cancer (OvCa) are treated with poly (ADP-ribose) polymerase inhibitors (PARPi). BC and OvCa tumors develop similar mechanisms of resistance to platinum-based agents and PARPi. This study aimed to identify microRNAs (miRs) inducing PARPi resistance in cancer cells that can be transferred by extracellular vesicles (EV). Methods: Olaparib-resistant (OlaR) cell lines were analyzed for 2,083 miRs using HTG miRNA Whole Transcriptomic Analysis (WTA) and NGS. Functional assays were performed in BRCA1-mutated TNBC and OvCa cell lines. In-silico analysis were performed using TCGA, GTEx, CCLE, GDSC, and GEO databases. Results: The miR-181 family (including miR-181a, p=0.001) was significantly upregulated in OlaR TNBC cell lines. High miR-181a levels occurred in tumor tissues of TNBC patients (p=0.001). miR-181a binds to the stimulator of interferon genes (STING) mRNA to promote STING mRNA degradation in OvCa. We hypothesized that miR-181a downregulates STING and downstream proinflammatory cytokines, to mediate PARPi resistance. miR-181a-overexpression induced olaparib resistance and STING downregulation in BRCA1-mutated TNBC cell lines. EV isolated from OlaR TNBC cell lines horizontally transferred miR-181a to non-resistant parental cell lines, which conferred PARPi-resistance and decreased STING. In clinical settings, STING levels were positively correlated with interferon gamma (IFNG) response scores (p=0.01). Low-IFNG response scores in HER2-negative BC patients showed a worse response to neoadjuvant treatment (p=0.001). Consistently, OlaR TNBC cell lines showed resistance to platinum-based drugs. OvCa cell lines resistant to cisplatin showed resistance to olaparib; but miR-181a knockout significantly improved olaparib sensitivity (p=0.001). Conclusions: High levels of miR-181a decrease STING pathway, correlate with IFNG scores, drive PARPi and platinum-based drug resistance. Horizontal miR-181a EVs transfer can facilitate drug resistance in cells. The miR-181a-STING axis can be used for predicting PARPi responses in TNBC and OvCa tumors. Citation Format: Matias A. Bustos, Takamichi Yokoe, Yoshiaki Shoji, Yuta Kobayashi, Shodai Mizuno, Tomohiro Murakami, Sreeja C. Sekhar, Matthew Knarr, Steven A. Vasilev, Analisa DiFeo, Ronny Drapkin, Dave S. Hoon. Extracellular vesicles transfer miR-181a to confer PARP inhibitor resistance and induce STING degradation in BRCA-mutated triple-negative breast and ovarian cancers 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 2013.

Abstract 2034: The NAE1 inhibitor MLN4924 sensitizes both BRCA1 wild type and mutant triple negative breast cancers to cisplatin by reducing the nucleotide excision repair protein XPC level

Abstract Background: Triple-negative breast cancer (TNBC) shows poor survival and prognosis, high recurrence, and poor response to conventional therapeutics. To develop novel therapeutics for TNBC, we explored the efficacy of the neddylation inhibitor, MLN4924. We showed that MLN4924 displayed increased sensitivity against TNBC compared to non-TNBC subtypes. Mechanistically, MLN4924 induced extensive re-replication and DNA damage leading to cell death. Furthermore, MLN4924 improved cisplatin efficacy by elevating the DNA damage levels. To demonstrate the mechanisms of MLN4924+cisplatin-mediated enhanced cell death, we examined the XPC level, a key factor in the nucleotide excision repair (NER) pathway, playing a central role in cisplatin damage repair. Neddylation of CUL4A promotes XPC ubiquitination which influences XPC binding to the DNA damage sites for NER. Methods: We examined the XPC protein level by Western blot assay and RNA level by Real Time PCR using both BRCA1-wild type (MDA-MB-231) and BRCA1-mutated (MDA-MB-436) cell lines and mouse xenograft tumor samples. We evaluated if the proteosome inhibitor MG132 stabilizes XPC ubiquitination and protein levels by treating these cells with MG132 for various times. We also overexpressed XPC in these cell lines and examined the effect on survival upon MLN4924 and MLN4924+cisplatin treatments. Results: Our results demonstrate that MLN4924 reduces XPC ubiquitination upon shorter drug treatment but reduces the protein level upon longer drug treatment in both BRCA1-wild type and BRCA1-mutated cell lines. MG132 treatment did not stabilize the XPC ubiquitination level upon shorter drug treatment but stabilized the protein level upon longer drug treatment. We also observed a reduction in the XPC protein level in tumor samples which correlated with the increase in the DNA damage level. Surprisingly, XPC overexpression improved the cell survival in both MLN4924- and MLN4924+cisplatin-treated BRCA1-wild type and mutated TNBC cells. Conclusion: We hypothesize that a reduction in the XPC ubiquitination and protein levels plays a role in cisplatin-induced DNA damage repair reducing NER efficiency and consequently increasing the DNA damage upon MLN4924+cisplatin treatment. Since overexpression of XPC results in improved survival of both MLN4924-and MLN4924+cisplatin-treated cells, we anticipate that XPC not only regulates cisplatin damage repair through NER but may have a broader role in MLN4924 sensitization beyond the NER pathway. Importantly, MLN4924 treatment does not affect the XPC mRNA level emphasizing that neddylation influences the XPC protein level. In summary, our research uncovers novel insights into the role of XPC in both MLN4924 and MLN4924+cisplatin sensitization, shedding light on potential avenues for innovative therapeutic strategies for TNBC patients. Citation Format: Shrilekha Misra, Mateusz Opyrchal, Alo Ray. The NAE1 inhibitor MLN4924 sensitizes both BRCA1 wild type and mutant triple negative breast cancers to cisplatin by reducing the nucleotide excision repair protein XPC level [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 2034.

Abstract 4913: Morphological feature discrepancies in wild-type vs. BRCA1/BRCA2 mutated high-grade serous ovarian cancer

Abstract Introduction: The understanding of morphological heterogeneity at the cellular level in High-Grade Serous Ovarian Cancer (HGSOC), particularly in relation to BRCA1 and BRCA2 mutations, is still an ongoing area of research. This study aims to elucidate the morphological features that distinguish wild-type (WT) tumors from those with BRCA1/BRCA2 mutations using deep learning models. Methods: A total of 300 H&E stained HGSOC slides were collected in a patient-wise manner and tumor areas were annotated by an expert pathologist. We used a convolutional neural network model with spatial attention pre-trained on pathological images to extract features from slides, and the features were clustered into 96 groups. Subsequently, a nuclei segmentation model was employed for precise cell segmentation, followed by measurement of cellular features including cell shape (area, eccentricity) and cell texture (dissimilarity, correlation). The assessment of cell texture evaluates the variation and uniformity in gray-level intensity across the cell. We performed independent t-tests on samples of 100 patches from each cluster, comparing cells of selected patches from the top-N clusters representing the highest proportion of each label. Results: H&E slides (n=300) include 69 (23%) BRCA1 mutants and 50 (16.7%) BRCA2 mutants. In Table1, negative t-statistics suggest that WT carcinoma cancer cells exhibit lower values for the measured features compared to BRCA mutants, whereas positive values denote higher values in WT. BRCA1 and BRCA2 mutant carcinoma cancer cells showed significantly larger areas and higher eccentricity than WT carcinoma cancer cells in all top-N clusters settings (N=3, 5, 10, 30). Furthermore, WT carcinoma cancer cells showed higher dissimilarity and reduced correlation compared to BRCA1 mutant carcinoma cells in four settings. Conclusions: Our observations in BRCA-mutated HGSOC cells enrich our understanding of tumor cell morphology with BRCA mutations. Table 1. Comparison of cell features between WT and BRCA mutants cell feature comparison top-3 clusters (t-statistics, p-value) top-5 clusters (t-statistics, p-value) top-10 clusters (t-statistics, p-value) top-30 clusters (t-statistics, p-value) area WT vs BRCA1 -37.41, <0.001 -50.2, <0.001 -37.53, <0.001 -85.95, <0.001 WT vs BRCA2 -42.14, <0.001 -50.61, <0.001 -16.57, <0.001 -51.98, <0.001 eccentricity WT vs BRCA1 -24.40, <0.001 -34.14, <0.001 -38.02, <0.001 -37.40, <0.001 WT vs BRCA2 -26.77, <0.001 -30.46, <0.001 -29.47, <0.001 -47.64, <0.001 dissimilarity WT vs BRCA1 55.17, <0.001 52.73, <0.001 103.57, <0.001 166.78, <0.001 WT vs BRCA2 -38.15, <0.001 -24.75, <0.001 0.2, <0.001 107.73, <0.001 correlation WT vs BRCA1 1.94, <0.001 -2.46, <0.001 -50.24, <0.001 -65.96, <0.001 WT vs BRCA2 87.62, <0.001 90.83, <0.001 52.6, <0.001 -48.90, <0.001 Citation Format: JaeHeon Lee, Hyunil Kim, Yongeun Lee, Yoon-La Choi, Kyungsoo Jung, Tae-Yeong Kwak, Sun Woo Kim, Hyeyoon Chang. Morphological feature discrepancies in wild-type vs. BRCA1/BRCA2 mutated high-grade serous ovarian 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 4913.

Abstract 4686: Identification of ART3 as a novel synthetic lethal partner of the BRCA1 mutation in breast cancer

Abstract Breast cancer (BC), the most prevalent malignancy in women, ranks fourth in cancer mortality as of 2022. Mutations in the BRCA genes significantly elevate BC risk and are associated with markedly reduced survival compared to non-carriers. These genes are crucial in homologous recombination, a mechanism essential for error-free DNA repair. Despite advancements, treatment options for BRCA mutation-driven cancers remain limited. Synthetic lethality (SL) has emerged as a promising strategy, with poly(ADP-ribose) polymerase inhibitors (PARPi) being the first developed drugs based on this principle. However, PARPi's effectiveness is limited, as nearly 40% of BRCA-mutated BCs are unresponsive, and resistance often develops in initial responders. Therefore, novel mutation-specific targeted therapies are urgently needed. In this study, we employed the novel computational method 'Mining Synthetic Lethals (MiSL)' to analyze TCGA pan-cancer primary tumor data, identifying ART3 as a potential SL partner of the BRCA1 germline mutation. Our approach focused on the intersection of genetic interactions and cancer vulnerabilities, providing a unique insight into SL relationships. siRNA-mediated silencing of ART3 in BRCA1-mutated cells consistently led to decreased cell viability, apoptosis induction, and G2/M cell cycle arrest. Following stable transfection with an inducible ART3 shRNA construct, we confirmed significant reduction in cell viability in BRCA1-deficient cells through colony formation assays. RNA sequencing of ART3 knockdown cells revealed transcriptional changes in genes involved in cell cycle progression, apoptosis, and growth and proliferation pathways compared with control cells. Immunofluorescent staining revealed increased DNA damage foci with decreased DNA repair in ART3 knockdown BRCA1-deficient cells. In conclusion, our study identifies ART3 as a novel SL partner of the BRCA1 mutation in BC. This discovery paves the way for developing new therapeutic strategies for BRCA1-mutated breast cancers and novel chemoprevention approaches for individuals carrying germline BRCA1 mutations. Future research will focus on further elucidating the molecular mechanisms underlying this SL interaction and exploring its therapeutic potential in clinical settings. Citation Format: Hannah Neiger, Xinyu Pei, Anh Nguyen, Wenjia Wang, Emily L. Siegler, James Zhou, Kristie Lau, Alexandra Tan, Yihui Shi. Identification of ART3 as a novel synthetic lethal partner of the BRCA1 mutation in breast 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 4686.

Induction of the DNA-Repair Gene POLQ only in BRCA1-mutant Breast-Cancer Cells by Methionine Restriction.

BRCA1/2 mutations in breast cancer cells impair homologous recombination and promote alternative end joining (Alt-EJ) for DNA-damage repair. DNA polymerase theta, encoded by POLQ, plays a crucial role in Alt-EJ, making it a potential therapeutic target, particularly in BRCA1/2-mutant cancers. Methionine restriction is a promising approach to target cancer cells due to their addiction to this amino acid. The present study investigated the expression of POLQ in BRCA1/2 wild-type and BRCA1-mutant breast cancer cells under methionine restriction. POLQ mRNA expression was measured using qRT-PCR in BRCA1/2 wild-type (MDA-MB-231) and BRCA1- mutant (HCC1937 and MDA-MB-436) breast-cancer cells under normal, or serum-restricted, or serum- and methionine-restricted conditions. Compared to BRCA1/2 wild-type cells, BRCA1-mutant cells displayed significantly higher basal POLQ expression in normal medium. Methionine restriction further increased POLQ expression in the BRCA1-mutant cells but decreased it in the BRCA1/2 wild-type cells. The present findings suggest that methionine restriction showed differential effects on POLQ expression, potentially impacting Alt-EJ activity, in BRCA1/2 wild-type and BRCA1-mutant breast-cancer cells. Further investigation is needed to explore the potential of combining methionine restriction with DNA-repair inhibitors, such as PARP inhibitors, to overcome drug resistance in BRCA1/2 mutant cancers.

Abstract IA001: Single strand DNA GAP accumulation as a functional biomarker for USP1 inhibitor sensitivity

Abstract Recent studies suggest that PARP inhibitors and POLQ inhibitors confer synthetic lethality in BRCA1-deficient tumors by accumulation of single-stranded DNA gaps (ssDNA gaps) at replication forks. Loss of USP1, a deubiquitinating enzyme, is also synthetic lethal with BRCA1 deficiency, and USP1 inhibitors are now undergoing clinical development for these cancers. Here, we show that USP1 inhibitors also promote the accumulation of ssDNA gaps during replication in BRCA1-deficient cells. USP1 inhibition increased monoubiquitinated PCNA at replication forks and resulted in accumulation of ssDNA gaps in BRCA1-deficient cancer cells. Knockdown of RAD18, the E3 ubiquitin ligase known to ubiquitinate PCNA, caused USP1 inhibitor resistance and suppression of ssDNA gaps. ssDNA gap accumulation induced by USP1 inhibition correlates with drug sensitivity of BRCA1-mutated cancer cells and overcomes PARP inhibitor resistance in cell line and xenograft models. Furthermore, USP1 inhibition was synergistic with PARP and POLQ inhibition in BRCA1-mutant cells, with enhanced ssDNA gap accumulation. A set of patient-derived ovarian cancer organoids (PDOs) were used to confirm the sensitivity of BRCA1-deficient cells to USP1 inhibition. Five PDOs were derived from patients with high grade-serous ovarian cancer (HGSOC). Among the five PDOs, two of them were from tumors harboring germline BRCA1 pathogenic mutations. BRCA1-mutant PDOs, but not BRCA1-WT PDOs, were sensitive to a USP1 inhibitor and to PARP inhibitor monotherapies. The accumulation of ssDNA gaps after treatment with a USP1 inhibitor or PARP inhibitor correlated with the sensitivity to these drugs in all the models tested. Moreover, the combination of a PARP inhibitor and USP1 inhibitor showed synergy in a BRCA1-WT model, which was resistant to both monotherapies. Interestingly, ssDNA gaps accumulated with the combination treatment and not with monotherapy in this model. Ovarian cancer PDOs therefore provide a powerful tool for rapid in vitro sensitivity testing. The detection of ssDNA gap accumulation may be a useful predictive biomarker for response to USP1 inhibition as monotherapy or in combination in ongoing clinical trials. Citation Format: Alan D. D'Andrea. Single strand DNA GAP accumulation as a functional biomarker for USP1 inhibitor sensitivity [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr IA001.

The ORFIUS complex regulates ORC2 localization at replication origins.

High-grade serous ovarian cancer (HGSC) is a lethal malignancy with elevated replication stress (RS) levels and defective RS and RS-associated DNA damage responses. Here we demonstrate that the bromodomain-containing protein BRD1 is a RS suppressing protein that forms a replication origin regulatory complex with the histone acetyltransferase HBO1, the BRCA1 tumor suppressor, and BARD1, ORigin FIring Under Stress (ORFIUS). BRD1 and HBO1 promote eventual origin firing by supporting localization of the origin licensing protein ORC2 at origins. In the absence of BRD1 and/or HBO1, both origin firing and nuclei with ORC2 foci are reduced. BRCA1 regulates BRD1, HBO1, and ORC2 localization at replication origins. In the absence of BRCA1, both origin firing and nuclei with BRD1, HBO1, and ORC2 foci are increased. In normal and non-HGSC ovarian cancer cells, the ORFIUS complex responds to ATR and CDC7 origin regulatory signaling and disengages from origins during RS. In BRCA1-mutant and sporadic HGSC cells, BRD1, HBO1, and ORC2 remain associated with replication origins, and unresponsive to RS, DNA damage, or origin regulatory kinase inhibition. ORFIUS complex dysregulation may promote HGSC cell survival by allowing for upregulated origin firing and cell cycle progression despite accumulating DNA damage, and may be a RS target.

Abstract B062: Loss of MED12 activates the TGFβ pathway to promote chemoresistance and replication fork stability in BRCA-deficient cells

Abstract Understanding chemoresistance mechanisms in BRCA-deficient cells will allow for identification of biomarkers for predicting tumor response to therapy, as well as the design of novel therapeutic approaches targeting this chemoresistance. Here, we show that the protein MED12, a component of the Mediator transcription regulation complex, plays an unexpected role in regulating chemosensitivity in BRCA-deficient cells. We found that loss of MED12 confers resistance to cisplatin and PARP inhibitors in both BRCA1- and BRCA2-deficient cells, which is associated with restoration of both homologous recombination and replication fork stability. Surprisingly, MED12-controlled chemosensitivity does not involve a function of the Mediator complex, but instead reflects a distinct role of MED12 in suppression of the TGFβ pathway. Importantly, we show that ectopic activation of the TGFβ pathway is enough to overcome the fork protection and DNA repair defects of BRCA-mutant cells, resulting in chemoresistance. Our work identifies the MED12-TGFβ module as an important regulator of genomic stability and chemosensitivity in BRCA-deficient cells. Citation Format: Lindsey M Pale, Ashna Dhoonmoon, Anastasia Hale, Kady A Dennis, Emily M Schleicher, Claudia M Nicolae, George-Lucian Moldovan. Loss of MED12 activates the TGFβ pathway to promote chemoresistance and replication fork stability in BRCA-deficient cells [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B062.

Genetic separation of Brca1 functions reveal mutation-dependent Polθ vulnerabilities

Homologous recombination (HR)-deficiency induces a dependency on DNA polymerase theta (Polθ/Polq)-mediated end joining, and Polθ inhibitors (Polθi) are in development for cancer therapy. BRCA1 and BRCA2 deficient cells are thought to be synthetic lethal with Polθ, but whether distinct HR gene mutations give rise to equivalent Polθ-dependence, and the events that drive lethality, are unclear. In this study, we utilized mouse models with separate Brca1 functional defects to mechanistically define Brca1-Polθ synthetic lethality. Surprisingly, homozygous Brca1 mutant, Polq−/− cells were viable, but grew slowly and had chromosomal instability. Brca1 mutant cells proficient in DNA end resection were significantly more dependent on Polθ for viability; here, treatment with Polθi elevated RPA foci, which persisted through mitosis. In an isogenic system, BRCA1 null cells were defective, but PALB2 and BRCA2 mutant cells exhibited active resection, and consequently stronger sensitivity to Polθi. Thus, DNA end resection is a critical determinant of Polθi sensitivity in HR-deficient cells, and should be considered when selecting patients for clinical studies.

Targeted DNA Damage Boost with Loncastuximab Tesirine in Combination with PARP Inhibitors in Diffuse Large B-Cell Lymphoma

MYC-over expressing lymphomas display inherent resistance to standard chemoimmunotherapy regimens and are characterised by genomic instability and constitutive activation of the DNA damage response (DDR) pathway. Loncastuximab tesirine (Lonca) is an antibody-drug conjugate directed against CD19, a surface antigen broadly expressed in B-cell malignancies. Upon CD19 binding, Lonca induces DNA damage by delivering a pyrrolobenzodiazepine dimer-based, DNA crosslinking warhead into target cells. Here we hypothesised that DDR inhibition could enhance DNA damage induced by Lonca in CD19-positive lymphoma cells. Since MYC-overexpressing cells mainly rely on PARP activity to attenuate endogenous MYC-induced replicative stress, we combined Lonca with Talazoparib (an FDA-approved PARP inhibitor), in a panel of 12 DLBCL cell lines (7 with MYC-rearrangement), and in vivo in a MYC/BCL-2-rearranged DLBCL PDX model. Lonca and Talazoparib showed significant antiproliferative activity in a dose and time dependent manner in most cell lines at clinically achievable concentrations. The highest sensitivity to both compounds was observed in a BRCA2 mutant cell line (DOHH2). These data are in line with the known synthetic lethality between BRCA mutations and platinum derivatives and PARP inhibitors. The addition of Talazoparib significantly enhanced the antiproliferative effects of Lonca in DLBCL cell lines irrespective of MYC/BCL2 rearrangements and TP53 genomic alterations. Of note, the highest efficacy of the combination was observed in MYC-rearranged and MYC-overexpressing cell lines. The combination of Lonca and Talazo sinergistically increased DNA damage as evaluated by comet assay, induced enhanced cell death and caused specific changes in cell cycle dynamics. Enhanced apoptosis was confirmed by Annexin/PI staining and caspase 3/7 cleavage, assessed by caspase Glo assay and Western Blot analyses. As previously shown (Fusani et al., ASH 2021), while Lonca and Talazoparib affected cell cycle inducing G2/M phase arrest, the combination specifically increased the percentage of cells arrested in the BrdU negative S phase of cell cycle. Upon combined treatment, we observed increased DDR activation with the evaluation of several DDR biomarkers such as phospho(p)-ATM, pCHK2 Thr68, pCHK1 Ser345, gH2AX. To better understand the molecular mechanism underlying this synergistic interaction, we performed RNA-Seq analysis in two representative cell lines (OCI-LY18 and SUDHL5). Interestingly while Lonca did not cause significant changes in gene expression profiling (GEP) after 24 hours of incubation, the combination resulted in specific GEP changes such as down-regulation of histone H2B and aurora kinase A (AURKA), genes mainly involved in S and G2/M transition of the cell cycle. Similar results were obtained by combining Talazoparib and different PARP inhibitors with the alkylating agent cisplatin, indicating a class effect. The synergistic interaction of Lonca and Talazoparib was further confirmed in vivo in a MYC/BCL-2 double hit PDX model. As previously shown (Fusani et al., ASH 2021), Lonca/Talazoparib combination did not result in enhanced DNA damage induction in PBMC-derived B cells from healthy donors. Importantly, PBMC-derived T cells from healthy donors did not show any sign of DNA damage accumulation upon exposure to Lonca, Talazoparib and the combination. These data provide the rationale for future therapeutic strategies based on selective induction of DNA damage in neoplastic B cells in combination with DDR inhibition in aggressive MYC-positive B cell lymphoma.

Analysis of the Relationship between PARP1 and BRCA1 Suggests PARP1 Gene Has a Role in Breast Cancer

Poly [ADP-ribose] polymerase 1 (PARP1), one of the genes in the PARP family, is mainly involved in the detection and repair of DNA damage in cells, and its upregulation has been associated with tumorigenesis. PARP1 is essential to all cells in the body as it ensures that DNA is replicated correctly. The PARP1 protein addresses repair of single-stranded breaks (SSBs) in DNA by initially binding near the point of break in the DNA. While it is bound to the region of the SSB, PARP1 transfers ADP ribosyl moiety from NAD+ to acceptor proteins. This leads to the recruitment of DNA repair proteins to the region of DNA breaks. The PARP1 protein also aids the double-stranded break (DSB) repair of DNA by recruiting the homologous recombination (HR) pathway proteins. Due to this role of PARP1 in DNA repair, it has been associated with cancer growth. Using databases, including UniProt, Xena Browser, and CBioPortal, this article explores the relationship between PARP1 mutations and BRCA1-mutated breast cancer. BRCA1 is a tumor suppressor gene, which is involved in DNA repair through the HR pathway. Therefore, in BRCA1-mutated cells, the lack of tumor suppressor factors leads to cancer growth. However, in a cell that has both BRCA1 mutations and PARP1 inhibition, DNA damage cannot be repaired, leading to apoptosis. Hence, PARP1 inhibitors have become essential in BRCA1-mutated breast cancers. There are several PARP1 inhibitors that are currently being used to treat breast cancer, which work using several mechanisms of action, including PARP1 trapping, which prevents the repair, transcription, and replication of DNA. This article also focuses on the clinical trials of three specific drugs, Olaparib, Iniparib, and Veliparib, which are used to treat breast cancer. However, due to the lack of understanding surrounding PARP1 inhibition mechanisms and potential drug combinations, more research needs to be done to understand potential biomarker targets and PARP1 inhibitor resistance.