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Supplementary data including supplementary figures S1 to S6 and supplementary tables S1 to S3.

Supplementary information on the used materials and methods.

Neuroblastoma tumors frequently overexpress the anti-apoptotic protein B-cell lymphoma/leukemia 2 (BCL-2). We previously showed that treating BCL-2–dependent neuroblastoma cells with the BCL-2 inhibitor venetoclax results in apoptosis, but unfortunately partial therapy resistance is observed. The current study describes the identification of drugs capable of resensitizing venetoclax-resistant neuroblastoma cells to venetoclax. To examine these effects, venetoclax resistance was induced in BCL-2–dependent neuroblastoma cell lines KCNR and SJNB12 by continuous exposure to high venetoclax concentrations. Non-resistant and venetoclax-resistant neuroblastoma cell lines were exposed to a 209-compound library in the absence and presence of venetoclax to identify compounds that were more effective in the venetoclax-resistant cell lines under venetoclax pressure. Top hits were further validated in combination with venetoclax using BCL-2–dependent neuroblastoma model systems. Overall, high-throughput drug screening identified the MDM2 inhibitor idasanutlin as a promising resensitizing agent for venetoclax-resistant neuroblastoma cell lines. Idasanutlin treatment induced BAX-mediated apoptosis in venetoclax-resistant neuroblastoma cells in the presence of venetoclax, whereas it caused p21-mediated growth arrest in control cells. In vivo combination treatment showed tumor regression and superior efficacy over single-agent therapies in a BCL-2–dependent neuroblastoma cell line xenograft and a patient-derived xenograft. However, xenografts less dependent on BCL-2 were not sensitive to venetoclax–idasanutlin combination therapy. This study demonstrates that idasanutlin can overcome resistance to the BCL-2 inhibitor venetoclax in preclinical neuroblastoma model systems, which supports clinical development of a treatment strategy combining the two therapies.

IntroductionMutations affecting the RAS-MAPK pathway occur frequently in relapsed neuroblastoma tumors and are associated with response to MEK inhibition in vitro. However, these inhibitors alone do not lead to tumor regression in vivo, indicating the need for combination therapy.Methods and resultsVia high-throughput combination screening, we identified that the MEK inhibitor trametinib can be combined with BCL-2 family member inhibitors, to efficiently inhibit growth of neuroblastoma cell lines with RAS-MAPK mutations. Suppressing the RAS-MAPK pathway with trametinib led to an increase in pro-apoptotic BIM, resulting in more BIM binding to anti-apoptotic BCL-2 family members. By favoring the formation of these complexes, trametinib treatment enhances sensitivity to compounds targeting anti-apoptotic BCL-2 family members. In vitro validation studies confirmed that this sensitizing effect is dependent on an active RAS-MAPK pathway. In vivo combination of trametinib with BCL-2 inhibitors led to tumor inhibition in NRAS-mutant and NF1-deleted xenografts.ConclusionTogether, these results show that combining MEK inhibition with BCL-2 family member inhibition could potentially improve therapeutic outcomes for RAS-MAPK-mutated neuroblastoma patients.

BackgroundImmunotherapy in high-risk neuroblastoma (HR-NBL) does not live up to its full potential due to inadequate (adaptive) immune engagement caused by the extensive immunomodulatory capacity of HR-NBL. We aimed to tackle one of the most notable immunomodulatory processes in neuroblastoma (NBL), absence of major histocompatibility complex class I (MHC-I) surface expression, a process greatly limiting cytotoxic T cell engagement. We and others have previously shown that MHC-I expression can be induced by cytokine-driven immune modulation. Here, we aimed to identify tolerable pharmacological repurposing strategies to upregulate MHC-I expression and therewith enhance T cell immunogenicity in NBL.MethodsDrug repurposing libraries were screened to identify compounds enhancing MHC-I surface expression in NBL cells using high-throughput flow cytometry analyses optimized for adherent cells. The effect of positive hits was confirmed in a panel of NBL cell lines and patient-derived organoids. Compound-treated NBL cell lines and organoids were cocultured with preferentially expressed antigen of melanoma (PRAME)-reactive tumor-specific T cells and healthy-donor natural killer (NK) cells to determine the in vitro effect on T cell and NK cell cytotoxicity. Additional immunomodulatory effects of histone deacetylase inhibitors (HDACi) were identified by transcriptome and translatome analysis of treated organoids.ResultsDrug library screening revealed MHC-I upregulation by inhibitor of apoptosis inhibitor (IAPi)- and HDACi drug classes. The effect of IAPi was limited due to repression of nuclear factor kappa B (NFκB) pathway activity in NBL, while the MHC-I-modulating effect of HDACi was widely translatable to a panel of NBL cell lines and patient-derived organoids. Pretreatment of NBL cells with the HDACi entinostat enhanced the cytotoxic capacity of tumor-specific T cells against NBL in vitro, which coincided with increased expression of additional players regulating T cell cytotoxicity (eg, TAP1/2 and immunoproteasome subunits). Moreover, MICA and MICB, important in NK cell cytotoxicity, were also increased by entinostat exposure. Intriguingly, this increase in immunogenicity was accompanied by a shift toward a more mesenchymal NBL cell lineage.ConclusionsThis study indicates the potential of combining (immuno)therapy with HDACi to enhance both T cell-driven and NKcell-driven immune responses in patients with HR-NBL.

Homozygous inactivation of the CDKN2A locus is one of the most common genomic aberrations in human cancer. The locus codes for two unrelated and distinctly regulated proteins: p14ARF and p16INK4a, which inhibit MDM2 and CDK4/6, respectively. Loss of CDKN2A is also a recurrent event in relapsed neuroblastoma, a childhood tumour that arises from neural crest cells. To examine the consequences of the loss of the two distinct gene transcripts in neuroblastoma, we used the CRISPR-Cas9 system to knockout p14, p16 and p14+p16 in SY5Y cells. RNA sequencing of the transcriptome revealed a striking shift towards an immature Schwann cell precursor-like phenotype with mesenchymal characteristics, specifically in the p16 and p14+p16 knockouts. High-throughput drug screening of p16 and p14+p16 knockout clones identified a large increase in sensitivity to EGFR inhibitors. On protein level, we were able to confirm that EGFR pathway activation is higher in p14+p16 knockout cells and that treatment with the EGFR inhibitor afatinib resulted in higher levels of apoptosis. Afatinib also reduced tumour growth in vivo in xenografts transplanted with p14+p16 knockout SY5Y cells. Overall, our study suggests that CDKN2A deletion in neuroblastoma relates to a phenotypic shift towards a more progenitor like state and increases sensitivity to EGFR inhibitors.

Background Currently ~50% of patients with the diagnosis of high-risk neuroblastoma will not survive due to relapsing or refractory disease. Recent innovations in immunotherapy for solid tumors are highly promising, but the low MHC-I expression of neuroblastoma represents a major challenge for T cell-mediated immunotherapy. Here, we propose a novel T cell-based immunotherapy approach for neuroblastoma, based on the use of TEG002, αβ-T cells engineered to express a defined γδ-T cell receptor, which are thought to recognize and kill target cells independent of MHC-I. In this pilot project we have tested the potential efficacy of TEG002 therapy as a novel treatment for neuroblastoma, with tumor organoids. Materials and Methods Effector cells were created from healthy donor peripheral blood T cells. The TEG002 cells were engineered by transducing αβ-T cells with a defined Vγ9Vδ2-T cell receptor. Both the untransduced αβ-T cells and the endogenous Vγ9Vδ2-T cells from the same healthy donor were used as controls in all experiments. Activation and killing of TEG002 was tested in a co-culture setting with neuroblastoma organoids. Supernatant of the co-culture was collected at 24 hours for IFNγ ELISA to measure activation of TEG002. The dynamics of cytotoxicity were analyzed over time from 0 till 72 hours, using the live-cell imaging system IncuCyte from Sartorius®. Killing was quantified using a Caspase3/7 Green dye and the IncuCyte software. Transcriptional profiling of the neuroblastoma organoids was done by RNA sequencing and MHC-I expression of the neuroblastoma organoids was determined by flow cytometry. Results We showed that 3 out of 6 neuroblastoma organoids could activate TEG002 as measured by IFNγ production. Transcriptional profiling of the neuroblastoma organoids showed that this effect correlates with an increased activity of processes involved in interferon signaling and extracellular matrix organization. Analysis of the dynamics of organoid killing by TEG002 over time confirmed that organoids which induced TEG002 activation were efficiently killed independently of their MHC-I expression. Of note, efficacy of TEG002 treatment was superior to donor-matched untransduced αβ-T cells or endogenous γδ-T cells. Conclusions We demonstrated that 50% of tested neuroblastoma organoids can effectively activate TEG002 and that killing of the organoids is independent of MHC-I expression. Hence, this pilot study identified TEG002 as a promising novel cellular product for immunotherapy for a subset of neuroblastoma tumors, warranting further investigations into its clinical application. Disclosure Information J.G.M. Strijker: None. E. Drent: A. Employment (full or part-time); Significant; Gadeta BV. J.J.F. van der Hoek: None. R. Pscheid: A. Employment (full or part-time); Significant; Gadeta BV. B. Koopmans: None. K. Ober: None. S.R. van Hooff: None. W.M. Kholosy: None. C. Coomans: A. Employment (full or part-time); Significant; Gadeta BV. A. Bisso: A. Employment (full or part-time); Significant; Gadeta BV. M. van Loenen: A. Employment (full or part-time); Significant; Gadeta BV. J.J. Molenaar: None. J. Wienke: None.

The treatment of children diagnosed with acute lymphoblastic leukemia (ALL) has improved significantly over recent decades, with 5-year event-free survival (EFS) approaching 85% [1]. However, 5-year EFS for infants diagnosed at less than 1 year of age with MLL-rearranged ALL remains less than 40% [2]. MLL-rearranged infant ALL is both clinically and biologically distinct from other childhood ALL subtypes, which is reflected by a unique gene expression profile [3], a remarkably silent mutational landscape [4], and pronounced resistance to currently applied chemotherapeutics [5].

Mutations affecting the RAS-MAPK pathway occur frequently in relapsed neuroblastoma tumors and are associated with response to MEK inhibition in vitro. However, these inhibitors alone do not lead to tumor regression in vivo, indicating the need for combination therapy. Through high throughput combination screening we identify Trametinib and inhibitors of the BCL2 family (Navitoclax and Venetoclax) as a promising combination in neuroblastoma cells with RAS-MAPK mutations. In these lines, inhibiting the RAS-MAPK pathway leads to Bim stabilization and increased sensitivity to compounds inhibiting Bim binding to Bcl2 family members. Combining Trametinib with BCL2 inhibitors causes increased growth inhibition compared to Trametinib only in NRAS mutant SKNAS xenografts, while BCL2 inihibitors alone do not affect growth of these tumors. These results show that MEK inhibitors and specific Bcl2 family member inhibitors are a potent combination for RAS-MAPK mutated neuroblastoma tumors.

Chromosome 17q gains are almost invariably present in high-risk neuroblastoma cases. Here, we perform an integrative epigenomics search for dosage-sensitive transcription factors on 17q marked by H3K27ac defined super-enhancers and identify TBX2 as top candidate gene. We show that TBX2 is a constituent of the recently established core regulatory circuitry in neuroblastoma with features of a cell identity transcription factor, driving proliferation through activation of p21-DREAM repressed FOXM1 target genes. Combined MYCN/TBX2 knockdown enforces cell growth arrest suggesting that TBX2 enhances MYCN sustained activation of FOXM1 targets. Targeting transcriptional addiction by combined CDK7 and BET bromodomain inhibition shows synergistic effects on cell viability with strong repressive effects on CRC gene expression and p53 pathway response as well as several genes implicated in transcriptional regulation. In conclusion, we provide insight into the role of the TBX2 CRC gene in transcriptional dependency of neuroblastoma cells warranting clinical trials using BET and CDK7 inhibitors., In high-risk neuroblastoma cases, gains in chromosome 17q are common. Here, the authors investigate the epigenomics and transcriptomics of neuroblastoma, identifying TBX2 as a core regulatory circuitry component enhancing the reactivation of DREAM targets by MYCN/FOXM1.

MLL-rearranged acute lymphoblastic leukemia (ALL) is characterized by deregulation of the epigenome and shows susceptibility towards epigenetic perturbators such as histone deacetylase (HDAC) inhibitors. Hence, HDACs represent attractive drug targets and a variety of small molecule HDAC inhibitors have been developed and evaluated for the treatment of hematological malignancies. However, most broad-spectrum inhibitors, which simultaneously target the majority of human HDAC isoforms, often induce toxicity, especially in combination with other therapeutic agents. Therefore, selective inhibition of only one or two HDAC isoforms may represent a better alternative, provided that disease-specific dependency on specific HDACs has been identified. We examined the effects of shRNA-mediated knock-down of the class II HDACs (i.e. HDAC4, HDAC5, HDAC6, HDAC7 and HDAC9) in the MLL-rearranged ALL cell lines SEM and ALL-PO. Except for HDAC9, loss of expression (both on the mRNA and protein level) of all HDACs led to strong reductions in viable cells (0.70 to 0.19-fold; p=0.02-0.0016) in both models due to apoptosis, cell cycle arrest, or a combination thereof. Next, we evaluated the in vitro efficacy of a variety of class II HDAC-specific inhibitors on a panel of MLL-rearranged ALL (n=5) using 4-day viability MTT assays. This revealed that the selective HDAC4/5 inhibitor LMK-235 was able to recapitulate the loss-of-function phenotype of HDAC4 and HDAC5. Dose response curves showed complete growth inhibition in MLL-rearranged ALL cell lines (n=5), as well as in primary MLL-rearranged infant ALL patient samples (n=4), with IC 50 values of ~100 nM and 40-100 nM, respectively. Importantly, at these concentrations, LMK-235 hardly affected whole bone marrow samples derived from healthy individuals (n=2), for which IC 50 values were ~1 µM. To further explore the potential of class II HDAC inhibitor-based therapeutic strategies, we performed a combinatorial drug screen to identify compounds that synergize with LMK-235. For this, a compound library (comprising >200 unique agents) was screened in the absence and presence of varying concentrations of LMK235 in the MLL-rearranged cell line models SEM and ALL-PO. This, and subsequent validation experiments in additional cell line models, revealed that Venetoclax (BCL2 inhibitor), Trametinib (MEK/ERK inhibitor), Ponatinib (multi-tyrosine kinase inhibitor) and Omipalisib (a PI3K/mTOR inhibitor) strongly synergized with LMK-235. Average ZIP synergy scores ranged from 10-30, with peak ZIP scores up to 40. Importantly, synergistic effects were consistent over all concentration combinations tested. The addition of 50-100 nM LMK-235 strongly reduced IC 50 values for Omipalisib, Ponatinib and Venetoclax (0.27-fold p=0.003, 0.11-fold p=0.0005, 0.75-fold p=0.0004, respectively) in both models. In preparation to assess the in vivo efficacy of LMK-235 in patient-derived xenograft (PDX) mouse models of MLL-rearranged infant ALL, pharmacokinetic/pharmacodynamic (PK/PD) analysis was performed in immunodeficient NSG mice (n=5). For this, mice were treated with 20 mg/kg of LMK-235, daily administered via intraperitoneal injections for a total of 29 days. While none of the mice showed signs of toxicity or weight loss, LMK-235 plasma levels were stably maintained at concentrations that are highly effective against MLL-rearranged ALL cells in vitro. Taken together, these data demonstrate that various class II HDAC isoforms are targetable vulnerabilities in MLL-rearranged ALL and that pharmaceutical inhibition of HDAC4/5 by LMK-235 represents an attractive therapeutic option. Moreover, high levels of synergy observed between this HDAC inhibitor and various agents belonging to drug classes already reported to be effective against MLL-rearranged ALL, warrants pre-clinical evaluation in vivo. Currently, the assessment of the in vivo efficacy of LMK-235 monotherapy in MLL-rearranged infant ALL PDX models is in progress, after which promising synergistic HDAC inhibitor-based drug combinations will be evaluated. To determine the additional therapeutic value, the efficacy of LMK-235 and promising synergistic combinations will be evaluated in the background of conventional combination chemotherapy, where PDX models will receive a mouse-adapted version of induction therapy currently applied for treatment of MLL-rearranged infant ALL patients. Disclosures No relevant conflicts of interest to declare.

BACKGROUND: The anti-apoptotic protein B cell lymphoma/leukaemia 2 (BCL-2) is highly expressed in the majority of all neuroblastomas. In previous preclinical studies, we have shown that treatment of BCL-2-dependent neuroblastoma with BCL-2 inhibitors leads to programmed cell death. These results have contributed to the initiation of a phase I trial to study the safety and pharmacokinetics of Venetoclax in children with relapsed or refractory neuroblastoma. AIM: The current study aims to identify and validate targeted combination strategies to prevent or overcome neuroblastoma resistance to Venetoclax. METHODS: Targeted drug candidates for combination treatment with Venetoclax were identified by high-throughput drug screening of non-resistant and Venetoclax-resistant BCL-2-dependent neuroblastoma cell lines. Top hits were subsequently tested more extensively in vitro and in vivo to validate the screening results. RESULTS: High-throughput drug screens identified the MDM2 inhibitor Idasanutlin as one of the strongest re-sensitizers for Venetoclax in Venetoclax-resistant BCL-2-dependent neuroblastoma cells with wild-type p53. Subsequent in vitro validation showed that Idasanutlin induced cyclin dependent kinase inhibitor 1 (p21)-mediated growth arrest in non-resistant neuroblastoma cells, but induced a BCL-2-associated X protein (BAX)-mediated apoptotic response in Venetoclax-resistant neuroblastoma cells in the presence of Venetoclax. In vivo combination of Venetoclax with Idasanultin resulted in a remarkably improved anticancer effect compared to single agent therapy, with very good partial and complete responses in BCL-2-dependent neuroblastoma xenografts. Combination screens additionally revealed that the clinically studied targeted inhibitors CUDC-907 (PI3K/HDAC), Prexasertib (CHK1) and Talazoparib (PARP1/2) improved the efficacy of Venetoclax more potently than ALK inhibitors in BCL-2-dependent neuroblastoma cells harboring ALK mutations. CONCLUSION: Our findings suggest that the clinical use of Venetoclax for the treatment of children with BCL-2-dependent neuroblastoma tumors can be improved by combination therapy with targeted inhibitors. The presence of additional neuroblastoma driving genomic events is not always predictive of the optimal combination strategy for BCL-2-dependent neuroblastoma subgroups. These findings should guide the design of combination Phase 2 trials of Venetoclax with other targeted compounds such as Idasanutlin, CUDC-907, Prexasertib and Talazoparib. Citation Format: M. Emmy M. Dolman, Laurel T. Bate-Eya, Lindy Vernooij, Bianca Koopmans, Lindy K. Alles, Anke H. Essing, Daphne Lelieveld, David A. Egan, Mark Kerstjens, Ronald W. Stam, Huib N. Caron, Jan J. Molenaar. Preclinical identification of Venetoclax combination strategies with Idasanutlin, CUDC-907, Prexasertib or Talazoparib for neuroblastoma treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2630.

BACKGROUND: Acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) represent the most common types of cancer among children. Although the survival rates of pediatric ALL and AML have improved substantially over the last decades, the prognosis for some subgroups of pediatric leukemia remain poor. MLL-rearranged infant ALL, MLL-rearranged AML, and NUP98-rearranged AML, for instance, still have 5-year event-free survival rates of only ~40%. Evidently, these high-risk subtypes of childhood leukemia urgently require new treatment strategies in order to improve clinical outcome. AIM: Identification of effective therapeutic drugs for high-risk leukemia subtypes harboring a translocation in the MLL or NUP98 gene, by using a drug repurposing strategy involving high-throughput screening of > 4000 compounds. METHODS: Primary leukemic cells derived from six patients with either MLL-rearranged infant ALL, pediatric MLL-rearranged AML, or pediatric NUP98-rearranged AML at diagnosis, were screened using commercially available drug libraries comprising a total of 4165 compounds. Drug sensitivity was assessed after 4 days treatment with 10 nM, 100 nM and 1000 nM of the library compounds using MTT assays. Potential hits were subsequently validated using cytotoxicity assays with a more extensive range of drug concentrations. RESULTS: The results of our drug screens showed that the most effective drugs, by far, were found for MLL-rearranged infant ALL. For MLL-rearranged AML the number of identified potent drugs was considerably less; notably, all of these compounds identified overlapped with the effective agents also found for MLL-rearranged infant ALL. Remarkably, for NUP98-translocated AML, only a few potential drug hits were identified, suggesting that this type of leukemia might be extremely chemo-resistant. In addition to novel candidate compounds, we also found several agents either recently described to have strong anti-leukemic effects against MLL-rearranged leukemia, such as the BCL2 inhibitors Venetoclax (ABT199) and Navitoclax (ABT263), or the MDM2 inhibitor Idasanutlin (RG7388), as well as finding drugs currently being used in the treatment of MLL-rearranged acute leukemias. Taken together, these observations indicate that high-throughput drug screening on primary patient samples is indeed able to identify effective compounds, validating our experimental approach. Interestingly, while validating newly identified drug hits, we observed a remarkable pattern for compounds effective against MLL-rearranged acute leukemia: the top hits seem to either directly or indirectly associate with p53 activity, albeit from various angles. CONCLUSION: Our data suggests a potential role for p53 in MLL-rearranged acute leukemia, and indicates that targeting p53 may well become an important therapeutic strategy for these types of childhood leukemia. Citation Format: Priscilla Wander, Sandra S. Pinhanços, Bianca Koopmans, M. Emmy M. Dolman, Pauline Schneider, Patricia Garrido Castro, Luke Jones, Susan T.C.J.M. Arentsen-Peters, Mark Kerstjens, Jan Molenaar, Huib N. Caron, Rob Pieters, Michel C. Zwaan, Ronald W. Stam. High-throughput drug library screening identifies potent drugs and novel drug targets for high-risk acute leukemia in children [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1925.