Atypical Teratoid Rhabdoid Tumor Cell Lines Research Articles

Modeling human brain rhabdoid tumor by inactivating tumor suppressor genes in induced pluripotent stem cells

Atypical teratoid/rhabdoid tumor (ATRT) is a rare childhood malignancy that originates in the central nervous system. Over ninety-five percent of ATRT patients have biallelic inactivation of the tumor suppressor gene SMARCB1. ATRT has no standard treatment, and a major limiting factor in therapeutic development is the lack of reliable ATRT models. We employed CRISPR/Cas9 gene-editing technology to knock out SMARCB1 and TP53 genes in human episomal induced pluripotent stem cells (Epi-iPSCs), followed by brief neural induction, to generate an ATRT-like model. The dual knockout Epi-iPSCs retained their stemness with the capacity to differentiate into three germ layers. High expression of OCT4 and NANOG in neurally induced knockout spheroids was comparable to that in two ATRT cell lines. Beta-catenin protein expression was higher in SMARCB1-deficient cells and spheroids than in normal Epi-iPSC-derived spheroids. Nucleophosmin, Osteopontin, and Ki-67 proteins were also expressed by the SMARCB1-deficient spheroids. In summary, the tumor model resembled embryonal features of ATRT and expressed ATRT biomarkers at mRNA and protein levels. Ribociclib, PTC-209, and the combination of clofilium tosylate and pazopanib decreased the viability of the ATRT-like cells. This disease modeling scheme may enable the establishment of individualized tumor models with patient-specific mutations and facilitate high-throughput drug testing.

SYST-12 LP-184, A NOVEL ACYLFULVENE-DERIVED TUMOR SITE ACTIVATED SMALL MOLECULE INHIBITS ADULT AND PEDIATRIC CNS TUMOR CELL GROWTH

Abstract Blood-brain barrier (BBB) permeable agents effective against recurrent, chemotherapy-resistant central nervous system (CNS) tumors are urgently needed, particularly in Glioblastoma multiforme (GBM) and atypical teratoid/rhabdoid tumors (ATRT). These represent extremely aggressive and lethal types of CNS malignancies. LP-184 is a next-generation acylfulvene class drug candidate and has received FDA orphan drug designations for the treatment of malignant gliomas and ATRT. LP-184 creates covalent DNA adducts that are selectively repaired via nucleotide excision repair (NER). Repair of LP-184-induced DNA damage is mediated by ERCC complexes. Consistent with this, we observed 3-6X decreased cancer cell viability in U87, M1123 and Mayo39 GBM cells treated with LP-184 in combination with the ERCC3 degrader Spironolactone (SP) relative to LP-184 alone. Mice bearing pre-established subcutaneous U87 xenografts were treated with SP alone, LP-184 alone or their combination. Tumors recurred after initial regression in 5/5 animals treated with LP-184 alone whereas tumors showed durable complete regression without recurrence in 4/5 animals treated with LP-184 + SP. Thus, LP-184 likely functions as a synthetically lethal agent in the presence of DNA repair deficiencies. LP-184 inhibited cell growth in CHLA06 and BT37 ATRT cell lines, with IC50s in the 20-25nM range. LP-184 induced apoptosis 96 hours after treatment in these ATRT cell lines as measured by immunofluorescence for cleaved caspase-3 and Western blot for c-PARP. LP-184 intravenous treatment at 4 mg/kg twice weekly for 2 weeks showed tumor regression in mice implanted with CHLA06 ATRT subcutaneous xenografts, with 112% tumor growth inhibition and 2/10 treated mice being tumor-free at study termination. LP-184 further showed favorable intracranial tumor bioavailability along with in vivo BBB permeability comparable to other CNS cancer drugs. These findings identify LP-184 as a promising new agent and support its further development for treating CNS tumors in adult and pediatric populations.

ATRT-17. CAR T CELL THERAPY TARGETING CLAUDIN-6 IS EFFECTIVE IN CELLULAR AND XENOGRAFT MODELS OF ATYPICAL TERATOID/RHABDOID TUMOR

Abstract Novel therapies are needed to for the treatment of atypical teratoid/rhabdoid tumor (ATRT), an aggressive brain tumor that predominantly affects young children and has an average 5-year survival under 50%. Claudin-6 (CLDN6) is a tight junction protein present during development and is expressed in up to 70% of ATRT specimens but not in normal tissue, making it a promising immunotherapeutic target. CLDN6-targeted chimeric antigen receptor (CAR) T cells in combination with a CAR T cell-amplifying mRNA vaccine have demonstrated antitumor activity against other CLDN6-expressing cancers in pre-clinical and a phase I adult trial (NCT04503278; Haanen J et al AACR, 2022). To assess the effectiveness of CLDN6-targeted CAR T cells against ATRT, we utilized a second-generation mRNA CAR with a 4-1BB costimulatory domain and single-chain variable fragment against CLDN6 (Reinhard et al, 2020). CLDN6 expression in patient-derived ATRT specimens was profiled by RNAseq (mean FPKM 11.4) and immunohistochemistry (positive staining in 53% of specimens). Tumor-derived cell lines were assessed for CLDN6 expression by flow cytometry. Co-culture of CLDN6-directed mRNA CAR T cells resulted in tumor-specific cytotoxicity compared to CD19-directed control CAR T cells in CLDN6-positive ATRT cell lines 7316-2187 (92% versus 15% at 10:1, p < 0.0001; 86% versus 0% at 5:1, p<0.0001) and 7316-2141 (75% versus 7% at 10:1, p<0.0001; 53% versus 0% at 5:1, p< 0.0001). Patient-derived, orthotopic xenograft ATRT models were created through intracranial injection of tumor cells into the cerebellum of NSG mice. Following engraftment with 7316-2141, repeated intratumoral administration of mRNA CLDN6 CAR T cells resulted in significant tumor regression (-1.9x108 vs. +2.4x109 p/sec/cm2/sr, p<0.001) and improved survival compared to mRNA CD19 CAR T cells (median OS not reached vs. 13 days, p=0.002). This work highlights the potential for targeting CLDN6 via CAR T cell therapy in patients with ATRT as a novel therapeutic strategy.

Abstract 3933: RRM2 inhibition by COH29 is a potential therapeutic strategy for atypical teratoid rhabdoid tumors

Abstract Introduction: Atypical teratoid rhabdoid tumors (ATRT) are a rare but aggressive malignancy in central nervous system, commonly occurring in early childhood. ATRT patients face a dismal prognosis despite aggressive therapy. Development of both effective and protective targeted therapy is an emerging necessity. It has been reported that RRM2 is a master driver of aggressiveness and a poor prognosis biomarker in several cancers. However, little is known about RRM2 function in ATRT. The aim of this study is to assess the roles of RRM2 in ATRT and elucidate the therapeutic potential of RRM2 to cure the ATRT. Methods: Expression of RRM2 was evaluated by molecular profiling analysis and was confirmed by IHC in both ATRT patients and PDX tissues. Follow-up in vitro studies used 3 different cell lines to elucidate the oncogenic role of RRM2 in ATRT cells. The efficacy of COH29, an RRM2 inhibitor, was assessed in vitro. ATRT model of SCID mice orthotopically injected with ATRT cells were used to test the efficiency of COH29 for in vivo. Western blot and RNA-sequencing were used to determine the mechanisms of RRM2 transcriptional activation in ATRT. Results: Molecular profiling results revealed that RRM2 was relatively highly expressed in ATRT tissues and cell lines. Clinical relevance analysis results showed that the RRM2 expression level was associated with poor prognosis among ATRT patients. Knockdown of RRM2 by shRNAs significantly reduced ATRT cells colonies formation, proliferation and migration. A similar but more pronounced inhibitory effect was observed when COH29 was used to target RMM2. Inhibition of RRM2 by shRNAs or COH29 significantly induced cell death via DNA damage and/or apoptosis pathways. In vivo results demonstrated that COH29 could suppressed ATRT tumor growth and extend mice overall survival. Conclusion: Our study identified RRM2 as a potential mediator of oncogenic cellular functions in ATRT cell lines. We propose that highly expressed RRM2 is associated with poor patient outcomes, and inhibition of RRM2 by COH29 may present a significant therapeutic value in ATRT. Citation Format: Le Hien Giang, Tai-Tong Wong, Che- Chang. RRM2 inhibition by COH29 is a potential therapeutic strategy for atypical teratoid rhabdoid tumors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3933.

Abstract 4875: The anti-tumor effects of GSK-3β inhibitor (9-1NG-41) in ETMR and ATRT pediatric brain tumors

Abstract Purpose Embryonal brain tumors (EBTs): ETMR (embryonal tumor with multilayered rosettes) and ATRT (atypical teratoid rhabdoid tumor) are aggressive malignancies with poor prognosis necessitating alternative strategies. GSK-3β is a serine threonine kinase often overexpressed in solid tumors and a positive regulator of NF-κB which promotes tumor growth and chemotherapy resistance. 9-ING-41 is a maleimide-based small molecule that crosses the blood brain barrier and selectively inhibits GSK-3β. Previously we demonstrated that 9-ING-41 decreases ETMR and ATRT cell viability through apoptosis and increases p53 signaling, however the exact mechanism leading to its activation is unknown. This study aims to determine the optimal dosing for 9-ING-41 and describe the phenotypic response of these cell lines to 9-ING-41 using cell viability assay, western blotting and neurosphere assay. This information will help further elucidate the mechanism of action for this drug. Methods ATRT cell lines ATRT 2141, ATRT-787199, ATRT 803499, LCH-091-07 and the ETMR cell line BT-183 were grown for 24hrs prior to 9-ING-41 treatment in DMEM and Neurocult medium, respectively. Cell viability was assessed after 72hrs of treatment using Cell Titer Glo 2.0. Western blots were analyzed for XIAP, cleaved caspase-3, p53, MDM2 after 24 and 48 hours at 200nM, 400nM and 600nM. Neurosphere assays were done by seeding two cells per well in a 96-well plate followed by treatment with 9-ING-41. Neurosphere frequency and size was monitored weekly for up to 4 weeks using Incucyte® S3 software. Pearson’s correlation graph was generated to determine the relationship between GSK-3β expression and sensitivity to 9-ING-41. Graph Pad Prism was used for statistical analysis and level of significance set to p=0.05. Results The IC50s of 9-ING-41 in cell lines ATRT 2141, ATRT-787199, ATRT 803499 and LCH-091-07 were 194nM, 558nM, 730nM & 5353nM, respectively. We observed decreased expression of NF-κB mediated anti-apoptotic marker XIAP and an increase in expression of apoptotic marker cleaved caspase-3 and tumor suppressor p53 in response to 9-ING-41. MDM2, a negative regulator of p53 had a significant increase in expression indicating it is not responsible for p53 increase which may suggest ATM pathway could be responsible for regulating p53 increase. GSK-3β expression in vitro, correlated with sensitivity to 9-ING-41. There was a dose dependent decrease in frequency and size of neurospheres in response to 9-ING-41. Conclusion 9-ING-41 decreases cell viability and neurosphere formation in ETMR and ATRT cell lines within clinically relevant doses. p53 stabilization is not mediated by MDM2 and may be downstream of the ATM pathway. Further studies are underway to demonstrate its efficacy in mouse models. Citation Format: Divya Gandra, Lauren Difabio, Kaitlyn H. Smith, Kimberly Q. McKinney, Giselle S. Sholler. The anti-tumor effects of GSK-3β inhibitor (9-1NG-41) in ETMR and ATRT pediatric brain tumors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4875.

351 Claudin 6 Expression in Atypical Teratoid/Rhabdoid Tumors is a Target for CAR-T Cell Therapy

INTRODUCTION: Novel therapies for atypical teratoid/rhabdoid tumor (ATRT) are desperately needed. Claudin-6 (CLDN6) is a tight junction protein present during early development and in some tumors, but not at appreciable levels in normal tissue. CLDN6-targeted chimeric antigen receptor (CAR) T cells with a CAR-T cell–amplifying RNA vaccine have demonstrated antitumor activity against CLDN6-expressing cancers in pre-clinical and clinical trials (NCT04503278; Haanen J et al AACR, 2022). METHODS: CLDN6 expression was assessed on primary ATRT specimens by RNAseq and immunohistochemistry and on tumor-derived cell lines by flow cytometry. CLDN6-positive and negative cell lines were co-cultured with CLDN6-targeting CAR-T cells and killing efficacy was measured. A second-generation mRNA CAR with a 4-1BB costimulatory domain and single-chain variable fragment directed against CLDN6 was used (Reinhard et al, 2020). Cell lines were modified with reporter assays and intracranial xenografts were created in NSG mice. RESULTS: 50% of specimens had CLDN6 expression greater than 2 FPKM (N = 28). Immunohistochemistry was positive in 53% of specimens (N = 15). Multiple CLDN6-positive ATRT cell lines were identified by flow cytometry. Co-culture of CLDN6-directed mRNA CAR-T cells with ATRT line 7316-2187 resulted in tumor-specific cytotoxicity versus CD19-directed control CAR-T cells (92% versus 15% at 10:1, p < 0.0001; 86% versus 0% at 5:1, p < 0.0001). Similar results were seen with an additional CLDN6-positive ATRT cell line 7316-2141 (75% versus 7% at 10:1, p < 0.0001; 53% versus 0% at 5:1, p < 0.0001). Both CLDN6- and CD19-directed CAR-T cells showed no cytotoxicity against a CLDN6-negative cell line, 7316-4149. Xenografts were successfully created, and ongoing work is evaluating locoregional administration of CLDN6-directed CAR-T cells. CONCLUSIONS: This work highlights the potential of targeting CLDN6 with CAR-T cell therapy as a novel treatment strategy for patients with ATRT.

Human Malignant Rhabdoid Tumor Antigens as Biomarkers and Potential Therapeutic Targets.

Simple SummaryAtypical teratoid rhabdoid tumor (ATRT) is a deadly type of human pediatric brain cancer without effective treatments. ATRT is mainly linked to the inactivation of a tumor suppressor gene, SMARCB1; however, additional biomarkers remain to be identified to develop novel therapeutic strategies. Therefore, different tumor antigens and extracellular matrix modulators were investigated in two human ATRT and one kidney malignant rhabdoid tumor cell lines and compared with the nonmalignant HEK293 cell line. Alpha-fetoprotein (AFP), mucin-16 (MUC16 or cancer antigen 125/CA125), osteopontin (OPN), and mesothelin (MSLN) are highly expressed in these human malignant rhabdoid cancer cell lines. Inhibiting MMPs using a small-molecule inhibitor decreased cell survival. This biomarker discovery process may lead to the identification of novel diagnostic and therapeutic strategies, such as the development of targeted and immunotherapies against cancer biomarkers, to treat cancer patients.Introduction: Atypical teratoid rhabdoid tumor (ATRT) is a lethal type of malignant rhabdoid tumor in the brain, seen mostly in children under two years old. ATRT is mainly linked to the biallelic inactivation of the SMARCB1 gene. To understand the deadly characteristics of ATRT and develop novel diagnostic and immunotherapy strategies for the treatment of ATRT, this study investigated tumor antigens, such as alpha-fetoprotein (AFP), mucin-16 (MUC16/CA125), and osteopontin (OPN), and extracellular matrix modulators, such as matrix metalloproteinases (MMPs), in different human malignant rhabdoid tumor cell lines. In addition, the roles of MMPs were also examined. Materials and methods: Five human cell lines were chosen for this study, including two ATRT cell lines, CHLA-02-ATRT and CHLA-05-ATRT; a kidney malignant rhabdoid tumor cell line, G401; and two control cell lines, human embryonic kidney HEK293 and HEK293T. Both ATRT cell lines were treated with a broad-spectrum MMP inhibitor, GM6001, to investigate the effect of MMPs on cell proliferation, viability, and expression of tumor antigens and biomarkers. Gene expression was examined using a reverse transcription polymerase chain reaction (RT-PCR), and protein expression was characterized by immunocytochemistry and flow cytometry. Results: All the rhabdoid tumor cell lines tested had high gene expression levels of MUC16, OPN, AFP, and MSLN. Low expression levels of neuron-specific enolase (ENO2) by the two ATRT cell lines demonstrated their lack of neuronal genotype. Membrane-type 1 matrix metalloproteinase (MT1-MMP/MMP-14) and tissue inhibitor of metalloproteinases-2 (TIMP-2) were highly expressed in these malignant rhabdoid tumor cells, indicating their invasive phenotypes. GM6001 significantly decreased ATRT cell proliferation and the gene expression of MSLN, OPN, and several mesenchymal markers, suggesting that inhibition of MMPs may reduce the aggressiveness of rhabdoid cancer cells. Conclusion: The results obtained from this study may advance our knowledge of the molecular landscapes of human malignant rhabdoid tumors and their biomarkers for effective diagnosis and treatment. This work analyzed the expression of human malignant rhabdoid tumor antigens that may serve as biomarkers for the development of novel therapeutic strategies, such as cancer vaccines and targeted and immunotherapies targeting osteopontin and mesothelin, for the treatment of patients with ATRT and other malignant rhabdoid tumors.

ATRT-01. Reconstitution of cGAS/ STING pathway via epigenetic reprogramming leads to anti-viral inflammatory signaling in Atypical teratoid rhabdoid tumors (ATRTs)

BACKGROUND: Atypical teratoid rhabdoid tumors (ATRTs) are highly aggressive brain tumors that affect young children characterized by biallelic inactivation of the SMARCB1 gene. Though patients benefit from multimodal therapy, there is no improvement in overall survival which necessitates the exploration of alternative approaches. Innate-based immune and epigenetic therapies have shown benefits in several cancers. The role of innate immune signaling has not been investigated in ATRTs. Our previous data from several ATRT cell lines showed loss of expression of key innate signaling components, like cGAS and STING that are needed for sensing extracellular dsDNA. Additionally, ATRT cell lines do not respond to STING agonists, like cGAMP or ISD. RESULTS: Co-treatment of ATRT cell lines, BT-12 and BT-16 with two epigenetic modulators, panobinostat and decitabine, leads to re-expression of cGAS and STING in a time-dependent manner. Furthermore, treatment with decitabine alone leads to demethylation of several CpG sites on the STING promoter and increased expression of STING mRNA. Panobinostat and decitabine co-treatment reconstitute STING-mediated innate signaling, as measured by IRF-3 and STAT1 phosphorylation and production of ISG-15 and IFIT-1 after treatment with cGAMP, a STING agonist. Co-treatment with panobinostat and decitabine also induced expression of antiviral pro-inflammatory chemokines/cytokines in ATRT cell lines, including type III IFN, IL-6, IL-8, IL-28, and IL-29. CONCLUSION: Our data suggest that ATRT cell lines are unresponsive to innate agonists possibly due to the loss of expression of key innate immune components. However, the cGAS/STING pathway is reactivated by epigenetic drugs, specifically the combination of panobinostat and decitabine. This is further potentiated by treating with STING agonists like cGAMP. Combination treatment of ATRT cell lines with panobinostat and decitabine also induced antiviral inflammatory signaling. This response could be a potential treatment modality to inhibit tumor growth and/or mediate cancer immunotherapy in these aggressive tumors.

ATRT-19. Functional genomics reveal distinct modulators of response to CDK4/6 inhibitors in ATRTs

Brain tumors are the leading cause of cancer-related deaths in children, and atypical teratoid rhabdoid tumors (ATRTs) are among the most common aggressive brain tumors in infants. With no standard-of-care treatment so far, ATRTs continue to have relatively low survival estimates, illustrating the urgent need for more efficacious treatment options. We have previously used genome-wide CRISPR/Cas9 knockout screens in combination with small-molecule drug assays to identify targetable vulnerabilities in ATRTs. CDK4/6 inhibitors, among the most promising drugs in our study with direct translational potential, are capable of inhibiting tumor growth due to mutual exclusive dependency of ATRTs on either CDK4 or CDK6. We here used genome-wide loss-of-function and gain-of-function strategies to identify modulators of response to CDK4/6 inhibition in ATRTs. Of note, while some well-known resistance mechanisms such as loss of RB1 or FBXW7 are shared by ATRT cell lines, we have also identified modulators of response to CDK4/6 inhibition with opposing effects across ATRT cell lines. As such, loss of AMBRA1, a recently described master regulator of D type cyclins, can either oppose the effects of or synergize with CDK4/6 inhibitors based on the cellular background. We are currently using a proteomics approach to further delineate the mechanism driving this functional heterogeneity of AMBRA1 in ATRTs. Our study will therefore provide deeper insights into the response of ATRTs to CDK4/6 inhibitors, which represent one of the most promising class of targeted agents for the treatment of ATRTs.

ATRT-13. An integrative analysis of the ATRT proteome unravels novel drug targets and refines molecular subgrouping

INTRODUCTION: Atypical teratoid/rhabdoid tumors (ATRT) represent frequent brain tumors in infants. In recent years, large-scale landscaping efforts on the epigenome and transcriptome of these tumors have unravelled a high degree of heterogeneity and three major molecular subgroups, termed ATRT-TYR, ATRT-SHH,ATRT-MYC, have been identified. The ATRT-proteome, in turn, still represents a largely unchartered territory. METHODS: We have performed a peptide-based screening approach to characterize the proteome of 40 ATRTs and six ATRT cell-lines. All of these samples had matching methylation data available and 28 also corresponding gene expression data. RESULTS: Unsupervised clustering recapitulated the previously described ATRT groups, revealing also a clear split of the SHH-subgroup in a supratentorial (SHH_1) and an infratentorial subgroup (SHH_2). Overall, we identified 7265 proteins, of which 1320 were differentially expressed between the groups, with an enrichment of spliceosome associated terms in SHH_1 and integrins/cell adhesions molecules in SHH_2. ATRT-MYC displayed an overrepresentation of immune cell markers and the TYR subgroup an enrichment of PI3K- as well as mTOR-signaling. Particularly, genes that have previously been described as signature genes for the ATRT-groups such as FABP7 in ATRT-SHH and OTX2 and MITF in ATRT-TYR were among the highly correlating genes that were both expressed in the proteome and the gene expression datasets. On top of this, our analysis revealed highly differentially expressed drug targets such as the tyrosine-kinase MARCKS (overexpressed in ATRT-TYR) not previously identified in ATRT transcriptome data, which warrant investigation by in vitro drug tests. CONCLUSION: Our data reveal the importance of previously described regulatory hubs in the ATRT subgroups, but additionally highlight novel drug targets that merit further exploration. Currently, drug treatment experiments in ATRT cell lines are ongoing to validate these proteins as drug targets, ultimately aiming to establish new therapeutic strategies in this deadly disease.

Targeting the TP53/MDM2 axis enhances radiation sensitivity in atypical teratoid rhabdoid tumors.

Atypical teratoid rhabdoid tumor (ATRT) is a highly aggressive pediatric brain tumor. Despite radiation, aggressive chemotherapy and autologous stem cell rescue, children usually have a poor survival time. In the present study, the role of TP53/MDM2 interaction in ATRT was investigated. A functional genomic screen identified the TP53/MDM2 axis as a therapeutic target in the central nervous system (CNS) ATRT. Gene expression analysis revealed that all ATRT sub-groups expressed high levels of MDM2, which is a negative regulator of TP53. Using cell viability, colony formation and methylcellulose assays it was found that genetic MDM2 inhibition with short hairpin RNA or chemical MDM2 inhibition with small molecule inhibitors, Nutlin3 and idasanutlin (RG7388) decreased the growth of ATRT cell lines. Furthermore, idasanutlin significantly decreased the growth of intracranial orthotopic ATRT brain tumors, as evaluated using T2 MRI, and prolonged survival time relative to control animals. MRI of intracranial tumors showed that diffusion coefficient, an effective marker for successful treatment, significantly increased with idasanutlin treatment showing tumor necrosis/apoptosis. Immunohistochemistry revealed an increased number of caspase-3-positive cells in the idasanutlin treatment group, confirming the induction of apoptosis in vivo. Using flow cytometry and western blot analysis we show that inhibition of MDM2 enhanced radiation sensitivity in vitro by potentiating DNA damage via the induction of the TP53/Bax/Puma proapoptotic axis. Furthermore, DNA damage was associated with increased mitochondrial reactive oxygen species accumulation. The present study demonstrated that MDM2 expression level was increased in ATRT patient samples and MDM2 inhibition suppressed ATRT cell growth in vitro, and leads to apoptosis in vivo. MDM2 inhibition potentiates DNA damage and sensitizes ATRT cells to radiation. These findings highlight the TP53/MDM2 axis as a rational therapeutic target in CNS ATRT.

Targeting of cyclin-dependent kinases in atypical teratoid rhabdoid tumors with multikinase inhibitor TG02.

Atypical teratoid rhabdoid tumors (ATRTs) are aggressive pediatric brain tumors with no current standard of care and an estimated median patient survival of 12 to 18 months. Previous genetic analyses have implicated cyclin D1 and enhancer of zeste homolog 2 (EZH2), a histone methyltransferase that is implicated in many cancers, as key drivers of tumorigenicity in ATRTs. Since the effects of EZH2 and cyclin D1 are facilitated by a host of cyclin-dependent kinases (CDKs), the authors sought to investigate the potential therapeutic effects of targeting CDKs in ATRTs with the multi-CDK inhibitor, TG02. Human ATRT cell lines BT12, BT37, CHLA05, and CHLA06 were selected for investigation. The effects of TG02 on cell viability, proliferation, clonogenicity, and apoptosis were assessed via Cell Counting Kit-8 assays, cell counting, clonogenic assays, and flow cytometry, respectively. Similar methods were used to determine the effects of TG02 combined with radiation therapy (RT) or cisplatin. Synergism indices for TG02-cisplatin combination therapy were calculated using CompuSyn software. TG02 was observed to significantly impair ATRT cell growth in vitro by limiting cell proliferation and clonogenicity, and by inducing apoptosis. TG02 inhibited ATRT cell proliferation and decreased cell viability in a dose-dependent manner with nanomolar half maximal effective concentration (EC50) values (BT12, 207.0 nM; BT37, 127.8 nM; CHLA05, 29.7 nM; CHLA06, 18.7 nM). TG02 (150 nM) dramatically increased the proportion of apoptotic ATRT cells 72 hours posttreatment (TG02 8.50% vs control 1.52% apoptotic cells in BT12, p < 0.0001; TG02 70.07% vs control 15.36%, p < 0.0001). Combination therapy studies revealed that TG02 acted as a potent radiosensitizer in ATRT cells (BT12 surviving fraction, RT 51.2% vs RT + TG02 21.7%). Finally, CompuSyn analysis demonstrated that TG02 acted synergistically with cisplatin against ATRT cells at virtually all therapeutic doses. These findings were consistent in cell lines that cover all three molecular subgroups of ATRTs. The results of this investigation have established that TG02 is an effective therapeutic against ATRTs in vitro. Given the lack of standard therapy for ATRTs, these findings help fill an unmet need and support further study of TG02 as a potential therapeutic option for patients with this deadly disease.

Abstract 4808: Preclinical studies of the combination of ONC201, radiotherapy and Temozolomide against GBM, DIPG and ATRT cell lines

Abstract The American Cancer Society predicts, in 2018, there will be ~23,880 new cases and 16,830 deaths caused by primary cancer of the brain and spinal cord, in the US. CNS tumors are the most common cause of cancer-related deaths in adolescents and young adults. First-in-class small-molecule imipridone ONC201 can act as a dual inhibitor of ERK/AKT and can induce an integrated stress response (ISR), pro-apoptotic TRAIL receptor DR5 activation, cancer stem cell depletion, and growth arrest. ONC201 crosses the blood brain barrier and has demonstrated clinical benefits in glioblastoma patients. Radiation therapy is used alone or in combination with surgery and/or chemotherapy such as Temozolomide in the treatment of primary or metastatic brain tumors. We hypothesized that ONC201 may synergize with radiotherapy and Temozolomide in brain tumor treatment. Glioblastoma (GBM), diffuse intrinsic pontine glioma (DIPG) and atypical teratoid rhabdoid tumor (ATRT) cell lines were tested in this study. Cell viability and colony formation assays were performed with ONC201 alone up to 20 μM or in combination with radiotherapy up to 8 Gy and Temozolomide up to 100 μM. Western blots were used to document apoptosis of treated cells. We observed synergy between ONC201 and radiation and between ONC201 and Temozolomide with the best combination indices of 0.51 and 0.21 respectively. Further studies are evaluating the role of dopamine receptors engaged by ONC201, the ISR and TRAIL pathway in the synergistic effect that would support further development of the triple combination therapy in brain tumors. Citation Format: Lanlan Zhou, Wafik S. El-Deiry. Preclinical studies of the combination of ONC201, radiotherapy and Temozolomide against GBM, DIPG and ATRT cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4808.

Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation

Biallelic inactivation of SMARCB1, encoding a member of the SWI/SNF chromatin remodeling complex, is the hallmark genetic aberration of atypical teratoid rhabdoid tumors (ATRT). Here, we report how loss of SMARCB1 affects the epigenome in these tumors. Using chromatin immunoprecipitation sequencing (ChIP-seq) on primary tumors for a series of active and repressive histone marks, we identified the chromatin states differentially represented in ATRTs compared with other brain tumors and non-neoplastic brain. Re-expression of SMARCB1 in ATRT cell lines enabled confirmation of our genome-wide findings for the chromatin states. Additional generation of ChIP-seq data for SWI/SNF and Polycomb group proteins and the transcriptional repressor protein REST determined differential dependencies of SWI/SNF and Polycomb complexes in regulation of diverse gene sets in ATRTs.

ATRT-24. CHROMATIN SEGMENTATION IN ATRT REVEALS AN IMPORTANT ROLE FOR RESIDUAL SWI/SNF MEMBERS

Although SMARCB1 mutations represent the only recurrent genetic aberration in atypical teratoid/rhabdoid tumors (ATRT), a comprehensive assessment of the epigenetic effect of SMARCB1 loss has not been attempted so far. To achieve this, we performed ChIP-sequencing for six histone marks (H3K4me1, H3K4me3, H3K27me3, H3K27Ac, H3K9me3, H3K36me3) and EZH2 in 11 primary ATRTs, encompassing all three molecular subgroups of ATRT. Chromatin segmentation analyses revealed that across all three subgroups a high percentage of ATRT epigenomes resides in a quiescent state and active enhancer states are significantly underrepresented as compared to non-neoplastic brain. We validated these findings in a SMARCB1-reexpressing ATRT cell line and also found an overall deincrease of H3K27Ac and H3K27me3 upon SMARCB1 reexpression. Interestingly, by comparing the genome wide distribution of EZH2 and H3K27me3, we also identified classes of ATRT-specific active genes bound by EZH2, but lackingH3K27me3, pointing at a non-canonical role of EZH2 in gene activation. ChIP-Sequencing of SMARCA4 in these samples revealed that many of these „EZH2 only” genes display a high signal of of this protein. Many of these genes (such as e.g. CCND2) were downregulated upon knock-down of SMARCA4 in ATRT cell lines. Adding to the overall characterization of the epigenome, we have shown that a number of genes - despite being bound by EZH2- are maintained in an active state by residual SWI/SNF complex binding. This sheds new light on the role of residual SWI/SNFSMARCA4 still being present in AT/RT and elucidates a mechanism by which AT/RT keep important tumor-genes in an active state.

Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors

We recently reported that atypical teratoid rhabdoid tumors (ATRTs) comprise at least two transcriptional subtypes with different clinical outcomes; however, the mechanisms underlying therapeutic heterogeneity remained unclear. In this study, we analyzed 191 primary ATRTs and 10 ATRT cell lines to define the genomic and epigenomic landscape of ATRTs and identify subgroup-specific therapeutic targets. We found ATRTs segregated into three epigenetic subgroups with distinct genomic profiles, SMARCB1 genotypes, and chromatin landscape that correlated with differential cellular responses to a panel of signaling and epigenetic inhibitors. Significantly, we discovered that differential methylation of a PDGFRB-associated enhancer confers specific sensitivity of group 2 ATRT cells to dasatinib and nilotinib, and suggest that these are promising therapies for this highly lethal ATRT subtype.

PTPS-29UBIQUITIN CARBOXYL TERMINAL HYDROLASE-L1 (UCH-L1) IS A TUMOR SUPPRESSOR IN ATYPICAL TERATOID RHABDOID TUMORS (ATRTs)

BACKGROUND: Atypical teratoid rhabdoid tumor (ATRTs) constitute 20% of brain tumors in young children (<3 yrs of age) and is characterized by bi-allelic mutations of the INI-1 gene. The cell of origin in this tumor is not known and the mechanism by which INI-1 causes tumor is still not clear. Ubiquitin carboxyl-terminal hydrolase isoenzyme 1 (UCHL1), is an abundant neuronal de-ubiquitinating enzyme which acts as a tumor suppressor gene that is inactivated by promoter methylation / gene deletion in several cancers as well as an oncogene with overexpression in other cancers. The role of UCHL1 in brain tumors has not yet been studied. METHODS/RESULTS: We identified UCHL1 is silenced in ATRT cell lines (BT-12, BT-16) along with absent basal expression of p53 and NOXA by western blotting. UCHL1 silencing is mediated by promoter hyper-methylation (detected by using methylation specific PCR (MSP)); and pharmacologic de-methylation reactivated UCHL1 expression in these cell lines along with expression of p53 and NOXA. Ectopic expression of UCHL1 dramatically inhibited the growth of ATRT cell lines (using colony forming assay and MTT assay) and increased sensitivity to radiation. The growth inhibition was mediated by promoting tumor cell apoptosis resulting from activating the p53 tumor suppressor pathway. CONCLUSIONS: We have shown that UCHL1 is silenced in ATRT cell lines and acts as a tumor suppressor gene. We hypothesize that loss of p53 function due to silencing of UCHL1 drives tumor formation in the background of bi-allelic INI1 mutation in ATRT. We will further test this hypothesis using patient derived primary cell cultures and animal models (using genetically engineered mouse models INI1 +/- / UCHL1-/- mice).

Abstract 3923: A role for fibroblast growth factor receptors in growth of atypical teratoid rhabdoid tumor cells and as potential therapeutic targets

Abstract Malignant rhabdoid tumors are characterized by the loss of the SWI/SNF complex subunit SMARCB1. Atypical Teratoid Rhabdoid Tumor (ATRT) is a rare form of pediatric MRT that occurs in the CNS. Current treatment modalities for this tumor type continue to be surgical resection, chemotherapy and radiotherapy, but overall survival is still relatively low for younger children with this disease. We initially tested the sensitivity of three ATRT cell lines to 48 chemotherapeutic agents and selective inhibitors. Our results indicated that two cell lines CHLA-04-ATRT and CHLA-05-ATRT were sensitive to FGFR inhibition. Further analysis of a panel of five ATRT cell lines indicated that the cell lines CHLA-04-ATRT, CHLA-05-ATRT, CHLA-266 and BT-12 were sensitive to the FGFR inhibitors PD173074, BGJ398 and AZD4547. Interestingly, the ATRT cell line CHLA-06-ATRT did not show sensitivity to FGFR inhibition. Analysis of FGFR protein expression by immunoblot analysis indicated that CHLA-04-ATRT and CHLA-266 cells expressed both FGFR1 and FGFR2, while the cell lines CHLA-05-ATRT and BT-12 expressed only FGFR1. The CHLA-06-ATRT cell line did not show expression of any FGFRs. We further demonstrated functional FGFR activity in the ATRT cell lines by treating growth factor-deprived ATRT cells with FGF-1 or FGF-2, both of which led to dose dependent cell growth only in the cell lines expressing FGFR1 or FGFR2. We are currently investigating the expression of FGFR isoforms in ATRT patient samples. Taken together, our results demonstrate a potential role for FGFR1 and FGFR2 in the survival and proliferation of ATRT cells and indicate that FGFRs could serve as potential targets for therapy in ATRT. Citation Format: David O. Azorsa, Oliver B. Pepper, Madhavi Chakravadhanula, David W. Lee, Justin J. Montoya, Victor Ozols, Ratan Bhardwaj, Robert J. Arceci. A role for fibroblast growth factor receptors in growth of atypical teratoid rhabdoid tumor cells and as potential therapeutic targets. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3923. doi:10.1158/1538-7445.AM2015-3923

Abstract 1613: β-lapachone: a novel targeted therapy for atypical teratoid rhabdoid tumors (ATRTs)

Abstract Atypical teratoid rhabdoid tumors (ATRTs) are aggressive malignant neoplasms that occur in the CNS, most commonly in children &amp;lt;3 years of age. Despite intensive chemo-radiotherapy and surgery, the outcomes for patients with this disease remain dismal, with ∼75% of patients dying from their disease at a median of 10 months after diagnosis. Thus, it is critical to identify and validate novel ATRT targets for new therapies. We found that the pathognomonic genetic lesion of ATRTs, loss of the SWI/SNF chromatin remodeling complex member INI1/hSNF5/SMARCB1, leads to high expression of NAD(P)H:quinone oxidoreductase 1 (NQO1), a two-electron oxidoreductase. Thus, we hypothesized that ATRTs will be vulnerable to drugs, such as ß-lapachone (ß-lap, ARQ761 in clinical form), that selectively kill NQO1-expressing cells. A panel of ATRT cell lines exhibited overall high NQO1 expression and low micromolar sensitivity to ß-lap (IC50 1.6-4 uM), with the exception of cell lines that were homozygous for the C609T NQO1 (*2) polymorphism, which exhibited no NQO1 activity and were resistant to ß-lap treatment (IC50 &amp;gt;15 uM). A two-hour pulse with ß-lap caused a burst of ROS-mediated DNA damage and PARP1 hyperactivation, resulting in NAD+ and ATP depletion and caspase-independent, mu-calpain-mediated apoptosis. Co-treatment with dicoumarol, a specific inhibitor of NQO1, prevented these effects by blocking the NQO1-dependent bioactivation of ß-lap. Low expression of NQO1 in normal brain and other pediatric tissues suggests a wide therapeutic window for ß-lap. These findings encourage the continued study of ß-lap and other NQO1 bioactivated therapeutics for the treatment of this recalcitrant disease. This work was supported by NIH/NCI R01 CA102972 to DAB and a REACH award from the Alex's Lemonade Stand Foundation to JFA and TWL. Citation Format: Zachary R. Moore, Sarai Stuart, Agnieszka Cholka, Ashwin Venkataraman, Jingying Xu, Anat Erdreich-Epstein, Dinesh Rakheja, David A. Boothman, James F. Amatruda, Theodore W. Laetsch. β-lapachone: a novel targeted therapy for atypical teratoid rhabdoid tumors (ATRTs). [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1613. doi:10.1158/1538-7445.AM2015-1613

Abstract 3107: The role of LIN28 in atypical teratoid rhabdoid tumor (ATRT) pathogenesis

Abstract Atypical teratoid rhabdoid tumor (ATRT) is a highly malignant brain tumor developing almost exclusively in children. It belongs to the embryonal brain tumor group which consists of primitive tumors recapitulating early embryogenesis of nervous system. It is known that loss of INI protein expression is the hallmark of ATRT pathogenesis. LIN28 is a key gene in embryonic development and maintenance of pluripotency in stem cells. Considering the primitive nature and young age onset of ATRT, LIN28 may be an important co-player in ATRT pathogenesis. We explored the expression and functional role of LIN28 in ATRT. In tumor tissues, LIN28 is highly expressed in ATRT compared with medulloblastomas, another embroynal tumor, whereas primary let-7 microRNA is down-regulated in ATRT. ATRT also showed higher expression of CCND1 and MYC and lower expression of CDKN1C. Knockdown of LIN28 with siRNA in ATRT cell lines resulted decreased cell viability, proliferation, and migration capability. Suppression of CCND1 and MYC expression and enhanced expression of CDKN1C were also observed. Knockdown of LIN28 lead to decreased expression of other pulripotency genes (OCT4 and NANOG) and signature of mesenchymal-epithelial transition was observed after suppression of LIN28. We then introduced wild-type INI1 into ATRT cells by transfection. Restoration of INI in ATRT cell lines lead to decreased expression of LIN28 and CCND1. These results showed that LIN28 is regulated by INI1 and that loss of INI1 protein in ATRT results in unopposed expression of LIN28 and related oncogenes such as CCND1, leading to tumorigenesis. Therefore, the strategic role of LIN28 in ATRT may be utilized as an important therapeutic target. Citation Format: Ji Hoon Phi, Seung Ah Choi, Yong Hwy Kim, Young-Hoon Kim, Chul-Kee Park, Kyu-Chang Wang, Seung-Ki Kim. The role of LIN28 in atypical teratoid rhabdoid tumor (ATRT) pathogenesis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3107. doi:10.1158/1538-7445.AM2014-3107