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BRCA1 mutations are associated with increased breast and ovarian cancer risk. BRCA1-mutant tumors are high-grade, recurrent, and often become resistant to standard therapies. Herein, we performed a targeted CRISPR-Cas9 screen and identified MEPCE, a methylphosphate capping enzyme, as a synthetic lethal interactor of BRCA1. Mechanistically, we demonstrate that depletion of MEPCE in a BRCA1-deficient setting led to dysregulated RNA polymerase II (RNAPII) promoter-proximal pausing, R-loop accumulation, and replication stress, contributing to transcription-replication collisions. These collisions compromise genomic integrity resulting in loss of viability of BRCA1-deficient cells. We also extend these findings to another RNAPII-regulating factor, PAF1. This study identifies a new class of synthetic lethal partners of BRCA1 that exploit the RNAPII pausing regulation and highlight the untapped potential of transcription-replication collision-inducing factors as unique potential therapeutic targets for treating cancers associated with BRCA1 mutations.

The lysine demethylase LSD1 (also called KDM1A) plays important roles in promoting multiple malignancies including both hematologic cancers and solid tumors. LSD1 targets histone and nonhistone proteins and can function as a transcriptional corepressor or coactivator. LSD1 has been reported to act as a coactivator of androgen receptor (AR) in prostate cancer and to regulate the AR cistrome via demethylation of its pioneer factor FOXA1. A deeper understanding of the key oncogenic programs targeted by LSD1 could help stratify prostate cancer patients for treatment with LSD1 inhibitors, which are currently under clinical investigation. In this study, we performed transcriptomic profiling in an array of castration-resistant prostate cancer (CRPC) xenograft models that are sensitive to LSD1 inhibitor treatment. Impaired tumor growth by LSD1 inhibition was attributed to significantly decreased MYC signaling, and MYC was found to be a consistent target of LSD1. Moreover, LSD1 formed a network with BRD4 and FOXA1 and was enriched at super-enhancer regions exhibiting liquid–liquid phase separation. Combining LSD1 inhibitors with BET inhibitors exhibited strong synergy in disrupting the activities of multiple drivers in CRPC, thereby inducing significant growth repression of tumors. Importantly, the combination treatment showed superior effects than either inhibitor alone in disrupting a subset of newly identified CRPC-specific super-enhancers. These results provide mechanistic and therapeutic insights for cotargeting two key epigenetic factors and could be rapidly translated in the clinic for CRPC patients. Significance: LSD1 drives prostate cancer progression by activating super-enhancer–mediated oncogenic programs, which can be targeted with the combination of LSD1 and BRD4 inhibitors to suppress the growth of CRPC.

Establishing causal links between inherited polymorphisms and cancer risk is challenging. Here, we focus on the single-nucleotide polymorphism rs55705857, which confers a sixfold greater risk of isocitrate dehydrogenase ( IDH) –mutant low-grade glioma (LGG). We reveal that rs55705857 itself is the causal variant and is associated with molecular pathways that drive LGG. Mechanistically, we show that rs55705857 resides within a brain-specific enhancer, where the risk allele disrupts OCT2/4 binding, allowing increased interaction with the Myc promoter and increased Myc expression. Mutating the orthologous mouse rs55705857 locus accelerated tumor development in an Idh1 R132H -driven LGG mouse model from 472 to 172 days and increased penetrance from 30% to 75%. Our work reveals mechanisms of the heritable predisposition to lethal glioma in ~40% of LGG patients.

The lysine demethylase LSD1 (also called KDM1A) plays important roles in promoting multiple malignancies including both hematologic cancers and solid tumors. LSD1 targets histone and nonhistone proteins and can function as a transcriptional corepressor or coactivator. LSD1 has been reported to act as a coactivator of androgen receptor (AR) in prostate cancer and to regulate the AR cistrome via demethylation of its pioneer factor FOXA1. A deeper understanding of the key oncogenic programs targeted by LSD1 could help stratify prostate cancer patients for treatment with LSD1 inhibitors, which are currently under clinical investigation. In this study, we performed transcriptomic profiling in an array of castration-resistant prostate cancer (CRPC) xenograft models that are sensitive to LSD1 inhibitor treatment. Impaired tumor growth by LSD1 inhibition was attributed to significantly decreased MYC signaling, and MYC was found to be a consistent target of LSD1. Moreover, LSD1 formed a network with BRD4 and FOXA1 and was enriched at super-enhancer regions exhibiting liquid–liquid phase separation. Combining LSD1 inhibitors with BET inhibitors exhibited strong synergy in disrupting the activities of multiple drivers in CRPC, thereby inducing significant growth repression of tumors. Importantly, the combination treatment showed superior effects than either inhibitor alone in disrupting a subset of newly identified CRPC-specific super-enhancers. These results provide mechanistic and therapeutic insights for cotargeting two key epigenetic factors and could be rapidly translated in the clinic for CRPC patients.Significance:LSD1 drives prostate cancer progression by activating super-enhancer–mediated oncogenic programs, which can be targeted with the combination of LSD1 and BRD4 inhibitors to suppress the growth of CRPC.

Supplementary data

Expression quantitative trait locus (eQTL) analysis has become an important tool in understanding the link between genetic variants and gene expression, ultimately helping to bridge the gap between risk SNPs and associated diseases. Recently, we identified and validated a specific case where the methylation of a CpG site can affect the relationship between the genetic variant and gene expression. To systematically evaluate this regulatory mechanism, we developed an extended eQTL mapping method named DNA methylation modulated eQTL (memo-eQTL). We performed memo-eQTL mapping in 128 normal prostate samples and discovered 1,731 memo-eQTLs, a vast majority of which have not been reported as eQTLs. We found that the methylation of the memo-eQTL CpG sites can either enhance or insulate the interaction between SNP and Gene expression by altering CTCF-based chromatin 3D structure. This study demonstrated the prevalence of memo-eQTLs, which can enable the identification of novel causal genes for traits or diseases associated with genetic variations.

Characterization of ENZ-resistant cell lines

Clinical characteristics of prostate cancer patients with matched diagnostic (archival) castration-sensitive and metastatic castration-resistant tissue biopsies

Results from CRISPR/Cas9 knockout screen in SU-DHL-4 cells.

Purpose:The efficacy of EZH2 inhibition has been modest in the initial clinical exploration of diffuse large B-cell lymphoma (DLBCL), yet EZH2 inhibitors are well tolerated. Herein, we aimed to uncover genetic and pharmacologic opportunities to enhance the clinical efficacy of EZH2 inhibitors in DLBCL.Experimental Design:We conducted a genome-wide sensitizing CRISPR/Cas9 screen with tazemetostat, a catalytic inhibitor of EZH2. The sensitizing effect of IKZF1 loss of function was then validated and leveraged for combination treatment with lenalidomide. RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing analyses were performed to elucidate transcriptomic and epigenetic changes underlying synergy.Results:We identified IKZF1 knockout as the top candidate for sensitizing DLBCL cells to tazemetostat. Treating cells with tazemetostat and lenalidomide, an immunomodulatory drug that selectively degrades IKAROS and AIOLOS, phenocopied the effects of the CRISPR/Cas9 screen. The combined drug treatment triggered either cell-cycle arrest or apoptosis in a broad range of DLBCL cell lines, regardless of EZH2 mutational status. Cell-line–based xenografts also showed slower tumor growth and prolonged survival in the combination treatment group. RNA-seq analysis revealed strong upregulation of interferon signaling and antiviral immune response signatures. Gene expression of key immune response factors such as IRF7 and DDX58 were induced in cells treated with lenalidomide and tazemetostat, with a concomitant increase of H3K27 acetylation at their promoters. Furthermore, transcriptome analysis demonstrated derepression of endogenous retroviruses after combination treatment.Conclusions:Our data underscore the synergistic interplay between IKAROS degradation and EZH2 inhibition on modulating epigenetic changes and ultimately enhancing antitumor effects in DLBCL.

Supplementary Data

Purpose:Although enzalutamide (ENZ) has been widely used to treat de novo or castration-resistant metastatic prostate cancer, resistance develops and disease progression is ultimately inevitable. There are currently no approved targeted drugs to specifically delay or overcome ENZ resistance.Experimental Design:We selected several ENZ-resistant cell lines that replicated clinical characteristics of the majority of patients with ENZ-resistant disease. A high-throughput pharmacologic screen was utilized to identify compounds with greater cytotoxic effect for ENZ-resistant cell lines, compared with parental ENZ-sensitive cells. We validated the potential hits in vitro and in vivo, and used knockdown and overexpression assays to study the dependencies in ENZ-resistant prostate cancer.Results:ABT199 (BCL-2 inhibitor) and IMD0354 (IKKB inhibitor) were identified as potent and selective inhibitors of cell viability in ENZ-resistant cell lines in vitro and in vivo which were further validated using loss-of-function assays of BCL-2 and IKKB. Notably, we observed that overexpression of BCL-2 and IKKB in ENZ-sensitive cell lines was sufficient for the emergence of ENZ resistance. In addition, we confirmed that BCL-2 or IKKB inhibitors suppressed the development of ENZ resistance in xenografts. However, validation of both BCL-2 and IKKB in matched castration-sensitive/resistant clinical samples showed that, concurrent with the development of ENZ/abiraterone resistance in patients, only the protein levels of IKKB were increased.Conclusions:Our findings identify BCL-2 and IKKB dependencies in clinically relevant ENZ-resistant prostate cancer cells in vitro and in vivo, but indicate that IKKB upregulation appears to have greater relevance to the progression of human castrate-resistant prostate cancer.

List of antibodies used for Western Blot analyses

Compound full list of two libraries

List of primers used for qPCR analyses

Suppl Figure 2. AR binds to PLZF locus and regulates its gene expression

Suppl Figure 1. AR cistrome analysis identifies androgen-activated genes

Supplementary Table 3. KEGG analysis of PLZF-repressed program

Suppl Figure 3. The impact of PLZF alternations on cell growth

Supplementary Information

MYC is a well characterized oncogenic transcription factor in prostate cancer, and CTCF is the main architectural protein of three-dimensional genome organization. However, the functional link between the two master regulators has not been reported. In this study, we find that MYC rewires prostate cancer chromatin architecture by interacting with CTCF protein. Through combining the H3K27ac, AR and CTCF HiChIP profiles with CRISPR deletion of a CTCF site upstream of MYC gene, we show that MYC activation leads to profound changes of CTCF-mediated chromatin looping. Mechanistically, MYC colocalizes with CTCF at a subset of genomic sites, and enhances CTCF occupancy at these loci. Consequently, the CTCF-mediated chromatin looping is potentiated by MYC activation, resulting in the disruption of enhancer-promoter looping at neuroendocrine lineage plasticity genes. Collectively, our findings define the function of MYC as a CTCF co-factor in three-dimensional genome organization.

Supplementary Table 2. PLZF Cistrome analysis

Suppl Figure 4. To evaluate the inhibitory effect of MAPK inhibitors on of PLZF depleted LNCaP cells

Supplementary Table 1. PLZF-regulated transcriptome

Summarycell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) has emerged as a promising non-invasive technology to detect cancers and monitor treatments. Several bioinformatics tools are available for cfMeDIP-seq data analysis. However, an easy to implement and flexible pipeline, particularly, for large-scale cfMeDIP-seq profiling, is still lacking. Here we present the MEDIPIPE, which provides a one-stop solution for cfMeDIP-seq data quality control, methylation quantification and sample aggregation. The major advantages of MEDIPIPE are: 1) it is easy to implement and reproduce with automatically deployed execution environments; 2) it can handle different experimental settings with a single input configuration file; 3) it is computationally efficient for large-scale cfMeDIP-seq profiling data analysis and aggregation.Availability and implementationThis pipeline is an open-source software under the MIT license and it is freely available athttps://github.com/yzeng-lol/MEDIPIPE.Contactyzeng@uhnresearch.caortrevor.pugh@utoronto.caorhansenhe@uhnresearch.caSupplementary informationSupplementary data are appended.

Genomic loss of RB1 is a common alteration in castration-resistant prostate cancer (CRPC) and is associated with poor patient outcomes. RB1 loss is also a critical event that promotes the neuroendocrine transdifferentiation of prostate cancer (PCa) induced by the androgen receptor (AR) signaling inhibition (ARSi). The loss of Rb protein disrupts the Rb-E2F repressor complex and thus hyperactivates E2F transcription activators. While the impact of Rb inactivation on PCa progression and linage plasticity has been previously studied, there is a pressing need to fully understand underlying mechanisms and identify vulnerabilities that can be therapeutically targeted in Rb-deficient CRPC. Using an integrated cistromic and transcriptomic analysis, we have characterized Rb activities in multiple CRPC models by identifying Rb-directly regulated genes and revealed that Rb has distinct binding sites and targets in CRPC with different genomic backgrounds. Significantly, we show that E2F1 chromatin binding and transcription activity in Rb-deficient CRPC are highly dependent on LSD1/KDM1A, and that Rb inactivation sensitizes CRPC tumor to the LSD1 inhibitor treatment. These results provide new molecular insights into Rb activity in PCa progression and suggest that targeting LSD1 activity with small molecule inhibitors may be a potential treatment strategy to treat Rb-deficient CRPC.

The introduction of high-throughput sequencing technologies has allowed for comprehensive RNA species detection, both coding and non-coding, which opened new avenues for the discovery of predictive and prognostic biomarkers. However the consistency of the detection of different RNA species depends on the RNA selection protocol used for RNA-sequencing. While preliminary reports indicated that non-coding RNAs, in particular circular RNAs, constitute a rich source of biomarkers predictive of drug response, the reproducibility of this novel class of biomarkers has not been rigorously investigated. To address this issue, we assessed the inter- lab consistency of circular RNA expression in cell lines profiled in large pharmacogenomic datasets. We found that circular RNA expression quantified from rRNA-depleted RNA-seq data is stable and yields robust prognostic markers in cancer. On the other hand, quantification of the expression of circular RNA from poly(A)-selected RNA-seq data yields highly inconsistent results, calling into question results from previous studies reporting their potential as predictive biomarkers in cancer. We have also identified median expression of transcripts and transcript length as potential factors influencing the consistency of RNA detection. Our study provides a framework to quantitatively assess the stability of coding and non-coding RNA expression through the analysis of biological replicates within and across independent studies.

Ribosome biogenesis plays a pivotal role in tumorigenesis by supporting robust protein translation. We investigate the functional and molecular mechanism of Zinc finger protein 545 (ZNF545), a transcriptional repressor for ribosomal RNA (rRNA), in colorectal cancer (CRC). ZNF545 was silenced in CRC compared to adjacent normal tissues (P Znf545knockout in mice accelerated CRC inApcMin/+and azoxymethane/dextran sulfate sodium-induced CRC. Mechanistically, we demonstrated that ZNF545 uses its two zinc finger clusters to bind to minimal rDNA promoter, where it assembled transcriptional repressor complex by interacting with KAP1.Znf545deletion in mouse embryonic fibroblasts not only increased rRNA transcription rate and the nucleolar size and number but also altered the nucleolar composition and architecture with an increased number of fibrillar centers surrounded by net-like dense fibrillar components. Consequently,Znf545deletion promoted the gene expression of translation machinery, protein translation, and cell growth. Consistent with its tumor-suppressive role, ZNF545 overexpression in CRC cells induced growth arrest and apoptosis. Finally, administration of rRNA synthesis inhibitor, CX-5461, inhibited CRC development inZnf545Δ/ΔApcMin/+mice. In conclusion, ZNF545 suppresses CRC through repressing rRNA transcription and protein translation. Targeting rRNA biosynthesis in ZNF545-silenced tumors is a potential therapeutic strategy for CRC.

Cancer stem cells (CSCs) are responsible for tumor progression, recurrence, and drug resistance. To identify genetic vulnerabilities of colon cancer, we performed targeted CRISPR dropout screens comprising 657 Drugbank targets and 317 epigenetic regulators on two patient-derived colon CSC-enriched spheroids. Next-generation sequencing of pooled genomic DNAs isolated from surviving cells yielded therapeutic candidates. We unraveled 44 essential genes for colon CSC-enriched spheroids propagation, including key cholesterol biosynthetic genes (HMGCR, FDPS, and GGPS1). Cholesterol biosynthesis was induced in colon cancer tissues, especially CSC-enriched spheroids. The genetic and pharmacological inhibition of HMGCR/FDPS impaired self-renewal capacity and tumorigenic potential of the spheroid models in vitro and in vivo. Mechanistically, HMGCR or FDPS depletion impaired cancer stemness characteristics by activating TGF-β signaling, which in turn downregulated expression of inhibitors of differentiation (ID) proteins, key regulators of cancer stemness. Cholesterol and geranylgeranyl diphosphate (GGPP) rescued the growth inhibitory and signaling effect of HMGCR/FDPS blockade, implying a direct role of these metabolites in modulating stemness. Finally, cholesterol biosynthesis inhibitors and 5-FU demonstrated antitumor synergy in colon CSC-enriched spheroids, tumor organoids, and xenografts. Taken together, our study unravels novel genetic vulnerabilities of colon CSC-enriched spheroids and suggests cholesterol biosynthesis as a potential target in conjunction with traditional chemotherapy for colon cancer treatment.

Cancers adapt to increasingly potent targeted therapies by reprogramming their phenotype. Here we investigated such a phenomenon in prostate cancer, in which tumours can escape epithelial lineage confinement and transition to a high-plasticity state as an adaptive response to potent androgen receptor (AR) antagonism. We found that AR activity can be maintained as tumours adopt alternative lineage identities, with changes in chromatin architecture guiding AR transcriptional rerouting. The epigenetic regulator enhancer of zeste homologue 2 (EZH2) co-occupies the reprogrammed AR cistrome to transcriptionally modulate stem cell and neuronal gene networks-granting privileges associated with both fates. This function of EZH2 was associated with T350 phosphorylation and establishment of a non-canonical polycomb subcomplex. Our study provides mechanistic insights into the plasticity of the lineage-infidelity state governed by AR reprogramming that enabled us to redirect cell fate by modulating EZH2 and AR, highlighting the clinical potential of reversing resistance phenotypes.

Mutations in SPOP E3 ligase gene are reportedly associated with genome-wide DNA hypermethylation in prostate cancer (PCa) although the underlying mechanisms remain elusive. Here, we demonstrate that SPOP binds and promotes polyubiquitination and degradation of histone methyltransferase and DNMT interactor GLP. SPOP mutation induces stabilization of GLP and its partner protein G9a and aberrant upregulation of global DNA hypermethylation in cultured PCa cells and primary PCa specimens. Genome-wide DNA methylome analysis shows that a subset of tumor suppressor genes (TSGs) including FOXO3, GATA5, and NDRG1, are hypermethylated and downregulated in SPOP-mutated PCa cells. DNA methylation inhibitor 5-azacytidine effectively reverses expression of the TSGs examined, inhibits SPOP-mutated PCa cell growth in vitro and in mice, and enhances docetaxel anti-cancer efficacy. Our findings reveal the GLP/G9a-DNMT module as a mediator of DNA hypermethylation in SPOP-mutated PCa. They suggest that SPOP mutation could be a biomarker for effective treatment of PCa with DNA methylation inhibitor alone or in combination with taxane chemotherapeutics., The molecular mechanism underlying the DNA hypermethylation phenotype observed in the SPOP-mutant prostate cancers is unclear. Here, the authors show that mutant SPOP induces global aberrant DNA methylation patterns through GLP/G9a and renders prostate cancer cells susceptible to DNA demethylating agents.

BACKGROUND AND AIMS Several studies have shown that expression of hepatic fibroblast growth factor 21 (FGF21) can be stimulated by glucagon-like peptide 1 (GLP-1)-based diabetes drugs. As GLP-1 receptor (GLP-1R) is unlikely to be expressed in hepatocytes, we aimed to compare such stimulation in mice and in mouse hepatocytes, determine the involvement of GLP-1R, and clarify whether FGF21 mediates certain functions of the GLP-1R agonist liraglutide. APPROACH AND RESULTS Liver FGF21 expression was assessed in mice receiving a daily liraglutide injection for 3 days or in mouse primary hepatocytes (MPHs) undergoing direct liraglutide treatment. The effects of liraglutide on metabolic improvement and FGF21 expression were then assessed in high-fat diet (HFD)-fed mice and compared with the effects of the dipeptidyl-peptidase 4 inhibitor sitagliptin. Animal studies were also performed in Glp1r-/- mice and liver-specific FGF21-knockout (lFgf21-KO) mice. In wild-type mouse liver that underwent RNA sequencing and quantitative reverse-transcription PCR, we observed liraglutide-stimulated hepatic Fgf21 expression and a lack of Glp1r expression. In MPHs, liraglutide did not stimulate Fgf21. In mice with HFD-induced obesity, liraglutide or sitagliptin treatment reduced plasma triglyceride levels, whereas their effect on reducing body-weight gain was different. Importantly, increased hepatic FGF21 expression was observed in liraglutide-treated mice but was not observed in sitagliptin-treated mice. In HFD-fed Glp1r-/- mice, liraglutide showed no beneficial effects and could not stimulate Fgf21 expression. In lFgf21-KO mice undergoing dietary challenge, the body-weight-gain attenuation and lipid homeostatic effects of liraglutide were lost or significantly reduced. CONCLUSIONS We suggest that liraglutide-stimulated hepatic Fgf21 expression may require GLP-1R to be expressed in extrahepatic organs. Importantly, we revealed that hepatic FGF21 is required for liraglutide to lower body weight and improve hepatic lipid homeostasis. These observations advanced our mechanistic understanding of the function of GLP-1-based drugs in NAFLD.

Metastatic prostate cancer remains a major clinical challenge and metastatic lesions are highly heterogeneous and difficult to biopsy. Liquid biopsy provides opportunities to gain insights into the underlying biology. Here, using the highly sensitive enrichment-based sequencing technology, we provide analysis of 60 and 175 plasma DNA methylomes from patients with localized and metastatic prostate cancer, respectively. We show that the cell-free DNA methylome can capture variations beyond the tumor. A global hypermethylation in metastatic samples is observed, coupled with hypomethylation in the pericentromeric regions. Hypermethylation at the promoter of a glucocorticoid receptor geneNR3C1is associated with a decreased immune signature. The cell-free DNA methylome is reflective of clinical outcomes and can distinguish different disease types with 0.989 prediction accuracy. Finally, we show the ability of predicting copy number alterations from the data, providing opportunities for joint genetic and epigenetic analysis on limited biological samples.

Androgen receptor (AR) messenger RNA (mRNA) alternative splicing variants (AR-Vs) are implicated in castration-resistant progression of prostate cancer (PCa), although the molecular mechanism underlying the genesis of AR-Vs remains poorly understood. The CDK12 gene is often deleted or mutated in PCa and CDK12 deficiency is known to cause homologous recombination repair gene alteration or BRCAness via alternative polyadenylation (APA). Here, we demonstrate that pharmacological inhibition or genetic inactivation of CDK12 induces AR gene intronic (intron 3) polyadenylation (IPA) usage, AR-V expression, and PCa cell resistance to the antiandrogen enzalutamide (ENZ). We further show that AR binds to the CCNK gene promoter and up-regulates CYCLIN K expression. In contrast, ENZ decreases AR occupancy at the CCNK gene promoter and suppresses CYCLIN K expression. Similar to the effect of the CDK12 inhibitor, CYCLIN K degrader or ENZ treatment promotes AR gene IPA usage, AR-V expression, and ENZ-resistant growth of PCa cells. Importantly, we show that targeting BRCAness induced by CYCLIN K down-regulation with the PARP inhibitor overcomes ENZ resistance. Our findings identify CYCLIN K down-regulation as a key driver of IPA usage, hormonal therapy–induced AR-V expression, and castration resistance in PCa. These results suggest that hormonal therapy–induced AR-V expression and therapy resistance are vulnerable to PARP inhibitor treatment.

Acute myeloid leukemia (AML) remains a devastating disease in need of new therapies to improve patient survival. Targeted adoptive T-cell therapies have achieved impressive clinical outcomes in some B-cell leukemias and lymphomas but not in AML. Double-negative T cells (DNTs) effectively kill blast cells from the majority of AML patients and are now being tested in clinical trials. However, AML blasts obtained from ∼30% of patients show resistance to DNT-mediated cytotoxicity; the markers or mechanisms underlying this resistance have not been elucidated. Here, we used a targeted clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) screen to identify genes that cause susceptibility of AML cells to DNT therapy. Inactivation of the Spt-Ada-Gcn5-acetyltransferase (SAGA) deubiquitinating complex components sensitized AML cells to DNT-mediated cytotoxicity. In contrast, CD64 inactivation resulted in resistance to DNT-mediated cytotoxicity. Importantly, the level of CD64 expression correlated strongly with the sensitivity of AML cells to DNT treatment. Furthermore, the ectopic expression of CD64 overcame AML resistance to DNTs in vitro and in vivo. Altogether, our data demonstrate the utility of CRISPR/Cas9 screens to uncover mechanisms underlying the sensitivity to DNT therapy and suggest CD64 as a predictive marker for response in AML patients.

Prostate cancers are considered to be immunologically ‘cold’ tumors given the very few patients who respond to checkpoint inhibitor (CPI) therapy. Recently, enrichment of interferon-stimulated genes (ISGs) predicted a favorable response to CPI across various disease sites. The enhancer of zeste homolog-2 (EZH2) is overexpressed in prostate cancer and known to negatively regulate ISGs. In the present study, we demonstrate that EZH2 inhibition in prostate cancer models activates a double-stranded RNA–STING–ISG stress response upregulating genes involved in antigen presentation, Th1 chemokine signaling and interferon response, including programmed cell death protein 1 (PD-L1) that is dependent on STING activation. EZH2 inhibition substantially increased intratumoral trafficking of activated CD8(+) T cells and increased M1 tumor-associated macrophages, overall reversing resistance to PD-1 CPI. Our study identifies EZH2 as a potent inhibitor of antitumor immunity and responsiveness to CPI. These data suggest EZH2 inhibition as a therapeutic direction to enhance prostate cancer response to PD-1 CPI.

Purpose: Although enzalutamide (ENZ) has been widely used to treat de novo or castration-resistant metastatic prostate cancer, resistance develops and disease progression is ultimately inevitable. There are currently no approved targeted drugs to specifically delay or overcome ENZ resistance. Experimental Design: We selected several ENZ-resistant cell lines that replicated clinical characteristics of the majority of patients with ENZ-resistant disease. A high-throughput pharmacologic screen was utilized to identify compounds with greater cytotoxic effect for ENZ-resistant cell lines, compared with parental ENZ-sensitive cells. We validated the potential hits in vitro and in vivo, and used knockdown and overexpression assays to study the dependencies in ENZ-resistant prostate cancer. Results: ABT199 (BCL-2 inhibitor) and IMD0354 (IKKB inhibitor) were identified as potent and selective inhibitors of cell viability in ENZ-resistant cell lines in vitro and in vivo which were further validated using loss-of-function assays of BCL-2 and IKKB. Notably, we observed that overexpression of BCL-2 and IKKB in ENZ-sensitive cell lines was sufficient for the emergence of ENZ resistance. In addition, we confirmed that BCL-2 or IKKB inhibitors suppressed the development of ENZ resistance in xenografts. However, validation of both BCL-2 and IKKB in matched castration-sensitive/resistant clinical samples showed that, concurrent with the development of ENZ/abiraterone resistance in patients, only the protein levels of IKKB were increased. Conclusions: Our findings identify BCL-2 and IKKB dependencies in clinically relevant ENZ-resistant prostate cancer cells in vitro and in vivo, but indicate that IKKB upregulation appears to have greater relevance to the progression of human castrate-resistant prostate cancer.

Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of non-Hodgkin lymphoma and represents a highly heterogeneous and aggressive disease. Up to 40% of all DLBCL patients experience treatment failure after the standard immunochemotherapy R-CHOP. Defining novel therapeutic strategies is therefore a pressing need. Reduced acetylation at histone 3 lysine 27 (H3K27ac) represents a pathogenetic hallmark of DLBCL and selective histone deacetylase 3 inhibition (HDAC3i) has recently emerged as a viable strategy to reverse abnormal epigenetic signatures and induce strong anti-tumor effects by increasing H3K27ac. Despite this compelling rationale, the overall response remains suboptimal, suggesting unrecognized mechanisms of resistance. To unbiasedly uncover sensitizers, we performed a genome-wide CRISPR screen and identified knockout (KO) of the top candidate GNAS (encoding G-protein α subunit, Gαs) for sensitizing resistant DLBCL cells to HDAC3i. The sensitizing effects on reduced viable cell number were only observed in GNAS KO cells treated with HDAC3i, but not in the control cells (“synthetic lethality”). We have validated this sensitizing phenotype in multiple resistant cell lines including three human DLBCL cell lines and one mouse B-cell lymphoma cell line. Interestingly, we showed that the sensitization was not related to the canonical G-protein functions but to novel regulatory mechanisms in viral mimicry activation and chromatin modification. Compared with the control conditions, the interaction between GNAS KO and HDAC3i has been linked with differential chromatin accessibility and endogenous retrovirus expression, upregulated double-stranded RNA expression, and increased phosphorylation of TBK1 whose activation plays a vital role in antiviral immune responses. Strikingly, a selective TBK1 degrader completely and specifically rescued the sensitizing phenotype in GNAS KO cells treated with HDAC3i, confirming the critical role of TBK1 in inducing sensitization. Furthermore, we identified potential immune interactions by exploring the clinical data from tumor samples of 309 DLBCL patients that low GNAS expression was correlated with cytokine and inflammatory signaling as well as stromal cell interactions in the tumor microenvironment, altogether associated with longer overall survival. These observations were aligned with our results in the mouse xenograft and allograft tumor experiments that GNAS KO with/without HDAC3i led to differential phenotypes. Overall, our research uncovers novel immunomodulating activities for potentiating the efficacy of epigenetic agents in non-Hodgkin lymphoma. This expands our understanding of novel interactions between immune and epigenetic regulation in lymphoma biology and provides new therapeutic opportunities for patients with resistant lymphoma who have poor prognoses and limited treatment options. Citation Format: Michael Y. He, Kit I. Tong, Mehran Bakhtiari, Ryder Whittaker Hawkins, Ting Liu, Yong Zeng, Noorhan Ghanem, Housheng Hansen He, Robert Kridel. Characterizing novel immunomodulating interactions for potentiating HDAC3 inhibition in non-Hodgkin lymphoma [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 1757.

Lysine-specific demethylase (LSD1) was initially identified as a transcriptional repressor through demethylation of mono/di-methylated histone 3 lysine 4 (H3K4me1/2). Subsequent work suggests that LSD1 may trigger gene activation via demethylating H3K9me1/2 in the context of steroid receptors. Our previous studies have confirmed that LSD1 functions broadly as a coactivator of androgen receptor (AR)-regulated enhancers but retains its H3K4 demethylation function at these sites. Importantly, our recent work revealed that LSD1 regulates the accessibility of active enhancers through the interaction with FOXA1, which functions as a pioneer transcription factor by facilitating AR access to chromatin LSD1 inhibition disrupts the global binding of FOXA1 by blocking the demethylation of K270 of FOXA1, leading to inhibition of AR binding and transcriptional activity. However, in addition to AR signaling, it remains largely unknown whether LSD1 regulates other critical oncogenic programs during prostate cancer (PCa) progression. In this study, we aimed to fully understand the functional targets of LSD1 in castration-resistant PCa (CRPC) models. We performed a large transcriptomic profiling of CRPC patient-derived xenograft (PDX) models that are sensitive to LSD1 inhibitors. Our analyses indicated that LSD1 inhibition targeted multiples oncogenic programs, including previously known pathways such as AR, FOXA1, and E2F, and a previously undefined pathway, MYC signaling. Through single-cell RNA-seq analysis in a CRPC PDX model, we confirmed that MYC signaling was decreased in the responsive tumor cells and identified a previously unknown molecular subtype, AR+/FOXA1+/LSD1low/RB1−, which was resistant to LSD1 inhibition. It is well known that MYC is driven by super-enhancers (SEs), which are regulated by BRD4 (bromodomain and extraterminal (BET) protein). We further evaluated LSD1, FOXA1 and BRD4 ChIP-seq and defined SEs by using H3K27ac ChIP-seq followed by ROSE analysis. We found that LSD1, FOXA1, and BRD4 co-occupied at MYC SEs and BRD4 was recruited by unmethylated FOXA1 but not K270-methylated FOXA1. In addition, we observed the puncta-like formation of LSD1/BRD4 marked nuclear condensates under confocal immunofluorescence microscopy. By examining the public datasets of H3K27ac ChIP-seq of samples with different stages of PCa development, we identified a subset of SEs which were distinctly activated in CRPC. Using multiple CRPC PDXs, we revealed that combining LSD1 inhibitors with BET inhibitors exhibited strong synergy possibly via disrupting the CRPC-specific SEs. In summary, this study reveals a novel oncogenic function of LSD1 in driving PCa progression by activating SE-driven oncogenic programs, such as MYC signaling. These results provide a strong therapeutic potential of combining inhibitors of LSD1 and BRD4 in treating CRPC. Citation Format: Mingyu Liu, Muqing Li, Dong Han, Zifeng Wang, Wanting Han, Housheng Hansen He, Shuai Gao, Changmeng Cai. LSD1 activates oncogenic super-enhancers in castration-resistant prostate cancer by forming nuclear condensates with BRD4. [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 4729.

Background: While castration-resistant PCa (CRPC) can be further treated with second-generation androgen deprivation therapies (ADTs), the tumor can quickly generate resistance through multiple mechanisms. One critical mechanism is that tumor cells can progress to AR-indifferent stem cell-like (SCL-PCa or SCLPC) or neuroendocrine-like CRPC (NE-PCa or NEPC) through lineage plasticity. However, the underlying molecular basis remains to be determined, and clinical treatment options for these aggressive CRPC subtypes are currently limited. FOXA1 and FOXA2, which are members of the FOXA (Forkhead Box A) protein family, are pioneer transcription factors. While FOXA1 is well known for its function as a critical pioneer factor of AR and pivotal for maintaining AR signaling, the molecular function of FOXA2 in PCa cells is poorly understood despite that FOXA2 is known to be overexpressed in NEPC. Moreover, since FOXA2, like FOXA1, is currently undruggable in the clinic, there is an urgent need to decipher the molecular basis for the chromatin binding of FOXA2 and identify druggable targets that regulate FOXA2 binding and activity in the aggressive FOXA2-positive CRPC. Methods: In the current study, we first examined the role of FOXA2 in tumorigenesis and metastasis by using various in vitro and in vivo assays including mouse subcutaneous injection and zebrafish embryo injection approaches. We then conducted integrated whole genomic transcriptome and cistrome analyses in SCLPC and NEPC cell line models to characterize the activity of FOXA2 on chromatin and to identify its collaborating transcription factors that may play specific functions in promoting SCLPC or NEPC using a series of biochemical and bioinformatic approaches. Results: We found that FOXA2 silencing decreased the growth and metastasis of SCLPC and NEPC cells. Importantly, we discovered that FOXA2 chromatin binding is tightly associated with binding of JUN family proteins (primarily c-Jun) and FOXA2 silencing dramatically interrupted the global chromatin binding of c-Jun and FOSL1. The transcription targets of FOXA2/AP-1 are highly enriched for neuroendocrine and plasticity associated genes and associated with poor clinical outcomes. Furthermore, we also found that FOXA2 chromatin binding is globally enhanced by an epigenetic factor LSD1, and LSD1 inhibition can repress FOXA2/AP-1 activity in multiple CRPC models. Conclusion: Overall, our data indicate that FOXA2 functions to maintain tumor growth and metastasis in SCLPC and NEPC models. Mechanistically, FOXA2 can act as a pioneer factor of AP-1 (c-Jun/FOSL1) and reprogram AP-1 transcription activity. This FOXA2/AP-1 axis is regulated by LSD1 via demethylating FOXA2 protein and LSD1 inhibition represses FOXA2-dependent CRPC tumor progression. These findings provide novel mechanistic insights into the molecular mechanisms for PCa lineage plasticity and treatment resistance. Citation Format: Zifeng Wang, Mingyu Liu, Songqi Zhang, Muqing Li, Susan Patalano, Jill A. Macoska, Dong Han, Shuai Gao, Hansen He, Changmeng Cai. LSD1 &8211mediated FOXA2/AP1 transcription program drives lineage plasticity in prostate cancer. [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 4753.

Establishing causal links between inherited polymorphisms and cancer risk is challenging. Here, we focus on the single nucleotide polymorphism rs55705857 (A>G), which confers a 6-fold increased risk of IDH-mutant low-grade glioma (LGG) and is amongst the highest genetic associations with cancer. By fine-mapping the locus, we reveal that rs55705857 itself is the causal variant and is associated with molecular pathways that drive LGG. Mechanistically, we show that rs55705857 resides within a brain-specific enhancer, where the risk allele disrupts OCT2/4 binding, allowing increased interaction with the Myc promoter and increased Myc expression. To functionally test rs55705857, we generated an IDH1R132H-driven LGG mouse model and show that mutating the highly conserved, orthologous mouse rs55705857 locus dramatically accelerated tumor development from 463 to 172 days and increased penetrance from 30% to 75%. Overall, our work generates new LGG models and reveals mechanisms of the heritable predisposition to lethal glioma in ∼40% of LGG-patients.

Prostate cancer is the most commonly diagnosed non-cutaneous cancers in North American men. While androgen deprivation has remained as the cornerstone of prostate cancer treatment, resistance ensues leading to lethal disease. Forkhead box A1 (FOXA1) encodes a pioneer factor that induces open chromatin conformation to allow the binding of other transcription factors. Through direct interactions with the Androgen Receptor (AR), FOXA1 helps to shape AR signaling that drives the growth and survival of normal prostate and prostate cancer cells. FOXA1 also possesses an AR-independent role of regulating epithelial-to-mesenchymal transition (EMT). In prostate cancer, mutations converge onto the coding sequence and cis-regulatory elements (CREs) of FOXA1, leading to functional alterations. In addition, FOXA1 activity in prostate cancer can be modulated post-translationally through various mechanisms such as LSD1-mediated protein demethylation. In this review, we describe the latest discoveries related to the function and regulation of FOXA1 in prostate cancer, pointing to their relevance to guide future clinical interventions.

RAS-MAPK signaling mediates processes critical to normal development including cell proliferation, survival, and differentiation. Germline mutation of RAS-MAPK genes lead to the Noonan-spectrum of syndromes. Here, we present a patient affected by a 6p-interstitial microdeletion with unknown underlying molecular etiology. Examination of 6p-interstitial microdeletion cases reveals shared clinical features consistent with Noonan-spectrum disorders including short stature, facial dysmorphia and cardiovascular abnormalities. We find the RAS-responsive element binding protein-1 (RREB1) is the common deleted gene in multiple 6p-interstitial microdeletion cases. Rreb1 hemizygous mice display orbital hypertelorism and cardiac hypertrophy phenocopying the human syndrome. Rreb1 haploinsufficiency leads to sensitization of MAPK signaling. Rreb1 recruits Sin3a and Kdm1a to control H3K4 methylation at MAPK pathway gene promoters. Haploinsufficiency of SIN3A and mutations in KDM1A cause syndromes similar to RREB1 haploinsufficiency suggesting genetic perturbation of the RREB1-SIN3A-KDM1A complex represents a new category of RASopathy-like syndromes arising through epigenetic reprogramming of MAPK pathway genes., Mutations in RAS-MAPK pathway genes are implicated in Noonan-spectrum, yet up to 20% of cases have unknown cause. Here, the authors identify RREB1 underlying a 6p microdeletion RASopathy-like syndrome and show that RREB1, SIN3A and KDM1A form a transcriptional repressive complex to control methylation of MAPK pathway genes.

FOXA1 functions as a pioneer transcription factor by facilitating the access to chromatin for steroid hormone receptors, such as androgen receptor and estrogen receptor1-4, but mechanisms regulating its binding to chromatin remain elusive. LSD1 (KDM1A) acts as a transcriptional repressor by demethylating mono/dimethylated histone H3 lysine 4 (H3K4me1/2)5,6, but also acts as a steroid hormone receptor coactivator through mechanisms that are unclear. Here we show, in prostate cancer cells, that LSD1 associates with FOXA1 and active enhancer markers, and that LSD1 inhibition globally disrupts FOXA1 chromatin binding. Mechanistically, we demonstrate that LSD1 positively regulates FOXA1 binding by demethylating lysine 270, adjacent to the wing2 region of the FOXA1 DNA-binding domain. Acting through FOXA1, LSD1 inhibition broadly disrupted androgen-receptor binding and its transcriptional output, and dramatically decreased prostate cancer growth alone and in synergy with androgen-receptor antagonist treatment in vivo. These mechanistic insights suggest new therapeutic strategies in steroid-driven cancers.