Mutations In Chromatin Regulators Research Articles

EZH2 mutations in follicular lymphoma distort H3K27me3 profiles and alter transcriptional responses to PRC2 inhibition

Mutations in chromatin regulators are widespread in cancer. Among them, the histone H3 lysine 27 methyltransferase Polycomb Repressive Complex 2 (PRC2) shows distinct alterations according to tumor type. This specificity is poorly understood. Here, we model several PRC2 alterations in one isogenic system to reveal their comparative effects. Focusing then on lymphoma-associated EZH2 mutations, we show that Ezh2Y641F induces aberrant H3K27 methylation patterns even without wild-type Ezh2, which are alleviated by partial PRC2 inhibition. Remarkably, Ezh2Y641F rewires the response to PRC2 inhibition, leading to induction of antigen presentation genes. Using a unique longitudinal follicular lymphoma cohort, we further link EZH2 status to abnormal H3K27 methylation. We also uncover unexpected variability in the mutational landscape of successive biopsies, pointing to frequent co-existence of different clones and cautioning against stratifying patients based on single sampling. Our results clarify how oncogenic PRC2 mutations disrupt chromatin and transcription, and the therapeutic vulnerabilities this creates.

Abstract 577: Deciphering the mechanism of the menin-MLL complex dependency in HCC

Abstract Liver cancer is the third leading cause of cancer-related death worldwide, with hepatocellular carcinoma (HCC) being the most common primary liver cancer (~90%). The 5-year survival rate of patients with advanced HCC is ~18% due to the late prognosis and the moderate clinical benefit of available systemic therapy options. Mutations in chromatin regulators were detected in ~50% of liver cancer. Since many chromatin regulators have been shown a dependency in various cancer types and can modulate therapy response, we focused on identifying new therapeutic targets of HCC among epigenetic modifiers and evaluating them as potential targets for future drug development. We constructed a CRISPR library of 6000 gRNAs targeting 737 genes involved in chromatin-mediated gene regulation. Using the epigenome-focused CRISPR/Cas9 screening in two-dimensional and three-dimensional settings in multiple liver cancer cell lines (HepG2, HLF, PLC/PRF5), we identified a list of epigenetic regulators as potential new targets in HCC. Two of them, MEN1 and ASH2L, are core subunits of the menin-MLL complex mediating H3K4 trimethylation (me3). We validated dependencies of HCC on MEN1 and ASH2L by performing a negative selection CRISPR/Cas9 competitive growth assay in HLF and PLC/PRF5 cell lines. Moreover, treatment of HCC cell lines (HLF, PLC/PRF5, HepG2) with recently developed menin inhibitor SNDX-5613 (revumenib) revealed a dose-dependent reduction in cell proliferation. To determine transcriptional changes associated with disruption of the menin-MLL complex, we performed RNA sequencing of HLF and PLC/PRF5 cells following either inhibition with 5µM SNDX-5613 for 4 days or knockout of the MEN1 or ASH2L gene. We observed the upregulation of KRAS and the oncogenic signature of TGFβ signaling pathways in all menin-MLL complex disrupting conditions. We did not detect global changes in H3K4me3 levels upon the menin inhibition or MEN1 or ASH2L knockouts assessed by immunoblotting. To explore the mechanism of the antiproliferative effect of the menin inhibition on HCC further, we evaluated changes in the binding of menin to chromatin and H3K4me3 levels in HCC cells by performing CUT&RUN following treatment of HLF cells with 5µM SNDX-5613 for 4 days. Menin inhibition led to a drastic removal of menin from the chromatin, while H3K4me3 levels were only mildly decreased. We identified 8765 genes near promoter regions with menin binding and H3K4me3 mark, of which 1952 genes were near regions with simultaneous loss of menin and decreased H3K4me3 levels upon menin inhibition. Integration of our genomics data revealed a list of 30 genes, which are downregulated upon menin inhibition in both HLF and PLC/PRF5 cells (FC≥1.5) and the direct targets of the menin-MLL complex in HLF cells, suggesting their potential role in HCC cell survival. Altogether, we anticipate that menin and ASH2L serve as promising targets and represent an appealing therapeutic strategy for HCC treatment. Citation Format: Margarita M. Dzama, Peyton C. Kuhlers, Jesse R. Raab. Deciphering the mechanism of the menin-MLL complex dependency in HCC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 577.

MDB-09. IMPACT OF PRDM6 ON CHROMATIN ACCESSIBILITY, GENE EXPRESSION, AND MEDULLOBLASTOMA FORMATION

Abstract Group 4 medulloblastoma (MB) is the most common medulloblastoma subgroup and shows high incidence of metastasis and late-onset relapse cases. These tumors lack a unifying oncogenic driver and treatment targets, despite extensive genomic characterization. Group 4 MBs are characterized by recurrent genetic alterations in chromatin modifiers and amplification of stemness genes. A substantial fraction of Group 4 MBs are characterized by enhancer hijacking through tandem duplication of SNCAIP, resulting in high expression of PRDM6, a putative transcriptional repressor and histone methyltransferase. Some PRDM6-overexpressing medulloblastoma cases show additional mutations in chromatin regulators and high MYCN expression. We set out to elucidate the impact and oncogenic potential of sustained PRDM6 expression in early neural stem cell populations and patient-derived medulloblastoma cells. We find that PRDM6 expression in human iPSC-derived neuroepithelial stem cells (NESCs) results in tumor growth in mice at low penetrance. Moreover, we find that PRDM6 expression in MYCN-overexpressing NESCs does not further alter tumor aggressiveness or survival in vivo. Notably, PRDM6 overexpression in the patient-derived Group 3 MYC-amplified D283-Med cell line causes significantly increased aggressiveness of tumor growth and shorter survival in mice. At the cellular level, PRDM6 localizes to the nucleus, suggesting a role in gene expression regulation. Consistent with this notion, ATAC-seq and RNA-seq analysis of PRDM6-NESCs and PRDM6-D283-Med cells reveals major changes in chromatin accessibility and gene expression, specifically upregulation of integrin family members and gene family members of focal adhesion and extracellular matrix receptor interaction pathways. We conclude that PRDM6 promotes tumor growth in NESCs and may play a role in tumor maintenance through interactions with the extracellular matrix and tumor microenvironment.

Iadademstat in combination with gilteritinib for patients with mutated FLT3 relapsed/refractory acute myeloid leukemia.

TPS7075 Background: Epigenetic dysregulation is a hallmark of acute myeloid leukemia (AML) and is caused by recurrent translocations and/or mutations in chromatin regulators and transcription factors, resulting in myeloid differentiation blockade and leukemic stem cell renewal. Accordingly, about 70% of recurring mutations in AML patients (pts) target regulators of gene expression, underscoring the potential of epigenetic therapies to change the disease natural history. Iadademstat (iada/ORY-1001) is a specific, oral, potent, covalent inhibitor of the epigenetic Lysine-Specific Demethylase 1 (LSD1/KDMA1) enzyme. In preclinical and clinical studies iada decreased leukemic stem cell survival and induced macrophage/monocytic differentiation of blasts. ALICE, a Ph2 study of iada in combination with azacitidine (aza), showed high complete remission (CR/CRi) rates and durable responses in treatment naïve, unfit AML pts without exacerbating the toxicity profile of aza (Salamero et al., Oral at ASH 2022). Despite improvements in AML therapy, relapsed and refractory (R/R) cases are frequent and contribute to the death of more than 50% of pts, particularly in those subpopulations with higher risk genetics, the largest of which (up to 30-40% AML pts) harbors fms-like tyrosine kinase 3 mutations (FLT3mut+). Use of the FLT3 inhibitor (FLT3i) gilteritinib as monotherapy for R/R pts resulted in improved outcomes but the duration of remission achieved is transient and often brief (CR rate: 20%; EFS: 2.8 months) per the ADMIRAL Ph3 study (Perl, et al., NEJM 2019). Preclinically, iada has marked synergy with FLT3i, particularly gilteritinib, in FLT3 wild-type and FLT3 mut+ AML cells and in derived cell lines resistant to venetoclax, azacitidine and FLT3is. Methods: Adult pts with ECOG 0-2 and FLT3 mut+ R/R AML, after 1 or 2 prior lines of therapy, will be enrolled. In escalation (3+3), up to 18 pts will receive iada at 75 to 150 ug, orally, in 5 days ON-2 days OFF schedule, with gilteritinib SoC. Up to approximate 14 pts will be expanded from pharmacologically active dose/s (per Project OPTIMUS). Primary endpoints of the study are safety and RP2D determination. Bayesian posterior probability efficacy monitoring will be performed periodically for each dose cohort. Bayesian efficacy futility and early stopping boundary will be applied. Posterior probability criterion (Prob (CR > 0.3) ≥ 0.60) at the end of the study will warrant further research. Safety in expansion will be evaluated continuously with a Bayesian stopping rule. Secondary endpoints include OS, EFS, CR, CR/CRh, ORR, TTR, DoR, and transfusion rate. Exploratory endpoints include PK, PD, MRD and gene mutational analysis. The study will run in 15 US sites. Additional sites will be added for a subsequent Phase 2 randomized controlled double-blinded FRIDA 2 study to assess the efficacy of this combination in R/R FLT3 mut+ AML. Clinical trial information: NCT05546580 .

Abstract 4754: Investigating the impact of hotspot mutations in a chromatin reader on leukemogenesis

Abstract Acute myeloid leukemia (AML) is one of the most aggressive forms of hematological malignancies with a low overall 5-year survival rate (< 26%). The mainstay of treatment for AML includes chemotherapy, but the response of a subset of patients to current treatment options remains poor. Thus, new therapeutic approaches are desperately needed. AML often arises from somatic mutations in chromatin regulators that result in uncontrolled proliferation and a block of differentiation in myeloid progenitor cells. As such, investigation of the role and molecular mechanism of chromatin regulator in AML is being actively pursued. Previously, we discovered the eleven-nineteen-leukemia (ENL) protein, a chromatin “reader” and transcription co-activator, as an unrecognized requirement for the survival of AML. We developed a potent and orally bioavailable small-molecule inhibitor of ENL, which displaces ENL from chromatin and blocks AML progression. Hotspot mutations have been found in ENL YEATS domains, both in Wilms tumor and in leukemia, and these mutations confer a gain of condensation property, leading to aberrant gene activation. However, the impact of ENL mutation on tumorigenesis is largely unknown. The over-arching goal of this project is to explore the impact of the hyper-activated ENL pathway (ENL mutation) in AML. Results from this project will elucidate how newly discovered chromatin reader mutations drive tumorigenesis and offer new biology insights that will facilitate both basic mechanistic studies and clinical studies. Citation Format: Yiman Liu, Qinglan Li, Sylvia Tang, Chujie Gong, Liling Wan. Investigating the impact of hotspot mutations in a chromatin reader on leukemogenesis. [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 4754.

The Frida Study: An Option for Mutated FLT3 Relapsed/Refractory Acute Myeloid Leukemia Patients with a Novel Iadademstat and Gilteritinib Combination Therapy

Background: Epigenetic dysregulation is a hallmark of acute myeloid leukemia (AML) and is caused by recurrent translocations and/or mutations in chromatin regulators and transcription factors, resulting in myeloid differentiation blockade and leukemic stem cell renewal. Accordingly, about 70% of recurring mutations in AML patients target regulators of gene expression, underscoring the potential of epigenetic therapies to change the natural history of the disease. Iadademstat (iada/ORY-1001) is a specific, oral, potent, covalent inhibitor of the epigenetic Lysine-Specific Demethylase 1 (LSD1/KDMA1) enzyme. Preclinical models demonstrate that exposure to iada decreases leukemic stem cell survival and preclinical and clinical studies shows iada's effect on inducing macrophage/monocytic differentiation of blast cells. Furthermore, a Phase 2 ongoing study of iada in combination with azacitidine (ALICE) shows high complete remission (CR)/ CR with incomplete count recovery (CRi) and durable responses in treatment naïve, unfit AML patients (pts) without exacerbating the toxicity profile of azacitidine (Salamero et al., Abstract P586 EHA 2022). Despite improvements in AML therapy, relapses remain a common challenge, contributing to the death of more than 50% of pts, particularly in those subpopulations with higher risk genetics, the largest of which (up to 30-40% of AML pts) harbor mutations in the fms-like tyrosine kinase 3 (FLT3) gene. Use of the FLT3 inhibitor (FLT3i) gilteritinib as monotherapy for relapsed/refractory (R/R) pts has resulted in improved outcomes but the duration of remission achieved is transient and often brief. The Phase 3 randomized ADMIRAL trial of gilteritinib revealed a CR rate of 20%; and an event-free-survival (EFS) of 2.8 months (Perl, et al., NEJM 2019). Preclinically, iada produces marked synergy with FLT3i, including gilteritinib, in FLT3 wild-type and mutated (FLT3 mut+) AML cells and in derived cell lines resistant to venetoclax, azacitidine and other FLT3is. The novel MOAs generating this synergy of the combination include activation of a pro-differentiative epigenetic and transcriptional program with simultaneous suppression of the activity of MYC target genes (Yashar, et al. 2022, https://doi.org/10.1101/2022.01.17.476469). The FRIDA clinical trial is designed to establish the safety, tolerability of the combination of iada plus gilteritinib and to identify the recommended phase 2 dose (RP2D) in FLT3 mut+ R/R AML specifically according to FDA's Project Optimus. Methods: Adult pts with body weight ≥50 Kg and ECOG 0-2, with FLT3 mut+ R/R AML, after 1 or 2 prior lines of therapy, will be enrolled. Up to 18 pts, in a 3+3 escalation phase, will receive iada at doses of 75 to 150 ug, orally, in 5 days ON - 2 days OFF schedule, with continuous gilteritinib, at 120 mg/day orally. In the expansion phase, up to 14 pts at the selected safe and pharmacologically active dose/s (determined based on all available data from escalation pts including PK, target engagement (TE), safety, tolerability, and emerging activity) will be enrolled. TE will be assessed with a proprietary validated chemo-probe assay for LSD1 occupancy in PBMCs. Primary endpoints of the study are safety and RP2D determination, based on the same 5 criteria outlined above. Bayesian posterior probability efficacy monitoring will be performed periodically for each dose cohort starting from the first 6 additional pts in the expansion phase (total of 12). Bayesian efficacy futility and early stopping boundary will be applied during the monitoring. Posterior probability criterion (Prob (θ>0.3) ≥ 0.60) at the end of the study will warrant additional development. The safety of the combination treatment will be also continuously evaluated during expansion following a Bayesian design stopping rule. Secondary endpoints include overall survival, EFS, CR, CR/CR with partial hematologic recovery (CRh), overall response rates, time to response, duration of response, and transfusion rate. Exploratory endpoints include measurable residual disease and gene mutational analysis. Pts who achieve a response can undergo hematopoietic stem cell transplant. The study plans to have 15 sites enrolling in the US. Additional sites will be added for a subsequent randomized controlled double-blinded FRIDA 2 study to assess the efficacy of the iada and gilteritinib combination in R/R FLT3 mut+ AML.

MODL-32. IMPACT OF PRDM6 ON CHROMATIN ACCESSIBILITY, GENE EXPRESSION, AND MEDULLOBLASTOMA FORMATION

Abstract Group 4 medulloblastoma (MB) is the most common medulloblastoma subgroup and shows high incidence of metastasis and late-onset relapse. Group 4 MBs lack a unifying oncogenic driver and treatment targets, despite extensive genomic characterization. Group 4 MBs are characterized by recurrent genetic alterations in chromatin modifiers, amplification of stemness genes, and putative enhancer "hijacking" events. A substantial fraction of Group 4 MBs are characterized by enhancer hijacking through tandem duplication of SNCAIP, resulting in high expression of PRDM6, a putative transcriptional repressor and histone methyltransferase. Some PRDM6-overexpressing MBs show additional mutations in chromatin regulators and high MYCN expression. We set out to elucidate the impact and oncogenic potential of sustained PRDM6 expression in early neural stem cell populations and patient-derived medulloblastoma cells. We find that PRDM6 expression in human iPSC-derived neuroepithelial stem cells (NESCs) results in tumor growth in mice, albeit at low penetrance. Moreover, we find that PRDM6 expression in MYCN-overexpressing NESCs does not further alter tumor aggressiveness or survival in vivo. Notably, PRDM6 overexpression in the patient-derived Group 3 MYC-amplified D283-Med cell line causes significantly increased aggressiveness of tumor growth and shorter survival in mice. At the cellular level, PRDM6 localizes to the nucleus, suggesting a role in gene expression regulation. Consistent with this notion, ATAC-seq and RNA-seq analysis of PRDM6-NESCs and PRDM6-D283-Med cells reveals major changes in chromatin accessibility and gene expression, including upregulation of integrin family members and genes related to focal adhesion and extracellular matrix-receptor interaction pathways. We conclude that PRDM6 promotes tumor growth in NESCs and may play a role in tumor maintenance through interactions with the extracellular matrix and tumor microenvironment.

Identification of clinical implications and potential prognostic models of chromatin regulator mutations in multiple myeloma

BackgroundWith the rapid development of next-generation sequencing (NGS) technologies, researchers are making efforts to reveal the genomic landscape of multiple myeloma (MM). However, the clinical significance of many mutations remains poorly defined due to the genetic heterogeneity of MM. To systematically explore the clinical implications of gene mutations and build practical prognostic models, we performed DNA sequencing in newly diagnosed MM patients.MethodsMM cells were purified from bone marrow aspirates using CD138 microbeads and subjected to sequencing with a 387-gene Panel. Nomogram was developed using Cox’s proportional hazards model, and candidate variables were screened by stepwise regression. Internal validation was carried out by the bootstrap method.ResultsBetween July 2016 and December 2020, a total of 147 patients were included in our study. We found patients with a higher mutational load had a significantly shorter progress-free survival (PFS) (19.0 vs. 32.0 months, P = 0.0098) and overall survival (OS) (3-year OS rates were 66.1% and 80.0%, P = 0.0290). Mutations in chromatin regulators (CRs) including KMT2C (14.3%), KMT2D (14.3%), EP300 (11.6%) and ARID gene family (31.3%) were highly frequent in newly diagnosed MM patients. Interestingly, proteins encoded by these genes could form a complex called KMT2C/D COMPASS (KCDCOMs). Patients with mutations of ARID gene family had a significantly shorter PFS (15.5 vs. 34.0 months, P = 0.0003) and OS (3-year OS rates were 64.9% and 81.0%, P = 0.0351) than patients without ARID gene mutations. Incorporating ARID gene mutations into the current staging system could successfully improve their prognostic performance. The PFS and OS nomogram models (including 1q21 copies, ARID gene mutations, extramedullary disease, mutational load and TP53 mutations) showed good predicting performance in both training and validation sets.ConclusionOur findings emphasized the importance of CRs mutations in newly diagnosed MM patients and indicated the mutations affecting KCDCOMs might promote the development of MM. High mutational load and harboring mutations in the ARID gene family were novel predictors of adverse prognosis in MM. Prognostic models based on gene mutations were commendably prognostic evaluation methods that could provide a reference for clinical practices.

Loss of H3K27 Methylation Identifies Poor Outcome in Adult-Onset Acute Myeloid Leukemia

Background: Acute myeloid leukemia (AML) is an epigenetically heterogeneous disease. The intensity of treatment is currently guided by cytogenetic and molecular genetic risk classifications; however these incompletely predict outcomes, requiring additional information for more accurate predictions. We aimed to identify potential prognostic implications of epigenetic modification of histone proteins, with a focus of H3K27 methylation in relation to mutations in chromatin, splicing and transcriptional regulators. Material and methods: Histone methylation mark expressions were evaluated in a cohort of 241 AML bone marrow (BM) and peripheral blood (PB) samples from patients admitted at the MD Anderson Cancer Center relative to their expression in CD34+ BM derived samples from healthy donors. Simultaneous analysis of 230 proteins was performed using the reverse phase protein array - a high-throughput, quantitative proteomic platform that enables identification of aberrant expressed proteins and the pathways they act in. Additional mutational analysis was performed on 65 BM samples. Results:H3K27Me3 was significantly lower in both BM and PB leukemic-derived samples compared to their expression in normal BM (figure 1A). A greater loss of H3K27Me3 associated with increased proliferative potential and shorter overall survival (OS) in the whole patient population (n=241, HR=0.64, 95% CI=0.47-0.87, p<0.01), as well as in subsets, e.g. cytogenetically normal AML (n=110, HR=0.62, 95% CI=0.40-0.97, p=0.03). To study the prognostic impact of H3K27Me3 in the context of cytogenetic aberrations and mutations, multivariate cox regression analysis was performed which identified H3K27Me3 level as an independent favorable prognostic factor in all (HR=0.74, 95%CI=0.57-0.95, p=0.02) as well as in P53 mutated AML (n=54, HR=0.48, 95%CI=0.26-0.87, p=0.02). A total of 78 AML patients had molecular data available for the major methylation affecting genes, i.e. IDH1, IDH2, DNMT3A and TET2. The level of H3K27Me3 was not prognostic in patients without any DNA methylation affecting mutation present, but patients with at least one mutation in any of these had better outcome when H3K27Me3 levels were high (highest tertile, figure 1A) compared to those with lower levels (median OS 7.1 vs. 24.1 months, HR=0.42, 95% CI=0.21-0.83, p=0.01, figure 1B). Mutations in U2AF1 and SRSF2 affect the spliceosome and are frequently found in antecedent hematological disorders (AHD), as well as are mutations in chromatin regulating genes ASXL1 and BCOR. We observed significant decreased H3K27Me3 in patients with these mutations corresponding with observed lower levels of H3K27Me3 in patients with AHD than those without (p=0.035). BCOR, SRSF2, U2AF1 and ASXL1 mutations confer poor prognosis in myeloid malignancies, however, in our cohort of 65 sequenced AML patients; not individual or a combination of these mutations were independent prognostic factors, but the degree of H3K27Me3 in these patients (HR= 0.49, 95% CI=0.25-0.95, p=0.03). To recognize dysregulated pathways in AML patients with the identified loss of H3K27Me3, we examined correlations of H3K27Me3 with the other 229 proteins on the array. H3K27Me3 is catalyzed by the polycomb group protein EZH2 and is linked to transcriptional repression via the formation of heterochromatin regions. To identify upregulated proteins and pathways upon the loss of H3K27Me3, we focused on significant negatively correlated proteins with H3K27Me3 leading us to the identification of 20 total and 6 phospho-proteins that showed increased expression upon decreased H3K27Me3. Functional enrichment analysis of this protein set revealed an upregulated anti-apoptotic phenotype. Conclusion:This study shows that proteomic profiling of epigenetic modifications on the histone level have clinical implications in AML and support the idea that epigenetic patterns contribute to a more accurate picture of the leukemic state complementing cytogenetic and molecular genetic subgrouping. Figure 1. A) Lower H3K27Me3 in BM and PB derived AML samples compared to normal CD34+. **** represents p<0.0001, ns = not significant. B) Overall survival probability in AML patients with any DNA methylation affecting mutation (i.e. IDH1/2, DNMT3A, TET2, n=53) according to H3K27Me3 low (blue) and high (orange) status. Figure 1 Disclosures No relevant conflicts of interest to declare.

Loss of UTX/KDM6A and the activation of FGFR3 converge to regulate differentiation gene-expression programs in bladder cancer

Bladder cancer prognosis is closely linked to the underlying differentiation state of the tumor, ranging from the less aggressive and most-differentiated luminal tumors to the more aggressive and least-differentiated basal tumors. Sequencing of bladder cancer has revealed that loss-of-function mutations in chromatin regulators and mutations that activate receptor tyrosine kinase (RTK) signaling frequently occur in bladder cancer. However, little is known as to whether and how these two types of mutations functionally interact or cooperate to regulate tumor growth and differentiation state. Here, we focus on loss of the histone demethylase UTX (also known as KDM6A) and activation of the RTK FGFR3, two events that commonly cooccur in muscle invasive bladder tumors. We show that UTX loss and FGFR3 activation cooperate to disrupt the balance of luminal and basal gene expression in bladder cells. UTX localized to enhancers surrounding many genes that are important for luminal cell fate, and supported the transcription of these genes in a catalytic-independent manner. In contrast to UTX, FGFR3 activation was associated with lower expression of luminal genes in tumors and FGFR inhibition increased transcription of these same genes in cell culture models. This suggests an antagonistic relationship between UTX and FGFR3. In support of this model, UTX loss-of-function potentiated FGFR3-dependent transcriptional effects and the presence of UTX blocked an FGFR3-mediated increase in the colony formation of bladder cells. Taken together, our study reveals how mutations in UTX and FGFR3 converge to disrupt bladder differentiation programs that could serve as a therapeutic target.

Abstract 5792: Preclinical antitumor activity of BMS-986158, an oral BET inhibitor, for the treatment of cancer

Abstract Background: Regulation and recognition of covalent chromatin modifications by cellular proteins are key determinants of gene expression. Bromodomain and extra-terminal (BET) proteins, including BRD2, BRD3, BRD4, and BRDT, bind directly to acetylated lysine on histone tails to promote gene transcription. Oncogenes such as c-MYC, BCL2, and ASCL1, are directly regulated by BET proteins. Here, we report the preclinical evaluation of BMS-986158, an orally bioavailable, potent, and selective BET inhibitor. Methods: BMS-986158 activity was assessed in tumor growth assays across solid and hematologic cancer cell lines in vitro and in vivo in patient-derived xenografts (PDX). Dose-response gene expression profiling of ex vivo blood from healthy donors was used to identify transcripts exhibiting a pharmacodynamic effect with BMS-986158 treatment. Results: Tumor growth inhibition (TGI) with BMS-986158 was observed across different solid and hematologic cancer cell lines. Mutations in chromatin regulators were identified among BMS-986158–sensitive cell lines. BMS-986158 also demonstrated antitumor activity (TGI ≥ 70%) in 24 of 82 PDX models tested (Table). Genetic alterations that correlate with BMS-986158 responsiveness will be presented. Finally, an ex vivo dose-response profiling study in healthy human blood identified 124 genes responsive to BMS-986158, including chemokines and chemokine receptors. Conclusions: BMS-986158, a potent and selective BET inhibitor, demonstrated robust anti-proliferative activity in vitro across a broad range of cancer cell lines. Consistent with the in vitro data, preclinical antitumor activity was observed in various PDX tumor models. Furthermore, gene expression profiling studies in human blood samples identified select target genes responsive to BMS-986158 treatment that may be useful as clinical pharmacodynamic markers. TGI assay in PDX modelsTumor TypeTotal sample, nResponders, naAdenocarcinoma319Lung squamous cell carcinoma217Breast cancer82Brain cancer10Colorectal cancer63Esophageal cancer31Gallbladder cancer21Head and neck cancer31Mixedb70Total8224a Responders were defined as having > 70% TGIb Mixed tumor types include large cell neuroendocrine carcinoma of the lung, liver, liver metastases from rectum, mixed adenocarcinoma, neuroendocrine tumor, and non-small cell lung cancer Citation Format: Susan Wee, Donald Jackson, Heshani Desilva, Maya Dajee, Julie Carman, Petra Ross-MacDonald, Jinping Gan, Richard A. Westhouse, Christine Huang, Zheng Yang, Michael Poss, John T. Hunt, Gregory D. Vite, Ashvinikumar V. Gavai. Preclinical antitumor activity of BMS-986158, an oral BET inhibitor, for the treatment of cancer [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 5792.

Long genes linked to autism spectrum disorders harbor broad enhancer-like chromatin domains.

Genetic variants associated with autism spectrum disorders (ASDs) are enriched in genes encoding synaptic proteins and chromatin regulators. Although the role of synaptic proteins in ASDs is widely studied, the mechanism by which chromatin regulators contribute to ASD risk remains poorly understood. Upon profiling and analyzing the transcriptional and epigenomic features of genes expressed in the cortex, we uncovered a unique set of long genes that contain broad enhancer-like chromatin domains (BELDs) spanning across their entire gene bodies. Analyses of these BELD genes show that they are highly transcribed with frequent RNA polymerase II (Pol II) initiation and low Pol II pausing, and they exhibit frequent chromatin–chromatin interactions within their gene bodies. These BELD features are conserved from rodents to humans, are enriched in genes involved in synaptic function, and appear post-natally concomitant with synapse development. Importantly, we find that BELD genes are highly implicated in neurodevelopmental disorders, particularly ASDs, and that their expression is preferentially down-regulated in individuals with idiopathic autism. Finally, we find that the transcription of BELD genes is particularly sensitive to alternations in ASD-associated chromatin regulators. These findings suggest that the epigenomic regulation of BELD genes is important for post-natal cortical development and lend support to a model by which mutations in chromatin regulators causally contribute to ASDs by preferentially impairing BELD gene transcription.

The Chromodomain Helicase DNA-Binding Chromatin Remodelers: Family Traits that Protect from and Promote Cancer.

A plethora of mutations in chromatin regulators in diverse human cancers is emerging, attesting to the pivotal role of chromatin dynamics in tumorigenesis. A recurrent theme is inactivation of the chromodomain helicase DNA-binding (CHD) family of proteins-ATP-dependent chromatin remodelers that govern the cellular machinery's access to DNA, thereby controlling fundamental processes, including transcription, proliferation, and DNA damage repair. This review highlights what is currently known about how genetic and epigenetic perturbation of CHD proteins and the pathways that they regulate set the stage for cancer, providing new insight for designing more effective anti-cancer therapies.

DNA methylation in urothelial carcinoma.

DNA methylation alterations are common in urothelial carcinoma, a prevalent cancer worldwide caused predominantly by chemical carcinogens. Recent studies have proposed sets of hypermethylated genes as promising diagnostic and prognostic biomarkers from urine or tissue samples, which require validation. Other studies have revealed intriguing links between specific carcinogens and DNA methylation alterations in cancer tissues or blood that might clarify carcinogenesis mechanisms and aid prevention. Like DNA methylation alterations, mutations in chromatin regulators are frequent, underlining the importance of epigenetic changes. However, the relations between the two changes and their functions in urothelial carcinogenesis remain unclear. Transcription factor genes with altered methylation deserve particular interest. Elucidating the functional impact of methylation changes is a prerequisite for their therapeutic targeting.

The chromatin regulator chd8 is a context-dependent mediator of cell survival in murine hematopoietic malignancies

Aberrant chromatin regulation is a frequent driver of leukemogenesis. Mutations in chromatin regulators often result in more stem-like cells that seed a bulk leukemic population. Inhibitors targeting these proteins represent an emerging class of therapeutics, and identifying further chromatin regulators that promote disease progression may result in additional drug targets. We identified the chromatin-modifying protein CHD8 as necessary for cell survival in a mouse model of BCR-Abl+ B-cell acute lymphoblastic leukemia. This disease has a poor prognosis despite treatment with kinase inhibitors targeting BCR-Abl. Although implicated as a risk factor in autism spectrum disorder and a tumor suppressor in prostate and lung cancer, the mechanism of CHD8’s activity is still unclear and has never been studied in the context of hematopoietic malignancies. Here we demonstrate that depletion of CHD8 in B-ALL cells leads to cell death. While multiple B cell malignancies were dependent on CHD8 expression for survival, T cell malignancies displayed milder phenotypes upon CHD8 knockdown. In addition, ectopic expression of the Notch1 intracellular domain in a T cell malignancy partially alleviated the detrimental effect of CHD8 depletion. Our results demonstrate that CHD8 has a context-dependent role in cell survival, and its inhibition may be an effective treatment for B lymphoid malignancies.

Enrichment of mutations in chromatin regulators in people with Rett syndrome lacking mutations in MECP2.

PurposeRett Syndrome (RTT) is a neurodevelopmental disorder caused primarily by de novo mutations (DNMs) in MECP2 and sometimes in CDKL5 and FOXG1. However, some RTT cases lack mutations in these genes.MethodsTwenty-two RTT cases without apparent MECP2, CDKL5, and FOXG1 mutations were subjected to both whole exome sequencing and single nucleotide polymorphism array-based copy number variant (CNV) analyses.ResultsThree cases had MECP2 mutations initially missed by clinical testing. Of the remaining 19 cases, 17 (89.5%) had 29 other likely pathogenic intragenic mutations and/or CNVs (10 cases had two or more). Interestingly, 13 cases had mutations in a gene/region previously reported in other NDDs, thereby providing a potential diagnostic yield of 68.4%. These mutations were significantly enriched in chromatin regulators (corrected p = 0.0068) and moderately in postsynaptic cell membrane molecules (corrected p = 0.076) implicating glutamate receptor signaling.ConclusionThe genetic etiology of RTT without MECP2, CDKL5, and FOXG1 mutations is heterogeneous, overlaps with other NDDs, and complex due to high mutation burden. Dysregulation of chromatin structure and abnormal excitatory synaptic signaling may form two common pathological bases of RTT.

Stalled replication forks within heterochromatin require ATRX for protection.

Expansive growth of neural progenitor cells (NPCs) is a prerequisite to the temporal waves of neuronal differentiation that generate the six-layered neocortex, while also placing a heavy burden on proteins that regulate chromatin packaging and genome integrity. This problem is further reflected by the growing number of developmental disorders caused by mutations in chromatin regulators. ATRX gene mutations cause a severe intellectual disability disorder (α-thalassemia mental retardation X-linked (ATRX) syndrome; OMIM no. 301040), characterized by microcephaly, urogenital abnormalities and α-thalassemia. Although the ATRX protein is required for the maintenance of repetitive DNA within heterochromatin, how this translates to disease pathogenesis remain poorly understood and was a focus of this study. We demonstrate that AtrxFoxG1Cre forebrain-specific conditional knockout mice display poly(ADP-ribose) polymerase-1 (Parp-1) hyperactivation during neurogenesis and generate fewer late-born Cux1- and Brn2-positive neurons that accounts for the reduced cortical size. Moreover, DNA damage, induced Parp-1 and Atm activation is elevated in progenitor cells and contributes to their increased level of cell death. ATRX-null HeLa cells are similarly sensitive to hydroxyurea-induced replication stress, accumulate DNA damage and proliferate poorly. Impaired BRCA1-RAD51 colocalization and PARP-1 hyperactivation indicated that stalled replication forks are not efficiently protected. DNA fiber assays confirmed that MRE11 degradation of stalled replication forks was rampant in the absence of ATRX or DAXX. Indeed, fork degradation in ATRX-null cells could be attenuated by treatment with the MRE11 inhibitor mirin, or exacerbated by inhibiting PARP-1 activity. Taken together, these results suggest that ATRX is required to limit replication stress during cellular proliferation, whereas upregulation of PARP-1 activity functions as a compensatory mechanism to protect stalled forks, limiting genomic damage, and facilitating late-born neuron production.

The Chromatin Regulator CHD8 Is a Context-Dependent Mediator of Cell Survival in Murine Hematopoietic Malignancies.

Aberrant chromatin regulation is a frequent driver of leukemogenesis. Mutations in chromatin regulators often result in more stem-like cells that seed a bulk leukemic population. Inhibitors targeting these proteins represent an emerging class of therapeutics, and identifying further chromatin regulators that promote disease progression may result in additional drug targets. We identified the chromatin-modifying protein CHD8 as necessary for cell survival in a mouse model of BCR-Abl+ B-cell acute lymphoblastic leukemia. This disease has a poor prognosis despite treatment with kinase inhibitors targeting BCR-Abl. Although implicated as a risk factor in autism spectrum disorder and a tumor suppressor in prostate and lung cancer, the mechanism of CHD8’s activity is still unclear and has never been studied in the context of hematopoietic malignancies. Here we demonstrate that depletion of CHD8 in B-ALL cells leads to cell death. While multiple B cell malignancies were dependent on CHD8 expression for survival, T cell malignancies displayed milder phenotypes upon CHD8 knockdown. In addition, ectopic expression of the Notch1 intracellular domain in a T cell malignancy partially alleviated the detrimental effect of CHD8 depletion. Our results demonstrate that CHD8 has a context-dependent role in cell survival, and its inhibition may be an effective treatment for B lymphoid malignancies.

Chromatin deregulation in disease.

The regulation of chromatin by epigenetic mechanisms plays a central role in gene expression and is essential for development and maintenance of cell identity and function. Aberrant chromatin regulation is observed in many diseases where it leads to defects in epigenetic gene regulation resulting in pathological gene expression programmes. These defects are caused by inherited or acquired mutations in genes encoding enzymes that deposit or remove DNA and histone modifications and that shape chromatin architecture. Chromatin deregulation often results in neurodevelopmental disorders and intellectual disabilities, frequently linked to physical and developmental abnormalities, but can also cause neurodegenerative diseases, immunodeficiency, or muscle wasting syndromes. Epigenetic diseases can either be of monogenic origin or manifest themselves as complex multifactorial diseases such as in congenital heart disease, autism spectrum disorders, or cancer in which mutations in chromatin regulators are contributing factors. The environment directly influences the epigenome and can induce changes that cause or predispose to diseases through risk factors such as stress, malnutrition or exposure to harmful chemicals. The plasticity of chromatin regulation makes targeting the enzymatic machinery an attractive strategy for therapeutic intervention and an increasing number of small molecule inhibitors against a variety of epigenetic regulators are in clinical use or under development. In this review, we will give an overview of the molecular lesions that underlie epigenetic diseases, and we will discuss the impact of the environment and prospects for epigenetic therapies.

Gain-of-function mutation of chromatin regulators as a tumorigenic mechanism and an opportunity for therapeutic intervention.

Somatic gain-of-function mutations that drive cancer pathogenesis are well established opportunities for therapeutic intervention, as demonstrated by the clinical efficacy of kinase inhibitors in kinase-mutant malignancies. Here, we discuss the recently discovered gain-of-function mutations in chromatin-regulatory machineries that promote the pathogenesis of cancer. The current understanding of the underlying molecular mechanisms and the therapeutic potential for direct chemical inhibition will be reviewed. Point mutations that increase the catalytic activity of EZH2 and NSD2 histone methyltransferases are found in distinct subsets of B-cell neoplasms, which promote cell transformation by elevating the global level of H3K27 tri-methylation or H3K36 di-methylation, respectively. In addition, mutations in histone H3 have been identified in certain pediatric cancers which cause reprogramming of H3K27 and H3K36 methylation by interfering with the histone methyltransferase activity. Finally, chromosomal translocations involving chromatin regulator genes can lead to the formation of fusion oncoproteins that directly modify chromatin as their mechanism of action. Although relatively rare in aggregate, gain-of-function mutations in chromatin regulators represent compelling therapeutic targets in genetically defined subsets of cancer patients. However, a broader clinical impact for epigenetic therapies in oncology will require an increased understanding of how nonmutated chromatin regulators function as cancer-specific dependencies.