SLFN11 Inactivation Induces Proteotoxic Stress and Sensitizes Cancer Cells to Ubiquitin Activating Enzyme Inhibitor TAK-243

Schlafen11 (SLFN11) inactivation occurs in approximately 50% of cancer cell lines and in a large fraction of patient tumor samples, which leads to chemoresistance. Therefore, new therapeutic approaches are needed to target SLFN11-deficient cancers. To that effect, we conducted a drug screen with the NCATS mechanistic drug library of 1,978 compounds in isogenic SLFN11-knockout (KO) and wild-type (WT) leukemia cell lines. Here we report that TAK-243, a first-in-class ubiquitin activating enzyme UBA1 inhibitor in clinical development, causes preferential cytotoxicity in SLFN11-KO cells; this effect is associated with claspin-mediated DNA replication inhibition by CHK1 independently of ATR. Additional analyses showed that SLFN11-KO cells exhibit consistently enhanced global protein ubiquitylation, endoplasmic reticulum (ER) stress, unfolded protein response (UPR), and protein aggregation. TAK-243 suppressed global protein ubiquitylation and activated the UPR transducers PERK, phosphorylated eIF2α, phosphorylated IRE1, and ATF6 more effectively in SLFN11-KO cells than in WT cells. Proteomic analysis using biotinylated mass spectrometry and RNAi screening also showed physical and functional interactions of SLFN11 with translation initiation complexes and protein folding machinery. These findings uncover a previously unknown function of SLFN11 as a regulator of protein quality control and attenuator of ER stress and UPR. Moreover, they suggest the potential value of TAK-243 in SLFN11-deficient tumors. SIGNIFICANCE: This study uncovers that SLFN11 deficiency induces proteotoxic stress and sensitizes cancer cells to TAK-243, suggesting that profiling SLFN11 status can serve as a therapeutic biomarker for cancer therapy.

Abstract LB-121: The novel ATR inhibitor M4344 and CHK1 inhibitor SRA737 overcome chemoresistance in SLFN11-negative cells in combination treatment with DNA-damaging agents

Precision medicine is an unmet need for DNA-damaging agents with potentially severe side effects. Loss of Schlafen 11 (SLFN11) expression is frequently detected in ~50% cancer cell lines of the NCI, the Broad Institute cancer cell line panel (CCLE), and the Genomics of Drug Sensitivity in Cancer project (GDSC). Deficiency of SLFN11 expression causes chemoresistance to a broad range of DNA-damaging agents, including topoisomerase I (TOP1) inhibitors, topoisomerase II (TOP2) inhibitors, alkylating agents, DNA synthesis inhibitors and PARP inhibitors. Moreover, gene silencing of SLFN11 is observed in small cell lung cancer patient-derived xenograft models with acquired drug resistance. To identify synthetic lethal therapeutic targets to overcome chemoresistance in SLFN11 deficient cells, we performed a genome-wide RNAi screen with the human druggable genome siRNA library by using camptothecin (CPT), a TOP1 inhibitor, in SLFN11 wild-type (WT) and knock-out (KO) prostate cancer DU145 cells. Gene Ontology analysis identified the inhibition of ATR-mediated DNA repair pathway genes (ATR, CHK1, BRCA2 and RPA1) is synergistic with CPT in SLFN11 KO cells, whereas inhibition of the RNA metabolism-related genes (POLR2, PSMD3, POLR2F and PSMD11) had higher combination effects in SLFN11 WT cells. The synergistic effects by depletion of ATR-mediated DNA repair pathway in SLFN11 KO cells were validated by additional siRNAs-mediated cell viability assays. To determine whether inhibition of ATR-mediated pathway can be applied clinically, we tested the new clinical ATR (M4344) and CHK1 (SRA737) inhibitors. Treatment with non-toxic-doses of M4344 and SRA737 reversed drug resistance of the SLFN11 KO cells to TOP1 inhibitors [CPT, and clinically used topotecan and LMP400 (indotecan)]. Additionally, the same synergistic effects by combination of the ATR/CHK1inhibitors and CPT were detected in isogenic CCRF-CEM SLFN11 WT and KO leukemic lymphoblasts cells and non-isogenic DMS114 and H446 small cell lung cancer cells. We also confirmed synergy with ATR/CHK1 inhibitors in combination of other clinical DNA-damaging agents (TOP2 inhibitor: etoposide, alkylating agent: cisplatin, and PARP inhibitor: talazoparib). Molecular changes induced by the combination treatment were examined in the cell cycle by assessing DAPI and EdU incorporation, cell death with Annexin V, and DNA damage response by confocal microscopy with M4344 and CPT. Co-treatment with ATR inhibitor and CPT resulted in G2/M arrest and apoptotic cell death, and formation of micronuclei and fragmented nuclei in SLFN11 KO cells, compared with SLFN11 WT cells. Collectively, our results provide a new therapeutic rationale for the clinical development of combination treatments of chemotherapeutic DNA-targeted agents with ATR/CHK1 inhibitors based on SLFN11 status.

Citation Format: Ukhyun Jo, Yasuhisa Murai, Junko Murai, Shar-yin N Huang, Sirisha Chakka, Lu Chen, Ken Cheng, Yves Pommier. The novel ATR inhibitor M4344 and CHK1 inhibitor SRA737 overcome chemoresistance in SLFN11-negative cells in combination treatment with DNA-damaging agents [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 LB-121.

Evaluating important change in cutaneous disease activity as an efficacy measure for clinical trials in dermatomyositis

BACKGROUND

Patients may experience improved quality of life (QoL) without complete clearance of skin disease. The Cutaneous Dermatomyositis Disease Area and Severity Index Activity (CDASI-A) score correlates with the Symptoms and Emotions subscales of Skindex-29, a measure of QoL, down to CDASI-A scores of 7 points (for Symptoms) and 10 points (for Emotions).

OBJECTIVES

Our goal was to define an important change in disease activity, as measured by the CDASI-A, that results in a meaningful change in QoL in patients with dermatomyositis.

METHODS

In 103 patients, we assessed the percentage change and actual change in CDASI-A scores needed to achieve a meaningful improvement in QoL, using linear regression models.

RESULTS

We found that meaningful improvement correlates with 7·86 points (P < 0·001) in Symptoms, and 10·29 points (P < 0·001) in Emotions, after correlating Skindex-29 to an established definition of meaningful change in the Dermatology Life Quality Index (DLQI). For patients with initial CDASI-A scores > 14 points, a 40% change in CDASI-A between the first two visits suggests a meaningful change in Skindex-29. In patients with moderate initial CDASI-A (15-26 points), the changes in CDASI-A resulting in meaningful changes in Symptoms and Emotions were 6 points (P < 0·001) and 7 points (P < 0·001), respectively. For initial CDASI-A scores in the severe range (27-35 points), an improvement in CDASI-A by 11 points (P = 0·030) and 9 points (P = 0·021) leads to a meaningful change in Symptoms and Emotions, respectively.

CONCLUSIONS

In patients with an initial CDASI-A score > 14 points, a 40% change in the CDASI-A score can be used to indicate a meaningful change in QoL in future dermatomyositis trials. What's already known about this topic? The Cutaneous Dermatomyositis Disease Area and Severity Index (CDASI) is a validated disease assessment tool used to capture the extent of cutaneous activity and damage. The Skindex-29 and Dermatology Life Quality Index are standardized and validated measures of quality of life (QoL) for clinical trials and correlate with CDASI Activity (CDASI-A) scores. What does this study add? We identified what change in Skindex-29 scores over two consecutive visits would indicate an important change (a minimal clinically important difference) in QoL. We determined which change in CDASI-A scores over two consecutive visits would lead to a meaningful change in QoL. For patients with an initial CDASI-A score > 14 points, a 40% change in the CDASI-A score over two visits is associated with a meaningful change in QoL. What are the clinical implications of this work? Clinical trials can consider using a 40% change in the CDASI-A score as an end point when assessing the clinical efficacy of drugs.

High-throughput screening with nucleosome substrate identifies small-molecule inhibitors of the human histone lysine methyltransferase NSD2

The histone lysine methyltransferase nuclear receptor-binding SET domain protein 2 (NSD2, also known as WHSC1/MMSET) is an epigenetic modifier and is thought to play a driving role in oncogenesis. Both NSD2 overexpression and point mutations that increase its catalytic activity are associated with several human cancers. Although NSD2 is an attractive therapeutic target, no potent, selective, and bioactive small molecule inhibitors of NSD2 have been reported to date, possibly due to the challenges of developing high-throughput assays for NSD2. Here, to establish a platform for the discovery and development of selective NSD2 inhibitors, we optimized and implemented multiple assays. We performed quantitative high-throughput screening with full-length WT NSD2 and a nucleosome substrate against a diverse collection of bioactive small molecules comprising 16,251 compounds. We further interrogated 174 inhibitory compounds identified in the primary screen with orthogonal and counter assays and with activity assays based on the clinically relevant NSD2 variants E1099K and T1150A. We selected five confirmed inhibitors for follow-up, which included a radiolabeled validation assay, surface plasmon resonance studies, methyltransferase profiling, and histone methylation in cells. We found that all five NSD2 inhibitors bind the catalytic SET domain and one exhibited apparent activity in cells, validating the workflow and providing a template for identifying selective NSD2 inhibitors. In summary, we have established a robust discovery pipeline for identifying potent NSD2 inhibitors from small-molecule libraries.

BRD4 facilitates DNA damage response and represses CBX5/Heterochromatin protein 1 (HP1)

Ovarian cancer (OC) is a heterogeneous disease characterized by defective DNA repair. Very few targets are universally expressed in the high grade serous (HGS) subtype. We previously identified that CHK1 was overexpressed in most of HGSOC. Here, we sought to understand the DNA damage response (DDR) to CHK1 inhibition and increase the anti-tumor activity of this pathway. We found BRD4 suppression either by siRNA or BRD4 inhibitor JQ1 enhanced the cytotoxicity of CHK1 inhibition. Interestingly, BRD4 was amplified and/or upregulated in a subset of HGSOC with statistical correlation to overall survival. BRD4 inhibition increased CBX5 (HP1α) level. CHK1 inhibitor induced DDR marker, γ-H2AX, but BRD4 suppression did not. Furthermore, nuclear localization of CBX5 and γ-H2AX was mutually exclusive in BRD4-and CHK1-inhibited cells, suggesting BRD4 facilitates DDR by repressing CBX5. Our results provide a strong rationale for clinical investigation of CHK1 and BRD4 co-inhibition, especially for HGSOC patients with BRD4 overexpression.

Identification of therapeutic targets applicable to clinical strategies in ovarian cancer

BACKGROUND

shRNA-mediated lethality screening is a useful tool to identify essential targets in cancer biology. Ovarian cancer (OC) is extremely heterogeneous and most cases are advanced stages at diagnosis. OC has a high response rate initially, but becomes resistant to standard chemotherapy. We previously employed high throughput global shRNA sensitization screens to identify NF-kB related pathways. Here, we re-analyzed our previous shRNA screens in an unbiased manner to identify clinically applicable molecular targets.

METHODS

We proceeded with siRNA lethality screening using the top 55 genes in an expanded set of 6 OC cell lines. We investigated clinical relevance of candidate targets in The Cancer Genome Atlas OC dataset. To move these findings towards the clinic, we chose four pharmacological inhibitors to recapitulate the top siRNA effects: Oxozeaenol (for MAP3K7/TAK1), BI6727 (PLK1), MK1775 (WEE1), and Lapatinib (ERBB2). Cytotoxic effects were measured by cellular viability assay, as single agents and in 2-way combinations. Co-treatments were evaluated in either sequential or simultaneous exposure to drug for short term and extended periods to simulate different treatment strategies.

RESULTS

Loss-of-function shRNA screens followed by short-term siRNA validation screens identified therapeutic targets in OC cells. Candidate genes were dysregulated in a subset of TCGA OCs although the alterations of these genes showed no statistical significance to overall survival. Pharmacological inhibitors such as Oxozeaenol, BI6727, and MK1775 showed cytotoxic effects in OC cells regardless of cisplatin responsiveness, while all OC cells tested were cytostatic to Lapatinib. Co-treatment with BI6727 and MK1775 at sub-lethal concentrations was equally potent to BI6727 alone at lethal concentrations without cellular re-growth after the drugs were washed off, suggesting the co-inhibition at reduced dosages may be more efficacious than maximal single-agent cytotoxic concentrations.

CONCLUSIONS

Loss-of-function screen followed by in vitro target validation using chemical inhibitors identified clinically relevant targets. This approach has the potential to systematically refine therapeutic strategies in OC. These molecular target-driven strategies may provide additional therapeutic options for women whose tumors have become refractory to standard chemotherapy.

Loss-of-function RNAi screens in breast cancer cells identify AURKB, PLK1, PIK3R1, MAPK12, PRKD2, and PTK6 as sensitizing targets of rapamycin activity

The use of molecularly targeted drugs as single agents has shown limited utility in many tumor types, largely due to the complex and redundant nature of oncogenic signaling networks. Targeting of the PI3K/AKT/mTOR pathway through inhibition of mTOR in combination with aromatase inhibitors has seen success in particular sub-types of breast cancer and there is a need to identify additional synergistic combinations to maximize the clinical potential of mTOR inhibitors. We have used loss-of-function RNAi screens of the mTOR inhibitor rapamycin to identify sensitizers of mTOR inhibition. RNAi screens conducted in combination with rapamycin in multiple breast cancer cell lines identified six genes, AURKB, PLK1, PIK3R1, MAPK12, PRKD2, and PTK6 that when silenced, each enhanced the sensitivity of multiple breast cancer lines to rapamycin. Using selective pharmacological agents we confirmed that inhibition of AURKB or PLK1 synergizes with rapamycin. Compound-associated gene expression data suggested histone deacetylation (HDAC) inhibition as a strategy for reducing the expression of several of the rapamycin-sensitizing genes, and we tested and validated this using the HDAC inhibitor entinostat in vitro and in vivo. Our findings indicate new approaches for enhancing the efficacy of rapamycin including the use of combining its application with HDAC inhibition.

Identification of novel molecular regulators of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced apoptosis in breast cancer cells by RNAi screening

INTRODUCTION

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) binds to its receptors, TRAIL-receptor 1 (TRAIL-R1) and TRAIL-receptor 2 (TRAIL-R2), leading to apoptosis by activation of caspase-8 and the downstream executioner caspases, caspase-3 and caspase-7 (caspase-3/7). Triple-negative breast cancer (TNBC) cell lines with a mesenchymal phenotype are sensitive to TRAIL, whereas other breast cancer cell lines are resistant. The underlying mechanisms that control TRAIL sensitivity in breast cancer cells are not well understood. Here, we performed small interfering RNA (siRNA) screens to identify molecular regulators of the TRAIL pathway in breast cancer cells.

METHODS

We conducted siRNA screens of the human kinome (691 genes), phosphatome (320 genes), and about 300 additional genes in the mesenchymal TNBC cell line MB231. Forty-eight hours after transfection of siRNA, parallel screens measuring caspase-8 activity, caspase-3/7 activity, or cell viability were conducted in the absence or presence of TRAIL for each siRNA, relative to a negative control siRNA (siNeg). A subset of genes was screened in cell lines representing epithelial TNBC (MB468), HER2-amplified breast cancer (SKBR3), and estrogen receptor-positive breast cancer (T47D). Selected putative negative regulators of the TRAIL pathway were studied by using small-molecule inhibitors.

RESULTS

The primary screens in MB231 identified 150 genes, including 83 kinases, 4 phosphatases, and 63 nonkinases, as potential negative regulators of TRAIL. The identified genes are involved in many critical cell processes, including apoptosis, growth factor-receptor signaling, cell-cycle regulation, transcriptional regulation, and DNA repair. Gene-network analysis identified four genes (PDPK1, IKBKB, SRC, and BCL2L1) that formed key nodes within the interaction network of negative regulators. A secondary screen of a subset of the genes identified in additional cell lines representing different breast cancer subtypes and sensitivities to TRAIL validated and extended these findings. Further, we confirmed that small-molecule inhibition of SRC or BCL2L1, in combination with TRAIL, sensitizes breast cancer cells to TRAIL-induced apoptosis, including cell lines resistant to TRAIL-induced cytotoxicity.

CONCLUSIONS

These data identify novel molecular regulators of TRAIL-induced apoptosis in breast cancer cells and suggest strategies for the enhanced application of TRAIL as a therapy for breast cancer.

Abstract B25: An unbiased functional screen identifies kinases essential to ovarian cancer cell survival

Ovarian cancer is the most lethal gynecologic cancer in USA. Many efforts including gene expression profiling, SNP analysis, comparative genomic hybridization, and exome sequencing have revealed that ovarian cancer is extremely heterogeneous. This implies that therapeutic strategy should be specifically designed based on molecular characteristics. Previously, we focused on investigating the functional role of NF-κB pathway in ovarian cancer initiation, propagation, and dissemination, performing two independent shRNA screens in the context of NF-κB signaling.

In this study, we have re-focused our efforts towards an unbiased loss-of-function screen across 4 ovarian cancer cell lines Caov3, Igrov1, Ovcar5, and A2780. Under the most stringent cut-off of 4 out of 4 cell lines with a p value of less than 0.05 and fold change less than 0.7, five genes including GUCY2F, MKNK2, PDK3, PIK3AP1, and WEE1 were identified as essential for ovarian cancer cell viability. When the stringency of analysis was relaxed to allow 3 out of 4 cell lines affected, a total of 55 genes were included. The most significant networks among these 55 genes were those of cell cycle, and cancer cell death and survival, as determined by Ingenuity Pathway Analysis. In order to validate and prioritize candidate genes, we focused siRNA lethality screening to the 55 genes in an expanded set of 6 ovarian cancer cell lines additionally including Skov3 and Ovcar8. Two siRNAs per gene (Qiagen) were tested in 384-well format. Transient transfection protocols such as seeding cell numbers, lipid to siRNA ratio, and incubation time were optimized in each individual cell line using positive and negative siRNA controls. Based on cell viability, 9 genes including EPHB1, FER, MAP3K7, MAP3K8, MGC42105 (NIM1), PRKCA, PLK1, ERBB2, and WEE1 were confirmed as essential in the initial shRNA screened 4 ovarian cancer cell lines, while six genes (EPHB1, FER, MAP3K7, PLK1, ERBB2, and WEE1) were identified in all 6 cell lines. To move these findings towards the clinic, we next investigated whether pharmacological inhibitors could recapitulate the siRNA effect. We tested 4 inhibitors: Oxozeaenol (for MAP3K7/TAK1), BI6727 (PLK1), MK1775 (WEE1), and Lapatinib (ERBB2). Using 2-fold serial dilutions in 6 cell lines, ranges of IC50 were determined based on cell proliferation and calculated by CompuSyn software. The ranges of IC50 were 1- 6 uM, 10 - 35 nM, and 0.2 - 0.6 uM for Oxozeaenol, BI6727, and MK1775, respectively. All 6 cell lines were resistant to Lapatinib at 10 uM, suggesting a kinase independent function of ERBB2 in ovarian cancer cells.

Single agent therapies often result in resistance and relapse. As such, our future work will include identification of predictive biomarkers for selecting drugs and the efficacy of sequential versus simultaneous treatment with these drugs in different combinations. In summary, a loss-of-function screening followed by validation using clinically relevant inhibitors helps us to identify essential targets in ovarian cancer and to systematically refine therapeutic strategies in ovarian cancer.

Citation Format: Marianne K. Kim, Sirisha Chakka, Natasha Caplen, Christina Annunziata. An unbiased functional screen identifies kinases essential to ovarian cancer cell survival. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr B25.

Integrated analysis of RNAi screens in pediatric rhabdomyosarcoma

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Background: Rhabdomyosarcoma (RMS) is the most common pediatric soft tissue sarcoma. Embryonal RMS (ERMS) are characterized by 11p15 LOH, while alveolar RMS (ARMS) harbor a translocation between PAX3 or PAX7 and FOXO1. Relapsed or metastatic RMS has a poor prognosis with a 5-year survival rate of 25%. We hypothesized that a reduction in proliferation of ARMS cell lines as result of the loss of function (LOF) of a specific protein via RNAi likely point to novel targets that exhibit “synthetic lethality” with the PAX3/7-FOXO1 translocation, and can be used to reveal unique ARMS vulnerabilities. Methods: We are using two complementary screening strategies to identify genes critical for RMS cell growth and survival. One RNAi screening strategy used an inducible LOF shRNA screen of 15,000 shRNA -5,000 genes- introduced into RH30 (ARMS) or RD (ERMS) cells. Data analysis after subtraction of targets related to common survival pathways revealed 40 genes with close association with RMS cell growth. Follow up analysis included further comparison of the effects of gene specific LOF in ARMS and ERMS cell lines and assessment in orthotopic xenografts. To increase the strength of our findings, we have also conducted parallel siRNA screens of the human kinome targeting 704 kinase genes (3 siRNAs per gene) in RH30 or RD cells. Results: Of the 40 genes identified by shRNA screening, 15 genes were identified as selectively needed for ARMS cell growth. Follow up analysis of one of these genes, TNK-2 (tyrosine kinase, non-receptor 2) in orthotopic xenografts, confirmed that LOF of TNK2 markedly decreases ARMS cell growth. The siRNA screen has identified a further putative 26 genes that selectively reduce ARMS cell growth. These screens have led us to focus on members of the ERK, PI3K and IGF1R pathways as potential targets for the treatment of ARMS. Conclusions: RNAi screening affords an unbiased method for the discovery and elucidation of gene function. Ongoing efforts are focused on the integration of results obtained to gain further insight into the signaling networks influencing alveolar rhabdomyosarcoma biology and thus identify a small group of druggable genes that could represent alveolar rhabdomyosarcoma specific vulnerabilities.