DNA-damaging Chemotherapeutics Research Articles

Immunohistochemical Evaluation of Schlafen 11 (SLFN11) Expression in Cancer in the Search of Biomarker-Informed Treatment Targets: A Study of 127 Entities Represented by 6658 Tumors.

Schlafen 11 (SLFN11), a DNA/RNA helicase, acts as a regulator of cellular response to replicative stress and irreversibly triggers replication block and cell death. Several preclinical in vitro studies and clinical trials established that SLFN11 expression predicts outcomes in patients with advanced cancer treated with DNA-damaging chemotherapeutics and more recently with poly(ADP-ribose) polymerase inhibitors. SLFN11 expression status remains unknown in many cancer types, especially in mesenchymal tumors. This study evaluated a cohort of well characterized 3808 epithelial and 2850 mesenchymal and neuroectodermal tumors for SLFN11 expression using immunohistochemistry. Nuclear SLFN11 expression was rare in some of the most common carcinomas, for example, hepatocellular (1%), prostatic (2%), colorectal (5%), or breast (16%) cancers. In contrast, other epithelial tumors including mesotheliomas (92%), clear cell renal cell carcinomas (79%), small cell lung cancers (76%), squamous cell carcinomas of the tonsil (89%) and larynx (71%), or ovarian serous carcinomas (69%) were mostly SLFN11-positive. Compared with epithelial malignancies, SLFN11 expression was overall higher in neuroectodermal and mesenchymal tumors. Most positive entities included desmoplastic small round cell tumor (100%), Ewing sarcoma (92%), undifferentiated sarcoma (92%), solitary fibrous tumor (91%), dedifferentiated liposarcoma (89%), synovial sarcoma (86%), and malignant peripheral nerve sheath tumor (85%). Also, this study identifies tumors with potentially worse response to DNA-damaging drugs including antibody drug conjugates due to the absence of SLFN11 expression. Such entities may benefit from alternative treatments or strategies to overcome SLFN11 deficiency-related drug resistance. Our approach and results should serve as a foundation for future biomarker-associated clinical trials.

LINC01021 Attenuates Expression and Affects Alternative Splicing of a Subset of p53-Regulated Genes.

Loss of the p53-inducible LINC01021 in p53-proficient CRC cell lines results in increased sensitivity to DNA-damaging chemotherapeutics. Here, we comprehensively analyze how LINC01021 affects the p53-induced transcriptional program. Using a CRISPR/Cas9-approach, we deleted the p53 binding site in the LINC01021 promoter of SW480 colorectal cancer cells and subjected them to RNA-Seq analysis after the activation of ectopic p53. RNA affinity purification followed by mass spectrometry was used to identify proteins associated with LINC01021. Loss of the p53-inducibility of LINC01021 resulted in an ~1.8-fold increase in the number of significantly regulated mRNAs compared to LINC01021 wild-type cells after ectopic activation of p53. A subset of direct p53 target genes, such as NOXA and FAS, displayed significantly stronger induction when the p53-inducibility of LINC01021 was abrogated. Loss of the p53-inducibility of LINC01021 resulted in alternative splicing of a small number of mRNAs, such as ARHGAP12, HSF2, and LYN. Several RNA binding proteins involved in pre-mRNA splicing were identified as interaction partners of LINC01021 by mass spectrometry. Our results suggest that LINC01021 may restrict the extent and strength of p53-mediated transcriptional changes via context-dependent regulation of the expression and splicing of a subset of p53-regulated genes.

Tolerance to colibactin correlates with homologous recombination proficiency and resistance to irinotecan in colorectal cancer cells

The bacterial genotoxin colibactin promotes colorectal cancer (CRC) tumorigenesis, but systematic assessment of its impact on DNA repair is lacking, and its effect on response to DNA-damaging chemotherapeutics is unknown. We find that CRC cell lines display differential response to colibactin on the basis of homologous recombination (HR) proficiency. Sensitivity to colibactin is induced by inhibition of ATM, which regulates DNA double-strand break repair, and blunted by HR reconstitution. Conversely, CRC cells chronically infected with colibactin develop a tolerant phenotype characterized by restored HR activity. Notably, sensitivity to colibactin correlates with response to irinotecan active metabolite SN38, in both cell lines and patient-derived organoids. Moreover, CRC cells that acquire colibactin tolerance develop cross-resistance to SN38, and a trend toward poorer response to irinotecan is observed in a retrospective cohort of CRCs harboring colibactin genomic island. Our results shed insight into colibactin activity and provide translational evidence on its chemoresistance-promoting role in CRC.

Targeting WEE1 kinase as a p53-independent therapeutic strategy in high-risk and relapsed acute lymphoblastic leukemia

BackgroundOutcomes for patients with relapsed acute lymphoblastic leukemia (ALL) are poor and there is a need for novel therapies to improve outcomes. Targeted inhibition of WEE1 with small-molecule inhibitor adavosertib (AZD1775) has emerged as a therapeutic strategy to sensitize cancer cells to DNA-damaging chemotherapeutics, particularly in the context of TP53-mutated tumors. However, WEE1 inhibition as a potential therapeutic strategy for patients with high-risk and relapsed ALL, including those with TP53 mutations, has not been definitively evaluated.MethodsAnti-leukemic effects of adavosertib were investigated using a relapsed TP53 isogenic cell model system, primary patient, and patient-derived ALL samples (n = 27) in an ex vivo co-culture model system with bone marrow-derived mesenchymal stem cells. Combination effects with drugs currently used for relapsed ALL were quantified by Excess over Bliss analyses. Investigations for alterations of cell cycle and apoptosis as well as related proteins were examined by flow cytometry and Western blot, respectively.ResultsOur study demonstrates the potent anti-leukemic activity of the clinically advanced WEE1 inhibitor adavosertib in a large majority (n = 18/27) of high-risk and relapsed ALL specimens at lower than clinically attainable concentrations, independent of TP53 mutation status. We show that treatment with adavosertib results in S-phase disruption even in the absence of DNA-damaging agents and that premature mitotic entry is not a prerequisite for its anti-leukemic effects. We further demonstrate that WEE1 inhibition additively and synergistically enhances the anti-leukemic effects of multiple conventional chemotherapeutics used in the relapsed ALL treatment setting. Particularly, we demonstrate the highly synergistic and cytotoxic combination of adavosertib with the nucleoside analog cytarabine and provide mechanistic insights into the combinational activity, showing preferential engagement of apoptotic cell death over cell cycle arrest. Our findings strongly support in vivo interrogation of adavosertib with cytarabine in xenograft models of relapsed and high-risk ALL.ConclusionsTogether, our data emphasize the functional importance of WEE1 in relapsed ALL cells and show WEE1 as a promising p53-independent therapeutic target for the improved treatment of high-risk and relapsed ALL.

LncRNA CTBP1-DT-encoded microprotein DDUP sustains DNA damage response signalling to trigger dual DNA repair mechanisms.

Sustaining DNA damage response (DDR) signalling via retention of DDR factors at damaged sites is important for transmitting damage-sensing and repair signals. Herein, we found that DNA damage provoked the association of ribosomes with IRES region in lncRNA CTBP1-DT, which overcame the negative effect of upstream open reading frames (uORFs), and elicited the novel microprotein DNA damage-upregulated protein (DDUP) translation via a cap-independent translation mechanism. Activated ATR kinase-mediated phosphorylation of DDUP induced a drastic ‘dense-to-loose’ conformational change, which sustained the RAD18/RAD51C and RAD18/PCNA complex at damaged sites and initiated RAD51C-mediated homologous recombination and PCNA-mediated post-replication repair mechanisms. Importantly, treatment with ATR inhibitor abolished the effect of DDUP on chromatin retention of RAD51C and PCNA, thereby leading to hypersensitivity of cancer cells to DNA-damaging chemotherapeutics. Taken together, our results uncover a plausible mechanism underlying the DDR sustaining and might represent an attractive therapeutic strategy in improvement of DNA damage-based anticancer therapies.

Abstract 1516: The role of protein tyrosine kinases in DNA mismatch repair

Abstract The DNA mismatch repair (MMR) pathway and its regulation are necessary for genomic stability. Cells deficient in MMR exhibit increased expansion and contraction of short repeat sequences in the genome, termed microsatellite instability (MSI). Loss of MMR also results in resistance to certain classes of DNA damaging chemotherapeutics. The standard treatment option for most patients includes chemotherapy, which has toxic side effects. Immunotherapy has recently been utilized as a treatment for various cancers. MSI-high cancers respond better to immunotherapy treatment compared to microsatellite stable (MSS) cancers. This increased response is believed to be due to the higher mutation frequencies associated with the MSI-high tumors, which lead to greater neoantigen production. The primary proteins required for MMR are known, however regulation of the pathway is not well understood. The MLH1 protein is critical for MMR and is required for the excision licensing of the daughter DNA strand. Loss or mutation of MLH1 leads to defective MMR, increased mutation frequency, and MSI. Recent studies by our laboratory and others have shown that treatment with a tyrosine kinase inhibitor, Imatinib, leads to decreased MLH1 protein expression, and resistance to MMR-dependent apoptosis. These observations suggest a link between Imatinib-sensitive protein tyrosine kinases (PTKs) and the regulation of MMR. We show that MLH1 protein reduction is not occurring at the mRNA level and is thought to be post-transcriptional. We have identified the Imatinib sensitive target most likely responsible for the MLH1 reduction phenotype. We show that the target protein and MLH1 have a physical interaction that likely prevents degradation targeting of MLH1 by the Hsp70 chaperone. A detailed understanding of MMR regulation by PTKs would significantly advance the knowledge in the field of MMR and have important implications for immunotherapy strategies. Citation Format: Hannah Daniels, Breanna Knicely, Eva M. Goellner. The role of protein tyrosine kinases in DNA mismatch repair [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1516.

Abstract 6384: Morphological and functional plasticity of mitochondria promotes chemotherapy resistance in triple negative breast cancer

Abstract Mitochondrial metabolism plays a key role in triple negative breast cancer (TNBC) aggressiveness. As TNBC has limited targeted therapy options, chemotherapies remain the mainstay treatment. Nearly 50% of TNBC patients harbor substantial residual cancer following chemotherapy, leading to high rates of recurrence. Using longitudinal biopsies from orthotopic patient-derived xenograft (PDX) models and TNBC patients, we found residual tumors following chemotherapy transitioned to a unique metabolic state characterized by high mitochondrial oxidative phosphorylation (oxphos). This state was transient, with tumors reverting to their baseline glycolysis-high phenotype when they were allowed to regrow in the absence of treatment. Using genomic sequencing and cellular barcode-mediated clonal tracking, we found this mechanism of chemoresistance arose in the absence of clonal selection, suggesting chemotherapy induced plastic (i.e., non-genomic) programs enabling cell survival following treatment. Blocking oxphos with an inhibitor of electron transport chain Complex I (IACS010759; PMID:29892070) was significantly more efficacious against residual than pre-treated tumors (PMID:30996079), providing evidence that dynamic metabolic phenotypes represent targetable therapeutic vulnerabilities for TNBC. Using longitudinal samples collected from PDX models undergoing treatments with anthracyclines, platinums, and/or taxanes, we visualized and quantified mitochondrial structure in two- and three-dimensions by electron microscopy. These studies revealed extensive alteration of mitochondrial structure and number in residual tumor cells, and these changes reverted when residual tumors were allowed to regrow in the absence of treatment. We then administered chemotherapeutics to human TNBC cells, revealing that DNA-damaging chemotherapeutics increased mitochondrial elongation, but microtubule poisons increased mitochondrial fragmentation. These findings suggested chemotherapeutics may alter the dynamics of mitochondrial fission and fusion in TNBC cells. These structural changes were accompanied by increased or decreased oxphos rates, glucose-driven TCA cycle flux, and mitochondrial content, respectively. Driving mitochondrial fusion by genetic or pharmacologic inhibition of the mitochondrial fission factor Drp1 increased oxphos and chemoresistance, whereas driving mitochondrial fission by genetic or pharmacologic inhibition of the mitochondrial fusion protein Opa1 decreased oxphos and chemoresistance. These findings provide evidence that modulating mitochondrial fission and fusion may be a promising strategy to overcome metabolic states contributing to chemoresistance in TNBC. Our ongoing investigations are aimed at rational targeted therapies and scheduling approaches to overcome chemoresistance in in vivo models of TNBC. Citation Format: Lily Baek, Junegoo Lee, Mariah J. Berner, Katherine E. Pendleton, Emily B. Goff, Karen Wang, James P. Barrish, Bora Lim, Philip J. Lorenzi, Weston Porter, Michael T. Lewis, Gloria V. Echeverria. Morphological and functional plasticity of mitochondria promotes chemotherapy resistance in triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6384.

Abstract PR009: Investigating dynamics of the mitochondrial network in triple negative breast cancer chemotherapy resistance

Abstract Triple negative breast cancer (TNBC) is an aggressive disease with extremely limited targeted therapeutic options. Thus, standard cytotoxic chemotherapies (typically sequential and/or combined anthracyclines, taxanes, and/or platinums) remain a mainstay treatment for this subtype of breast cancer. Nearly 50% of TNBC patients harbor substantial residual cancer burden following standard chemotherapy treatment, leading to high rates of recurrence and death (PMID:28135148). Using longitudinal biopsies from orthotopic patient-derived xenograft (PDX) models and TNBC patients, we found that residual tumors following chemotherapy transitioned to a unique metabolic state characterized by high mitochondrial oxidative phosphorylation (oxphos). This metabolic state was transient, with tumors reverting to their baseline glycolysis-high phenotype when they were allowed to regrow in the absence of treatment. Using genomic sequencing and cellular barcode-mediated clonal tracking, we found this mechanism of chemoresistance arose in the absence of clonal selection, suggesting chemotherapy induced plastic (i.e., non-genomic) programs enabling cell survival following treatment. Oxphos inhibition using a specific inhibitor of electron transport chain Complex I (IACS010759; PMID:29892070) was significantly more efficacious against residual, rather than treatment-naive tumors (PMID:30996079), providing evidence that dynamic metabolic phenotypes represent targetable therapeutic vulnerabilities for TNBC. Mechanisms controlling mitochondrial bioenergetics are numerous but their roles in driving metabolic phenotypes of chemoresistant TNBC are not understood. We find that residual tumor cells following chemotherapy treatment have altered mitochondrial network morphology. Mitochondrial fission and fusion are well established regulators of mitochondrial morphology, yet their functional impacts on bioenergetic output of mitochondria is highly context dependent. Our analyses of mitochondrial structure in TNBC cells and PDX tumors reveal that while DNA-damaging chemotherapeutics (anthracyclines, platinums) increased mitochondrial elongation, microtubule-stabilizing chemotherapeutics (taxanes) increased mitochondrial fragmentation. This was accompanied by increased or decreased oxphos rates and mitochondrial content, respectively. Interestingly, these structural changes were reverted in PDX tumors that were allowed to regrow in the absence of treatment, suggesting mitochondrial adaptations are plastic in vivo. Using pharmacologic agents in TNBC cells, we found that mitochondrial fusion increased oxphos and chemoresistance, whereas mitochondrial fission decreased oxphos and chemoresistance. Further, knockdown of OPA1 or MFN2, mediators of mitochondrial inner and outer membrane fusion, respectively, diminished mitochondrial fusion, oxphos, and chemoresistance. Based on these findings, we hypothesize therapeutic targeting of mediators of mitochondrial network adaptability may be a promising strategy to overcome plastic metabolic states indued by chemotherapeutics in TNBC. Citation Format: Lily Baek, Mariah Berner, Junegoo Lee, Katherine Pendleton, Karen Wang, Emily B. Goff, James P. Barrish, Bora Lim, Michael T. Lewis, Philip L. Lorenzi, Weston Porter, Gloria V. Echeverria. Investigating dynamics of the mitochondrial network in triple negative breast cancer chemotherapy resistance [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr PR009.

Polycarcin V induces DNA-damage response and enables the profiling of DNA-binding proteins.

To maintain genomic integrity and avoid diseases, the DNA-damage response (DDR) not only detects and repairs DNA lesions, but also contributes to the resistance to DNA-damaging chemotherapeutics. Targeting the DDR plays a significant role in drug discovery using the principle of synthetic lethality. The incomplete current knowledge of the DDR encouraged us to develop new strategies to identify and study its components and pathways. Polycarcin V, belonging to the C-aryl glycoside natural products, is a light-activatable DNA-intercalating agent that causes DNA damage by forming a covalent [2+2] cycloadduct with thymine residue under 365-450 nm of light irradiation in a DNA-sequence-independent manner. Taking advantage of the light-activatable feature and temporal control of DDR, we designed and synthesized polycarcin V-based bifunctional chemical probes, including one that cross-links DNA to DNA-binding protein to explore the DDR induced by polycarcin V and uncover novel DNA-protein interactions. Utilizing this chemical probe and activity-based protein profiling-stable isotope labeling with amino acids in cell culture, we identified 311 DNA-binding protein candidates, including known DDR factors and additional proteins that may be of interest in discovering new biology. We validated our approach by showing that our probe could specifically cross-link proteins involved in nucleotide excision repair (NER) that repair bulky DNA adducts. Our studies showed that the [2+2] cycloadduct formed by polycarcin V could indeed be repaired by NER in vivo. As a DNA-damaging agent, polycarcin V or its drug-like derivative plus blue light showed promising properties for psoriasis treatment, suggesting that it may itself hold promise for clinic applications.

Abstract P4-01-08: Morphological and functional plasticity of mitochondria in chemoresistant triple negative breast cancer

Abstract BACKGROUND: Neoadjuvant chemotherapy (NACT) used for triple negative breast cancer (TNBC) eradicates tumors in only 45% of patients. TNBC patients with substantial residual cancer burden have poor metastasis free and overall survival rates. Therefore, understanding the mechanisms of resistance to standard chemotherapy is essential. Our previous studies found mitochondrial oxidative phosphorylation (OXPHOS) was elevated and was a unique therapeutic dependency of residual tumor cells that survived after NACT. Mitochondria are morphologically plastic and dynamic organelles that continuously cycle between fission and fusion to maintain mitochondrial integrity and metabolic homeostasis. Mitochondrial fusion is thought to support OXPHOS through maintenance of the mitochondrial genome (mtDNA) which encodes 13 subunits of electron transport chain complexes. On the other hand, mitochondrial fission can be the precursor to mitophagy, the selective degradation of damaged mitochondria. We are investigating how mitochondrial structure dynamics impact metabolic states driving chemoresistance in TNBC. Methods We used a previously characterized orthotopic patient-derived xenograft (PDX) mouse model derived from the primary tumor of a treatment-naïve metastatic TNBC patient. After treatment with a standard NACT regimen, combined Adriamycin (aka doxorubicin) and cyclophosphamide (AC), we observed initial partial response followed by tumor regrowth. We collected PDX tumors at three time points: pre-treatment, post-AC residual (when tumors reached the volume nadir), and post-AC tumors that later regrew to the starting tumor volume. We used transmission electron microscopy (TEM) and immunohistochemical (IHC) analysis of human mitochondria to assess mitochondrial morphology and mass, respectively. For in vitro assays, we assessed mitochondria morphology, mtDNA content, and OXPHOS activity in TNBC cells treated with two different types of chemotherapeutic drugs, DNA-damaging agents (doxorubicin and carboplatin) and a microtubule-stabilizing agent (paclitaxel). To examine metabolic adaptations upon chemotherapy, we conducted 13C-glucose and glutamine flux metabolomics. To pharmaceutically perturb mitochondrial morphology, we used Mdivi-1 and Silibinin, known to induce mitochondrial fusion and fission, respectively. We assessed cell growth by Incucyte real-time imaging. Results: Analyses of residual PDX tumors after in vivo AC treatment revealed increased mitochondrial content, and increased average mitochondrial length in residual tumor cells. Metabolomic analysis of TNBC cells revealed all three chemotherapies induced glucose, but not glutamine, flux through the TCA cycle. Flux through glycolysis was not affected by chemotherapies. Treatment with doxorubicin and carboplatin, increased mitochondrial elongation, mtDNA content, and OXPHOS activity. Conversely, paclitaxel treatment reduced mitochondrial length and OXPHOS activity. We observed Mdivi-1 induced fusion concomitant with increased OXPHOS activity, while treatment with Silibinin reduced fusion and decreased OXPHOS. We next tested if induction of mitochondrial fission enhanced chemosensitivity. Sequential treatment of TNBC cells with DNA-damaging chemotherapeutics followed by Silibinin perturbed OXPHOS and resulted in enhanced cell killing. Conclusion: These findings establish a functional role for mitochondrial structure in chemotherapeutic response and metabolic reprogramming, which may confer a survival advantage to TNBC cells. Given the increased chemosensitivity we observed after pharmacologic inhibition of mitochondrial fusion, our study suggests perturbing mitochondrial structure adaptations may provide an opportunity to overcome TNBC chemoresistance in the neoadjuvant setting. Citation Format: Lily Mokryun Baek, Junegoo Lee, James P. Barrish, Bora Lim, Jeffrey T. Chang, Phillip L. Lorenzi, Weston Porter, Gloria V. Echeverria. Morphological and functional plasticity of mitochondria in chemoresistant triple negative breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P4-01-08.

New Synthetic Lethality Re-Sensitizing Platinum-Refractory Cancer Cells to Cisplatin In Vitro: The Rationale to Co-Use PARP and ATM Inhibitors.

The pro-apoptotic tumor suppressor BIN1 inhibits the activities of the neoplastic transcription factor MYC, poly (ADP-ribose) polymerase-1 (PARP1), and ATM Ser/Thr kinase (ATM) by separate mechanisms. Although BIN1 deficits increase cancer-cell resistance to DNA-damaging chemotherapeutics, such as cisplatin, it is not fully understood when BIN1 deficiency occurs and how it provokes cisplatin resistance. Here, we report that the coordinated actions of MYC, PARP1, and ATM assist cancer cells in acquiring cisplatin resistance by BIN1 deficits. Forced BIN1 depletion compromised cisplatin sensitivity irrespective of Ser15-phosphorylated, pro-apoptotic TP53 tumor suppressor. The BIN1 deficit facilitated ATM to phosphorylate the DNA-damage-response (DDR) effectors, including MDC1. Consequently, another DDR protein, RNF8, bound to ATM-phosphorylated MDC1 and protected MDC1 from caspase-3-dependent proteolytic cleavage to hinder cisplatin sensitivity. Of note, long-term and repeated exposure to cisplatin naturally recapitulated the BIN1 loss and accompanying RNF8-dependent cisplatin resistance. Simultaneously, endogenous MYC was remarkably activated by PARP1, thereby repressing the BIN1 promoter, whereas PARP inhibition abolished the hyperactivated MYC-dependent BIN1 suppression and restored cisplatin sensitivity. Since the BIN1 gene rarely mutates in human cancers, our results suggest that simultaneous inhibition of PARP1 and ATM provokes a new BRCAness-independent synthetic lethal effect and ultimately re-establishes cisplatin sensitivity even in platinum-refractory cancer cells.

Abstract 2144: STAT3 regulates the expression of XRCC1 in triple negative breast cancer

Abstract Background: Base excision repair (BER) addresses base lesions and abasic sites induced by endogenous and exogenous environmental stresses. XRCC1 is a scaffold protein that facilitates and coordinates the BER repair machinery. Alterations in the protein and gene expression of XRCC1 have been observed in a multitude of cancers, including triple negative breast cancers (TNBC). Increased expression of XRCC1 is associated with aggressiveness and resistance to DNA damaging chemotherapeutics. However, only two transcription factors, E2F1 and Sp1 have been implicated in the transcriptional regulation of XRCC1 to date. Methods: Utilizing promoter luciferase, transcription factor promoter binding ELISA, and chromatin immunoprecipitation (CHiP), STAT3 binding was identified and mapped in the XRCC1 promoter. Results: In the current study, we identify a STAT3 binding site within the XRCC1 promoter. Importantly, STAT3 regulation of XRCC1 appears to be constitutive in TNBC cell line models where STAT3 is highly activated. In HEK293T cells, the STAT3 binding site shows low occupancy under basal growth condition, but STAT3 regulation of XRCC1 can be stimulated by cytokine or mitogenic signaling by IL-6 and epidermal growth factor (EGF). Summary: STAT3 conditionally regulates XRCC1 under specific stress conditions to promote BER. In TNBC, the overexpression of XRCC1 by activated STAT3 likely contributes to increased resistance to DNA damaging chemotherapeutics. Citation Format: Griffin M. Wright, Natalie R. Gassman. STAT3 regulates the expression of XRCC1 in triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2144.

Activated STAT3 Is a Novel Regulator of the XRCC1 Promoter and Selectively Increases XRCC1 Protein Levels in Triple Negative Breast Cancer.

Base Excision Repair (BER) addresses base lesions and abasic sites induced by exogenous and endogenous stressors. X-ray cross complementing group 1 (XRCC1) functions as a scaffold protein in BER and single-strand break repair (SSBR), facilitating and coordinating repair through its interaction with a host of critical repair proteins. Alterations of XRCC1 protein and gene expression levels are observed in many cancers, including colorectal, ovarian, and breast cancer. While increases in the expression level of XRCC1 are reported, the transcription factors responsible for this up-regulation are not known. In this study, we identify the signal transducer and activator of transcription 3 (STAT3) as a novel regulator of XRCC1 through chromatin immunoprecipitation. Activation of STAT3 through phosphorylation at Y705 by cytokine (IL-6) signaling increases the expression of XRCC1 and the occupancy of STAT3 within the XRCC1 promoter. In triple negative breast cancer, the constitutive activation of STAT3 upregulates XRCC1 gene and protein expression levels. Increased expression of XRCC1 is associated with aggressiveness and resistance to DNA damaging chemotherapeutics. Thus, we propose that activated STAT3 regulates XRCC1 under stress and growth conditions, but constitutive activation in cancers results in dysregulation of XRCC1 and subsequently BER and SSBR.

Small-molecule screen reveals synergy of cell cycle checkpoint kinase inhibitors with DNA-damaging chemotherapies in medulloblastoma.

Medulloblastoma (MB) consists of four core molecular subgroups with distinct clinical features and prognoses. Treatment consists of surgery, followed by radiotherapy and cytotoxic chemotherapy. Despite this intensive approach, outcome remains dismal for patients with certain subtypes of MB, namely, MYC-amplified Group 3 and TP53-mutated SHH. Using high-throughput assays, six human MB cell lines were screened against a library of 3208 unique compounds. We identified 45 effective compounds from the screen and found that cell cycle checkpoint kinase (CHK1/2) inhibition synergistically enhanced the cytotoxic activity of clinically used chemotherapeutics cyclophosphamide, cisplatin, and gemcitabine. To identify the best-in-class inhibitor, multiple CHK1/2 inhibitors were assessed in mice bearing intracranial MB. When combined with DNA-damaging chemotherapeutics, CHK1/2 inhibition reduced tumor burden and increased survival of animals with high-risk MB, across multiple different models. In total, we tested 14 different models, representing distinct MB subgroups, and data were validated in three independent laboratories. Pharmacodynamics studies confirmed central nervous system penetration. In mice, combination treatment significantly increased DNA damage and apoptosis compared to chemotherapy alone, and studies with cultured cells showed that CHK inhibition disrupted chemotherapy-induced cell cycle arrest. Our findings indicated CHK1/2 inhibition, specifically with LY2606368 (prexasertib), has strong chemosensitizing activity in MB that warrants further clinical investigation. Moreover, these data demonstrated that we developed a robust and collaborative preclinical assessment platform that can be used to identify potentially effective new therapies for clinical evaluation for pediatric MB.

Vulnerability to low-dose combination of irinotecan and niraparib in ATM-mutated colorectal cancer

BackgroundDespite the advancements in new therapies for colorectal cancer (CRC), chemotherapy still constitutes the mainstay of the medical treatment. For this reason, new strategies to increase the efficacy of chemotherapy are desirable. Poly-ADP-Ribose Polymerase inhibitors (PARPi) have shown to increase the activity of DNA damaging chemotherapeutics used in the treatment of CRC, however previous clinical trials failed to validate these results and pointed out dose-limiting toxicities that hamper the use of such combinations in unselected CRC patients. Nevertheless, in these studies little attention was paid to the mutational status of homologous recombination repair (HRR) genes.MethodsWe tested the combination of the PARPi niraparib with either 5-fluorouracil, oxaliplatin or irinotecan (SN38) in a panel of 12 molecularly annotated CRC cell lines, encompassing the 4 consensus molecular subtypes (CMSs). Synergism was calculated using the Chou-Talalay method for drug interaction. A correlation between synergism and genetic alterations in genes involved in homologous recombination (HR) repair was performed. We used clonogenic assays, mice xenograft models and patient-derived 3D spheroids to validate the results. The induction of DNA damage was studied by immunofluorescence.ResultsWe showed that human CRC cell lines, as well as patient-derived 3D spheroids, harboring pathogenic ATM mutations are significantly vulnerable to PARPi/chemotherapy combination at low doses, regardless of consensus molecular subtypes (CMS) and microsatellite status. The strongest synergism was shown for the combination of niraparib with irinotecan, and the presence of ATM mutations was associated to a delay in the resolution of double strand breaks (DSBs) through HRR and DNA damage persistence.ConclusionsThis work demonstrates that a numerically relevant subset of CRCs carrying heterozygous ATM mutations may benefit from the combination treatment with low doses of niraparib and irinotecan, suggesting a new potential approach in the treatment of ATM-mutated CRC, that deserves to be prospectively validated in clinical trials.

1951P Niraparib and irinotecan combination in ATM-mutated colorectal cancer

Despite the advancement in new therapies in colorectal cancer (CRC), chemotherapy still constitutes the mainstay of the treatment. Poly-ADP-Ribose Polymerase inhibitors (PARPi) have the potential to increase the activity of DNA damaging chemotherapeutics such as 5-fluorouracil (5FU), oxaliplatin and irinotecan, even if dose-limiting toxicities have emerged at the currently used doses in previous clinical trials in molecularly unselected CRC patients. We tested the combination of the PARPi niraparib (MK-4827) with either 5-fluorouracil, oxaliplatin or irinotecan (SN38) in a panel of 12 molecularly annotated CRC cell lines, encompassing the 4 consensus molecular subtypes (CMSs). Synergism was calculated using the Chou-Talalay method for drug interaction. A correlation between synergism and genetic alterations in genes involved in homologous recombination (HR) repair was performed. We used clonogenic assays, mice xenograft models and patient-derived 3D spheroids to validate the results. The induction of DNA damage was studied by immunofluorescence. Irinotecan/SN38 is the best candidate for combination with niraparib, showing strong synergism is 6/12 cell lines. Synergism was independent from CMS and microsatellite status. Strong synergistic activity of low-dose combinations of SN38 and niraparib was found in cell lines carrying a pathogenic mutation in ATM by induction of DNA double strand breaks. The strong activity of the low-dose combination was further confirmed in clonogenic assays and in mice xenografts. The presence of an ATM mutation predicted the activity of the combination in a model of patient-derived 3D spheroid. This work demonstrates that the subset of CRCs carrying heterozygous ATM mutations may benefit from a combination treatment with low doses of niraparib and irinotecan. These data suggest a new potential approach in the treatment of ATM-mutated CRC, up to 10% in large datasets, that deserves to be validated prospectively in clinical trials.

Abstract 1386: 5-FU-induces PD-L1 in the absence of p53 via ATM dependent activation of STAT3

Abstract Background: 5-Fluorouracil (5-FU) is an antimetabolite DNA damaging chemotherapeutics that forms the backbone for treatment of colorectal cancer (CRC) and currently it is the most commonly used anti-cancer drug. Despite the central role played by p53 in regulating DNA-damage response, its role in regulating response to 5-FU remains unclear. Methods: To better understand how p53 status differentially affects response to 5-FU, we conducted a detailed phenotypic analysis of the effects of 5FU alone or in combination with Oxaliplatin on cell cycle, DNA damage, cell death, DNA repair and consequent signaling across a panel of p53 isogenic, null and mutant CRC cell lines. Results: This revealed that while 5-FU induce both p53 dependent and independent cell death, the effects on cell cycle are profoundly different, with p53 deficient cells accumulating in S-phase with prolongated double strand breaks. This is not observed in p53 proficient cells, which are protected from these effects by induction of the p53 target gene p21/CDKN1A limiting cell cycle and enforcing suppression of cell cycle genes. Notably in both p53 or p21 deficient cells 5-FU results in sustained DNA damage-signaling through ATR and ATM in p53 deficient cells which preferentially arrest in S-phase. Importantly, these cells exhibit significant induction of cell surface expression of programmed death ligand-1 (PD-L1), which is enhanced by ATR inhibition concomitant with increased ATM activation. Further analysis indicates that transcriptional induction of PD-L1 is mediated through STAT3 in an interferon independent manner. Conclusion: This work adds significantly to our understanding of how p53 status impacts 5FU induced cell cycle arrest and response in CRC patients and have important implications for understanding 5-FU response, particularly in future combinations with immune checkpoint inhibitors. Citation Format: Tamas Sessler, Fiammetta Falcone, Peter Gallagher, Timothy Wright, Kienan Savage, Daniel B. Longley, Simon S. McDade. 5-FU-induces PD-L1 in the absence of p53 via ATM dependent activation of STAT3 [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1386.

Wee1 Inhibition Enhances the Anti-Tumor Effects of Capecitabine in Preclinical Models of Triple-Negative Breast Cancer.

Triple-negative breast cancer (TNBC) is an aggressive subtype defined by lack of hormone receptor expression and non-amplified HER2. Adavosertib (AZD1775) is a potent, small-molecule, ATP-competitive inhibitor of the Wee1 kinase that potentiates the activity of many DNA-damaging chemotherapeutics and is currently in clinical development for multiple indications. The purpose of this study was to investigate the combination of AZD1775 and capecitabine/5FU in preclinical TNBC models. TNBC cell lines were treated with AZD1775 and 5FU and cellular proliferation was assessed in real-time using IncuCyte® Live Cell Analysis. Apoptosis was assessed via the Caspase-Glo 3/7 assay system. Western blotting was used to assess changes in expression of downstream effectors. TNBC patient-derived xenograft (PDX) models were treated with AZD1775, capecitabine, or the combination and assessed for tumor growth inhibition. From the initial PDX screen, two of the four TNBC PDX models demonstrated a better response in the combination treatment than either of the single agents. As confirmation, two PDX models were expanded for statistical comparison. Both PDX models demonstrated a significant growth inhibition in the combination versus either of the single agents. (TNBC012, p < 0.05 combo vs. adavosertib or capecitabine, TNBC013, p < 0.01 combo vs. adavosertib or capecitabine.) An enhanced anti-proliferative effect was observed in the adavosertib/5FU combination treatment as measured by live cell analysis. An increase in apoptosis was observed in two of the four cell lines in the combination when compared to single-agent treatment. Treatment with adavosertib as a single agent resulted in a decrease in p-CDC2 in a dose-dependent manner that was also observed in the combination treatment. An increase in γH2AX in two of the four cell lines tested was also observed. No significant changes were observed in Bcl-xL following treatment in any of the cell lines. The combination of adavosertib and capecitabine/5FU demonstrated enhanced combination effects both in vitro and in vivo in preclinical models of TNBC. These results support the clinical investigation of this combination in patients with TNBC, including those with brain metastasis given the CNS penetration of both agents.

Abstract P1-19-25: Wee1 inhibition enhances the anti-tumor effects of capecitabine in preclinical models of triple negative breast cancer

Abstract Background: Triple-negative breast cancer (TNBC) is an aggressive subtype defined by lack of hormone receptor expression and non-amplified HER2. TNBC accounts for approximately 15% of breast cancer cases, however, is associated with an increased risk of cancer recurrence, brain metastasis, and death due to metastatic breast cancer. Mutations in p53 are common in TNBC, occurring in approximately 85% of tumors. While a number of promising targeted therapies are on the horizon in TNBC including immunotherapy, there remains an unmet need for active targeted therapies where chemotherapy remains the standard treatment for metastatic disease and results in a median survival of 12-18 months. Adavosertib (AZD1775) is a potent, small molecule, ATP-competitive inhibitor of the Wee1 kinase that potentiates the activity of many DNA-damaging chemotherapeutics and is currently in clinical development for multiple indications. AZD1775 potentiates the activity of DNA-damaging and antimetabolite chemotherapeutics in preclinical models without TP53-deficiency, possibly due to baseline replicative stress or compromised DNA repair proficiency. A previous unbiased screen of CTEP compounds in TNBC PDX models demonstrated that the combination of adavosertib and capecitabine/5FU had greater anti-proliferative effects than either of the single agents. The purpose of this study was to further investigate the combination of adavosertib and capecitabine/5FU in preclinical TNBC models. Methods: HCC1937, CAL51, MDA-MB-231 and MDA-MB-468 cells were plated in 96-well plates and exposed to increasing concentrations of adavosertib, 5FU, or the combination. Cellular proliferation was assessed in real-time using IncuCyte® Live Cell Analysis. Apoptosis was assessed via the Caspase-Glo 3/7 assay system. Western blotting was used to assess changes in expression of CDC2, phospho-CDC2, H2AX, and Bcl-xL. TNBC PDX models CU_TNBC_012 and CU_TNBC_013 were treated with vehicle, adavosertib, capecitabine, or the combination and assessed for tumor growth inhibition. Results: From the initial PDX screen, two of the four TNBC PDX models demonstrated a better response in the combination treatment than either of the single agents. As confirmation, two PDX models were expanded for statistical comparison. Both PDX models demonstrated a significant growth inhibition in the combination versus either of the single agents. (TNBC012, p&amp;lt;0.05 combo vs adavosertib or capecitabine, TNBC013, p&amp;lt;0.01 combo vs adavosertib or capecitabine ). An enhanced antiproliferative effect was observed in the adavosertib/5FU combination treatment as measured by live cell analysis. An increase in apoptosis was observed in two of the four cell lines in the combination when compared to single agent treatment. Treatment with single agent adavosertib resulted in an increase in p-cdc2 in a dose dependent manner that was also observed in the combination treatment. Similar results were observed with γH2AX in two of the four cell lines tested. No significant changes were observed in Bcl-xL following treatment in any of the cell lines. Conclusions: The combination of adavosertib and capecitabine/5-FU demonstrated enhanced combination effects both in vitro and in vivo in preclinical models of TNBC. These results support the clinical investigation of this combination in patients with TNBC, including those with brain metastasis given the CNS penetration of both agents. Citation Format: Todd M Pitts, Dennis M Simmons, Kyrie Dailey, Stacey M Bagby, Sarah J Hartman, Betelehem W Yacob, Brian Gittleman, John J Tentler, Diana Cittely, D. Ryan Ormond, Wells A Messersmith, S Gail Eckhardt, Jennifer R Diamond. Wee1 inhibition enhances the anti-tumor effects of capecitabine in preclinical models of triple negative breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P1-19-25.

Structure-Guided Optimization of Replication Protein A (RPA)-DNA Interaction Inhibitors.

Replication protein A (RPA) is the major human single stranded DNA (ssDNA)-binding protein, playing essential roles in DNA replication, repair, recombination, and DNA-damage response (DDR). Inhibition of RPA-DNA interactions represents a therapeutic strategy for cancer drug discovery and has great potential to provide single agent anticancer activity and to synergize with both common DNA damaging chemotherapeutics and newer targeted anticancer agents. In this letter, a new series of analogues based on our previously reported TDRL-551 (4) compound were designed to improve potency and physicochemical properties. Molecular docking studies guided molecular insights, and further SAR exploration led to the identification of a series of novel compounds with low micromolar RPA inhibitory activity, increased solubility, and excellent cellular up-take. Among a series of analogues, compounds 43, 44, 45, and 46 hold promise for further development of novel anticancer agents.