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Supplementary Figures S1 to S13 Supplementary Figure S1: Summary of clinical samples analyzed for BRD4 protein expression and SPOP mutational status The clinical samples used in this study were from a population of metastatic castration resistant prostate cancer (mCRPC) patients treated at The Royal Marsden Hospital. Patients with sufficient formalin fixed paraffin embedded (FFPE) tissue from diagnostic (archival) hormone sensitive prostate cancer (HSPC) biopsies (n=53) and same patient, matched, CRPC biopsies (n=38) were analyzed for nuclear BRD4 expression by immunohistochemistry (dark grey shading). Clinical correlations were determined as shown (yellow shading). Twenty-seven (of 53) diagnostic (archival) HSPC biopsies and 12 (of 38) mCRPC biopsies had next generation sequencing (NGS) available to determine SPOP mutational analysis (light grey shading). Supplementary Figure S2: BRD4 immunohistochemistry validation Immunohistochemistry (A), immunofluorescence (B) and western blot (C) analysis of BRD4 protein expression in LNCaP95 cells transfected with overexpression plasmid, control siRNA or BRD4 siRNA for 72 hours (magnification 200x; scale bar 50 µm). Supplementary Figure S3: BRD4 protein expression in SPOP mutant prostate cancer Expression (H-score) of nuclear BRD4 expression in 27 (of 53) HSPC and 12 (of 38) CRPC biopsies with next generation sequencing available to determine SPOP mutational analysis. Median H-score and interquartile range is shown. Supplementary Figure S4: AR-V7 and BRD4 protein expression in prostate cancer cell lines AR-FL, AR-V7, C-MYC, BRD4 and GAPDH protein expression determined by western blot analysis of prostate cancer cell lines. Supplementary Figure S5: JQ1 treatment downregulates AR-V7 protein expression in androgen dependent and independent prostate cancer cell lines LNCaP95 (A), VCaP (B) and 22Rv1 (C) were treated with vehicle (DMSO 0.1%) or various concentrations of JQ1 (0.1 µM, 0.5 µM, 1.0 µM, 2.5 µM and 5.0 µM) for 48 hours. The effect of JQ1 treatment on AR-FL, AR-V7 and C-MYC protein expression was determined. Single representative western blot shown from three separate experiments. Supplementary Figure S6: I-BET151 treatment effects on BET family protein expression LNCaP95 (A), VCaP (B) and 22Rv1 (C) were treated with vehicle (DMSO 0.1%) or various concentrations of I-BET151 (0 µM, 0.1µM, 0.5µM, 1.0 µM, 2.5 µM and 5.0 µM) for 48 hours. The effect of I-BET151 treatment on BRD2, BRD3 and BRD4 RNA expression was determined. Mean RNA expression (normalized to B2M and vehicle; defined as 1.0) with standard deviation from three individual experiments is shown (unless otherwise stated). p-values (*p=

Triple-negative breast cancers (TNBC) are resistant to standard-of-care chemotherapy and lack known targetable driver gene alterations. Identification of novel drivers could aid the discovery of new treatment strategies for this hard-to-treat patient population, yet studies using high-throughput and accurate models to define the functions of driver genes in TNBC to date have been limited. Here, we employed unbiased functional genomics screening of the 200 most frequently mutated genes in breast cancer, using spheroid cultures to model in vivo–like conditions, and identified the histone acetyltransferase CREBBP as a novel tumor suppressor in TNBC. CREBBP protein expression in patient tumor samples was absent in 8% of TNBCs and at a high frequency in other tumors, including squamous lung cancer, where CREBBP-inactivating mutations are common. In TNBC, CREBBP alterations were associated with higher genomic heterogeneity and poorer patient survival and resulted in upregulation and dependency on a FOXM1 proliferative program. Targeting FOXM1-driven proliferation indirectly with clinical CDK4/6 inhibitors (CDK4/6i) selectively impaired growth in spheroids, cell line xenografts, and patient-derived models from multiple tumor types with CREBBP mutations or loss of protein expression. In conclusion, we have identified CREBBP as a novel driver in aggressive TNBC and identified an associated genetic vulnerability in tumor cells with alterations in CREBBP and provide a preclinical rationale for assessing CREBBP alterations as a biomarker of CDK4/6i response in a new patient population.Significance:This study demonstrates that CREBBP genomic alterations drive aggressive TNBC, lung cancer, and lymphomas and may be selectively treated with clinical CDK4/6 inhibitors.

Supplementary Methods

Enrichment analysis from TCGA RNA-seq and RPPA data comparing CREBBPaltered versus wild-type patients.

Purpose: Persistent androgen receptor (AR) signaling drives castration-resistant prostate cancer (CRPC) and confers resistance to AR-targeting therapies. Novel therapeutic strategies to overcome this are urgently required. We evaluated how bromodomain and extra-terminal (BET) protein inhibitors (BETi) abrogate aberrant AR signaling in CRPC.Experimental Design: We determined associations between BET expression, AR-driven transcription, and patient outcome; and the effect and mechanism by which chemical BETi (JQ1 and GSK1210151A; I-BET151) and BET family protein knockdown regulates AR-V7 expression and AR signaling in prostate cancer models.Results: Nuclear BRD4 protein expression increases significantly (P ≤ 0.01) with castration resistance in same patient treatment-naïve (median H-score; interquartile range: 100; 100–170) and CRPC (150; 110–200) biopsies, with higher expression at diagnosis associating with worse outcome (HR, 3.25; 95% CI, 1.50–7.01; P ≤ 0.001). BRD2, BRD3, and BRD4 RNA expression in CRPC biopsies correlates with AR-driven transcription (all P ≤ 0.001). Chemical BETi, and combined BET family protein knockdown, reduce AR-V7 expression and AR signaling. This was not recapitulated by C-MYC knockdown. In addition, we show that BETi regulates RNA processing thereby reducing alternative splicing and AR-V7 expression. Furthermore, BETi reduce growth of prostate cancer cells and patient-derived organoids with known AR mutations, AR amplification and AR-V7 expression. Finally, BETi, unlike enzalutamide, decreases persistent AR signaling and growth (P ≤ 0.001) of a patient-derived xenograft model of CRPC with AR amplification and AR-V7 expression.Conclusions: BETi merit clinical evaluation as inhibitors of AR splicing and function, with trials demonstrating their blockade in proof-of-mechanism pharmacodynamic studies. Clin Cancer Res; 24(13); 3149–62. ©2018 AACR.

Supplementary Figure Legends for Figures S1 to S13

Phosphorylated, acetylated peptides and total proteins identified in HAP1 CREBBP WT and mutant spheroids.

Validation screen of the top 50 ranked genes in 2D and 3D.

Gene list for the spheroid screen

Supplementary Materials and Methods

Supplementary Tables 1 to 10 Supplementary Table 1: Cell lines ATCC - american type culture collection, FBS - fetal bovine serum, CSS - charcoal stripped serum, * - LNCaP95 cells were kindly provided by Drs. Alan K Meeker and Jun Luo (Johns Hopkins University, Baltimore, Maryland, USA), NA - non-applicable, ^ - phenol red free, BPE/EGF - bovine pituitary extract and human recombinant epidermal growth factor. Supplementary Table 2: ON-TARGETplus siRNA pools for gene expression knock down Supplementary Table 3: TaqMan probes for qRT-PCR analysis Supplementary Table 4: Primary antibodies for western blot analysis Supplementary Table 5: AR regulated genes included in AR activity score Supplementary Table 6: Patient baseline characteristics at prostate cancer diagnosis N - number, SD - standard deviation, IQR - interquartile range, NR - not recorded, PSA - prostate specific antigen, NA - non-applicable. ^5 patient without PSA values; one value >2000 (analyzed as 2000) *All cases adenocarcinoma 1Student's t-test 2Fisher's Exact Test 3Wilcoxon Rank-Sum Test Supplementary Table 7: Cellular pathways regulated by I-BET151 treatment Cellular pathways annotated by CellMap (C), Reactome (R), KEGG (K), NCI PID (N), Panther (P) and BioCarta (B) with p value 0.2 and

ObjectivesSynovium is acutely affected following joint trauma and contributes to post-traumatic osteoarthritis (PTOA) progression. Little is known about discrete cell types and molecular mechanisms in PTOA synovium. We aimed to describe synovial cell populations and their dynamics in PTOA, with a focus on fibroblasts. We also sought to define mechanisms of synovial Wnt/β-catenin signalling, given its emerging importance in arthritis.MethodsWe subjected mice to non-invasive anterior cruciate ligament rupture as a model of human joint injury. We performed single-cell RNA-sequencing to assess synovial cell populations, subjected Wnt-GFP reporter mice to joint injury to study Wnt-active cells, and performed intra-articular injections of the Wnt agonist R-spondin 2 (Rspo2) to assess whether gain of function induced pathologies characteristic of PTOA. Lastly, we used cultured fibroblasts, macrophages and chondrocytes to study how Rspo2 orchestrates crosstalk between joint cell types.ResultsWe uncovered seven distinct functional subsets of synovial fibroblasts in healthy and injured synovium, and defined their temporal dynamics in early and established PTOA. Wnt/β-catenin signalling was overactive in PTOA synovium, and Rspo2 was strongly induced after injury and secreted exclusively by Prg4hilining fibroblasts. Trajectory analyses predicted that Prg4hilining fibroblasts arise from a pool of Dpp4+ mesenchymal progenitors in synovium, with SOX5 identified as a potential regulator of this emergence. We also showed that Rspo2 orchestrated pathological crosstalk between synovial fibroblasts, macrophages and chondrocytes.ConclusionsSynovial fibroblasts assume distinct functional identities during PTOA in mice, and Prg4hilining fibroblasts secrete Rspo2 that may drive pathological joint crosstalk after injury.

Genomic instability is a hallmark of cancer, and has a central role in the initiation and development of breast cancer1,2. The success of poly-ADP ribose polymerase inhibitors in the treatment of breast cancers that are deficient in homologous recombination exemplifies the utility of synthetically lethal genetic interactions in the treatment of breast cancers that are driven by genomic instability3. Given that defects in homologous recombination are present in only a subset of breast cancers, there is a need to identify additional driver mechanisms for genomic instability and targeted strategies to exploit these defects in the treatment of cancer. Here we show that centrosome depletion induces synthetic lethality in cancer cells that contain the 17q23 amplicon, a recurrent copy number aberration that defines about 9% of all primary breast cancer tumours and is associated with high levels of genomic instability4–6. Specifically, inhibition of polo-like kinase 4 (PLK4) using small molecules leads to centrosome depletion, which triggers mitotic catastrophe in cells that exhibit amplicon-directed overexpression of TRIM37. To explain this effect, we identify TRIM37 as a negative regulator of centrosomal pericentriolar material. In 17q23-amplified cells that lack centrosomes, increased levels of TRIM37 block the formation of foci that comprise pericentriolar material—these foci are structures with a microtubule-nucleating capacity that are required for successful cell division in the absence of centrosomes. Finally, we find that the overexpression of TRIM37 causes genomic instability by delaying centrosome maturation and separation at mitotic entry, and thereby increases the frequency of mitotic errors. Collectively, these findings highlight TRIM37-dependent genomic instability as a putative driver event in 17q23-amplified breast cancer and provide a rationale for the use of centrosome-targeting therapeutic agents in treating these cancers. TRIM37 overexpression promotes centrosome dysfunction that drives genomic instability in breast cancer cell lines containing the recurrent 17q23 amplicon, revealing a vulnerability that can be targeted to eliminate cancer cells.

Aims: The Scottish Transfusion and Laboratory Support in Trauma Group (TLSTG) previously reviewed all National Code Red activations between June 1st 2013 and October 31st 2015, generating a number of recommendations to be adopted to optimise the transfusion support given to patients following major trauma in Scotland. A repeat National survey was undertaken for all patients for whom Code Red was activated between 1st November 2015 and 31st December 2017. Methods: A clinical and transfusion lead for each centre entered anonymised data onto a secure electronic database (REDCap). Results: During the study period there were 66 activations (24 South-East of Scotland, 32 West, 10 East). Mean age was 45 years and 88% were male. Mean Injury Severity Score (ISS) was 28 with 75% blunt trauma. 93% (62/66) of Code Red patients received blood components with a 300% increase in pre-hospital transfusion (48 vs 16 patients; p

The Scottish Transfusion and Laboratory Support in Trauma (TLST) group previously audited all National Code Red activations between June 1st 2013 and October 31st 2015, generating a number of recommendations to be adopted to optimise the transfusion support given to patients following major trauma in Scotland. A repeat audit was undertaken for all patients for whom a Code Red was activated between 1st November 2015 and 31st December 2017.A clinical and transfusion lead for each centre entered anonymised data onto a secure electronic database (REDCAP; http://www.project-redcap.org) the server of which is held within the University of Edinburgh. This database was maintained by the Edinburgh study team. Each of Scotland’s pre-hospital trauma teams who take patients to hospitals where Code Red Policy is in place, and the receiving hospitals, agreed to enter data into the National Code Red audit for all patients for whom a Code Red was activated during the study period. The project was deemed a service evaluation by the South East Scotland Research Ethics committee (Ref: NR/1408AB11) and therefore did not require full ethics submission. The project was also registered with each hospital’s clinical effectiveness/governance teams where available, and a favourable Caldicott opinion was obtained.Abstract 042 Figure 1Flow chart showing transfusion events and outcomes of code red patientsAbstract 042 Figure 2Ratio of the mean number of concentrated red cells (CRC) and fresh frozen plasma (FFP) transfused to code red patients at 30 minute intervalsAbstract 042 Table 166 activations (24 South-East of Scotland, 32 West, 10 East). Mean age 45 years, 88% male patients. 93% of Code Red patients received blood components with a 300% increase in pre-hospital transfusion (48 patients; 73%); median time from 999 call to Code Red activation reduced to 37 minutes from 70 minutes; 78% patients received pre-hospital TXA (improved from 70%). CRC:FFP ratios improved in comparison to 2013–15. Survival to discharge increased (63% to 66%) despite increased ISS.Code Red practice has improved since our last audit. There are still improvements to be made in TXA administration and time to blood products.

Summary paragraphPoly-(ADP-ribose) polymerase inhibitors (PARPi) elicit anti-tumour activity in homologous recombination defective cancers by promoting cytotoxic, chromatin-bound, “trapped” PARP1. How cells process trapped PARP1 remains unclear. By exploiting wild-type or trapping-resistant PARP1 transgenes combined with either a rapid immunoprecipitation mass-spectrometry of endogenous proteins (RIME)-based approach, or PARP1 Apex2-proximity labelling linked to mass-spectrometry, we generated proteomic profiles of trapped and non-trapped PARP1 complexes. This combined approach identified an interaction between trapped PARP1 and the ubiquitin-regulated p97 ATPase (aka VCP). Subsequent experiments demonstrated that upon trapping, PARP1 is SUMOylated by the SUMO-ligase PIAS4 and subsequently ubiquitinated by the SUMO-targeted E3-ubiquitin ligase, RNF4, events that promote p97 recruitment and p97 ATPase-mediated removal of trapped-PARP1 from chromatin. Consistent with this, small molecule p97 complex inhibitors, including a metabolite of the clinically-used drug disulfiram (CuET) that acts as a p97 sequestration agent, prolong PARP1 trapping and thus enhance PARPi-induced cytotoxicity in homologous recombination-defective tumour cells and patient-derived tumour organoids. Taken together, these results suggest that p97 ATPase plays a key role in the processing of trapped PARP1 from chromatin and the response of homologous recombination defective tumour cells to PARPi.

To identify approaches to target DNA repair vulnerabilities in cancer, we discovered nanomolar potent, selective, low molecular weight (MW), allosteric inhibitors of the polymerase function of DNA polymerase Polθ, including ART558. ART558 inhibits the major Polθ-mediated DNA repair process, Theta-Mediated End Joining, without targeting Non-Homologous End Joining. In addition, ART558 elicits DNA damage and synthetic lethality in BRCA1- or BRCA2-mutant tumour cells and enhances the effects of a PARP inhibitor. Genetic perturbation screening revealed that defects in the 53BP1/Shieldin complex, which cause PARP inhibitor resistance, result in in vitro and in vivo sensitivity to small molecule Polθ polymerase inhibitors. Mechanistically, ART558 increases biomarkers of single-stranded DNA and synthetic lethality in 53BP1-defective cells whilst the inhibition of DNA nucleases that promote end-resection reversed these effects, implicating these in the synthetic lethal mechanism-of-action. Taken together, these observations describe a drug class that elicits BRCA-gene synthetic lethality and PARP inhibitor synergy, as well as targeting a biomarker-defined mechanism of PARPi-resistance., Polθ has been recently identified as a therapeutic target in cancer but specific inhibitors are currently unavailable. Here, the authors identify small molecule inhibitors of Polθ’s polymerase activity which elicit BRCA1/2 synthetic lethality, enhance the effect of PARP inhibitors and target PARP inhibitor resistance caused by 53BP1/Shieldin pathway defects.

Triple-negative breast cancers (TNBC) are resistant to standard-of-care chemotherapy and lack known targetable driver gene alterations. Identification of novel drivers could aid the discovery of new treatment strategies for this hard-to-treat patient population, yet studies using high-throughput and accurate models to define the functions of driver genes in TNBC to date have been limited. Here, we employed unbiased functional genomics screening of the 200 most frequently mutated genes in breast cancer, using spheroid cultures to model in vivo–like conditions, and identified the histone acetyltransferase CREBBP as a novel tumor suppressor in TNBC. CREBBP protein expression in patient tumor samples was absent in 8% of TNBCs and at a high frequency in other tumors, including squamous lung cancer, where CREBBP-inactivating mutations are common. In TNBC, CREBBP alterations were associated with higher genomic heterogeneity and poorer patient survival and resulted in upregulation and dependency on a FOXM1 proliferative program. Targeting FOXM1-driven proliferation indirectly with clinical CDK4/6 inhibitors (CDK4/6i) selectively impaired growth in spheroids, cell line xenografts, and patient-derived models from multiple tumor types with CREBBP mutations or loss of protein expression. In conclusion, we have identified CREBBP as a novel driver in aggressive TNBC and identified an associated genetic vulnerability in tumor cells with alterations in CREBBP and provide a preclinical rationale for assessing CREBBP alterations as a biomarker of CDK4/6i response in a new patient population. Significance: This study demonstrates that CREBBP genomic alterations drive aggressive TNBC, lung cancer, and lymphomas and may be selectively treated with clinical CDK4/6 inhibitors.

To target DNA repair vulnerabilities in cancer, we discovered nanomolar potent, selective, low molecular weight (MW), allosteric inhibitors of the polymerase function of DNA polymerase Polθ, including ART558. ART558 inhibits the major Polθ-mediated DNA repair process, Theta-Mediated End Joining (TMEJ), without targeting Non-Homologous End Joining. Moreover, we show that exposure to ART558 can elicit DNA damage and synthetic lethality in BRCA1- or BRCA2-mutant tumor cells and enhances the effects of a PARP inhibitor. Genetic perturbation screening revealed that defects in the 53BP1/Shieldin complex, which are a cause of PARP inhibitor resistance, result in in vitro and in vivo sensitivity to Polθ polymerase inhibitors. Mechanistically, ART558 increases biomarkers of single-stranded DNA and synthetic lethality in 53BP1-defective cells. The inhibition of DNA nucleases that promote end-resection, such as Exo1 or Blm-Dna2 reversed these effects, implicating these in the synthetic lethal mechanism-of-action. Taken together, these observations describe a drug class that elicits BRCA-gene synthetic lethality and PARP inhibitor synergy, as well as targeting a biomarker-defined mechanism of PARPi-resistance. Citation Format: Diana Zatreanu, Helen Robinson, Omar Alkhatib, Marie Boursier, Harry Finch, Lerin Geo, Diego Grande, Vera Grinkevich, Robert Heald, Sophie Langdon, Jayesh Majithiya, Claire McWhirter, Niall Martin, Shaun Moore, Joana Neves, Eeson Rajendra, Marco Ranzani, Theresia Schaedler, Martin Stockley, Kimberley Wiggins, Rachel Brough, Sandhya Sridhar, Aditi Gulati, Nan Shao, Luted Badder, Daniela Novo, Eleanor Knight, Rebecca Marlow, Syed Haider, Elsa Callen, Graeme Hewitt, Joost Schimmel, Remko Prevo, Christina Alli, Amanda Ferdinand, Cameron Bell, Peter Blencowe, Chris Bot, Mathew Calder, Mark Charles, Jayne Curry, Tennyson Ekwuru, Andre Nussenzweig, Marcel Tijsterman, Andrew N. Tutt, Simon Boulton, Geoff Higgins, Stephen J. Pettitt, Graeme C. Smith, Christopher J. Lord. Targeting PARP inhibitor resistance with Polθ inhibitors [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 5697.

// Jeffrey C. Francis 1 , Amy Capper 1 , Jian Ning 2 , Eleanor Knight 2 , Johann de Bono 3 and Amanda Swain 1, 2 1 Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK 2 Tumour Profiling Unit, The Institute of Cancer Research, London SW3 6JB, UK 3 Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK Correspondence to: Amanda Swain, email: amanda.swain@icr.ac.uk Keywords: aggressive invasive prostate cancer; prostate cancer mouse models; cell lineage plasticity; epithelial to mesenchymal transition Received: May 18, 2017 Accepted: July 03, 2017 Published: January 10, 2018 ABSTRACT Aggressive lethal prostate cancer is characterised by tumour invasion, metastasis and androgen resistance. Understanding the mechanisms by which localised disease progresses to advanced lethal stages is key to the development of effective therapies. Here we have identified a novel role for the transcription factor, SOX9, as a driver of aggressive invasive prostate cancer. Using genetically modified mouse models, we show that increased Sox9 expression in the prostate epithelia of animals with Pten loss leads to a highly invasive phenotype and metastasis. In depth analysis of these mice and related in vitro models reveals that SOX9 acts a key regulator of various processes that together promote tumour progression. We show that this factor promotes cell lineage plasticity with cells acquiring properties of basal stem cells and an increase in proliferation. In addition, increased SOX9 leads to changes in cytoskeleton and adhesion, deposition of extracellular matrix and epithelia to mesenchyme transition, properties of highly invasive cells. Analysis of castrated mice showed that the invasive phenotype driven by SOX9 is independent of androgen levels. Our study has identified a novel driver of prostate cancer progression and highlighted the cellular and molecular processes that are regulated by Sox9 to achieve invasive disease.

Background: Leptomeningeal metastasis remains a devastating development in breast cancer, with a median survival of 3-4 months, no widely accepted standard treatment, and limited access to trials of novel therapies. In addition, lack of access to leptomeningeal metastatic material hampers the pre-clinical investigation of the disease process and molecular drivers. This project uses CSF as a liquid biopsy to characterise BCLM, through genomic analysis of the cell-free DNA (cfDNA), and the development of pre-clinical BCLM models by the expansion of CSF disseminated tumour cells. Methods: CSF (surplus to clinical requirements) and blood were collected from patients undergoing evaluation of leptomeningeal metastasis. cfDNA was extracted from CSF and plasma, and subjected to ultra-low pass whole genome sequencing (ulpWGS) to assess tumour-derived cfDNA fraction. Samples with >10% tumour fraction underwent whole exome sequencing, along with matched archival primary tumour, archival extra-cranial metastatic site(s) and germline DNA. CSF cells were expanded in vitro (to establish 3D patient-derived organoids (PDOs). Results: Cohort demographics are shown in Table 1. Whole exome sequencing (WES) in 21 patients reveals that 65.2% of variants found in CSF cfDNA were not shared with the primary tumour or other matched samples. Phylogenetic analysis shows a divergent evolution from extra-cranial metastatic sites, represented by plasma cfDNA (n = 12) and/or metastatic site tissue DNA (n = 7). The most frequently mutated cancer-associated genes in CSF were MUC16 (12/21), TP53 (11/21), CDH1 (10/21), and KMT2D (7/21). The common occurrence of CDH1 loss-of-function mutations was in keeping with the large number of lobular cases, however were also discovered in CSF of two cases with E-cadherin positive ductal primary tumours. Furthermore, mutations (including frameshift indels) in JAK family proteins (JAK1, JAK3 and TYK2) were present in 5/21 cases, and were private to CSF in 4/21. Potential actionable gene alterations private to CSF include; IDH2 (3/21), GLI1 (3/21), PIK3CA (2/21) and PTCH1 (2/21). Further, there was an enrichment for somatic BRCA1/2 mutations (5/21, 2 private to CSF) indicating potential for platinum and/or PARP inhibitor therapy in these individuals. Patient-derived organoids (PDOs) were established using CSF tumour cells from 3 ER+/HER2- and 2 TNBC BCLM cases. WES of PDOs revealed high concordance with genomic variants identified in the matched CSF cfDNA. Therapeutic compound testing revealed 3/5 PDOs did not display sensitivity to methotrexate, the most commonly used BCLM intrathecal treatment. Patient-derived xenograft (PDX) models have been established by mammary fat pad, intraductal, intracardiac and intracerebroventricular injection routes. Conclusion/future plans: WES of CSF cfDNA provides insight into genomic changes in BCLM, including the divergent evolution, and BCLM specific alterations, some of which are potentially targetable. Parallel PDO and PDX models are being used to validate potential drivers and therapeutic targets. Treatment options beyond intrathecal methotrexate are urgently needed and in future might be molecularly tailored based on alterations discovered by CSF cfDNA sequencing. Table 1. Clinical demographicsDemographicsMedian, years (range)Age at BC diagnosis45 (24 – 66)Time from primary BC to BCLM4.7 (0.7 – 14.7)Time from first metastasis to BCLM1.2 (0.0 – 6.5)Histological Typen (%)Lobular10 (48)Ductal8 (38)Mixed ductal/lobular3 (14)Immuno-histochemical phenotypen (%)ER+ HER2-13 (62)TNBC5 (24)ER+ HER2+2 (9)ER- HER2+1 (5)Metastatic sitesn (%)No other metastatic sites (BCLM only)3 (14)Bone12 (57)Serosal8 (38)Brain6 (29)Liver4 (19)Ovary4 (19) Citation Format: Amanda Fitzpatrick, Marjan Iravani, Adam Mills, Eleanor Knight, Thanussuyah Alaguthurai, Vandna Shah, Alicia Okines, Nick Turner, Mark Harries, Syed Haider, Andrew Tutt, Clare Isacke. Genomic profiling of breast cancer leptomeningeal metastasis (BCLM) reveals a divergent evolution and therapeutic targets [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD13-03.

Background Deletion of the chromatin remodeler chromodomain helicase DNA-binding protein 1 (CHD1) is a common genomic alteration found in human prostate cancers (PCas). CHD1 loss represents a distinct PCa subtype characterized by SPOP mutation and higher genomic instability. However, the role of CHD1 in PCa development in vivo and its clinical utility remain unclear. Patients and methods To study the role of CHD1 in PCa development and its loss in clinical management, we generated a genetically engineered mouse model with prostate-specific deletion of murine Chd1 as well as isogenic CHD1 wild-type and homozygous deleted human benign and PCa lines. We also developed patient-derived organoid cultures and screened patients with metastatic PCa for CHD1 loss. Results We demonstrate that CHD1 loss sensitizes cells to DNA damage and causes a synthetic lethal response to DNA damaging therapy in vitro, in vivo, ex vivo, in patient-derived organoid cultures and in a patient with metastatic PCa. Mechanistically, CHD1 regulates 53BP1 stability and CHD1 loss leads to decreased error-free homologous recombination (HR) repair, which is compensated by increased error-prone non-homologous end joining (NHEJ) repair for DNA double-strand break (DSB) repair. Conclusions Our study provides the first in vivo and in patient evidence supporting the role of CHD1 in DSB repair and in response to DNA damaging therapy. We uncover mechanistic insights that CHD1 modulates the choice between HR and NHEJ DSB repair and suggest that CHD1 loss may contribute to the genomic instability seen in this subset of PCas.

Despite robust responses to androgen deprivation therapy and AR targeting therapies (including abiraterone and enzalutamide), nearly all cases of advanced prostate cancer progress to lethal mCRPC and develop therapeutic resistance. This progression is associated with persistent AR signaling, in part due to expression of constitutively active AR splice variants that include AR variant 7 (AR-V7). We show that AR-V7 expression in patient biopsies (protein) and circulating tumor cells (RNA) associates with poor outcome from mCRPC. Therapies that regulate AR-V7 and induce robust anticancer responses are required to confirm the clinical importance of AR-V7 in mCRPC. One such promising approach, currently in clinical trials, is inhibitors of BET family proteins, which include BRD2, BRD3, and BRD4. Preclinical studies have shown that BRD4 binds to AR at the androgen response element and facilitates the recruitment of the transcriptional machinery. We show that BRD4 protein expression increases as patients develop mCRPC and at diagnosis associates with patient outcome and more advanced disease. In addition, through RNAseq analysis we show that expression levels of BRD2, 3, and 4 in mCRPC associated with degree of AR activity. We, and others, have shown that the use of BET inhibitors (BETi) in vitro on AR/AR-V7 expressing cell lines not only decreased AR activity but also preferentially decreased the production on AR-V7 mRNA. In light of BETi having efficacy against BRD2, 3, and 4, and all isoforms being expressed in mCRPC, we explored the effect of genetic knockdown of each isoform. We show that BETi treatment is sufficient to decrease AR-V7 mRNA and protein in CRPC cell lines. Moreover, we demonstrate that BRD4 knockdown, and to a greater extent, the combination of BRD2, 3, and 4 knockdown blocked AR and AR-V7 signaling. Furthermore, C-MYC knockdown did not recapitulate the effect of BETi and led to an increase in AR signaling. Consistent with these findings, BETi and the combination of BRD2, 3, and 4 knockdown reduced the growth of CRPC cell lines. To further investigate whether BETi is sufficient to inhibit AR-V7 production in patients with mCRPC, we treated patient-derived organoids (PDOs) and a mouse xenograft (PDX) grown from patient metastatic biopsies who had progressed on enzalutamide and/or abiraterone. In this study 4 out of 9 PDOs were sensitive to BETi. Consistent with cell culture experiments, BETi treatment of PDO and PDX led to downregulation of both AR-V7 mRNA and protein expression, and growth inhibition. In light of the pleotropic effects of BETi on cancer cell biology and potential for treatment-related toxicities, we explored whether we could identify critical factors for BETi mediated AR-V7 regulation in CRPC. The ability of BETi to regulate AR-V7 may suggest an effect of BETi on pre-mRNA splicing of AR resulting in the observed decrease of AR-V7 expression. RNAseq analysis of the AR-V7 expressing CRPC cell line LNCaP95 treated with BETi demonstrated an increase in total splicing. Despite this, focused analysis of splicing factors and spliceosome components identified a subset of eight splicing factors being downregulated by BETi treatment, including one yet-uncharacterized factor (splicing factor B; Sf-B) that is crucial for AR-V7 expression and LNCaP95 cell growth. In addition, mCRPC patients who express high levels of Sf-B had a significantly poorer outcome and the protein structure of Sf-B is druggable using the drug discovery knowledgebase canSAR. Based on our results, we propose that inhibition of Sf-B may lead to decreased splicing and expression of AR-V7; providing a novel approach to target AR-V7 in mCRPC. Citation Format: Adam Sharp, Jon Welti, Wei Yuan, Ines Figueiredo, Veronica Gil, Daniel Nava Rodrigues, Maryou Lambros, Eleanor Knight, Jian Ning, Jeff Francis, David Dolling, Lorna Pope, Antje Neeb, Gunther Boysen, Yezi Zhu, Mateus Crespo, Alec Paschalis, Jun Luo, Stephen Plymate, Bissan Al-Lazikani, Amanda Swain, Johann de Bono. Targeting the bromodomain and extra-terminal (BET) family proteins and beyond in metastatic castration-resistant prostate cancer (mCRPC): Overcoming aberrant androgen receptor (AR) signaling [abstract]. In: Proceedings of the AACR Special Conference: Prostate Cancer: Advances in Basic, Translational, and Clinical Research; 2017 Dec 2-5; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(16 Suppl):Abstract nr A067.

Persistent androgen receptor (AR) signaling is key to the development and progression of metastatic castration resistant prostate cancer (mCRPC). This is in part due to expression of constitutively active AR splice variants like AR variant 7 (ARV7), confering resistance to current anti-androgens including enzalutamide (E) and abiraterone (A). To improve the outcome for patients with mCRPC, new therapeutic strategies to overcome AR and ARV7 oncogenic signaling are urgently required. The inhibition of co-factors modulating AR signaling are currently being investigated as novel strategies to treat mCRPC. One promising candidate is BRD4, a member of the BET protein family, that binds the AR on androgen response elements and facilitates the recruitment of the transcriptional machinery. BET inhibitors (BETi) have been shown to regulate AR and ARV7 signalling, however, the exact mechanism of ARV7 regulation remains unclear. As BETi are currently being explored in clinical trials of unstratified patients with mCRPC, we investigated their potential mechanism of action in CRPC cell lines, patient derived organoids (PDOs) and a patient derived mouse xenograft (PDX). Here we demonstrate that nuclear expression of BRD4 and ARV7 increases as patients develop resistance to E and/or A and inhibition of BRD4 by BETi is sufficient to block AR and ARV7 signalling in mCRPC. Both inhibition of BRD4 by BETi and genetic knockdown of BRD4 reduced the growth of CRPC cell lines and led to down-regulation of AR and ARV7 at the mRNA and protein level. To further investigate whether BETi is sufficient to inhibit ARV7 activity in patients with mCRPC, we treated patient derived organoids (PDOs) and a mouse xenograft (PDX) grown from metastatic biopsies of patients resistant to E and/or A with BETi. In this study 5 out of 10 PDOs were sensitive to BETi. Consistent with the cell culture experiments, BETi treatment of the PDX led to down-regulation of both ARV7 mRNA and protein expression. Mechanistically, BETi might inhibit pre-mRNA splicing of AR resulting in the observed decrease of ARV7 expression. However, RNAseq analysis of the ARV7 expressing CRPC cell line LNCaP95 demonstrated an increase in total splicing events including skipped exons, retained introns, mutually exclusive exons, alternative 5’ splice site and alternative 3’ splice site after BETi treatment. Despite this, focused analysis of splicing factors and spliceosome components identified a subset of eight splicing factors being down-regulated by BET inhibition including one yet uncharacterized factor that is crucial for ARV7 expression in LNCaP95 cells. Based on our results we propose a model that BETi mediated inhibition of this novel ARV7-mRNA splicing factor may lead to decreased splicing and subsequent expression of ARV7 at both mRNA and protein level; providing a novel approach to target ARV7 in mCRPC. Citation Format: Jonathan Welti, Adam Sharp, Ines Figueiredo, Wei Yuan, Daniel Nava Rodrigues, Veronica S. Gil, Eleanor Knight, Jian Ning, Jeff Francis, Antje Neeb, Gunther Boysen, Amanda Swain, Johann S. de Bono. Bromodomain and extra-terminal motif protein inhibitors (BETi) in metastatic castration resistant prostate cancer (mCRPC): A novel mechanism for regulating androgen receptor variant 7 (ARV7) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1515. doi:10.1158/1538-7445.AM2017-1515

A broad range of technologies have been developed to enable three dimensional (3D) cell culture. Few if any however are adaptable for routine everyday use in a straightforward and cost effective manner. Alvetex(®) is a rigid highly porous polystyrene scaffold designed specifically to enable routine 3D cell culture. The scaffold is engineered into thin membranes that fit into conventional cell culture plasticware. The material is inert and offers a polystyrene substrate familiar to cell biologists worldwide. The 3D geometry of the scaffold provides the environment in which cells grow, differentiate, and function to form close relationships with adjacent cells thus creating the equivalent of a thin tissue layer in vitro. This chapter introduces the features required by a technology that enables routine 3D cell culture. Using Alvetex(®) as a product that satisfies these requirements, its application is demonstrated for the growth of a recognised cell line. Procedures detailing the use of Alvetex(®) for 3D cell culture are provided. This is followed by a series of detailed methods describing ways to analyse such cultures including histological techniques, immunocytochemistry, and scanning electron microscopy. Examples of data generated from these methods are shown in the corresponding figures. Additional notes are also included where further information about certain procedures is required. The use of Alvetex(®) in combination with these methods will enable investigators to routinely produce complex 3D cultures to research the growth, differentiation, and function of cells in new ways.

A broad range of technologies have been developed to enable three dimensional (3D) cell culture. Few if any however are adaptable for routine everyday use in a straightforward and cost effective manner. Alvetex(®) is a rigid highly porous polystyrene scaffold designed specifically to enable routine 3D cell culture. The scaffold is engineered into thin membranes that fit into conventional cell culture plasticware. The material is inert and offers a polystyrene substrate familiar to cell biologists worldwide. The 3D geometry of the scaffold provides the environment in which cells grow, differentiate, and function to form close relationships with adjacent cells thus creating the equivalent of a thin tissue layer in vitro. This chapter introduces the features required by a technology that enables routine 3D cell culture. Using Alvetex(®) as a product that satisfies these requirements, its application is demonstrated for the growth of a recognised cell line. Procedures detailing the use of Alvetex(®) for 3D cell culture are provided. This is followed by a series of detailed methods describing ways to analyse such cultures including histological techniques, immunocytochemistry, and scanning electron microscopy. Examples of data generated from these methods are shown in the corresponding figures. Additional notes are also included where further information about certain procedures is required. The use of Alvetex(®) in combination with these methods will enable investigators to routinely produce complex 3D cultures to research the growth, differentiation, and function of cells in new ways.