Lou, Zhenkun

Abstract Pancreatic adenocarcinoma remains one of the most lethal malignancies, primarily due to its robust resistance to genotoxic therapies, such as chemotherapy and radiotherapy. Understanding the mechanisms underlying this resistance is essential to improve clinical outcomes. In this study, we identified trimethylguanosine synthase 1 (TGS1), previously known for its role in RNA modification, as a critical mediator of homologous recombination (HR) repair that specifically contributes to resistance in pancreatic adenocarcinoma. TGS1 was significantly overexpressed in pancreatic adenocarcinoma tissues, correlating strongly with advanced disease stages, therapy resistance, and poor patient prognosis. Following DNA damage, ATM kinase phosphorylated TGS1 at serine residues S389 and S531, which mediated its direct interaction with BRCA1 and subsequent recruitment of BRCA1 to DNA damage sites. The phosphorylation-dependent interaction enhanced HR repair efficiency, enabling cancer cells to survive genotoxic stress. Depletion or pharmacologic inhibition of TGS1 induced HR deficiency and markedly enhanced sensitivity to DNA-damaging agents, particularly PARP inhibitors, in pancreatic adenocarcinoma cell lines in vitro and in both cell line– and patient-derived xenograft models in vivo. Collectively, these findings uncover an ATM–TGS1–BRCA1 signaling axis that promotes DNA repair and resistance to genotoxic therapies in pancreatic cancer, positioning TGS1 as a promising predictive biomarker and therapeutic target to enhance treatment efficacy. Significance: The ATM–TGS1–BRCA1 signaling axis is a critical regulator of DNA repair that can be targeted to overcome genotoxic therapy resistance, providing a promising therapeutic strategy that could transform pancreatic cancer treatment.

Metastatic castration-resistant prostate cancer (mCRPC) progresses aggressively and resists existing therapies. Although poly(ADP-ribose) polymerase inhibitors (PARPis) benefit a subset of patients with mCRPC and BRCA1/2 deficiencies, therapeutic options remain limited for those without such mutations. Here, we uncover a critical role for the ATM-TRMT10A-BRCA1 signaling axis in regulating homologous recombination (HR) repair and PARPi sensitivity. We demonstrate that ATM phosphorylates TRMT10A at serine-28 after DNA damage, promoting BRCA1 recruitment and efficient HR repair. TRMT10A deletion disrupts HR repair, sensitizing cells to PARPis. Moreover, TRMT10A is up-regulated in mCRPC through stabilization by USP10. Targeting USP10 with spautin-1 induces TRMT10A degradation and enhances tumor sensitivity to PARPis in cell-derived xenografts and patient-derived xenograft models. These findings identify TRMT10A as a therapeutic vulnerability in mCRPC and demonstrate that combined inhibition of PARP and USP10 offers a promising synthetic lethal strategy for a broader group of patients lacking classical BRCA mutations.

CDK12 primarily functions as a transcription regulatory cyclin-dependent kinase (CDK) that controls mRNA elongation, splicing, and polyadenylation. The CDK12 gene is implicated in human cancers since it is frequently mutated and/or deleted in prostate and ovarian cancer but paradoxically amplified in breast cancer. Here, we demonstrate that CDK12 promotes serine-933 phosphorylation of DNA2, a nuclease/helicase critical for replication fork stress regulation, and the phosphorylation subsequently facilitates DNA2 polyubiquitination and degradation mediated by the APC/C CDC20 E3 ubiquitin ligase. CDK12 inactivation induces but amplification suppresses genome-wide expression of interferon response and antigen processing and presentation machinery genes in ovarian and breast cancer cells, respectively. Besides causing aberrant DNA2 stabilization, replication stress, genomic instability, and cytosolic double-stranded DNA (dsDNA) accumulation, CDK12 loss also triggers cGAS–STING activation and innate immune response, which can be reversed by forced expression of replication protein A (RPA) subunits or DNA2 depletion. Our findings identify DNA2 as a phosphorylation substrate of CDK12, connecting CDK12 to cell cycle regulation. These data also reveal DNA2 protein destruction as a critical mechanism that dictates genomic instability, cGAS–STING signaling activation, and innate immune response in CDK12-deregulated cancers.

Oncogene expression can cause replication stress (RS), leading to DNA double-strand breaks (DSBs) that require repair through pathways such as homologous recombination, nonhomologous end-joining, and microhomology-mediated end-joining (MMEJ). Cyclin D1 (encoded by CCND1 ) is a well-known oncoprotein overexpressed in cancer; however, its role in RS is unknown. Using mantle cell lymphoma (MCL) as a naturally occurring model of cyclin D1 overexpression, we examined the impact of cyclin D1 on RS and DSB repair mechanisms. Cyclin D1 overexpression elevated RS, increased DNA damage, especially during mitosis, and caused specific upregulation of MMEJ. Furthermore, cyclin D1 activated polymerase theta ( POLQ ) transcription by binding its promoter loci, driving POLΘ-mediated MMEJ that is essential to withstand cyclin D1–induced RS. Moreover, concurrent ATM deficiency further intensified RS, enhanced POLQ expression, and heightened reliance on MMEJ-mediated DNA damage repair. Consequently, inhibition of POLΘ in cyclin D1–overexpressed settings further exacerbated RS, causing single-strand DNA gap accumulations and chromosomal instability, ultimately leading to apoptosis, an effect amplified in ATM-deficient cells. Targeting MMEJ via POLΘ inhibition is therefore an effective strategy in the context of cyclin D1 overexpression and ATM deficiency and may provide a unique therapeutic approach for treating MCL and other malignancies characterized by similar alterations.

Triple-negative breast cancer (TNBC) represents the most malignant subtype of breast cancer. The clinical application of PARP inhibitors (PARPi) is limited by the low frequency of BRCA1/2 mutations in TNBC. Here, we identified that MTAP deletion sensitized genotoxic agents in our clinical cohort of metastatic TNBC. Further study demonstrated that MTAP deficiency or inhibition rendered TNBC susceptibility to chemotherapeutic agents, particularly PARPi. Mechanistically, targeting MTAP that synergized with PARPi by disrupting the METTL16-MAT2A axis involved in methionine metabolism and depleting in vivo s-adenosylmethionine (SAM) levels. Exhausted SAM in turn impaired PARPi-induced DNA damage repair through attenuation of MRE11 recruitment and end resection by diminishing MRE11 methylation. Notably, brain metastatic TNBC markedly benefited from a lower dose of PARPi and MTAP deficiency/inhibition synergy due to the inherently limited methionine environment in the brain. Collectively, our findings revealed a feed-forward loop between methionine metabolism and DNA repair through SAM, highlighting a therapeutic strategy of PARPi combined with MTAP deficiency/inhibition for TNBC.

e24015 Background: Anthracyclines are effective cancer therapeutics but can cause cardiotoxicity. Recent studies suggest a connection between efficacy and toxicity in that the effects of anthracyclines on cancer cells leads to the release of interleukin 1-alpha (IL-1⍺), which negatively impacts cardiomyocyte metabolism and thereby cardiac function. This observation was made in in vivo and in vitro models of acute myeloid leukemia (AML); whether this holds true for other cancer cell lines remains unclear. Methods: Herein we characterized the cytokine profile of 9 cancer cell lines exposed to doxorubicin (1 µM for 24 hours) and then tested the effects of interleukin 1-alpha (IL-1⍺, 50-150 ng/mL) on the viability and metabolism of neonatal cardiomyocyte. We used Seahorse to assess cardiomyocyte glycolysis via extracellular acidification rate (ECAR) and mitochondrial oxidative phosphorylation based on the oxygen consumption rate (OCR). Results: As outlined in Table 1, different hematological and breast cancer cell lines showed a range of cytokine profile in response to doxorubicin exposure. Of the cytokines with putative action on cardiomyocyte metabolism IL-1⍺was one of the most induced in 3 out of 5 murine breast cancer, murine B- and T-cell lymphoma, as well as murine and human AML human and murine cell lines. Doxorubicin did not induce IL-1⍺ expression in macrophage cell lines (RAW) or directly in cardiomyocytes. Exposing neonatal cardiomyocytes to different concentrations of IL-1⍺ did not decrease but rather increased OCR and especially ECAR. Conclusions: These data confirm the release of IL-1⍺ from AML as well as several, but not all breast cancer cell lines. Furthermore, purified IL-1⍺ increased oxidative phosphorylation and glycolysis in murine neonatal cardiomyocytes. These data point out heterogeneity in the cytokine release pattern from anthracycline-treated cancer cell lines and their impact on cardiomyocyte metabolism. Further studies are required to define the nuances of crosstalk between cancer and the heart and its contribution to the variation in cardiotoxicity risk. Cytokine profile of cancer cell lines. Cytokines RAW Neonatal MC38HuPD-L1 EMT6 JC E0771 4T1 B Lymphoma: A20 T Lymphoma: E.G7-OVA AML Human: THP-1 AML mouse: C1498 ICAM-1, CD54 ++ ++ ++ ++ ++ ++ IL-1α IL-1F1 + + + + + + + IL-10 + + IL-16 ++ ++ ++ CXCL10/CRG-2 ++ + ++ ++ ++ ++ ++ ++ ++ M-CSF ++ ++ ++ + ++ ++ ++ ++ + RANTES CCL5 + ++ ++ ++ ++ TNF-α +++ + ++ + + + + +

Abstract Poly ADP ribose polymerase inhibitors (PARPi) are being investigated in combination with photon and proton radiotherapy in clinical trials of pediatric and adult malignancies. The precise mechanisms of PARPi radiosensitization, and whether differences in photon and proton-mediated relative efficacy exist, have not been fully elucidated. To study mechanisms of PARPi radiosensitization we investigated the effects of PARPi in combination with photons and two different ionizing densities of protons delivered at the entrance (ENT) or the Bragg peak (BP) of the profile (dose-averaged LET [LETd] 2.2 and 7.0 keV/µm, respectively) of a 76.8 MeV proton beam after observing an extreme tumor and normal tissue response in an 18-year-old female patient with high grade glioma treated veliparib and proton therapy in a Children’s Oncology Group clinical trial. BRCA1/2 wild-type hTERT RPE-1, U2OS, and MDA-MB-231 cells were hypersensitive to the combination of veliparib and proton BP, with enhanced relative biological effectiveness (RBE) at 2 Gy values of 1.7, 1.4, and 1.3, respectively. Similar findings were observed with talazoparib and olaparib, suggesting that PARP trapping efficiency was not a major influence on the proton BP RBE. Further, we did not observe differences in transcription replication conflict between the different proton ionizing densities. Unexpectedly, DNA fiber assays revealed more elongated replication fork tracks in PARPi treated cells 60 minutes after proton BP compared with proton ENT, indicative of accelerated replication fork progression. To assess gap formation in the vicinity of nascent DNA we treated cells with the ssDNA-specific S1 nuclease and found that the lengths of CldU-labeled tracks were significantly reduced in cells treated with the PARPi/proton BP combination, suggestive of greater gap formation at replication forks. We postulated that more ssDNA gaps were being converted to DSBs during replication as we further observed that PARPi/proton BP resulted in increased γH2AX foci at 4- and 24-hours after treatment. Consistent with increased DSB formation, a higher proportion of cells arrested in the G2/M phase of the cell cycle at 24 hours following PARPi/proton BP. Despite being arrested in G2/M when homologous recombination is active, there was a significant increase in 53BP1 and a decrease in RAD51 recruitment, indicative of upregulated repair by more error-prone non-homologous end-joining (NHEJ) repair pathway. The enhanced proton BP RBE in PARPi treated cells was abrogated upon knockdown of XRCC4, a critical component of NHEJ repair pathway, suggesting that toxic NHEJ may be contributing to the enhanced proton BP RBE. In conclusion, PARPi renders cells hypersensitive to high LET BP proton irradiation. Enhancing the LET in combination with PARPi warrants further investigation to overcome therapeutic resistance. Citation Format: Yiqun Han, Qin Zhou, Anna Olson, Cameron M. Callaghan, Bin Chen, Nicholas B. Remmes, Meng Xu Welliver, Zheming Wu, Daniel K. Ebner, Jake A. Kloeber, Zhenkun Lou, Robert W. Mutter. Poly ADP ribose polymerase inhibitors potentiate proton therapy end-of-range relative biological effective dose by increasing replication stress [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4689.

Abstract The TopBP1-ATR axis is critical for maintaining genomic stability during DNA replication stress, yet the precise regulation of TopBP1 in replication stress responses remains poorly understood. In this study, we identified PHD and Ring Finger Domains 1 (PHRF1) as an important ATR activator through its interaction with TopBP1. Our analysis revealed a correlation between PHRF1 and genomic stability in cancer patients. Mechanistically, PHRF1 is recruited to DNA lesions in a manner dependent on its PHD domain and histone methylation. Subsequently, PHRF1 mono-ubiquitinates TopBP1 at lysine 73, which enhances the TopBP1-ATR interaction and activates ATR. Depletion of PHRF1 disrupts ATR activation and sensitizes cells to replication stress-inducing agents. Furthermore, conditional knockout of Phrf1 in mice leads to early lethality and impaired ATR-Chk1 axis signaling. Collectively, our findings establish PHRF1 as a novel E3 ligase for TopBP1, coordinating the replication stress response by enhancing TopBP1-ATR signaling.

Abstract The phosphorylation of histone H2A.X into γH2A.X is a crucial early event in the DNA damage response, marking DNA damage sites and initiating repair processes. While ATM kinase is traditionally recognized as the primary mediator of H2A.X phosphorylation, our study identifies serine/threonine kinase 39 (STK39) as a novel enhancer of this critical signaling pathway. We demonstrate that after DNA damage, STK39 undergoes phosphorylation by the ATM kinase, facilitating its interaction with the Mre11-Rad50-Nbs1 complex and subsequent recruitment to chromatin. This recruitment enables STK39 to further phosphorylate H2A.X, thus amplifying γH2A.X production and promoting homologous recombination repair. Notably, we observe a significant upregulation of STK39 in pancreatic adenocarcinoma (PAAD) tissues, correlating with heightened resistance to PARPi therapy. Furthermore, we demonstrate the synergistic efficacy of combining STK39 inhibition with PARP inhibitors in suppressing and reversing PAAD growth. This study not only provides new insights into the molecular dynamics of H2A.X phosphorylation but also highlights the therapeutic potential of targeting STK39 to enhance PARPi sensitivity in PAAD (created with BioRender).