CRISPR/Cas9 Screen in Gastric Cancer Patient-Derived Organoids Reveals KDM1A-NDRG1 Axis as a Targetable Vulnerability

Viability CRISPR screens have proven indispensable in parsing genome function. However, their application in new, more physiologically relevant culturing systems like patient-derived organoids (PDOs) has been much slower. To probe epigenetic contribution to gastric cancer (GC), the third leading cause of cancer-related deaths worldwide, the first negative selection CRISPR screen in GC PDOs that faithfully preserve primary tumor characteristics is performed. Extensive quality control measurements showing feasibility of CRISPR screens in primary organoid culture are provided. The screen reveals the histone lysine demethylase-1A (KDM1A) to constitute a GC vulnerability. Both genetic and pharmacological inhibition of KDM1A cause organoid growth retardation. Further, it is shown that most of KDM1A cancer-supporting functions center on repression of N-myc downstream regulates gene-1 (NDRG1). De-repression of NDRG1 by KDM1A inhibitors (KDM1Ai) causes inhibition of Wnt signaling and a strong G1 cell cycle arrest. Finally, by profiling 20 GC PDOs, it is shown that NDRG1 upregulation predicts KDM1Ai response with 100% sensitivity and 82% specificity in the tested cohort. Thus, this work pioneers the use of negative selection CRISPR screens in patient-derived organoids, identifies a marker of KDM1Ai response, and accordingly a cohort of patients who may benefit from such therapy.

3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma

Ependymoma is a tumor of the brain or spinal cord. The two most common and aggressive molecular groups of ependymoma are the supratentorial ZFTA-fusion associated and the posterior fossa ependymoma group A. In both groups, tumors occur mainly in young children and frequently recur after treatment. Although molecular mechanisms underlying these diseases have recently been uncovered, they remain difficult to target and innovative therapeutic approaches are urgently needed. Here, we use genome-wide chromosome conformation capture (Hi-C), complemented with CTCF and H3K27ac ChIP-seq, as well as gene expression and DNA methylation analysis in primary and relapsed ependymoma tumors, to identify chromosomal conformations and regulatory mechanisms associated with aberrant gene expression. In particular, we observe the formation of new topologically associating domains ('neo-TADs') caused by structural variants, group-specific 3D chromatin loops, and the replacement of CTCF insulators by DNA hyper-methylation. Through inhibition experiments, we validate that genes implicated by these 3D genome conformations are essential for the survival of patient-derived ependymoma models in a group-specific manner. Thus, this study extends our ability to reveal tumor-dependency genes by 3D genome conformations even in tumors that lack targetable genetic alterations.

Abstract 3886: 3D genome conformation analysis in ST-EPN-ZFTA ependymoma identifies RCOR2 as a potential target

Ependymoma (EPN) is a tumor of the central nervous system that occurs in children and adults. Childhood EPNs are one of the most aggressive pediatric brain tumors, arising both in infratentorial and supratentorial (ST) regions of the brain. Molecular profiling has identified distinct subgroups of ependymomas, including ST-EPN-ZFTA and PF-EPN-A as the most common and most aggressive ones in children. To this date, the only curative and indispensable treatment option is surgical resection followed by radiation. Unfortunately, there are no targeted therapies in clinical use. However, EPN cells have been extremely difficult to culture and expand in vitro, which explains why molecular studies on EPN cells have been hampered. This shortcoming has recently been overcome by establishing EPN models including human cell lines and organoids as well as patient derived xenografts (PDX). 3D genome conformation analysis has emerged as a powerful approach to understand tumor development and to identify novel drug targets for the treatment of different tumors. In this project we have used genome-wide chromosome conformation capture (Hi-C), complemented with H3K27ac (active enhancers) as well as gene expression in primary ependymoma tumors and cell lines to identify regulatory mechanisms underlying aberrant expression of genes that are essential for ependymoma tumorigenesis. Results of this study showed that the fusion between ZFTA and RELA leads to the formation of new regulatory environments that are recurrently associated with aberrant overexpression of RCOR2 only in ST-EPN-ZFTA ependymoma cells. Indeed, compared to all other ependymoma subgroups as well as to normal brain, RCOR2 is significantly upregulated only in ST-EPN-ZFTA patient samples. To test oncogenic relevance of RCOR2 for growth and maintenance, we depleted RCOR2 by RNAi and observed a strongly reduced cell survival in several ST-EPN-ZFTA cell lines but not or to a lesser extent in PF-EPN-A cells. Since RCOR2 is an adaptor protein lacking enzymatic activity, we looked at the expression of the proteins known as an interacting partner of RCOR2. Lysine-histone demethylase 1 (LSD1) is one of them and its expression in ST-EPN-ZFTA significantly correlates with RCOR2 expression. We therefore hypothesized that ST-EPN-ZFTA cells may be sensitive to LSD1 depletion, too. Indeed, depletion of LSD1 by RNAi resulted in a strong growth inhibition in ST-EPN-ZFTA cells, but not in PF-EPN-A cells. However, none of the tested LSD1 inhibitors exerted anti-proliferative activity at clinically reachable doses in the ST-EPN-ZFTA cells indicating a potential LSD1 non-enzymatic function in this particular tumor type. In summary, our study nominates RCOR2 as a oncogenic gene specific for ST-EPN-ZFTA ependymomas. Current studies focus on the identification of other interacting partners of the RCOR2-LSD1 complex and how to target these for therapeutic approaches.

Citation Format: Aylin Camgöz, Konstantin Okonechnikov, Owen Chapman, Monika Maurmann, Frank Buchholz, Stefan Pfister, Lukas Chavez, Marcel Kool. 3D genome conformation analysis in ST-EPN-ZFTA ependymoma identifies RCOR2 as a potential target [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 3886.

Abstract 3885: USP7 is an interaction partner of EZHIP and potential druggable target in PFA ependymomas

Ependymomas (EPN) are tumors of the central nervous system (CNS) that can arise in the supratentorial brain (ST-EPN), hindbrain or posterior fossa (PF-EPN), or anywhere in the spinal cord (SP-EPN), both in children and adults. Molecular profiling has identified distinct subgroups and subtypes in each of the anatomic compartments. In the posterior fossa, three subgroups have been identified: PFA, PFB and PF-SE. Of them, PFA ependymomas are characterized by a young median age at diagnosis, an overall balanced genome and a bad clinical outcome (56% 10-year overall survival). Standard therapy consists of tumor resection and radiotherapy, but working chemo- or targeted therapies will be essential to improve patient outcomes. Recently, we and others identified enhancer of zeste inhibiting protein (EZHIP) as potential main driver of PFA tumorigenicity. By inhibiting EZH2, the catalytic subunit of the polycomb repressive complex 2 (PRC2), EZHIP prevents the distribution of the epigenetic repressor mark H3K27me3. However, since EZHIP does not possess any known enzymatic functions itself, it does not serve as the druggable target urgently needed for PFA tumors. Thus, interaction partners are one main focus of ongoing PFA research. In this project, we focused on the ubiquitin-specific protease 7 (USP7), a well-known regulator of cancer pathways with a variety of inhibitors available, which was observed to interact with EZHIP in non-PFA cell lines before. We were able to confirm this interaction of EZHIP and USP7 in PFA cells in vitro by co-immunoprecipitation and mass spectrometry, and could show that the EZHIP-USP7 interaction is independent of EZH2, a separate interactor of both. Functionally, we are testing the hypothesis that USP7 de-ubiquitinates EZHIP, thereby preventing its proteasomal degradation and thus stabilizing the protein. As EZHIP expression is essential to PFA cell survival, we aim to target EZHIP indirectly by interfering with its stability regulation via USP7. RNAi-based knockdown (KD) experiments have been used to test a susceptibility of PFA cells to a loss of USP7, focusing on effects on cell proliferation and apoptosis, but also investigating gene expression changes provoked by a change in USP7 levels. Moreover, multiple USP7 inhibitors already highly affect the survival of different PFA cell lines in vitro. Ongoing experiments with PFA patient-derived xenograft (PDX) models will hopefully confirm the strong effect of USP7 inhibitors in PFA, and help to improve targeted therapy for PFA patients.

Citation Format: Anne Jenseit, Aylin Camgöz, Monika Mauermann, Stefan M. Pfister, Marcel Kool. USP7 is an interaction partner of EZHIP and potential druggable target in PFA ependymomas [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 3885.

EPEN-18. Oncogenic 3D genome conformations identify novel therapeutic targets in ependymoma

Ependymoma (EPN) is an aggressive pediatric tumor that occurs throughout the central nervous system. The two most aggressive molecular subgroups of EPN are the supratentorial ZFTA-fusion associated group (ST-EPN-ZFTA) and the posterior fossa group A (PF-EPN-A). Although the molecular characteristics underlying the tumorigenesis of these subgroups have been extensively studied, these tumors remain difficult to treat. Hence, innovative therapeutic approaches are urgently needed. Here, we used genome-wide chromosome conformation capture (Hi-C), complemented with CTCF (insulators) and H3K27ac (active enhancers) ChIP-seq, as well as gene expression and whole-genome DNA methylation profiling in primary and relapsed EPN tumors and cell lines, to identify chromosomal rearrangements and regulatory mechanisms underlying aberrant expression of genes that are essential for EPN tumorigenesis. By integrating these heterogenous data types, we have observed the formation of new topologically associated domains (‘neo-TADs’) caused by intra- and inter-chromosomal structural variants in both tumors. In addition, we observed 3D chromatin complexes of regulatory elements, and the replacement of CTCF insulators by DNA hyper-methylation in PF-EPN-A tumors. These tumor-specific 3D genome conformations can be associated with the transcriptional upregulation of nearby genes. Through inhibition experiments we validated that these newly identified genes, including RCOR2, ITGA6, LAMC1, and ARL4C, are highly essential for the survival of patient-derived EPN cell lines in a disease subgroup-specific manner. Thus, our study identifies novel potential therapeutic vulnerabilities in EPN and extends our ability to reveal tumor-dependency genes and pathways by oncogenic 3D genome conformations even in tumors that lack known genetic alterations.

EPEN-03. USP7 is an interaction partner of EZHIP and potential druggable target in PFA ependymomas

Ependymomas (EPN) arise in the supratentorial brain (ST-EPN), posterior fossa (PF-EPN), or the spinal cord (SP-EPN), in children and adults. Molecular profiling has identified distinct subgroups in each location. Among the three molecular subgroups of PF-EPN, PFAs are characterized by young median age at diagnosis, an overall balanced genome and bad clinical outcome (56 % 10-year OS). Therapy involves tumor resection and radiotherapy, but the role of chemo- or targeted therapies remains to be defined. Recently, we and others identified enhancer of zeste inhibiting protein (EZHIP) as potential driver of PFAs. By inhibiting EZH2, catalytic subunit of the polycomb repressive complex 2 (PRC2), EZHIP prevents the distribution of the epigenetic repressor mark H3K27me3. However, since EZHIP does not possess any known enzymatic functions, it does not seem to be the druggable target urgently searched for in PFA. We therefore focused on essential and potentially druggable interactions. Here, we present ubiquitin-specific protease 7 (USP7), a known cancer regulator with multiple inhibitors available, which has been shown to interact with EZHIP in non-PFA cells. We confirmed this interaction in PFA cells by co-immunoprecipitation and mass spectrometry, and showed that the EZHIP-USP7 interaction is independent of EZH2, a separate interactor of both. Functionally, we show that USP7 de-ubiquitinates EZHIP, preventing its degradation and thus stabilizing it. As EZHIP is essential for PFA cell survival, we aim to target EZHIP indirectly by affecting its stability regulation via USP7. Knockdown experiments showed a susceptibility of PFA cells to a USP7 loss, focusing on proliferation, apoptosis, and expressional changes induced by altered USP7 levels. Moreover, USP7 inhibitors highly affected the survival of different PFA cell lines at a low micromolar IC50 in vitro and in vivo treatments of PFA patient-derived xenografts with USP7 inhibitors are ongoing, hopefully helping to improve targeted therapies for PFA ependymoma patients.

RNAi-Mediated Screen of Primary AML Cells Nominates MDM4 as a Therapeutic Target in NK-AML with DNMT3A Mutations

DNA-methyltransferase 3A (DNMT3A) mutations belong to the most frequent genetic aberrations found in adult acute myeloid leukemia (AML). Recent evidence suggests that these mutations arise early in leukemogenesis, marking leukemic progenitors and stem cells, and persist through consolidation chemotherapy, providing a pool for AML relapse. Currently, there are no therapeutic approaches directed specifically against this cell population. To unravel therapeutically actionable targets in mutant DNMT3A-driven AML cells, we have performed a focused RNAi screen in a panel of 30 primary AML samples, all carrying a DNMT3A R882 mutation. As one of the strongest hits, we identified MDM4 as a gene essential for proliferation of primary DNMT3A^WT/R882X AML cells. We analyzed a publicly available RNA-Seq dataset of primary normal karyotype (NK) AML samples and found a trend towards MDM4 transcript overexpression particularly in DNMT3A-mutant samples. Moreover, we found that the MDM2/4 inhibitor ALRN-6924 impairs growth of DNMT3A^WT/R882X primary cells in vitro by inducing cell cycle arrest through upregulation of p53 target genes. Our results suggest that MDM4 inhibition is a potential target in NK-AML patients bearing DNMT3A R882X mutations.

EZHIP: a new piece of the puzzle towards understanding pediatric posterior fossa ependymoma

Ependymomas (EPN) are tumors of the central nervous system (CNS) that can arise in the supratentorial brain (ST-EPN), hindbrain or posterior fossa (PF-EPN) or anywhere in the spinal cord (SP-EPN), both in children and adults. Molecular profiling studies have identified distinct groups and subtypes in each of these anatomical compartments. In this review, we give an overview on recent findings and new insights what is driving PFA ependymomas, which is the most common group. PFA ependymomas are characterized by a young median age at diagnosis, an overall balanced genome and a bad clinical outcome (56% 10-year overall survival). Sequencing studies revealed no fusion genes or other highly recurrently mutated genes, suggesting that the disease is epigenetically driven. Indeed, recent findings have shown that the characteristic global loss of the repressive histone 3 lysine 27 trimethylation (H3K27me3) mark in PFA ependymoma is caused by aberrant expression of the enhancer of zeste homolog inhibitory protein (EZHIP) or in rare cases by H3K27M mutations, which both inhibit EZH2 thereby preventing the polycomb repressive complex 2 (PRC2) from spreading H3K27me3. We present the current status of the ongoing work on EZHIP and its essential role in the epigenetic disturbance of PFA biology. Comparisons to the oncohistone H3K27M and its role in diffuse midline glioma (DMG) are drawn, highlighting similarities but also differences between the tumor entities and underlying mechanisms. A strong focus is to point out missing information and to present directions of further research that may result in new and improved therapies for PFA ependymoma patients.

FOXR2 Stabilizes MYCN Protein and Identifies Non-MYCN-Amplified Neuroblastoma Patients With Unfavorable Outcome

Clinical outcomes of patients with neuroblastoma range from spontaneous tumor regression to fatality. Hence, understanding the mechanisms that cause tumor progression is crucial for the treatment of patients. In this study, we show that FOXR2 activation identifies a subset of neuroblastoma tumors with unfavorable outcome and we investigate the mechanism how FOXR2 relates to poor outcome in patients.

Comparative RNAi Screens in Isogenic Human Stem Cells Reveal SMARCA4 as a Differential Regulator

Large-scale RNAi screens are a powerful approach to identify functions of genes in a cell-type-specific manner. For model organisms, genetically identical (isogenic) cells from different cell types are readily available, making comparative studies meaningful. However, large-scale screens in isogenic human primary cells remain challenging. Here, we show that RNAi screens are possible in genetically identical human stem cells, using induced pluripotent stem cells as intermediates. The screens revealed SMARCA4 (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4) as a stemness regulator, while balancing differentiation distinctively for each cell type. SMARCA4 knockdown in hematopoietic stem and progenitor cells caused impaired self-renewal in vitro and in vivo with skewed myeloid differentiation; whereas, in neural stem cells, it impaired self-renewal while biasing differentiation toward neural lineage, through combinatorial SWI/SNF subunit assembly. Our findings pose a powerful approach for deciphering human stem cell biology and attribute distinct roles to SMARCA4 in stem cell maintenance.

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Comparative RNAi screens on isogenic hHSPCs and hNSCs, using iPSCs as bridging cell type

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SMARCA4 is a differential regulator of self-renewal and differentiation

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SMARCA4 loss impairs HSPC engraftment in vivo and myeloid differentiation in vitro

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SMARCA4 loss in NSCs causes exit from self-renewal and biased neural differentiation