Oncogenic Program Research Articles

Small-Molecule Inhibition of the Acyl-Lysine Reader ENL as a Strategy against Acute Myeloid Leukemia.

AML is a poor-prognosis disease for which new therapeutic approaches are desperately needed. We developed an orally bioavailable inhibitor of ENL, demonstrated its potent efficacy in MLL-rearranged and NPM1-mutated AML, and determined its mechanisms of action. These biological and chemical insights will facilitate both basic research and clinical translation. This article is highlighted in the In This Issue feature, p. 2483.

IRF4 as an Oncogenic Master Transcription Factor.

Simple SummaryMaster transcription factors regulate essential developmental processes and cellular maintenance that characterize cell identity. Many of them also serve as oncogenes when aberrantly expressed or activated. IRF4 is one of prime examples of oncogenic master transcription factors that has been implicated in various mature lymphoid neoplasms. IRF4 forms unique regulatory circuits and induces oncogenic transcription programs through the interactions with upstream pathways and binding partners. IRF4 is a transcription factor in the interferon regulatory factor (IRF) family. Since the discovery of this gene, various research fields including immunology and oncology have highlighted the unique characteristics and the importance of IRF4 in several biological processes that distinguish it from other IRF family members. In normal lymphocyte development and immunity, IRF4 mediates critical immune responses via interactions with upstream signaling pathways, such as the T-cell receptor and B-cell receptor pathways, as well as their binding partners, which are uniquely expressed in each cell type. On the other hand, IRF4 acts as an oncogene in various mature lymphoid neoplasms when abnormally expressed. IRF4 induces several oncogenes, such as MYC, as well as genes that characterize each cell type by utilizing its ability as a master regulator of immunity. IRF4 and its upstream factor NF-κB form a transcriptional regulatory circuit, including feedback and feedforward loops, to maintain the oncogenic transcriptional program in malignant lymphoid cells. In this review article, we provide an overview of the molecular functions of IRF4 in mature lymphoid neoplasms and highlight its upstream and downstream pathways, as well as the regulatory circuits mediated by IRF4.

FOXA1 regulates alternative splicing in prostate cancer.

SummaryDysregulation of alternative splicing in prostate cancer is linked to transcriptional programs activated by AR, ERG, FOXA1, and MYC. Here, we show that FOXA1 functions as the primary orchestrator of alternative splicing dysregulation across 500 primary and metastatic prostate cancer transcriptomes. We demonstrate that FOXA1 binds to the regulatory regions of splicing-related genes, including HNRNPK and SRSF1. By controlling trans-acting factor expression, FOXA1 exploits an “exon definition” mechanism calibrating alternative splicing toward dominant isoform production. This regulation especially impacts splicing factors themselves and leads to a reduction of nonsense-mediated decay (NMD)-targeted isoforms. Inclusion of the NMD-determinant FLNA exon 30 by FOXA1-controlled oncogene SRSF1 promotes cell growth in vitro and predicts disease recurrence. Overall, we report a role for FOXA1 in rewiring the alternative splicing landscape in prostate cancer through a cascade of events from chromatin access, to splicing factor regulation, and, finally, to alternative splicing of exons influencing patient survival.

Neuron-Glial Interactions in Health and Brain Cancer.

Brain tumors are devastating diseases of the central nervous system. Brain tumor pathogenesis depends on both tumor-intrinsic oncogenic programs and extrinsic microenvironmental factors, including neurons and glial cells. Glial cells (oligodendrocytes, astrocytes, and microglia) make up half of the cells in the brain, and interact with neurons to modulate neurodevelopment and plasticity. Many brain tumor cells exhibit transcriptomic profiles similar to macroglial cells (oligodendrocytes and astrocytes) and their progenitors, making them likely to subvert existing neuron-glial interactions to support tumor pathogenesis. For example, oligodendrocyte precursor cells, a putative glioma cell of origin, can form bona fide synapses with neurons. Such synapses are recently identified in gliomas and drive glioma pathophysiology, underscoring how brain tumor cells can take advantage of neuron-glial interactions to support cancer progression. In this review, it is briefly summarized how neurons and their activity normally interact with glial cells and glial progenitors, and it is discussed how brain tumor cells utilize neuron-glial interactions to support tumor initiation and progression. Unresolved questions on these topics and potential avenues to therapeutically target neuron-glia-cancer interactions in the brain are also pointed out.

Discovery of Small-Molecule Degraders of the CDK9-Cyclin T1 Complex for Targeting Transcriptional Addiction in Prostate Cancer.

Aberrant hyperactivation of cyclins results in carcinogenesis and therapy resistance in cancers. Direct degradation of the specific cyclin or cyclin-dependent kinase (CDK)-cyclin complex by small-molecule degraders remains a great challenge. Here, we applied the first application of hydrophobic tagging to induce degradation of CDK9-cyclin T1 heterodimer, which is required to keep productive transcription of oncogenes in cancers. LL-K9-3 was identified as a potent small-molecule degrader of CDK9-cyclin T1. Quantitative and time-resolved proteome profiling exhibited LL-K9-3 induced selective and synchronous degradation of CDK9 and cyclin T1. The expressions of androgen receptor (AR) and cMyc were reduced by LL-K9-3 in 22RV1 cells. LL-K9-3 exhibited enhanced anti-proliferative and pro-apoptotic effects compared with its parental CDK9 inhibitor SNS032 and suppressed downstream signaling of CDK9 and AR more effectively than SNS032. Moreover, LL-K9-3 inhibited AR and Myc-driven oncogenic transcriptional programs and exerted stronger inhibitory effects on several intrinsic target genes of AR than the monomeric CDK9 PROTAC (Thal-SNS032).

A multi-omic dissection of super-enhancer driven oncogenic gene expression programs in ovarian cancer

The human genome contains regulatory elements, such as enhancers, that are often rewired by cancer cells for the activation of genes that promote tumorigenesis and resistance to therapy. This is especially true for cancers that have little or no known driver mutations within protein coding genes, such as ovarian cancer. Herein, we utilize an integrated set of genomic and epigenomic datasets to identify clinically relevant super-enhancers that are preferentially amplified in ovarian cancer patients. We systematically probe the top 86 super-enhancers, using CRISPR-interference and CRISPR-deletion assays coupled to RNA-sequencing, to nominate two salient super-enhancers that drive proliferation and migration of cancer cells. Utilizing Hi-C, we construct chromatin interaction maps that enable the annotation of direct target genes for these super-enhancers and confirm their activity specifically within the cancer cell compartment of human tumors using single-cell genomics data. Together, our multi-omic approach examines a number of fundamental questions about how regulatory information encoded into super-enhancers drives gene expression networks that underlie the biology of ovarian cancer.

Connecting Metabolic Rewiring With Phenotype Switching in Melanoma.

Melanoma is a complex and aggressive cancer type that contains different cell subpopulations displaying distinct phenotypes within the same tumor. Metabolic reprogramming, a hallmark of cell transformation, is essential for melanoma cells to adopt different phenotypic states necessary for adaptation to changes arising from a dynamic milieu and oncogenic mutations. Increasing evidence demonstrates how melanoma cells can exhibit distinct metabolic profiles depending on their specific phenotype, allowing adaptation to hostile microenvironmental conditions, such as hypoxia or nutrient depletion. For instance, increased glucose consumption and lipid anabolism are associated with proliferation, while a dependency on exogenous fatty acids and an oxidative state are linked to invasion and metastatic dissemination. How these different metabolic dependencies are integrated with specific cell phenotypes is poorly understood and little is known about metabolic changes underpinning melanoma metastasis. Recent evidence suggests that metabolic rewiring engaging transitions to invasion and metastatic progression may be dependent on several factors, such as specific oncogenic programs or lineage-restricted mechanisms controlling cell metabolism, intra-tumor microenvironmental cues and anatomical location of metastasis. In this review we highlight how the main molecular events supporting melanoma metabolic rewiring and phenotype-switching are parallel and interconnected events that dictate tumor progression and metastatic dissemination through interplay with the tumor microenvironment.

YAP induces an oncogenic transcriptional program through TET1-mediated epigenetic remodeling in liver growth and tumorigenesis.

Epigenetic remodeling is essential for oncogene-induced cellular transformation and malignancy. In contrast to histone post-translational modifications, how DNA methylation is remodeled by oncogenic signaling remains poorly understood. The oncoprotein YAP, a coactivator of the TEAD transcription factors mediating Hippo signaling, is widely activated in human cancers. Here, we identify the 5-methylcytosine dioxygenase TET1 as a direct YAP target and a master regulator that coordinates the genome-wide epigenetic and transcriptional reprogramming of YAP target genes in the liver. YAP activation induces the expression of TET1, which physically interacts with TEAD to cause regional DNA demethylation, histone H3K27 acetylation and chromatin opening in YAP target genes to facilitate transcriptional activation. Loss of TET1 not only reverses YAP-induced epigenetic and transcriptional changes but also suppresses YAP-induced hepatomegaly and tumorigenesis. These findings exemplify how oncogenic signaling regulates the site specificity of DNA demethylation to promote tumorigenesis and implicate TET1 as a potential target for modulating YAP signaling in physiology and disease.

Molecular Docking Studies to Evaluate Small Molecule Inhibitors of Wnt/Betacatenin Signaling Pathway

Canonical Wnt pathway or β catenin dependent pathway is one of the highly conserved signalling pathway which can control gene expression and regulate cell proliferation, cell adhesion, cell migration, cell polarity and organogenesis. Abnormal regulation of β catenin in the canonical wnt signalling pathway leads to transcription of several genes involved in oncogenic programs. Aberrant signalling of the canonical wnt pathway was observed in several types of cancers including hepatocarcinoma, colorectal cancer and lung cancer. Many small molecules were observed to have the potential to block the aberrant wnt signalling pathway by allosteric binding and inhibiting β catenin molecule. The current study involves screening for ligands which can have strong allosteric binds to β catenin and inhibit wnt signalling pathway. Molecular docking studies were used to evaluate the binding capacity of the selected ligands. Curcumin, Cardamonin, FH535 and ICRT-3 were used as ligands for the molecular docking study with β catenin binding Transcription factor -4 receptor. All chosen ligands have exhibited significant binding energies with the receptor. The highest -9.518272 kcal/mol with Cardamonin followed by -9.28359 kcal/mol with FH535, -8.422604 kcal/mol with curcumin and the least -8.407231 kcal/mol with ICRT-3. All the ligands showed at least 1 hydrogen bond with the target receptor whereas Cardamonin showed 3 hydrogen bonds. Curcumin is a close second forming 2 hydrogen bonds while FH535 and ICRT-3 form only 1 hydrogen bond. The 2D interactions of the ligand and the molecule are visualised by using chimera. We observed Cardamonin to have a very strong binding affinity with the target receptor. Cardamonin can be a suitable drug candidate and might have the potential to inhibit the β catenin dependent wnt signalling pathway.

Abstract 5729: Dynamic phase separation of the androgen receptor and its coactivators to regulate gene expression

Abstract Numerous cancers, including prostate cancer (PCa), have been shown to be addicted to transcription programs driven by specific genomic sites known as superenhancers (SEs). Recently, it has been proposed that the robust transcription of genes at such SEs is enabled by the formation of phase-separated condensates by transcription factors and coactivators with intrinsically disordered regions. The androgen receptor (AR), the main oncogenic driver in PCa, contains large disordered regions and is co-recruited with the transcriptional coactivator MED1 to SEs in androgen-dependent prostate cancer cells, thereby promoting oncogenic transcriptional programs. In this work, we show that AR-rich, liquid-like foci form in prostate cancer models upon androgen stimulation. We reveal that foci formation correlates with AR transcriptional activity, which can be modulated by changing cellular foci content genetically or chemically. We also demonstrate that the transcriptional coactivator MED1 plays an essential role in the formation of transcriptionally active AR-rich foci and that AR antagonists that block cofactor recruitment or DNA binding hinder foci formation and thus AR transcriptional activity. The liquid like properties of the condensates were also validated in-vitro by using recombinant AR protein. Using clinical specimens, we detected the interaction between AR and MED1 in advanced forms of prostate cancer and not in benign tissues. These results suggest that enhanced compartmentalization of AR and coactivators at SEs may play an important role in the activation of oncogenic transcription programs in androgen-dependent PCa. A better understanding of the assembly and the regulation of these AR-rich compartments may provide novel therapeutic options for PCa by targeting downstream events of androgen activation and DNA binding of AR. Citation Format: Fan Zhang, Maitree Biswas, Joseph Lee, Shreyas Lingadahalli, Samantha Wong, Christopher Wells, Neetu Saxena, Bei Sun, Ana K. Parra-Nuñez, Christophe Sanchez, Jane Foo, Novia Chan, Lauren Ung, Nabeel Khan, Umut Berkay Altıntaş, Jennifer M. Bui, Yuzhuo Wang, Ladan Fazli, Paul S. Rennie, Nathan Lack, Artem Cherkasov, Martin E. Gleave, Joerg Gsponer, Nada Lallous. Dynamic phase separation of the androgen receptor and its coactivators to regulate gene expression [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 5729.

Abstract 422: Novel approach to destabilization of oncogenic mutant p53 and therapeutic implications

Abstract Introduction: Mutant p53 drives several hallmarks of cancer through a gain-of-function oncogenic program. The oncogenicity of mutant p53 includes sustained proliferation, increased survival and resistance to therapy, increased invasion and metastasis, and genomic instability. The oncogenicity of mutant p53 is related to its stability and accumulation in cells by evading degradation by the proteasome. Therefore, destabilization of mutant p53 has been sought as a therapeutic strategy, but so far without clinical success. We and others observe that proteasome inhibitors cause paradoxical depletion of mutant p53 in lung cancer cell lines. Objectives: In this project, we sought to determine the mechanism(s) of mutant p53 depletion by proteasome inhibition and its therapeutic implications in lung cancer. Methods: Human lung cancer cell lines bearing mutant p53 and wildtype p53 (WTp53) were used in this study. An isogenic panel of cell lines with mutant p53, WTp53 and a vector control was also used to determine mutant p53 dependency of the observed effects. Western blotting, immunoprecipitation, siRNA technology, DNA transfection were used for protein detection, protein-protein interactions, gene knock-down and overexpression respectively. Cycloheximide chase assay was used to determine protein degradation. The cancer genome atlas (TCGA) analysis was performed using the cBioPortal platform. Results: Proteasome inhibitors resulted in depletion of mutant p53 in the lung cancer cell line H1975. This effect was also confirmed using the isogenic model described above. Depletion of mutant p53 occurred through a degradation mechanism and was time dependent. While WTp53 accumulated at initial timepoints of proteasome inhibition, mutant p53 did not accumulate but instead depleted with time. This suggested that the proteasome is not the primary mechanism for mutant p53, in contrast to WTp53. Since autophagy is an alternative mechanism of protein degradation in eukaryotes, we evaluated for, and found evidence of autophagy upon proteasome inhibition. We further showed that autophagic degradation of mutant p53 could involve the heat shock protein 70. Our TCGA data analysis showed proteasome genes amplification in mutant p53 lung cancers, suggesting a possible functional dependency. Furthermore, RNA sequencing analysis showed upregulation of most proteasome genes upon stable expression of the R273H mutant in p53-null lung cancer cell line. Finally, in vitro cell viability assays using two different proteasome inhibitors showed increased sensitivity of the lung cancer cell line with mutant p53 compared to WTp53. Conclusion: The cumulative evidence of proteasome hyperactivity, degradation of mutant p53 and in vitro evidence of increased susceptibility of mutant p53 lung cancer cell lines suggests that proteasome inhibitors warrant a closer attention for therapeutic targeting of mutant p53 in lung cancer. Citation Format: Eziafa I. Oduah, Larisa Litovchick, Steven R. Grossman. Novel approach to destabilization of oncogenic mutant p53 and therapeutic implications [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 422.

Abstract 3729: Discovery of orally bioavailable SMARCA2/4 dual degraders for treatment of acute myeloid leukemia

Abstract Background: The BAF (SWI/SNF) chromatin remodeling complex comprises of two mutually exclusive ATPases, SMARCA2 (BRM) and SMARCA4 (BRG1), that affect the mobilization and positioning of nucleosomes on DNA and thereby regulates important cellular functions including transcription, DNA recombination, DNA repair and chromosome decatenation during mitosis. SMARCA4 is frequently overexpressed in several types of cancers. Overexpression has been linked to increased proliferation and survival, as well as aggressive tumors and poor prognosis. SMARCA4 knockdown in these tumors lead to inhibition of proliferation and increased sensitivity to known chemotherapeutic agents, supporting the validity of targeting SMARCA4. Genetic silencing studies have established that the oncogenic activity of tumors lacking SMARCA4 is primarily driven by SMARCA2-containing residual SWI/SNF complex, suggesting the importance of dual inhibition of SMARCA2 and SMARCA4. While SMARCA4 is known to play a vital role in maintaining the oncogenic transcription program and driving proliferation in leukemia, the impact of dual SMARCA2 and SMARCA4 inhibition/degradation in acute myeloid leukemia (AML) is largely unexplored. Methods and Results: As part of the initial design plan, selective SMARCA2/4 Bromodomain inhibitors and specific ligands of several E3 ligases were chosen to arrive at different degrader designs. A choice of linkers and different exit vectors were considered to construct a variety of hetero bifunctional molecules. Our proprietary ternary complex modeling algorithm, ALMOND (ALgorithm for MOdeling Neosubstrate Degraders) helped in prioritizing the designs. Short listed compounds were synthesized and profiled in multiple cellular assays to understand their degradation potential. Several compounds that degrade SMARCA2, SMARCA4 & PBRM1 with pico molar DC50 were identified. These compounds have shown very potent anti-proliferative activity in both SMARCA2/4 proficient (MV-4-11, VCaP etc) and SMARCA4 mutant cell lines (SK-MEL-5 & RERF-LC-A1 etc). Further, potent compounds were optimized for their pharmacokinetic properties. Multiple lead compounds with low IV clearance and good oral bioavailability in rodents were identified. Advanced lead compounds are currently being evaluated in rodent tolerability and PK-PD experiments to select doses for the efficacy study. Conclusions: Highly potent degraders of SMARCA2, SMARCA4 & PBRM1 were identified by conjugating selective SMARCA2/4 Bromodomain inhibitors and several E3 ligase specific ligands. Further optimization of the linkers resulted in compounds with improved pharmacokinetic profile and very good oral bioavailability in rodents. Highly potent and orally available degraders of SMARCA2, SMARCA4 are efficacious in AML xenograft models and advanced profiling of candidate molecule is in progress. Citation Format: Chandrasekhar Abbineni, Leena Khare, Bilash Kuila, Abdul Rawoof Khaji, Dhaytadak Bhagwan Mahadeo, Sandeep Vitthal Dukare, Bhagya M S Kumar, Suraj T Gore, Vijay Kamal Ahuja, Amit A Dhudashiya, Raghavendra N R, Nagesh Gowda, Charamanna K B, Kiran Aithal B, Samiulla D S, Subhendu Mukherjee, Thomas Antony, Sanjeev Giri, Shekar Chelur, Kavitha Nellore, Girish Daginakatte, Murali Ramachandra, Susanta Samajdar. Discovery of orally bioavailable SMARCA2/4 dual degraders for treatment of acute myeloid leukemia [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 3729.

Abstract 5728: A druggable FOXA1-glucocorticoid receptor transcriptional axis drives tumor growth in NSCLC

Abstract FOXA1 is a pioneer factor that is essential to steroid receptor function in hormone-dependent adenocarcinomas, including breast and prostate cancer. FOXA1 expression is also observed in other tumors of epithelial lineage such as non-small cell lung cancer (NSCLC), but whether and how it is required for tumor growth in these contexts is not known. Analyzing data from genome-scaled pooled loss-of-function screens, we identified and validated a subset of NSCLC cell lines with reduced cellular fitness following FOXA1 knockout. We performed a rapid immunoprecipitation and mass spectrometry of endogenous proteins (RIME) screen to nominate candidate factors that may cooperate with FOXA1 to mediate oncogenic transcription programs. This screen revealed a chromatin-localized interaction between FOXA1 and the glucocorticoid receptor (GR). Depletion of GR expression using shRNA or CRISPR/Cas9 suppressed the proliferation of FOXA1-dependent, but not FOXA1-independent NSCLC models, suggesting GR specifically contributes to tumor growth in the FOXA1-dependent context. To assess the potential therapeutic utility of targeting the FOXA1-GR signaling axis, we employed two structurally distinct ligand antagonists of GR from ORIC Pharmaceuticals: ORIC-101, a steroidal antagonist, and OP-4954, a non-steroidal antagonist. Both antagonists inhibited dexamethasone stimulated GR-transactivation of a glucocorticoid response element (GRE)-luciferase reporter with equal potency. However, proliferation and colony formation of the FOXA1/GR-dependent NSCLC cells were only inhibited upon treatment with ORIC-101, and not OP-4954. Gene expression analysis uncovered a discrete set of GR target genes, including SFTPB, TRAF4 and SGK1, whose expression was reduced by ORIC-101 but unaffected or even induced by OP-4954. The specific inhibition of GR target gene expression and attendant induction of apoptosis by ORIC-101 suggest a hierarchy of GR targets relevant to the FOXA1/GR-growth program in NSCLC. Finally, we evaluated the in vivo therapeutic potential of ORIC-101 using NSCLC xenografts and found that single-agent ORIC-101 exhibited potent antitumor effects in these models. Taken together, these data establish a model of FOXA1-GR-dependent tumor growth amongst a subset of NSCLCs and demonstrate that effective blockade of this complex is a rational therapeutic avenue to be explored in the clinic. Citation Format: Madeline Dorso. A druggable FOXA1-glucocorticoid receptor transcriptional axis drives tumor growth in NSCLC [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 5728.

Abstract 1461: ETV6 deficiency and microsatellite enhancers drive transcriptional dysregulation in B-lymphoblastic leukemia

Abstract Subtypes of B-lymphoblastic leukemia (B-ALL) are defined by unique genetic aberrations and gene expression programs. ETV6-RUNX1+ (E-R+) B-ALL, a common pediatric subtype, shares a gene activation signature with “ETV6-RUNX1-like” B-ALL that lacks the E-R fusion gene. Both E-R+ and E-R-like B-ALL show frequent inactivating mutations or deletions of ETV6, which encodes an ETS family transcriptional repressor (core binding motif GGAA/T). Signature genes overexpressed in E-R+ B-ALL, such as EPOR and PIK3C3, were shown to sustain the malignant phenotype. We performed H3K27ac ChIP-Seq and ATAC-Seq on 26 B-cell cancer cell lines to identify subtype-specific active enhancer-like elements. Unbiased K-means clustering identified distal elements that were selectively acetylated in four E-R+ B-ALL cell lines (all with inactivation of the second ETV6 allele) and in a fifth B-ALL cell line with biallelic ETV6 deletion. Motif analysis of this cluster showed strong enrichment for tandem repeats of the sequence “GGAA” (p<10-100). Repeats with ≥6 tandem copies of “GGAA” were selectively acetylated and accessible in H3K27ac ChIP-Seq and ATAC-Seq datasets from primary patient samples of E-R+ B-ALL, but not from other genetic subtypes that lack ETV6 aberrations. Doxycycline-inducible expression of ETV6 in ETV6-deficient, E-R+ B-ALL cells led to significant growth inhibition. Restored ETV6 bound extensively to GGAA repeats (80% of ETV6 binding sites), repressed repeat enhancer acetylation, and repressed expression of adjacent E-R+ signature genes (n=40). Repression of a published E-R+ signature gene set was significant by GSEA analysis (p<0.001). Direct CRISPR-interference repression of 6 GGAA repeat enhancers led to significant downregulation of their associated E-R+ signature genes, including EPOR and PIK3C3. GGAA repeat enhancers are a known driver of Ewing sarcoma, where they are activated by oncogenic fusions of the ETS activators FLI1 or ERG. Active GGAA repeat enhancers and repeat-regulated genes in E-R+ B-ALL show only partial overlap with repeat-regulated genes in Ewings, possibly due to tissue-specific factors. Wild-type ERG and FLI1 are highly expressed in B-ALL. We found that knockdown of ERG, but not FLI1, led to significant downregulation of repeat enhancer-regulated E-R+ signature genes in B-ALL. ChIP-Seq showed that the ERG binds nearly all active GGAA repeat enhancers in three ETV6-deficient B-ALL cell lines, but not in ETV6-intact B-ALL. We identify GGAA repeat enhancers, sustained by ETV6 deficiency and strong ERG expression, as a unifying mechanism for a subtype-specific oncogenic gene expression program in B-ALL. Our findings may have crucial implications for E-R+ B-ALL modeling, as most GGAA repeats are not conserved between mice and humans. Mechanisms that activate leukemia-specific repeat enhancers may represent appealing targets for future therapeutic development. Citation Format: Joshua W. Goldman, Rohan Kodgule, Alexander C. Monovich, Travis Saari, Cody N. Hall, Niharika Rajesh, Juhi Gupta, Athalee Aguilar, Noah Brown, Mark Y. Chiang, Marcin P. Cieslik, Russell J. Ryan. ETV6 deficiency and microsatellite enhancers drive transcriptional dysregulation in B-lymphoblastic leukemia [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 1461.

Abstract 6086: Clonal biallelic inactivation of NF2 is an evolutionary bottleneck that exposes a vulnerability to CDK7 inhibition in mesothelioma

Abstract Background: Mesothelioma, a cancer caused by asbestos is lethal and lacks molecularly targeted therapy. The tumor suppressor NF2 constitutes a frequent, positively selected somatic alteration warranting synthetic lethal approaches to target this driver. NF2 inactivation drives nuclearization of YAP to mediate TEAD dependent oncogenic transcriptional program. YAP is stabilized by CDK7 through phosphorylation of S169/S128/S90, inhibiting the E3 ligase complex CDL4DCAF12. We hypothesized that biallelic NF2 inactivation would be vulnerable to augmentation of CRL4DCAF12 through inhibition of CDK7. Methods: 50 Patients (the MEDUSA cohort) undergoing routine extended pleurectomy decortications consented to have multiregional sampling of their mesotheliomas at resection at 4-5 stereotyped locations, followed by multiregional whole exome sequencing (mWES 200x), phylogenetic deconvolution and transfer learning to examine evolutionary trajectories. Bulk RNA sequencing enabled gene set enrichment analysis, and spatial YAP phenotyping using tissue microarrays were conducted on the mWES profiled cohort. Primary cell lines were generated from a subset of mesotheliomas and whole exome sequenced. Results: NF2 exhibited biallelic inactivation involving copy number/mutation allelic heterogeneity in 42% of mesotheliomas. Double hits were predominantly clonal. Hippo signalosome exhibited additional clonal somatic alterations in 26% of mesotheliomas, with biallelic inactivation being observed in LATS2 (8%) and LATS1 (4%). Transfer learning identified NF2 inactivation as a predominantly secondary clonal event, constituting an evolutionary bottleneck. Random forest analysis revealed YAP dependent transcription, epithelial mesenchymal transition and spindle checkpoint transcriptional signature enrichments in NF2 double hit mesotheliomas. We conducted drug screening of NF2 wild type versus inactivated primary mesothelioma cell lines, which revealed selective sensitivity to CDK7 inhibitors THZ1 and YKL-5-124 in NF2 inactivated but not wild type MEDUSA cell lines. Conclusions: NF2 biallelic inactivation constitutes an evolutionary bottleneck during early mesothelioma evolution, associated with a specific vulnerability to CDK7 highlighting a potential path to clinical stratified therapy. Citation Format: Essa Y. Baitei, Min Zhang, Qianqian Sun, Jin-Li Luo, Philip Zhang, Tamihiro Kamata, James Harber, Aleksandra Bzura, Peter W. Jordan, Charlotte Poile, Alan Dawson, Apostolos Nakas, Cathy Richards, Hongji Yang, Ed Hollox, Dean A. Fennell. Clonal biallelic inactivation of NF2 is an evolutionary bottleneck that exposes a vulnerability to CDK7 inhibition in mesothelioma [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 6086.

Abstract 701: Loss of PRC2 enforces a mesenchymal neural crest stem cell phenotype in NF1-deficient cancer through activation of core transcription factors

Abstract Objective: Recurrent mutations in the polycomb repressive complex 2 (PRC2) occur in ~80% of malignant peripheral nerve sheath tumors (MPNST), which originate from NF1-deficient Schwann cells. In MPNST, PRC2 loss results in a diverse set of transcriptomic and phenotypic consequences, including gain of acetylated H3K27 (H3K27ac) accompanying the loss of trimethylated H3K27 (H3K27me3), hyperactivated Ras signaling, and tumor escape from immune surveillance. Mechanistic understanding of how PRC2 loss results in these diverse consequences remains unresolved. Methods: To delineate the oncogenic mechanisms mediated by PRC2 loss, we engineered MPNST cell lines to dynamically reassemble a functional PRC2 and evaluated the transcriptomic and epigenetic consequences of PRC2 restoration. We further extended these finding using single cell RNA sequencing (scRNAseq) from human MPNST. Results: Through integrative analysis of RNAseq and H3K27me3 ChIP-seq in PRC2-deficient MPNST cells, we identified 6134 H3K27me3 peaks gained when a functional PRC2 was restored. Of the 876 significantly altered genes, 699 genes were downregulated, and 177 genes were upregulated when a restored PRC2 caused genome-wide redistribution of H3K27me3 peaks. Detailed mechanistic dissection of these PRC2-regulated genes revealed a two-pronged oncogenic process mediated by PRC2 loss and they cooperatively contribute to the tumorigenesis of MPNST. First, PRC2 loss leads to the upregulation of a transcriptional circuit that remodels the enhancer landscape of MPNST cells and establishes an enhancer-driven transcription factor, FOXC1, as a master regulator and thus a core vulnerability of the cell. Second, PRC2 loss reduces type I interferon (IFN) signaling and antigen presentation as a downstream consequence of the upregulated Ras signaling. These data were further integrated with scRNAseq of human MPNST. Importantly, we discovered that the PRC2-deficient tumor cells have a corrupted transcriptional program characteristic of a mesenchymal precursor cell found during the trajectory of normal Schwann cell development. Interestingly, malignant cells expressing high levels of IFN and antigen presentation genes were missing in the metastatic MPNST, potentially allowing the tumor cell to escape the immune surveillance. The transcriptional circuit established by PRC2-regulated FOXC1 and its downstream targets sustains the malignant program in both primary and metastatic MPNST. Conclusion: In summary, we discovered the activation of a lineage specific oncogenic transcription program in PRC2-deficient MPNST, which is characteristic of a neural crest-derived mesenchymal stem cell. Our findings provide mechanistic understanding of the inherent metastatic potential, chemotherapy and radiotherapy resistance, and immune escape that are clinically characteristic of these tumors. Citation Format: Xiyuan Zhang, Hannah E. Lou, Vishaka Gopalan, Zhihui Liu, Hilda Jafarah, Haiyan Lei, Paige Jones, Carly M. Sayers, Marielle E. Yohe, Prashant Chittiboina, Brigitte C. Widemann, Carol J. Thiele, Michael C. Kelly, Sridhar Hannenhalli, Jack F. Shern. Loss of PRC2 enforces a mesenchymal neural crest stem cell phenotype in NF1-deficient cancer through activation of core transcription factors [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 701.

Abstract 3592: Targeting SWI/SNF ATPases in enhancer-addicted human cancers

Abstract In mammalian cells, DNA is wrapped around histone octamers (collectively referred to as nucleosomes) which form a physical barrier to all DNA-based processes. The switch/sucrose non-fermentable (SWI/SNF) is a multi-subunit chromatin remodeling complex that uses energy from ATP hydrolysis to reposition or eject nucleosomes at non-coding regulatory elements, thereby enabling access to the underlying DNA for transcriptional activation. Notably, the SWI/SNF complex plays a crucial role in chromatin remodeling and is recurrently altered in over 20% of human cancers, with the revised complex in cancer cells enabling central oncogenic gene programs. Yet, no studies have assessed the therapeutic efficacy of complete SWI/SNF inactivation across human cancers. Here, we developed a proteolysis targeting chimera (PROTAC) degrader of ATPase subunits of the SWI/SNF complex, SMARCA2 and SMARCA4. In a panel with over 90 normal and cancer cell lines from 18 different lineages, we found MYC-driven multiple myeloma and androgen receptor (AR)/forkhead box A1 (FOXA1)-positive prostate and breast cancers to be preferentially sensitive to dual SMARCA2 and SMARCA4 degradation relative to benign prostate as well as other cancer cell lines, including cancer cell lines with inactivating SMARCA4 mutations. We found complete SWI/SNF ATPase degradation to instantaneously compact the cis-regulatory elements that are bound and activated by transcription factors that drive cancer proliferation, namely MYC, IRF4, TCF3, AR, FOXA1, and ERG. This ensued in parallel untethering of these oncogenic drivers from the chromatin, with subsequent chemical decommissioning of their core enhancer circuitry and attenuation of downstream gene programs. Furthermore, using chromatin conformation assays we found SWI/SNF inactivation to disrupt super-enhancer and promoter DNA looping interactions that wire supra-physiologic expression of the MYC, AR, ERG, IRF4, and TCF3 oncogenes themselves, thereby tempering their expression in cancer cells. Treatment with the SMARCA2/4 degrader alone induced potent inhibition of tumor growth in cell line-derived xenograft models of multiple myeloma, as well as prostate cancer, and synergized with AR antagonists, inducing disease remission in several drug-resistant disease models. Notably, no major toxicities were seen in mice upon prolonged treatment with the SMARCA2/4 degrader, including no indications of thrombocytopenia, gastrointestinal goblet cell depletion, or germ cell degeneration—all being major toxicities associated with the BRD4-targeting therapeutics. To our knowledge, this study is the first preclinical proof of concept that targeted obstruction of chromatin accessibility at non-coding regulatory elements can be a potent therapeutic strategy in enhancer-addicted tumors, warranting the safety and efficacy assessments of SWI/SNF inhibitors and degraders in human clinical trials. Citation Format: Abhijit Parolia, Lanbo Xiao, Yuanyuan Qiao, Pushpinder Bawa, Sanjana Eyunni, Eleanor Young, Rahul Mannan, Sandra E. Carson, Yu Chang, Yuping Zhang, James George, Mustapha Jaber, Fengyun Su, Rui Wang, Sanjita Sasmal, Leena Khare, Subhendu Mukerjee, Chandrasekhar AbbinenI, Kiran Aithal, Xuhong Cao, Yuzhuo Wang, Susanta Samajdar, Murali Ramachandra, Arul M. Chinnaiyan. Targeting SWI/SNF ATPases in enhancer-addicted human cancers [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 3592.

Abstract 411: Reversibility of tumor adaptations to PI3K inhibition decreases as a function of time

Abstract The PI3K pathway is a key regulator of metabolism, cell proliferation and migration and some of its components (e.g. PIK3CA, HER2 and PTEN) are frequently altered in cancer by genetic events that deregulate its output. However, inhibitors of components of the pathway have only modest antitumor effects and, in some instances, have resulted in “tumor flares” in patients upon cessation of therapy. Low efficacy has been attributed to toxicity and to adaptive resistance. Inhibition of the PI3K pathway has been associated with relief of feedback inhibition of receptor signaling (RTKs) by a variety of mechanisms including increased receptor expression and decreased expression of the PTEN phosphatase, a major negative regulator of the pathway. Now we show that changes in expressions of RTKs, PTEN, anti-apoptosis proteins like Mcl1 and transcription factors known to drive oncogenic and survival programs in tumors like c-Myc, c-Jun, FOXOs are induced upon continuous long-term PI3K inhibition (2 weeks and longer). These changes increase as a function of duration of inhibition and become less reversible with time in drug. Unbiased clustering of RNA seq of cells treated with PI3K inhibitors revealed clusters of gene expression changes based upon short or long-term inhibition. Correspondingly the mRNA of the RTKs and transcription factors change with similar kinetics as that of the proteins and become less reversible with duration of inhibition. Moreover, the persister cells treated with PI3K inhibitors for 2 weeks or longer grow faster than the treatment naive cells upon drug removal both in vitro and in vivo and the degree of reversibility of the increased proliferation rate is inversely proportional to the duration of inhibition. Persister cells treated with PI3K inhibitors for more than two weeks have higher levels of expression of a set of transcription factors, RTKs, Mcl1 and of pAKT after one week of drug wash-out and are less sensitive to re-inhibition of PI3K. Combined inhibition of PI3K with Mcl1 inhibitors lead to greater reduction of cell proliferation and increased cell death.This suggests that continuous long-term inhibition of PI3K leads to a chronic adaptive state driven by relief of negative feedback which becomes less reversible with increasing duration of inhibition. Cells undergoing long term inhibition have higher steady state levels of components of the pathway leading to increased cell growth upon drug removal as compared to untreated cells. The data suggests that induction of adaptive resistance is in part responsible for the continued persistence of tumor masses after the initial response to targeted therapy. We hypothesize that pulsatile targeted inhibition with short intervals off therapy could avoid development of chronic adaptation. Intermittent administration of PI3K inhibitor combinations that cause potent induction of cell death may result in improved therapeutic outcomes. Citation Format: Radha Mukherjee, Elisa de Stanchina, Sarat Chandarlapaty, Neal Rosen. Reversibility of tumor adaptations to PI3K inhibition decreases as a function of time [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 411.

Abstract 2647: RVU120, a selective CDK8/CDK19 inhibitor, demonstrates efficacy against hormone-independent breast cancer cells in vitro and in vivo

Abstract Breast cancer (BC) is a complex and heterogenous disease, and various approaches have been used to classify BC into several subtypes to improve diagnostic and therapeutic outcomes. One of the features of BC is deregulated transcription, which allows for classification of the disease based on gene expression signature into four basic types: Luminal A, Luminal B, HER2-enriched, and triple negative (TNBC)/basal-like. Novel therapeutic approaches targeting oncogenic transcriptional programs may represent a promising strategy, in particular for TNBC, where the lack of common genetic alterations has so far limited the development of targeted therapies. The CDK8 module functions as a master coordinator of transcription, bridging enhancers and core promoters. Meta-analysis of curated TCGA data reveals that >15% of all BC have increased expression of CDK8 and/or CDK19, and that elevated expression of both genes is associated with decreased overall survival. High CDK8 expression is inversely correlated with the expression of estrogen receptor (ER) and positively correlated with occurrence of TP53 mutations. RVU120 is a specific, low nM, selective inhibitor of CDK8/CDK19, currently being tested in a first-in-human Phase Ib clinical trial in patients with metastatic or advanced solid tumors progressing from previous lines of therapy (ClinicalTrials.gov: NCT05052255). In order to establish a rationale for treatment of BC with RVU120 we have interrogated a panel of cell lines representing various subtypes of BC. These studies revealed that TNBC and ER-/PR-/HER2+ cells were highly sensitive to RVU120 and also to two other non-related CDK8/19 inhibitors, indicating a class effect. In contrast, CDK8/19 inhibitors were not able to inhibit mitogenic effect of estrogen, confirming differential efficacy in hormone - independent BC. Detailed transcriptional profiling of RVU120-responder cells revealed high enrichment of STAT3 target genes, SOX4 target genes and gene hallmarks of epithelial to mesenchymal transition (EMT), signatures associated with invasiveness and stemness. Non-responder cells were characterized by enrichment of transcriptional signatures of ER activity. Further proteomic profiling show that the top responder cells were the Mesenchymal Stem-Like (MSL) molecular subtype of TNBC and were positive for transactivated pSTAT3. Transcriptomic RNAseq profiling of MSL TNBC cell lines indicated that among genes inhibited by RVU120 there was high enrichment of STAT1 (interferon signature), STAT3 (IL6- signaling) and STAT5 (IL2 signaling) dependent genes. Single agent efficacy of RVU120 has been confirmed in subcutaneous TNBC xenograft models in vivo at well tolerated doses. Overall, these studies provide rationale for further development of RVU120 in TNBC patients. Citation Format: Urszula Pakulska, Marta Obacz, Aniela Gołas, Milena Mazan, Magdalena Masiejczyk, Agata Stachowicz, Justyna Martyka, Michał Combik, Kinga Kęska, Katarzyna Wiklik, Kristina Goller, Elżbieta Adamczyk, Krzysztof Brzózka, Tomasz Rzymski. RVU120, a selective CDK8/CDK19 inhibitor, demonstrates efficacy against hormone-independent breast cancer cells in vitro and in vivo [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 2647.

Abstract 3717: KMT2D loss cooperates with PTCH loss for medulloblastoma genesis

Abstract We have previously reported that the histone H3 lysine 4 methyltransferase KMT2D (also called MLL4, MLL2, and ALR; a transcriptional coactivator) is required for neuronal differentiation of human neuron-committed NT2/D1 embryonal carcinoma stem cells. Notably, we have shown that brain-specific knockout of Kmt2d alone induces spontaneous medulloblastoma (MB) in mice and that Kmt2d loss in the brain highly upregulates several oncogenic signaling programs and downregulates tumor suppressor genes. Consistent with this, our analysis of several publicly available databases indicates that Kmt2d is the most frequently mutated epigenetic modifier (8%‒10%) in MB. In this study, we sought to assess whether Kmt2d loss cooperates with another oncogenic event in MB genesis. Particularly, PTCH (also known as PTCH1), a potent MB-signaling suppressor, is one of the most frequently mutated genes in MB, and KMT2D mutations co-occur with PTCH mutations more than with many other mutations in MB. Therefore, we determined the effect of Kmt2d loss on of Ptch+/--driven MB genesis by generating and analyzing Nestin-Cre Kmt2dfl/+ Ptch+/- mice. Our results showed that heterozygous loss of Kmt2d strongly increased the genesis and incidence of Ptch+/--driven MB. Supporting this, immunohistochemistry staining of Ki-67 (a proliferation marker) showed that heterozygous loss of Kmt2d in Ptch+/--driven MB highly increased the proliferation of MB cells. Our transcriptomic analysis showed that heterozygous Kmt2d loss upregulated tumor-promoting programs, including G-protein-coupled receptor signaling and oxidation-reduction process. In line with this, heterozygous Kmt2d loss upregulated oncogenic kinases (e.g., phospho-AKT1 and phospho-ERK) that may be downstream of G-protein-coupled receptor signaling. Mechanistically, our results indicate that these tumor-promoting programs are repressed, at least in part, by the transcription-repressive and tumor-suppressive factor (s) NCOR2, whose expression is activated by KMT2D. Our results would be the first to provide molecular insights into how co-losses of an epigenetic modifier and an MB-signaling suppressor cooperate for MB genesis. Our new mouse model would be helpful in future preclinical therapeutic experiments for MB treatment. Our findings suggest that targeting oncogenic effectors downstream of KMT2D loss can be considered a potential therapeutic strategy for MB treatment. Citation Format: Shilpa S. Dhar, Calena J. Brown, Ali S. Rizvi, Janak R. Abraham, Roy V. Sillitoe, Kaifu Chen, Min Gyu Lee. KMT2D loss cooperates with PTCH loss for medulloblastoma genesis [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 3717.