γH2AX Foci Research Articles

BUB1 regulates non-homologous end joining pathway to mediate radioresistance in triple-negative breast cancer

BackgroundTriple-negative breast cancer (TNBC) is a highly aggressive form of breast cancer subtype often treated with radiotherapy (RT). Due to its intrinsic heterogeneity and lack of effective targets, it is crucial to identify novel molecular targets that would increase RT efficacy. Here we demonstrate the role of BUB1 (cell cycle Ser/Thr kinase) in TNBC radioresistance and offer a novel strategy to improve TNBC treatment.MethodsGene expression analysis was performed to look at genes upregulated in TNBC patient samples compared to other subtypes. Cell proliferation and clonogenic survivals assays determined the IC50 of BUB1 inhibitor (BAY1816032) and radiation enhancement ratio (rER) with pharmacologic and genomic BUB1 inhibition. Mammary fat pad xenografts experiments were performed in CB17/SCID. The mechanism through which BUB1 inhibitor sensitizes TNBC cells to radiotherapy was delineated by γ-H2AX foci assays, BLRR, Immunoblotting, qPCR, CHX chase, and cell fractionation assays.ResultsBUB1 is overexpressed in BC and its expression is considerably elevated in TNBC with poor survival outcomes. Pharmacological or genomic ablation of BUB1 sensitized multiple TNBC cell lines to cell killing by radiation, although breast epithelial cells showed no radiosensitization with BUB1 inhibition. Kinase function of BUB1 is mainly accountable for this radiosensitization phenotype. BUB1 ablation also led to radiosensitization in TNBC tumor xenografts with significantly increased tumor growth delay and overall survival. Mechanistically, BUB1 ablation inhibited the repair of radiation-induced DNA double strand breaks (DSBs). BUB1 ablation stabilized phospho-DNAPKcs (S2056) following RT such that half-lives could not be estimated. In contrast, RT alone caused BUB1 stabilization, but pre-treatment with BUB1 inhibitor prevented stabilization (t1/2, ~8 h). Nuclear and chromatin-enriched fractionations illustrated an increase in recruitment of phospho- and total-DNAPK, and KAP1 to chromatin indicating that BUB1 is indispensable in the activation and recruitment of non-homologous end joining (NHEJ) proteins to DSBs. Additionally, BUB1 staining of TNBC tissue microarrays demonstrated significant correlation of BUB1 protein expression with tumor grade.ConclusionsBUB1 ablation sensitizes TNBC cell lines and xenografts to RT and BUB1 mediated radiosensitization may occur through NHEJ. Together, these results highlight BUB1 as a novel molecular target for radiosensitization in women with TNBC.

Conofolidine: A Natural Plant Alkaloid That Causes Apoptosis and Senescence in Cancer Cells.

Natural products contribute substantially to anticancer therapy; the plant kingdom provides an important source of molecules. Conofolidine is a novel Aspidosperma-Aspidosperma bisindole alkaloid isolated from the Malayan plant Tabernaemontana corymbosa. Herein, we report conofolidine's broad-spectrum anticancer activity together with that of three other bisindoles-conophylline, leucophyllidine, and bipleiophylline-against human-derived breast, colorectal, pancreatic, and lung carcinoma cell lines. Remarkably, conofolidine was able to induce apoptosis (e.g., in MDA-MB-468 breast) or senescence (e.g., in HT-29 colorectal) in cancer cells. Annexin V-FITC/PI, caspase activation, and PARP cleavage confirmed the former while positive β-gal staining corroborated the latter. Cell cycle perturbations were evident, comprising S-phase depletion, accompanied by downregulated CDK2, and cyclins (A2, D1) with p21 upregulation. Confocal imaging of HCT-116 cells revealed an induction of aberrant mitotic phenotypes-membrane blebbing, DNA-fragmentation with occasional multi-nucleation. DNA integrity assessment in HCT-116, MDA-MB-468, MIAPaCa-2, and HT-29 cells showed increased fluorescent γ-H2AX during the G1 cell cycle phase; γ-H2AX foci were validated in HCT-116 and MDA-MB-468 cells by confocal microscopy. Conofolidine increased oxidative stress, preceding apoptosis- and senescence-induction in most carcinoma cell lines as seen by enhanced ROS levels accompanied by increased NQO1 expression. Collectively, we present conofolidine as a putative potent anticancer agent capable of inducing heterogeneous modes of cancerous cell death in vitro, encouraging further preclinical evaluations of this natural product.

Fully automated viability and toxicity screening—A reliable all‐in‐one attempt

AbstractBackgroundThe CRISPR/Cas9 technology is nowadays a common tool for genome editing to achieve new insights into, for example, diagnostics and therapeutics in cancer and genetic disorders. Cell proliferation and anticancer drug response studies are widely used to evaluate the impact of editing. However, these assays are often time‐consuming, expensive, and reproducibility is an issue. To overcome this, we developed a fast and cheap assay that combines a fully automated multispectral fluorescence microscopy platform with a nuclei staining and open‐source software analysis.MethodsHere, we generated different LEDGF/p75 model cell lines to validate the effect on proliferation and chemosensitivity. Therefore, a fast protocol for an optimized all‐in‐one attempt for cytotoxicity screenings and proliferation analysis of adherent cells in a 96‐well plate format was established using differential staining with two fluorescent dyes (Hoechst 33342 and propidium iodide) for live/dead cell discrimination. Subsequently, an automated cell nuclei count and analysis were performed using bioimage informatics.ResultsWith the new established assay technology, up to 50,000 cells/well can be detected and analyzed in a 96‐well plate, resulting in a fast and accurate verification of viability and proliferation with consistency of 98% compared to manual counting. Our screening revealed that LEDGF depletion using CRISPR/Cas9 showed a diminished proliferation and chemosensitivity independent of cell line origin. Moreover, LEDGF depletion caused a significant increase in 𝛾H2AX foci, indicating a substantial increase in DNA double strand breaks. LEDGF/p75 overexpression enhanced proliferation and chemoresistance underlining the role of LEDGF in DNA damage response.ConclusionIndependent of cancer cell type, LEDGF/p75 is a central player in DNA damage repair and is implicated in chemoresistance. Moreover, our automated fluorescence biosensor technology allowed fast and reliable data acquisition without any fixation or additional washing steps. Additionally, data analysis was implemented using the modular open‐source software that can be adapted as needed.

СВЯЗЬ МЕЖДУ КЛЕТОЧНЫМ СТАРЕНИЕМ И ИЗМЕНЕНИЯМИ КОЛИЧЕСТВА И РАЗМЕРОВ ФОКУСОВ ФОСФОРИЛИРОВАННОГО ГИСТОНА Н2AX В ОБЛУЧЕННЫХ ФИБРОБЛАСТАХ ЧЕЛОВЕКА

Purpose: To analyze the relationship between cellular aging and changes in the number and size of phosphorylated histone H2AX (γH2AX) foci in human fibroblasts and their descendants (up to 15 passages) after exposure to low and high doses of X-ray radiation. Material and methods: The work was performed on a culture of human skin fibroblasts. Cells were irradiated in the exponential growth phase on an X-ray biological unit RUB RUST-M1 (Russia), equipped with two X-ray emitters, at a dose rate of 40 mGy/min (dose 100 mGy) or 850 mGy/min (doses 2000 and 5000 mGy) and temperature 4˚C. Immunocytochemical staining was used to assess the number and size of γH2AX foci and the proportion of proliferating cells using antibodies to γH2AX and Ki67 (a cell proliferation marker protein), respectively. To assess cellular senescence, the proportion of cells positive for senescence-associated β-galactosidase (CA-β-gal(+)) was analyzed. Statistical and mathematical analysis of the obtained data was carried out using the statistical software package Statistica 8.0 (StatSoft). Results: The studies showed that irradiation of cultured human fibroblasts at a low dose (100 mGy) does not lead to statistically significant changes in the number and size of γH2AX foci, as well as the proportion of non-proliferating and senescent cells in the progenies of irradiated cells up to the 15th passage after irradiation. The phenomenon of aging-associated persistence of an increased number and size of γH2AX foci in passages of cells irradiated at a dose of 5000 mGy was discovered. Mathematical analysis of the relationship between changes in the proportion of CA-β-gal(+) cells, the number and size of γH2AX foci in populations of irradiated cells indicates that radiation-induced cellular aging is more associated with the size, rather than the number, of γH2AX foci.

The impact of dose rate on responses of human lens epithelial cells to ionizing irradiation

The knowledge on responses of human lens epithelial cells (HLECs) to ionizing radiation exposure is important to understand mechanisms of radiation cataracts that are of concern in the field of radiation protection and radiation therapy. However, biological effects in HLECs following protracted exposure have not yet fully been explored. Here, we investigated the temporal kinetics of γ-H2AX foci as a marker for DNA double-strand breaks (DSBs) and cell survival in HLECs after exposure to photon beams at various dose rates (i.e., 150 kVp X-rays at 1.82, 0.1, and 0.033 Gy/min, and 137Cs γ-rays at 0.00461 Gy/min (27.7 cGy/h) and 0.00081 Gy/min (4.9 cGy/h)), compared to those in human lung fibroblasts (WI-38). In parallel, we quantified the recovery for DSBs and cell survival using a biophysical model. The study revealed that HLECs have a lower DSB repair rate than WI-38 cells. There is no significant impact of dose rate on cell survival in both cell lines in the dose-rate range of 0.033–1.82 Gy/min. In contrast, the experimental residual γ-H2AX foci showed inverse dose rate effects (IDREs) compared to the model prediction, highlighting the importance of the IDREs in evaluating radiation effects on the ocular lens.

CD276 enhances sunitinib resistance in clear cell renal cell carcinoma by promoting DNA damage repair and activation of FAK-MAPK signaling pathway.

This study aimed to explore the effect of CD276 expression on the sunitinib sensitivity of clear cell renal cell carcinoma (ccRCC) cell and animal models and the potential mechanisms involved. CD276 expression levels of ccRCC and normal samples were analyzed via online databases and real-time quantitative PCR (RT-qPCR). CD276 was knocked down in ccRCC cell models (sunitinib-resistant 786-O/R cells and sunitinib-sensitive 786-O cells) using shRNA transfection, and the cells were exposed to a sunitinib (2 µM) environment. Cells proliferation was then analyzed using MTT assay and colony formation experiment. Alkaline comet assay, immunofluorescent staining, and western blot experiments were conducted to assess the DNA damage repair ability of the cells. Western blot was also used to observe the activation of FAK-MAPK pathway within the cells. Finally, a nude mouse xenograft model was established and the nude mice were orally administered sunitinib (40mg/kg/d) to evaluate the in vivo effects of CD276 knockdown on the therapeutic efficacy of sunitinib against ccRCC. CD276 was significantly upregulated in both ccRCC clinical tissue samples and cell models. In vitro experiments showed that knocking down CD276 reduced the survival rate, IC50 value, and colony-forming ability of ccRCC cells. Knocking down CD276 increased the comet tail moment (TM) values and γH2AX foci number, and reduced BRCA1 and RAD51 protein levels. Knocking down CD276 also decreased the levels of p-FAK, p-MEK, and p-ERK proteins. Knocking down CD276 effectively improved the sensitivity of ccRCC cell and animal models to sunitinib treatment.

Exploring Southern Ecuador's Traditional Medicine: Biological Screening of Plant Extracts and Metabolites.

Ecuador stands as a nation inheriting a profound ancestral legacy in the utilization of medicinal plants, reflective of the rich biodiversity embraced by various ethnic groups. Despite this heritage, many of these therapeutic resources remain insufficiently explored concerning their toxicity and potential pharmacological effects. This study focused on a comprehensive evaluation of cytotoxicity and the potential subcellular targets within various extracts and nine isolated metabolites from carefully selected medicinal plants. Assessing their impact on the breast cancer cell line (MCF7), we subsequently examined the most active fractions for effects on the cell cycle, microtubule network, centrosome duplication, γH2AX foci, and E-cadherin. The investigated crude extracts and isolated compounds from Ecuadorian medicinal plants demonstrated cytotoxic effects, influencing diverse cellular pathways. These findings lend credence to the traditional uses of Ecuadorian medicinal plants, which have served diverse therapeutic purposes. Moreover, they beckon the exploration of the specific chemicals, whether in isolation or combination, responsible for these observed activities.

Cutibacterium acnes invades prostate epithelial cells to induce BRCAness as a possible pathogen of prostate cancer

AbstractBackgroundAbundant evidence suggests that chronic inflammation is linked to prostate cancer and that infection is a possible cause of prostate cancer.MethodsTo identify microbiota or pathogens associated with prostate cancer, we investigated the transcriptomes of 20 human prostate cancer tissues. We performed de novo assembly of nonhuman sequences from RNA‐seq data.ResultsWe identified four bacteria as candidate microbiota in the prostate, including Moraxella osloensis, Uncultured chroococcidiopsis, Cutibacterium acnes, and Micrococcus luteus. Among these, C. acnes was detected in 19 of 20 prostate cancer tissue samples by immunohistochemistry. We then analyzed the gene expression profiles of prostate epithelial cells infected in vitro with C. acnes and found significant changes in homologous recombination (HR) and the Fanconi anemia pathway. Notably, electron microscopy demonstrated that C. acnes invaded prostate epithelial cells and localized in perinuclear vesicles, whereas analysis of γH2AX foci and HR assays demonstrated impaired HR repair. In particular, BRCA2 was significantly downregulated in C. acnes–infected cells.ConclusionsThese findings suggest that C. acnes infection in the prostate could lead to HR deficiency (BRCAness) which promotes DNA double‐strand breaks, thereby increasing the risk of cancer development.

Muscone restores anoikis sensitivity in TMZ-resistant glioblastoma cells by suppressing TOP2A via the EGFR/Integrin β1/FAK signaling pathway

BackgroundTemozolomide (TMZ) resistance is the main obstacle faced by glioblastoma multiforme (GBM) treatment. Muscone, one of the primary active pharmacological ingredients of Shexiang (Moschus), can cross the blood-brain barrier (BBB) and is being investigated as an antineoplastic medication. However, muscone treatment for GBM has received little research, and its possible mechanisms are still unclear. PurposeThis study aims to evaluate the effect and the potential molecular mechanism of muscone on TMZ-resistant GBM cells. MethodsThe differentially expressed genes (DEGs) between TMZ-resistant GBM cells and TMZ-sensitive GBM cells were screened using GEO2R. By progressively raising the TMZ concentration, a relatively stable TMZ-resistant human GBM cell line was established. The drug-resistance traits of U251-TR cells were assessed via the CCK-8 assay and Western Blot analysis of MGMT and TOP2A expression. Cell viability, cell proliferation, cell migration ability, and drug synergism were detected by the CCK-8 assay, colony formation assay, wound healing assay, and drug interaction relationship test, respectively. Anoikis was quantified by Calcein-AM/EthD-1 staining, MTT assay, and flow cytometry. Measurements of cell cycle arrest, apoptosis, mitochondrial membrane potential (MMP), and reactive oxygen species (ROS) were performed using cell cycle staining, Annexin V-FITC/PI labeling, JC-1 assay, and ROS assay, respectively. DNA damage was measured by TUNEL assay, alkaline comet assay, and γ-H2AX foci assay. GEPIA was used to investigate the link between the anoikis marker (FAK)/drug resistance gene and critical proteins in the EGFR/Integrin β1 signaling pathway. Molecular docking was used to anticipate the probable targets of muscone. The intracellular co-localization and expression of EGFR and FAK were shown using immunofluorescence. The U251-TR cell line stably overexpressing EGFR was constructed using lentiviral transduction to assess the involvement of EGFR-related signaling in anoikis resistance. Western Blot was employed to detect the expression of migration-related proteins, cyclins, anoikis-related proteins, DNA damage/repair-related proteins, and associated pathway proteins. ResultsDEGs analysis identified 97 deregulated chemotherapy-resistant genes and 3779 upregulated genes in TMZ-resistant GBM cells. Subsequent experiments verified TMZ resistance and the hyper-expression of DNA repair-related genes (TOP2A and MGMT) in continuously low-dose TMZ-induced U251-TR cells. Muscone exhibited dose-dependent inhibition of U251-TR cell migration and proliferation, and its co-administration with TMZ showed the potential for enhanced therapeutic efficacy. By downregulating FAK, muscone reduced anoikis resistance in anchorage-independent U251-TR cells. It also caused cell cycle arrest in the G2/M phase by upregulating p21 and downregulating CDK1, CDK2, and Cyclin E1. Muscone-induced anoikis was accompanied by mitochondrial membrane potential collapse, ROS production, an increase in the BAX/Bcl-2 ratio, as well as elevated levels of Cytochrome c (Cyt c), cleaved caspase-9, and cleaved caspase-3. These findings indicated that muscone might trigger mitochondrial-dependent anoikis via ROS generation. Moreover, significant DNA damage, DNA double-strand breaks (DSBs), the formation of γ-H2AX foci, and a reduction in TOP2A expression are also associated with muscone-induced anoikis. Overexpression of EGFR in U251-TR cells boosted the expression of Integrin β1, FAK, β-Catenin, and TOP2A, whereas muscone suppressed the expression levels of EGFR, Integrin β1, β-Catenin, FAK, and TOP2A. Muscone may influence the expression of the key DNA repair enzyme, TOP2A, by suppressing the EGFR/Integrin β1/FAK pathway. ConclusionWe first demonstrated that muscone suppressed TOP2A expression through the EGFR/Integrin β1/FAK pathway, hence restoring anoikis sensitivity in TMZ-resistant GBM cells. These data suggest that muscone may be a promising co-therapeutic agent for enhancing GBM treatment, particularly in cases of TMZ-resistant GBM with elevated TOP2A expression.

Ataxia Telengectesia Protein Influences Bleomycin-Induced DNA Damage in Human Fibroblast Cells.

Human cancer is caused mainly by exposure to genotoxic chemicals; therefore, cellular defence mechanisms against genotoxic stress are crucial. Genetic factors are essential to maintaining genome stability and play a vital role in overcoming this by repairing the genome damage caused by any agent in order to prevent chromosomal instability. To examine the influence of the genetic makeup in specific ataxia-telangiectasia (ATM), we have examined non-cancerous fibroblast cell lines (HLF, AG1522 and L6) and cells with ATM mutated deficiency (GM4405). Cell lines were exposed in vitro to bleomycin (0, 40 and 80 µg/mL). The induced DNA damages were measured using endpoints including the micronucleus assay (MN) to measure chromosome damage and gamma-H2AX (γ-H2AX) assay to measure DNA damage/repair foci formation. An increase in DNA damage were observed in bleomycin-treated cells compared to unexposed controls (p < 0.05). A concentration-dependent increase of MN and γ-H2AX foci was observed and the sensitivity differed among the cell lines as follows: GM4405 > HLF > AG1522 > L6 for MN frequency and HLF > AG1522 > GM4405 > L6 for γ-H2AX foci. These findings suggest that the genetic makeup of the cellular genome would play an essential role in repairing bleomycin-induced DNA damage. Signalling of DNA damage, and the genes responsible for the repair process, could contribute to the differential susceptibility of different tissues to carcinomas induced by environmental mutagens.

Abstract PO2-04-14: Dual Inhibition of WEE1 and PKMYT1 Synergistically Overcomes CDK4/6 Inhibitor Resistance in Breast Cancer

Abstract Cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) are approved for the treatment of advanced estrogen receptor-positive, HER2-negative (ER+ve) breast cancer when combined with endocrine therapy. However, the emergence of resistance to CDK4/6 inhibitors poses a significant clinical challenge. This study investigates the mechanisms underlying CDK4/6 inhibitor resistance and identifies a common occurrence of high replication stress in triple-negative breast cancer (TNBC) and CDK4/6 inhibitor-resistant ER+ve breast cancers. While ER+ve breast cancer patients have benefited from targeted therapy, TNBC patients, particularly those without germline BRCA1/2 or PALB2 mutations, lack effective treatment options. TNBC and CDK4/6 inhibitor-resistant ER+ve breast cancer cells exhibit an increased dependence on cell cycle arrest to repair replication stress-induced DNA damage. Failure to exit the cell cycle results in excessive DNA damage, thereby limiting their proliferative potential. Based on these findings, we hypothesize that dual inhibition of WEE1 and PKMYT1, two kinases involved in G2/M cell cycle transition and crucial for cell cycle arrest and DNA damage repair, could synergistically inhibit tumor growth. Although WEE1 and PKMYT1 share a common function in promoting G2/M cell cycle transition through CDK1 phosphorylation, their functions are not entirely redundant, suggesting that targeting both kinases may elicit a synergistic response. Recent clinical trials have shown resistance to WEE1-targeted monotherapies, emphasizing the need for combining WEE1 inhibitors with other agents, such as PKMYT1 inhibitors. We demonstrate the synergistic effects of WEE1 inhibitor (MK1775/AZD1775) and PKMYT1 inhibitor (RP6306) in a panel of TNBC and ER+ve breast cancer cells with acquired palbociclib resistance (PalboR). Combination treatment with both inhibitors leads to excessive unrepaired DNA damage, as indicated by increased γH2AX foci following 48 hours of combination treatment, whereas single-agent treatments induce significantly lower levels of DNA damage. Furthermore, we observed the AZD1775/RP6306 combination decreases the expression of the DNA repair protein Rad51 in PalboR cells. To evaluate the clinical potential of dual WEE1 and PKMYT1 inhibition, we generated organoids from metastatic breast cancer lesions of patients who had progressed on CDK4/6 inhibitors for ex vivo studies. Our results demonstrate that dual inhibition of WEE1 and PKMYT1 is more effective than single-agent treatments in eliminating CDK4/6 inhibitor-resistant organoids. Additionally, using patient-derived xenograft mouse models from patients who had progressed on palbociclib and endocrine treatment, we show that the AZD1775/RP6306 combination exhibits superior tumor suppression effects compared to single agents. Overall, this study highlights the potential therapeutic benefits of dual inhibition of WEE1 and PKMYT1 in overcoming CDK4/6 inhibitor resistance in TNBC and ER+ve breast cancer patients. These findings provide a rationale for future clinical trials aimed at exploring the clinical utility of this combination therapy. Citation Format: Mei-Kuang Chen, Grace DeAlessandro, Tuyen Bui, Khandan Keyomarsi. Dual Inhibition of WEE1 and PKMYT1 Synergistically Overcomes CDK4/6 Inhibitor Resistance in 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 PO2-04-14.

Dynamic role of CUL4B in radiation-induced intestinal injury-regeneration.

CUL4B, a crucial scaffolding protein in the largest E3 ubiquitin ligase complex CRL4B, is involved in a broad range of physiological and pathological processes. While previous research has shown that CUL4B participates in maintaining intestinal homeostasis and function, its involvement in facilitating intestinal recovery following ionizing radiation (IR) damage has not been fully elucidated. Here, we utilized in vivo and in vitro models to decipher the role of CUL4B in intestinal repair after IR-injury. Our findings demonstrated that prior to radiation exposure, CUL4B inhibited the ubiquitination modification of PSME3, which led to the accumulation of PSME3 and subsequent negative regulation of p53-mediated apoptosis. In contrast, after radiation, CUL4B dissociated from PSME3 and translocated into the nucleus at phosphorylated histones H2A (γH2AX) foci, thereby impeding DNA damage repair and augmenting p53-mediated apoptosis through inhibition of BRCA1 phosphorylation and RAD51. Our study elucidated the dynamic role of CUL4B in the repair of radiation-induced intestinal damage and uncovered novel molecular mechanisms underlying the repair process, suggesting a potential therapeutic strategy of intestinal damage after radiation therapy for cancers.

Stromal Rigidity Stress Accelerates Pancreatic Intraepithelial Neoplasia Progression and Chromosomal Instability via Nuclear Protein Tyrosine Kinase 2 Localization

Since the mechanotransduction by stromal stiffness stimulates the rupture and repair of the nuclear envelope in pancreatic progenitor cells, accumulated genomic aberrations are under selection in the tumor microenvironment. Analysis of cell growth, micronuclei, and γH2AX foci links to mechanotransduction pressure in vivo during serial orthotopic passages of mouse KrasLSL-G12D/+;Trp53flox/flox;Pdx1-Cre (KPC) cancer cells in the tumor and in migrating through the size-restricted 3μm micropores. To search for pancreatic cancer cell-of-origin, analysis of single-cell datasets revealed that the ECM shapes an alternate route of acinar-ductal transdifferentiation of acinar cells into a central hub of elegantly restrained TOP2A-overexpressing cancer cells that spread out as unique cancer clusters with copy number amplifications in MYC-PTK2 locus and PIK3CA. High-PTK2 expression is associated with 171 differentially methylated CpG loci, 319 differentially expressed genes, and poor overall survival in TCGA-PAAD patients. Abolished RGD-integrin signaling by disintegrin KG blocked the PTK2 phosphorylation, increased cancer apoptosis, decreased VAV1 expression, and prolonged overall survival in the KPC mice. Decreases of αSMA deposition in the CD248 knockout KPC mice remodel the tissue stroma and downregulated TOP2A expression in the epithelium. In summary, stromal stiffness induces the onset of cells-of-origin of cancer by ectopic TOP2A expression, and the genomic amplification of MYC-PTK2 locus via alternative transdifferentiation of pancreatic progenitor cells is the vulnerability useful for disintegrin KG treatment against cells-of-origin cancer.

Abstract LB397: Simultaneous CRISPR-Cas9 induced double strand breaks causes chromosomal catastrophe in pancreatic cancers: A parallel comparison with ionizing radiation

Abstract CRISPR-Cas9, a highly effective gene editing tool, is a molecular scissor that induces double strand breaks (DSBs) at its targeted genomic locations. Ionizing radiation (IR), in contrast, generates DSBs and other DNA lesions, making it potentially more toxic than CRISPR-Cas9 induced DSBs. Alternatively, CRISPR-Cas9 might be more toxic as the Cas9 activity would continue if the DSB were repaired to wild type, resulting in more scissions per target. We designed multitarget sgRNAs targeting 0-16 sites in the human genome and performed similar dose-response experiments with IR (0-10 Gy) over 21 days on two pancreatic cancer (PC) cell lines. Growth inhibition was measured through clonogenicity and alamarBlue assays, and γ-H2AX staining performed to calculate DSBs. Surviving colonies from sgRNA transduction underwent whole genome sequencing (WGS) and targeted deep sequencing to quantify mutations. Cell growth was assessed through cell counting and sgRNA tag survival over time. Chromosomal changes were elucidated through chromosome breakage assays and XY FISH. We found that cytotoxicity increased as a function of both IR dose and number of sgRNA target site. At a comparable number of DSBs, CRISPR-Cas9 demonstrated higher cytotoxicity (~44% growth inhibition from 5-target sgRNA, ~15 γ-H2AX foci in the PC cells) compared to IR (9% inhibition from 0.5 Gy, ~25 foci). WGS of 5-cutter treated cells also revealed ~13 CRISPR-Cas9 induced DSBs in the PC cells. &amp;gt;99% cytotoxicity was achieved with 12-target sgRNA and 8 Gy. Moreover, sequencing of surviving colonies from sgRNA-treated cells confirmed lack of widespread off-target events. Notably, no surviving colonies could be obtained from the 12- and 16-cutter treated Panc10.05 cells and 8-14 cutters treated TS0111 cells.Both CRISPR-Cas9 and IR assays demonstrated delayed cell death, and cell death began 7 days after transduction of multitarget sgRNAs. Cytogenetic analyses on cells transduced with a 14-cutter sgRNA over 21 days revealed accumulation of karyotypic abnormalities peaking at day 14, and polyploidization peaking at day 10 and decreasing by day 21. Structural variant (SV) analyses from WGS data showed that the number of SVs per colony increased and peaked in 6-cutter colonies (average = 42 SVs), then decreased in 8- and 14-cutter colonies. Finally, surviving colonies that were resistant to 5-, 8-, and 16-cutter sgRNAs were re-challenged with their original multitarget sgRNA, 12-, and 14-cutter sgRNAs. Re-treating with original sgRNA showed no growth inhibition, while &amp;gt;95% cytotoxicity was observed by re-challenging them with 12- or 14-cutter sgRNAs.In conclusion, CRISPR-Cas9 kills pancreatic cancers by inducing chromosomal catastrophe, and resistance to original set of CRISPR-Cas9 induced DSBs can be easily overcome by targeting different sites. For the same number of DSBs, CRISPR-Cas9 was surprisingly more toxic than IR. Citation Format: Selina Shiqing K. Teh, Akhil Kotwal, Eitan Halper-Stromberg, Laura Morsberger, Kirsten Bowland, Alexis Bennett, Michael Goldstein, Ying S. Zou, James R. Eshleman. Simultaneous CRISPR-Cas9 induced double strand breaks causes chromosomal catastrophe in pancreatic cancers: A parallel comparison with ionizing radiation [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 LB397.

Discovery and characterization of sgRNA-sequence-independent DNA cleavage from CRISPR/Cas9 in mouse embryos

The CRISPR/Cas9 system can induce off-target effects in programmed gene editing, but there have been few reports on cleavage detection and their affection in embryo development. To study these events, sgRNAs with different off-target rates were designed and compared after micro-injected into mouse zygotes, and γH2AX was used for DNA cleavage sites analysis by immunostaining and CUT&Tag. Although the low off-target sgRNA were usually selected for production gene editing animals, γH2AX immunofluorescence indicated that there was a relative DSB peak at 15 h after Cas9 system injection, and the number of γH2AX foci at the peak was significantly higher in the low off-target sgRNA-injected group than in the control group. Further, the result of CUT&Tag sequencing analysis showed more double-strand breaks (DSBs) related sequences were detected in low off-target sgRNA-injected group than control and the distribution of DSB related sequences had no chromosome specificity. Gene Ontology (GO) annotation analysis of the DSB related sequences showed that these sequences were mainly concentrated at genes associated with some important biological processes, molecular functions, and cell components. In a conclusion, there are many sgRNA-sequence-independent DSBs in early mouse embryos when the Cas9 system is used for gene editing and the DSB related sequence could be detected and characterized in the genome. These results and method should also be considered in using or optimizing the Cas9 system.

Abstract 1987: PARP inhibitor (PARPi) rechallenge shows differential sensitivity in PARPi olaparib-resistant BRCA1-mutated (BRCA1m) high-grade serous ovarian cancer (HGSC)

Abstract Background: PARPis have changed the treatment paradigm in HGSC, particularly for women with BRCA mutations. PARPi, olaparib (O), is a standard of care maintenance therapy following platinum-based chemotherapy in newly diagnosed BRCA-mutated (BRCAm) HGSC. But patients ultimately develop resistance to O. We investigated whether rechallenge with different PARPi monotherapy could cause cytotoxicity in BRCAm HGSC after becoming O-resistant. We also aimed to identify possible mechanisms of actions of PARPi’s differential sensitivity. Methods: We developed a PARPi-resistant line (UWB-OlaJR) from BRCA1m PARPi-sensitive cells (UWB1.289) by gradient exposure of O with initial lower doses to a final concentration of 20 μM over 10 months. Four PARPis including O, niraparib (N), talazoparib (T), and veliparib (V) were tested. Cell growth was assessed using 5-day XTT and 10-day clonogenic assays. DNA damage and homologous recombination (HR) repair activity were evaluated using immunofluorescence (IF) staining of γH2AX and RAD51 foci, respectively. Replication fork (RF) dynamics was measured by DNA fiber assay. All data were repeated in triplicate and analyzed using t-test or one-way ANOVA. Data were shown as mean ± SD and P &amp;lt; 0.05 was considered statistically significant. Results: 5-day XTT assay shows a 53.7-fold increase in resistance to O in UWB-OlaJR relative to UWB1.289 (IC50 2.2 μM vs. 118.1 μM). Cross-resistance was observed with other 3 PARPis, showing increased IC50 values compared to its parental line (V: 23.4-fold, N: 160.5-fold, T: 229.6-fold). However, 10-day clonogenic assay showed no resistance against N (1.09-fold) and T (0.51-fold) in UWB-OlaJR, indicating differential sensitivity to different PARPis by a long-term cytotoxicity measure. Surprisingly, γH2AX foci did not increase in response to PARPis in UWB-OlaJR compared to UWB1.289 (O: 2.58-fold, V: 2.33-fold; N: 2.89-fold, T: 2.58-fold; all P &amp;lt; 0.05), suggesting possible restored DNA repair function. All four PARPis induced replication stress in both O-sensitive and -resistant cell lines as evidenced by decreased RF speed compared to untreated group (O: 0.57- and 0.7-fold, V: 0.68- and 0.74-fold, N: 0.47- and 0.47-fold, T: 0.47- and 0.52-fold; all P &amp;lt; 0.001). Notably, N and T treatments reduced fork speed to a greater extent than O and V in UWB-OlaJR. However, RF protection was not affected when UWB-OlaJR treated with different PARPis compared to UWB1.289 (O: 0.89-fold, V: 0.87-fold, N: 0.71-fold, T: 0.83-fold; all P &amp;lt; 0.05), suggesting that differential sensitivity to different PARPis was unlikely due to modulation of RF stabilization. Conclusions: Our findings demonstrate different PARPis may induce varied levels of cytotoxicity and replication stress in O-resistant BRCA1m HGSC, possibly via modulating alternative RF dynamics besides RF protection. Citation Format: Chi-Ting Shih, Tzu-Ting Huang, Jayakumar R. Nair, Jung-Min Lee. PARP inhibitor (PARPi) rechallenge shows differential sensitivity in PARPi olaparib-resistant BRCA1-mutated (BRCA1m) high-grade serous ovarian cancer (HGSC) [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 1987.

Abstract 689: BUB1 interferes with the repair of radiation-induced DNA damage to radiosensitize triple-negative breast cancer

Abstract Triple-negative breast cancer (TNBC) is associated with locoregional recurrence and low survival rates. Novel molecular targets are expected to improve the efficacy of radiation therapy (RT) in TNBC. BUB1, a mitotic checkpoint Serine/Threonine-protein kinase is known to impact chromosomal segregation during mitosis. However, its precise role in DNA damage repair in response to RT remains largely unknown. We demonstrated that BUB1 is overexpressed in BC (vs. normal breast) and considerably raised in TNBC with poor survival outcomes using differential gene expression analysis. In multiple TNBC cell lines, cell proliferation assays revealed that pharmacological (BAY1816032) or genomic (CRISPR) ablation of BUB1 was cytotoxic. Using clonogenic survival assays, we observed that BUB1 ablation radiosensitized TNBC cell lines (SUM159, MDA-MB-231, MDA-MB-468, BT-549) while its ablation did not radiosensitized breast epithelial cells (MCF10A). Furthermore, by depleting endogenous BUB1 (siRNAs and CRISPR) and reintroducing wild-type (WT) or kinase-dead (KD) BUB1, we demonstrated that inhibition of BUB1 kinase function is responsible for the radiosensitization phenotype. BUB1 ablation increased tumor doubling time in SUM159 xenografts when combined with radiation. Ki67 levels were also reduced in these tumors, confirming the efficacy of the combined treatment. BUB1 ablation led to persistent radiation-induced DNA DSB (gH2AX foci) indicating decreased DNA-DSB repair. BLRR assays confirmed that BUB1 impacts the non-homologous end joining (NHEJ) pathway. Biochemical analyses showed that BUB1 ablation stabilized total- and phospho- DNAPKcs (S2056) following RT such that half-lives could not be estimated. In contrast, RT alone caused BUB1 stabilization, but pre-treatment with BUB1i and DNAPKi prevented stabilization. To evaluate the recruitment of DDR proteins to the chromatin following RT, soluble nuclear and chromatin-enriched fractionations were performed which illustrated an increase in recruitment of phospho- and total-DNAPK, KAP1, and ATM to chromatin indicating that BUB1 is important in the activation and recruitment of critical NHEJ proteins to DSBs. In addition, BUB1 staining of TNBC TMAs demonstrated significant correlation between BUB1 protein expression with tumor grade and stage in TNBC patients. Our findings demonstrate that ablation of BUB1 sensitizes TNBC cell lines and xenograft to RT and BUB1 mediated radiosensitization may occur through NHEJ. Our results suggest that BUB1 may serve as a novel molecular target for radiosensitization in women with TNBC. Citation Format: Sushmitha Sriramulu, Shivani Thoidingjam, Pin Li, Stephen L. Brown, Farzan Siddiqui, Benjamin Movsas, Michael Green, Corey Speers, Shyam Nyati. BUB1 interferes with the repair of radiation-induced DNA damage to radiosensitize triple-negative 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 689.

Abstract 4777: A small-molecule SMUG1 activator enhances repair of 5-hydroxymethyl-2’-deoxyuridine-mediated pyrimidine lesions in DNA

Abstract Background: Pharmacological upregulation of DNA repair pathways presents a potentially promising approach for cancer prevention in populations that are genetically high-risk. SMUG1, an enzyme involved in base excision repair, removes uracil and certain oxidized bases from DNA to mitigate adverse genotoxic and mutagenic effects and represents a promising target for cancer therapy. A growing body of evidence suggests that SMUG1 is involved in tumorigenesis, and deficiency of SMUG1 correlates with poor prognosis in several cancers. We hypothesize that upregulation of SMUG1 by a small molecule activator may be a viable strategy for reducing tumorigenesis in at-risk populations. We report on the properties of SU0547 - a SMUG1 activator that was derived from the EGFR inhibitor drug gefitinib - which shows reduced kinase inhibition and potent activation of SMUG1 both in vitro and in human cell lines. Methods: MTT proliferation assays were used to screen for toxicity and to determine the effect of SU0547 on 5-hydroxymethyl-2’-deoxyuridine (5-hmdU)-treated cell lines. The effect of the compound on SMUG1 expression was determined by Western blot and RT-qPCR while its effect on DSBs via γH2AX expression in 5-hmdU-treated cells was determined by immunofluorescence and Western blot. Results: SU0547 activates SMUG1 by 347 ± 50% in vitro at 100 nM, with an AC50 of 2.55 ± 0.62 µM. We examined whether it can modulate SMUG1 activity in a panel of human cell lines by artificially inducing DNA damage with the native SMUG1 substrate 5-hmdU and treating cells with the activator. In all five human cancer cell lines tested, SU0547 caused the cells to become significantly more resistant to 5-hmdU by factors of 2.1 to 5.3-fold. A series of CRISPR-Cas9 generated SMUG1 KO cell lines showed resistance to 5-hmdU and SU0547 had no effect on these treated cells, confirming that this activator acts on endogenous SMUG1. To determine the effect of the activator on double-strand breaks (DSBs), cells were treated with 5-hmdU with or without the compound and DSBs were visualized and quantitated by examining γH2AX foci. 5-hmdU treatment induced γH2AX foci while SU0547 treatment significantly reduced these foci to near or below baseline levels. These results were confirmed using Western blot quantitation of γH2AX. Conclusions: We envision that this activator will serve as a useful tool for further studying the role of SMUG1 in mediating 5-hmdU toxicity and will enable the testing of our hypothesis that enhancing DNA repair processes may serve to inhibit mutagenesis and slow progression of pre-neoplastic lesions to invasive cancers associated with genomic instability. Citation Format: Lisa A. McPherson, Yixuan Gao, Shanthi Adimoolam, Samyuktha Suresh, David L. Wilson, Ishani Das, Elizabeth R. Park, Christine S. Ng, Yong Woong Jun, James M. Ford, Eric T. Kool. A small-molecule SMUG1 activator enhances repair of 5-hydroxymethyl-2’-deoxyuridine-mediated pyrimidine lesions in DNA [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 4777.

Abstract 2885: O-carborane-entrapped polymeric Micelles for Proton Boron Capture Therapy

Abstract Introduction: Proton boron capture therapy (PBCT) has the potential to enhance the biological effectiveness of proton therapy, based on proton-boron fusion reactions (11B + p → 3α + 8.7 MeV), which produce 3 α particles. In this study, we formulated o-carborane, a high boron content cage-like compound, into a polymeric micelle (M-carb) as a delivery tool to achieve effective delivery of the boronated compound to cancer cells and validated the enhancement of the biological effectiveness of proton therapy promoted by the uptake of o-carborane-entrapped in the micelle. Methods: O-carborane was effectively entrapped into an amphiphilic block copolymer to yield a stable polymeric micelle. The size and surface charge of the resulting M-carb were characterized by dynamic light scattering (DLS) and the uptake of M-carb in MIA PaCa-2 pancreatic cancer cells was measured by inductively coupled plasma mass spectrometry (ICP-MS). A colony formation assay was employed to assess the impact of M-carb on the survival of MIA PaCa-2 cells irradiated with a proton beam at the entrance and distal Spread-Out Bragg Peak (SOBP) positions at doses ranging from 0, 2, 5, and 8 Gy. The γH2AX foci were quantified by immunofluorescence to assess treatment-induced DNA double-strand breaks. Boron phenylalanine (BPA) was used as a control boron-carrying agent. Results: O-carborane-entrapped polymeric micelles (M-carb) had a diameter of about 60 nm and a relatively narrow size distribution (polydispersity index ~0.15) and possessed a slight negative charge. After 6 h incubated with M-carb at an equivalent concentration of 200 µM boron, MIA PaCa-2 cells were found to have taken up ~45 ng 11Boron per million cells. The colony formation assay demonstrated a significant decrease in the survival rate of MIA PaCa-2 cells after 8 Gy proton irradiation in the presence of 40 ppm of boron (corresponding to 4.61 µM BPA or 0.46 µM carborane) compared to irradiation treatment alone (p&amp;lt;0.05). At 8 Gy, the survival rates were 0.10, 0.07, and 0.04 for the following irradiation conditions: i) irradiation alone; ii) in the presence of BPA; in the presence of M-carb. At 2 and 5 Gy, these survival rate values were 0.78, 0.69, and 0.69 and 0.33, 0.19, and 0.16, respectively. Importantly, M-carb alone at the concentration used in proton irradiation experiments displayed no cytotoxicity. Immunofluorescence assays revealed that at both 2 Gy and 5 Gy, BPA and M-carb significantly increased γH2AX foci compared to irradiation alone (p&amp;lt;0.0001). Conclusion: M-carb was efficiently taken up by MIA PaCa-2 cells. PBCT mediated by M-carb or BPA enhanced the relative biological effectiveness of proton therapy with consequent improvement of its cell-killing efficacy in pancreatic cancer cells. This approach holds promise for advancing proton therapy as a new treatment modality for pancreatic cancer. Citation Format: Qiu-Xu Teng, Guodong Zhang, Haiyan Chen, Filipa Mendes, Narayan Sahoo, Célia Fernandes, António Paulo, Chun Li. O-carborane-entrapped polymeric Micelles for Proton Boron Capture Therapy [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 2885.

Abstract 2506: Novel biomarkers that predict response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer

Abstract Background: Neoadjuvant chemoradiotherapy (nCRT) followed by surgery is standard of care for locally advanced rectal cancer (LARC). About 20% patients receiving nCRT alone experience a pathologic complete response (pCR), while up to 25% patients exhibit a poor response. Currently, there is no biomarker to predict response to nCRT. We hypothesized that inherited ability to recognize and repair DNA damage, especially lethal double-strand breaks (DSBs), manifest in lymphocytes, would yield a reproducible test predicting therapeutic response to nCRT. Methods: Expression of DNA damage response (DDR) proteins was studied using peripheral blood lymphocytes (PBLs) from LARC patients and healthy controls. PBLs from LARC patients collected either before nCRT or after a standard course of ~5.5 weeks of nCRT were assessed by immunofluorescence (IF) for phospho-γH2AXSer139 and by Luminex multi-analyte platform (xMAP) approaches. The xMAP assay was modified from a qualitative to a semi-quantitative assay that measures the following DDR-associated proteins- total ATR, phospho-γH2AXSer139, total MDM2, phospho-Chk1S345, phospho-Chk2T68, phospho-p53S15, total p21. The analytical performance of the assay was assessed with vendor-provided reference controls and banked PBLs from healthy controls (n=50). LARC patients were segregated by neoadjuvant rectal (NAR) score to determine if tested biomarkers correlated with nCRT response. We used two independent sets of LARC biospecimens for xMAP analysis (set 1, n=48; set 2, n=44). Results: IF-based assessment: Using PBLs from LARC patients, we found that poor responders (PoR; NAR score&amp;gt;14; n=21) had significantly lower γH2AX foci than complete responders (CR; NAR score&amp;lt;1; n=21) (P&amp;lt;0.0001, logistic regression). No significant difference was observed in positive γH2AX foci from PBLs drawn pre-nCRT versus post-nCRT from the same patient (p=0.4961, n=11, Wilcoxon test). xMAP assay performance: The performance assessment showed linear sample curves, precision with acceptable inter- and intra-assay coefficients of variability, and high reproducibility with ~1% outliers identified in replicates. Clinical associations using xMAP assay: levels of six proteins (ATR, p-γH2AXSer139, MDM2, p-Chk1S345, p-Chk2T68, p-p53S15) significantly differentiated CRs from PoRs (p-values and False Discovery Rate ⇐ 1e-5). The strongest associations with nCRT response were observed for: ATR, MDM2 and γH2AX. Conclusion: 1) we standardized an xMAP assay to assess DDRs in human PBLs, and 2) found novel biomarkers that predict response to nCRT in LARC patients using minimally invasive PBL biospecimen. In ongoing work, we are using a larger biospecimen set to establish clinical validity parameters. Citation Format: Adria Hasan, Elena V. Demidova, Philip Czyzewicz, Karthik Devarajan, Margret B. Einarson, Donald Baldwin, Erica A. Golemis, Joshua E. Meyer, Sanjeevani Arora. Novel biomarkers that predict response to neoadjuvant chemoradiotherapy in locally advanced rectal 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 2506.