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Liang CC, Greenhough LA, Masino L, Maslen S, Bajrami I, Tuppi M, Skehel M, Taylor IA, West SC. Mechanism of single-stranded DNA annealing by RAD52-RPA complex. Nature 2024:10.1038/s41586-024-07347-7. [PMID: 38658755 DOI: 10.1038/s41586-024-07347-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/22/2024] [Indexed: 04/26/2024]
Abstract
RAD52 is important for the repair of DNA double-stranded breaks1,2, mitotic DNA synthesis3-5 and alternative telomere length maintenance6,7. Central to these functions, RAD52 promotes the annealing of complementary single-stranded DNA (ssDNA)8,9 and provides an alternative to BRCA2/RAD51-dependent homologous recombination repair10. Inactivation of RAD52 in homologous-recombination-deficient BRCA1- or BRCA2-defective cells is synthetically lethal11,12, and aberrant expression of RAD52 is associated with poor cancer prognosis13,14. As a consequence, RAD52 is an attractive therapeutic target against homologous-recombination-deficient breast, ovarian and prostate cancers15-17. Here we describe the structure of RAD52 and define the mechanism of annealing. As reported previously18-20, RAD52 forms undecameric (11-subunit) ring structures, but these rings do not represent the active form of the enzyme. Instead, cryo-electron microscopy and biochemical analyses revealed that ssDNA annealing is driven by RAD52 open rings in association with replication protein-A (RPA). Atomic models of the RAD52-ssDNA complex show that ssDNA sits in a positively charged channel around the ring. Annealing is driven by the RAD52 N-terminal domains, whereas the C-terminal regions modulate the open-ring conformation and RPA interaction. RPA associates with RAD52 at the site of ring opening with critical interactions occurring between the RPA-interacting domain of RAD52 and the winged helix domain of RPA2. Our studies provide structural snapshots throughout the annealing process and define the molecular mechanism of ssDNA annealing by the RAD52-RPA complex.
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Affiliation(s)
| | | | | | | | | | - Marcel Tuppi
- The Francis Crick Institute, London, UK
- Abcam, Cambridge Biomedical Campus, Cambridge, UK
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2
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Pettitt SJ, Shao N, Zatreanu D, Frankum J, Bajrami I, Brough R, Krastev DB, Roumeliotis TI, Choudhary JS, Lorenz S, Rust A, de Bono JS, Yap TA, Tutt ANJ, Lord CJ. A HUWE1 defect causes PARP inhibitor resistance by modulating the BRCA1-∆11q splice variant. Oncogene 2023; 42:2701-2709. [PMID: 37491606 PMCID: PMC10473960 DOI: 10.1038/s41388-023-02782-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/07/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023]
Abstract
Although PARP inhibitors (PARPi) now form part of the standard-of-care for the treatment of homologous recombination defective cancers, de novo and acquired resistance limits their overall effectiveness. Previously, overexpression of the BRCA1-∆11q splice variant has been shown to cause PARPi resistance. How cancer cells achieve increased BRCA1-∆11q expression has remained unclear. Using isogenic cells with different BRCA1 mutations, we show that reduction in HUWE1 leads to increased levels of BRCA1-∆11q and PARPi resistance. This effect is specific to cells able to express BRCA1-∆11q (e.g. BRCA1 exon 11 mutant cells) and is not seen in BRCA1 mutants that cannot express BRCA1-∆11q, nor in BRCA2 mutant cells. As well as increasing levels of BRCA1-∆11q protein in exon 11 mutant cells, HUWE1 silencing also restores RAD51 nuclear foci and platinum salt resistance. HUWE1 catalytic domain mutations were also seen in a case of PARPi resistant, BRCA1 exon 11 mutant, high grade serous ovarian cancer. These results suggest how elevated levels of BRCA1-∆11q and PARPi resistance can be achieved, identify HUWE1 as a candidate biomarker of PARPi resistance for assessment in future clinical trials and illustrate how some PARPi resistance mechanisms may only operate in patients with particular BRCA1 mutations.
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Affiliation(s)
- Stephen J Pettitt
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
| | - Nan Shao
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Diana Zatreanu
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Jessica Frankum
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Ilirjana Bajrami
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rachel Brough
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Dragomir B Krastev
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | | | | | - Sonja Lorenz
- Max Planck Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Alistair Rust
- The Institute of Cancer Research, London, SW3 6JB, UK
| | - Johann S de Bono
- The Institute of Cancer Research, The Royal Marsden Hospital, Downs Road, Sutton, Surrey, SM2 5PT, UK
| | - Timothy A Yap
- The Institute of Cancer Research, The Royal Marsden Hospital, Downs Road, Sutton, Surrey, SM2 5PT, UK
- University of Texas MD Anderson Cancer Center, 1400 Holcombe Blvd, Houston, TX, 77030, USA
| | - Andrew N J Tutt
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
| | - Christopher J Lord
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
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3
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Bajrami I, Walker C, Krastev DB, Weekes D, Song F, Wicks AJ, Alexander J, Haider S, Brough R, Pettitt SJ, Tutt ANJ, Lord CJ. Sirtuin inhibition is synthetic lethal with BRCA1 or BRCA2 deficiency. Commun Biol 2021; 4:1270. [PMID: 34750509 PMCID: PMC8575930 DOI: 10.1038/s42003-021-02770-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/06/2021] [Indexed: 02/06/2023] Open
Abstract
PARP enzymes utilise NAD+ as a co-substrate for their enzymatic activity. Inhibition of PARP1 is synthetic lethal with defects in either BRCA1 or BRCA2. In order to assess whether other genes implicated in NAD+ metabolism were synthetic lethal with BRCA1 or BRCA2 gene defects, we carried out a genetic screen, which identified a synthetic lethality between BRCA1 and genetic inhibition of either of two sirtuin (SIRT) enzymes, SIRT1 or SIRT6. This synthetic lethal interaction was replicated using small-molecule SIRT inhibitors and was associated with replication stress and increased cellular PARylation, in contrast to the decreased PARylation associated with BRCA-gene/PARP inhibitor synthetic lethality. SIRT/BRCA1 synthetic lethality was reversed by genetic ablation of either PARP1 or the histone PARylation factor-coding gene HPF1, implicating PARP1/HPF1-mediated serine ADP-ribosylation as part of the mechanistic basis of this synthetic lethal effect. These observations suggest that PARP1/HPF1-mediated serine ADP-ribosylation, when driven by SIRT inhibition, can inadvertently inhibit the growth of BRCA-gene mutant cells.
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Affiliation(s)
- Ilirjana Bajrami
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Callum Walker
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Dragomir B Krastev
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Daniel Weekes
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Feifei Song
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Andrew J Wicks
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - John Alexander
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Syed Haider
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rachel Brough
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Stephen J Pettitt
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK.
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
| | - Andrew N J Tutt
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
| | - Christopher J Lord
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK.
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
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4
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Chabanon RM, Morel D, Eychenne T, Colmet-Daage L, Bajrami I, Dorvault N, Garrido M, Meisenberg C, Lamb A, Ngo C, Hopkins SR, Roumeliotis TI, Jouny S, Hénon C, Kawai-Kawachi A, Astier C, Konde A, Del Nery E, Massard C, Pettitt SJ, Margueron R, Choudhary JS, Almouzni G, Soria JC, Deutsch E, Downs JA, Lord CJ, Postel-Vinay S. PBRM1 Deficiency Confers Synthetic Lethality to DNA Repair Inhibitors in Cancer. Cancer Res 2021; 81:2888-2902. [PMID: 33888468 DOI: 10.1158/0008-5472.can-21-0628] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022]
Abstract
Inactivation of Polybromo 1 (PBRM1), a specific subunit of the PBAF chromatin remodeling complex, occurs frequently in cancer, including 40% of clear cell renal cell carcinomas (ccRCC). To identify novel therapeutic approaches to targeting PBRM1-defective cancers, we used a series of orthogonal functional genomic screens that identified PARP and ATR inhibitors as being synthetic lethal with PBRM1 deficiency. The PBRM1/PARP inhibitor synthetic lethality was recapitulated using several clinical PARP inhibitors in a series of in vitro model systems and in vivo in a xenograft model of ccRCC. In the absence of exogenous DNA damage, PBRM1-defective cells exhibited elevated levels of replication stress, micronuclei, and R-loops. PARP inhibitor exposure exacerbated these phenotypes. Quantitative mass spectrometry revealed that multiple R-loop processing factors were downregulated in PBRM1-defective tumor cells. Exogenous expression of the R-loop resolution enzyme RNase H1 reversed the sensitivity of PBRM1-deficient cells to PARP inhibitors, suggesting that excessive levels of R-loops could be a cause of this synthetic lethality. PARP and ATR inhibitors also induced cyclic GMP-AMP synthase/stimulator of interferon genes (cGAS/STING) innate immune signaling in PBRM1-defective tumor cells. Overall, these findings provide the preclinical basis for using PARP inhibitors in PBRM1-defective cancers. SIGNIFICANCE: This study demonstrates that PARP and ATR inhibitors are synthetic lethal with the loss of PBRM1, a PBAF-specific subunit, thus providing the rationale for assessing these inhibitors in patients with PBRM1-defective cancer. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/11/2888/F1.large.jpg.
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MESH Headings
- Animals
- Apoptosis
- Ataxia Telangiectasia Mutated Proteins/antagonists & inhibitors
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Renal Cell/drug therapy
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/pathology
- Cell Proliferation
- DNA Repair
- DNA-Binding Proteins/deficiency
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Kidney Neoplasms/drug therapy
- Kidney Neoplasms/genetics
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/pathology
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Poly(ADP-ribose) Polymerase Inhibitors/pharmacology
- Synthetic Lethal Mutations
- Transcription Factors/deficiency
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Roman M Chabanon
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Daphné Morel
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
- Université Paris Saclay, Université Paris-Sud, Faculté de Médicine, Le Kremlin Bicêtre, France
| | - Thomas Eychenne
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Léo Colmet-Daage
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Ilirjana Bajrami
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Nicolas Dorvault
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Marlène Garrido
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Cornelia Meisenberg
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, London, United Kingdom
| | | | - Carine Ngo
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Suzanna R Hopkins
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, London, United Kingdom
| | | | - Samuel Jouny
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Clémence Hénon
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | | | - Clémence Astier
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Asha Konde
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Elaine Del Nery
- Institut Curie, PSL Research University, Department of Translational Research, The Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | | | - Stephen J Pettitt
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Raphaël Margueron
- Institut Curie, PSL Research University, INSERM Unit U934, CNRS UMR 3215, Paris, France
| | - Jyoti S Choudhary
- Functional Proteomics Team, The Institute of Cancer Research, London, United Kingdom
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS, UMR 3664, Equipe Labellisée Ligue contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris-VI, CNRS, UMR3664, Paris, France
| | - Jean-Charles Soria
- Université Paris Saclay, Université Paris-Sud, Faculté de Médicine, Le Kremlin Bicêtre, France
| | - Eric Deutsch
- Université Paris Saclay, Université Paris-Sud, Faculté de Médicine, Le Kremlin Bicêtre, France
- INSERM UMR1030 Molecular Radiotherapy and Therapeutic Innovations, Gustave Roussy, Villejuif, France
| | - Jessica A Downs
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, London, United Kingdom
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom.
| | - Sophie Postel-Vinay
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France.
- Université Paris Saclay, Université Paris-Sud, Faculté de Médicine, Le Kremlin Bicêtre, France
- Drug Development Department, DITEP, Gustave Roussy, Villejuif, France
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5
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Fugger K, Bajrami I, Silva Dos Santos M, Young SJ, Kunzelmann S, Kelly G, Hewitt G, Patel H, Goldstone R, Carell T, Boulton SJ, MacRae J, Taylor IA, West SC. Targeting the nucleotide salvage factor DNPH1 sensitizes BRCA-deficient cells to PARP inhibitors. Science 2021; 372:156-165. [PMID: 33833118 PMCID: PMC7610649 DOI: 10.1126/science.abb4542] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 12/31/2020] [Accepted: 02/24/2021] [Indexed: 12/13/2022]
Abstract
Mutations in the BRCA1 or BRCA2 tumor suppressor genes predispose individuals to breast and ovarian cancer. In the clinic, these cancers are treated with inhibitors that target poly(ADP-ribose) polymerase (PARP). We show that inhibition of DNPH1, a protein that eliminates cytotoxic nucleotide 5-hydroxymethyl-deoxyuridine (hmdU) monophosphate, potentiates the sensitivity of BRCA-deficient cells to PARP inhibitors (PARPi). Synthetic lethality was mediated by the action of SMUG1 glycosylase on genomic hmdU, leading to PARP trapping, replication fork collapse, DNA break formation, and apoptosis. BRCA1-deficient cells that acquired resistance to PARPi were resensitized by treatment with hmdU and DNPH1 inhibition. Because genomic hmdU is a key determinant of PARPi sensitivity, targeting DNPH1 provides a promising strategy for the hypersensitization of BRCA-deficient cancers to PARPi therapy.
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Affiliation(s)
- Kasper Fugger
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | | | | | | | | | - Geoff Kelly
- MRC Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Graeme Hewitt
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Harshil Patel
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Thomas Carell
- Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, Building F, 81377 Munich, Germany
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - James MacRae
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ian A Taylor
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stephen C West
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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6
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Dreyer SB, Upstill-Goddard R, Paulus-Hock V, Paris C, Lampraki EM, Dray E, Serrels B, Caligiuri G, Rebus S, Plenker D, Galluzzo Z, Brunton H, Cunningham R, Tesson M, Nourse C, Bailey UM, Jones M, Moran-Jones K, Wright DW, Duthie F, Oien K, Evers L, McKay CJ, McGregor GA, Gulati A, Brough R, Bajrami I, Pettitt S, Dziubinski ML, Candido J, Balkwill F, Barry ST, Grützmann R, Rahib L, Johns A, Pajic M, Froeling FEM, Beer P, Musgrove EA, Petersen GM, Ashworth A, Frame MC, Crawford HC, Simeone DM, Lord C, Mukhopadhyay D, Pilarsky C, Tuveson DA, Cooke SL, Jamieson NB, Morton JP, Sansom OJ, Bailey PJ, Biankin AV, Chang DK. Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer. Gastroenterology 2021; 160:362-377.e13. [PMID: 33039466 PMCID: PMC8167930 DOI: 10.1053/j.gastro.2020.09.043] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Continuing recalcitrance to therapy cements pancreatic cancer (PC) as the most lethal malignancy, which is set to become the second leading cause of cancer death in our society. The study aim was to investigate the association between DNA damage response (DDR), replication stress, and novel therapeutic response in PC to develop a biomarker-driven therapeutic strategy targeting DDR and replication stress in PC. METHODS We interrogated the transcriptome, genome, proteome, and functional characteristics of 61 novel PC patient-derived cell lines to define novel therapeutic strategies targeting DDR and replication stress. Validation was done in patient-derived xenografts and human PC organoids. RESULTS Patient-derived cell lines faithfully recapitulate the epithelial component of pancreatic tumors, including previously described molecular subtypes. Biomarkers of DDR deficiency, including a novel signature of homologous recombination deficiency, cosegregates with response to platinum (P < .001) and PARP inhibitor therapy (P < .001) in vitro and in vivo. We generated a novel signature of replication stress that predicts response to ATR (P < .018) and WEE1 inhibitor (P < .029) treatment in both cell lines and human PC organoids. Replication stress was enriched in the squamous subtype of PC (P < .001) but was not associated with DDR deficiency. CONCLUSIONS Replication stress and DDR deficiency are independent of each other, creating opportunities for therapy in DDR-proficient PC and after platinum therapy.
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Affiliation(s)
- Stephan B Dreyer
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Rosie Upstill-Goddard
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | | | - Clara Paris
- Department of Pharmacological Faculty, Université Grenoble Alpes, Saint-Martin-d'Heres, France
| | - Eirini-Maria Lampraki
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Eloise Dray
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas
| | - Bryan Serrels
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - Giuseppina Caligiuri
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Selma Rebus
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Dennis Plenker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York
| | - Zachary Galluzzo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York
| | - Holly Brunton
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Richard Cunningham
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Mathias Tesson
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Craig Nourse
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Ulla-Maja Bailey
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Marc Jones
- Stratified Medicine Scotland, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Kim Moran-Jones
- College of Medicine, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Derek W Wright
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Fraser Duthie
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; Department of Pathology, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Karin Oien
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; Department of Pathology, Queen Elizabeth University Hospital, Glasgow, United Kingdom; Greater Glasgow and Clyde Bio-repository, Pathology Department, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Lisa Evers
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Colin J McKay
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | | | - Aditi Gulati
- Cancer Research UK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Rachel Brough
- Cancer Research UK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Ilirjana Bajrami
- Cancer Research UK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Stephan Pettitt
- Cancer Research UK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Michele L Dziubinski
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Juliana Candido
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Frances Balkwill
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Simon T Barry
- Bioscience, Oncology, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Cambridge, United Kingdom
| | - Robert Grützmann
- Department of Surgery, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Lola Rahib
- Pancreatic Cancer Action Network, Manhattan Beach, California
| | - Amber Johns
- The Kinghorn Cancer Centre, Darlinghurst and Garvan Institute of Medical Research, Sydney, Australia
| | - Marina Pajic
- The Kinghorn Cancer Centre, Darlinghurst and Garvan Institute of Medical Research, Sydney, Australia
| | - Fieke E M Froeling
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York; Epigenetics Unit, Department of Surgery and Cancer, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Phillip Beer
- Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Elizabeth A Musgrove
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | | | - Alan Ashworth
- Department of Pathology, Queen Elizabeth University Hospital, Glasgow, United Kingdom; University of California-San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Margaret C Frame
- Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - Howard C Crawford
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Diane M Simeone
- Pancreatic Cancer Center, Perlmutter Cancer Center, New York University Langone Health, New York, New York
| | - Chris Lord
- Cancer Research UK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Debabrata Mukhopadhyay
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Jacksonville, Florida
| | | | - David A Tuveson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York
| | - Susanna L Cooke
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Nigel B Jamieson
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Jennifer P Morton
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Owen J Sansom
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas
| | - Peter J Bailey
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom; South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, Australia.
| | - David K Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom; South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, Australia.
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7
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Chabanon RM, Morel D, Colmet-Daage L, Eychenne T, Dorvault N, Bajrami I, Garrido M, Hopkins S, Meisenberg C, Lamb A, Roumeliotis T, Jouny S, Astier C, Konde A, Almouzni G, Choudhary J, Soria JC, Downs J, Lord CJ, Postel-Vinay S. Abstract 1058: Targeting chromatin remodeling-associated genetic vulnerabilities in cancer: PBRM1 defects are synthetic lethal with PARP and ATR inhibitors. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Aim: Polybromo-1 (PBRM1), a specific subunit of the pBAF chromatin remodeling complex, is frequently inactivated in cancer. For example, 40% of clear cell Renal Cell Carcinoma (ccRCC) and 15% of cholangiocarcinoma present deleterious PBRM1 mutations. There is currently no precision medicine-based therapeutic approach that targets PBRM1 defects. To identify novel, targeted therapeutic strategies for PBRM1-defective cancers, we carried out high-throughput functional genomics and drug screenings followed by in vitro and in vivo validation studies.
Methods: High-throughput siRNA-drug sensitization and drug sensitivity screens evaluating > 150 cancer-relevant small molecules in dose-response were performed in Pbrm1 siRNA-transfected mouse embryonic stem cells (mES) and isogenic PBRM1-KO or -WT HAP1 cells, respectively. After identification of PBRM1-selective small molecules, revalidation was carried out in a series of in-house-generated isogenic models of PBRM1 deficiency - including 786-O (ccRCC), A498 (ccRCC), U2OS (osteosarcoma) and H1299 (non-small cell lung cancer) human cancer cell lines - and non-isogenic ccRCC models, using multiple clinical compounds. Mechanistic dissection was performed using immunofluorescence, RT-qPCR, western blotting, DNA fiber assay, transcriptomics, proteomics and DRIP-sequencing to evaluate markers of DNA damage response (DDR), replication stress and cell-autonomous innate immune signaling. Preclinical data were integrated with TCGA tumor data.
Results: Parallel high-throughput drug screens independently identified PARP inhibitors (PARPi) as being synthetic lethal with PBRM1 defects - a cell type-independent effect which was exacerbated by ATR inhibitors (ATRi) and which we revalidated in vitro in isogenic and non-isogenic systems and in vivo in a xenograft model. PBRM1 defects were associated with increased replication fork stress (higher γH2AX and RPA foci levels, decreased replication fork speed and increased ATM checkpoint activation), R-loop accumulation and enhanced genomic instability in vitro; these effects were exacerbated upon PARPi exposure. In patient tumor samples, we also found that PBRM1-mutant cancers possessed a higher mutational load. Finally, we found that ATRi selectively activated the cGAS/STING cytosolic DNA sensing pathway in PBRM1-deficient cells, resulting in increased expression of type I interferon genes.
Conclusion: PBRM1-defective cancer cells present increased replication fork stress, R-loop formation, genome instability and are selectively sensitive to PARPi and ATRi through a synthetic lethal mechanism that is cell type-independent. Our data provide the pre-clinical rationale for assessing PARPi as a monotherapy or in combination with ATRi or immune-modulating agents in molecularly-selected patients with PBRM1-defective cancers.
Citation Format: Roman Merial Chabanon, Daphné Morel, Léo Colmet-Daage, Thomas Eychenne, Nicolas Dorvault, Ilirjana Bajrami, Marlène Garrido, Suzanna Hopkins, Cornelia Meisenberg, Andrew Lamb, Theo Roumeliotis, Samuel Jouny, Clémence Astier, Asha Konde, Geneviève Almouzni, Jyoti Choudhary, Jean-Charles Soria, Jessica Downs, Christopher J. Lord, Sophie Postel-Vinay. Targeting chromatin remodeling-associated genetic vulnerabilities in cancer: PBRM1 defects are synthetic lethal with PARP and ATR inhibitors [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1058.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Samuel Jouny
- 3Institute of Cancer Research, London, United Kingdom
| | | | - Asha Konde
- 3Institute of Cancer Research, London, United Kingdom
| | | | | | - Jean-Charles Soria
- 6Université Paris-Sud/Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Jessica Downs
- 3Institute of Cancer Research, London, United Kingdom
| | | | - Sophie Postel-Vinay
- 7Gustave Roussy Cancer Campus and U981 INSERM, ATIP-Avenir group, Villejuif, France
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8
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Brunton H, Caligiuri G, Cunningham R, Upstill-Goddard R, Bailey UM, Garner IM, Nourse C, Dreyer S, Jones M, Moran-Jones K, Wright DW, Paulus-Hock V, Nixon C, Thomson G, Jamieson NB, McGregor GA, Evers L, McKay CJ, Gulati A, Brough R, Bajrami I, Pettitt SJ, Dziubinski ML, Barry ST, Grützmann R, Brown R, Curry E, Pajic M, Musgrove EA, Petersen GM, Shanks E, Ashworth A, Crawford HC, Simeone DM, Froeling FEM, Lord CJ, Mukhopadhyay D, Pilarsky C, Grimmond SE, Morton JP, Sansom OJ, Chang DK, Bailey PJ, Biankin AV, Chang DK, Cooke SL, Dreyer S, Grimwood P, Kelly S, Marshall J, McDade B, McElroy D, Ramsay D, Upstill-Goddard R, Rebus S, Hair J, Jamieson NB, McKay CJ, Westwood P, Williams N, Duthie F, Biankin AV, Johns AL, Mawson A, Chang DK, Scarlett CJ, Brancato MAL, Rowe SJ, Simpson SH, Martyn-Smith M, Thomas MT, Chantrill LA, Chin VT, Chou A, Cowley MJ, Humphris JL, Mead RS, Nagrial AM, Pajic M, Pettit J, Pinese M, Rooman I, Wu J, Tao J, DiPietro R, Watson C, Steinmann A, Lee HC, Wong R, Pinho AV, Giry-Laterriere M, Daly RJ, Musgrove EA, Sutherland RL, Grimmond SM, Waddell N, Kassahn KS, Miller DK, Wilson PJ, Patch AM, Song S, Harliwong I, Idrisoglu S, Nourbakhsh E, Manning S, Wani S, Gongora M, Anderson M, Holmes O, Leonard C, Taylor D, Wood S, Xu C, Nones K, Fink JL, Christ A, Bruxner T, Cloonan N, Newell F, Pearson JV, Quinn M, Nagaraj S, Kazakoff S, Waddell N, Krisnan K, Quek K, Wood D, Samra JS, Gill AJ, Pavlakis N, Guminski A, Toon C, Asghari R, Merrett ND, Pavey D, Das A, Cosman PH, Ismail K, O’Connnor C, Lam VW, McLeod D, Pleass HC, Richardson A, James V, Kench JG, Cooper CL, Joseph D, Sandroussi C, Crawford M, Gallagher J, Texler M, Forest C, Laycock A, Epari KP, Ballal M, Fletcher DR, Mukhedkar S, Spry NA, DeBoer B, Chai M, Zeps N, Beilin M, Feeney K, Nguyen NQ, Ruszkiewicz AR, Worthley C, Tan CP, Debrencini T, Chen J, Brooke-Smith ME, Papangelis V, Tang H, Barbour AP, Clouston AD, Martin P, O’Rourke TJ, Chiang A, Fawcett JW, Slater K, Yeung S, Hatzifotis M, Hodgkinson P, Christophi C, Nikfarjam M, Mountain A, Eshleman JR, Hruban RH, Maitra A, Iacobuzio-Donahue CA, Schulick RD, Wolfgang CL, Morgan RA, Hodgin M, Scarpa A, Lawlor RT, Beghelli S, Corbo V, Scardoni M, Bassi C, Tempero MA, Nourse C, Jamieson NB, Graham JS. HNF4A and GATA6 Loss Reveals Therapeutically Actionable Subtypes in Pancreatic Cancer. Cell Rep 2020; 31:107625. [PMID: 32402285 PMCID: PMC9511995 DOI: 10.1016/j.celrep.2020.107625] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 11/05/2019] [Accepted: 04/17/2020] [Indexed: 12/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) can be divided into transcriptomic subtypes with two broad lineages referred to as classical (pancreatic) and squamous. We find that these two subtypes are driven by distinct metabolic phenotypes. Loss of genes that drive endodermal lineage specification, HNF4A and GATA6, switch metabolic profiles from classical (pancreatic) to predominantly squamous, with glycogen synthase kinase 3 beta (GSK3β) a key regulator of glycolysis. Pharmacological inhibition of GSK3β results in selective sensitivity in the squamous subtype; however, a subset of these squamous patient-derived cell lines (PDCLs) acquires rapid drug tolerance. Using chromatin accessibility maps, we demonstrate that the squamous subtype can be further classified using chromatin accessibility to predict responsiveness and tolerance to GSK3β inhibitors. Our findings demonstrate that distinct patterns of chromatin accessibility can be used to identify patient subgroups that are indistinguishable by gene expression profiles, highlighting the utility of chromatin-based biomarkers for patient selection in the treatment of PDAC.
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Affiliation(s)
- Holly Brunton
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Giuseppina Caligiuri
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland
| | - Richard Cunningham
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland
| | - Rosie Upstill-Goddard
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland
| | - Ulla-Maja Bailey
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Ian M Garner
- Epigenetics Unit, Department of Surgery & Cancer, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Craig Nourse
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Stephan Dreyer
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK
| | - Marc Jones
- Stratified Medicine Scotland Innovation Centre, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - Kim Moran-Jones
- Stratified Medicine Scotland Innovation Centre, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - Derek W Wright
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland
| | - Viola Paulus-Hock
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Colin Nixon
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Gemma Thomson
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Nigel B Jamieson
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK
| | - Grant A McGregor
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Lisa Evers
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland
| | - Colin J McKay
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK
| | - Aditi Gulati
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Rachel Brough
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Ilirjana Bajrami
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Stephen J Pettitt
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Michele L Dziubinski
- Department of Molecular and Integrative Physiology, University of Michigan, 4304 Rogel Cancer Center Drive, Ann Arbor, MI 48109, USA
| | - Simon T Barry
- Bioscience, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Robert Grützmann
- Department of Surgery, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Robert Brown
- Epigenetics Unit, Department of Surgery & Cancer, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Edward Curry
- Epigenetics Unit, Department of Surgery & Cancer, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | | | | | - Marina Pajic
- The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst and Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Elizabeth A Musgrove
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland
| | | | - Emma Shanks
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Alan Ashworth
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK; UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94158, USA
| | - Howard C Crawford
- Department of Molecular and Integrative Physiology, University of Michigan, 4304 Rogel Cancer Center Drive, Ann Arbor, MI 48109, USA
| | - Diane M Simeone
- Pancreatic Cancer Center, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Fieke E M Froeling
- Epigenetics Unit, Department of Surgery & Cancer, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Christopher J Lord
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Debabrata Mukhopadhyay
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Jacksonville, FL 32224, USA
| | | | - Sean E Grimmond
- University of Melbourne Centre for Cancer Research, University of Melbourne, Melbourne 3010, VIC, Australia
| | - Jennifer P Morton
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Owen J Sansom
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - David K Chang
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK; South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Peter J Bailey
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK; Department of General Surgery, University of Heidelberg, Heidelberg 69120, Germany.
| | - Andrew V Biankin
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, Scotland; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK; South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
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9
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Chabanon RM, Muirhead G, Krastev DB, Adam J, Morel D, Garrido M, Lamb A, Hénon C, Dorvault N, Rouanne M, Marlow R, Bajrami I, Cardeñosa ML, Konde A, Besse B, Ashworth A, Pettitt SJ, Haider S, Marabelle A, Tutt AN, Soria JC, Lord CJ, Postel-Vinay S. PARP inhibition enhances tumor cell-intrinsic immunity in ERCC1-deficient non-small cell lung cancer. J Clin Invest 2019; 129:1211-1228. [PMID: 30589644 PMCID: PMC6391116 DOI: 10.1172/jci123319] [Citation(s) in RCA: 200] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 12/18/2018] [Indexed: 12/17/2022] Open
Abstract
The cyclic GMP-AMP synthase/stimulator of IFN genes (cGAS/STING) pathway detects cytosolic DNA to activate innate immune responses. Poly(ADP-ribose) polymerase inhibitors (PARPi) selectively target cancer cells with DNA repair deficiencies such as those caused by BRCA1 mutations or ERCC1 defects. Using isogenic cell lines and patient-derived samples, we showed that ERCC1-defective non-small cell lung cancer (NSCLC) cells exhibit an enhanced type I IFN transcriptomic signature and that low ERCC1 expression correlates with increased lymphocytic infiltration. We demonstrated that clinical PARPi, including olaparib and rucaparib, have cell-autonomous immunomodulatory properties in ERCC1-defective NSCLC and BRCA1-defective triple-negative breast cancer (TNBC) cells. Mechanistically, PARPi generated cytoplasmic chromatin fragments with characteristics of micronuclei; these were found to activate cGAS/STING, downstream type I IFN signaling, and CCL5 secretion. Importantly, these effects were suppressed in PARP1-null TNBC cells, suggesting that this phenotype resulted from an on-target effect of PARPi on PARP1. PARPi also potentiated IFN-γ-induced PD-L1 expression in NSCLC cell lines and in fresh patient tumor cells; this effect was enhanced in ERCC1-deficient contexts. Our data provide a preclinical rationale for using PARPi as immunomodulatory agents in appropriately molecularly selected populations.
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Affiliation(s)
- Roman M. Chabanon
- Université Paris Saclay, Université Paris-Sud, Faculté de médicine, Le Kremlin Bicêtre, Paris, France
- ATIP-Avenir group, Inserm U981, Gustave Roussy, Villejuif, France
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre and
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Gareth Muirhead
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre and
| | - Dragomir B. Krastev
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre and
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Julien Adam
- ATIP-Avenir group, Inserm U981, Gustave Roussy, Villejuif, France
| | - Daphné Morel
- Université Paris Saclay, Université Paris-Sud, Faculté de médicine, Le Kremlin Bicêtre, Paris, France
- ATIP-Avenir group, Inserm U981, Gustave Roussy, Villejuif, France
| | - Marlène Garrido
- ATIP-Avenir group, Inserm U981, Gustave Roussy, Villejuif, France
| | | | - Clémence Hénon
- Université Paris Saclay, Université Paris-Sud, Faculté de médicine, Le Kremlin Bicêtre, Paris, France
- ATIP-Avenir group, Inserm U981, Gustave Roussy, Villejuif, France
| | - Nicolas Dorvault
- ATIP-Avenir group, Inserm U981, Gustave Roussy, Villejuif, France
| | - Mathieu Rouanne
- Université Paris Saclay, Université Paris-Sud, Faculté de médicine, Le Kremlin Bicêtre, Paris, France
- Inserm U1015, Gustave Roussy, Villejuif, France
| | - Rebecca Marlow
- The Breast Cancer Now Research Unit, King’s College London, London, United Kingdom
| | - Ilirjana Bajrami
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre and
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Marta Llorca Cardeñosa
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre and
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
- Biomedical Research Institute INCLIVA, Hospital Clinico Universitario Valencia, University of Valencia, Valencia, Spain
| | - Asha Konde
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre and
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Benjamin Besse
- Université Paris Saclay, Université Paris-Sud, Faculté de médicine, Le Kremlin Bicêtre, Paris, France
- Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
| | - Stephen J. Pettitt
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre and
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Syed Haider
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre and
| | - Aurélien Marabelle
- Inserm U1015, Gustave Roussy, Villejuif, France
- Département d’Innovations Thérapeutiques et Essais Précoces (DITEP), Gustave Roussy, Villejuif, France
| | - Andrew N.J. Tutt
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre and
- The Breast Cancer Now Research Unit, King’s College London, London, United Kingdom
| | - Jean-Charles Soria
- Université Paris Saclay, Université Paris-Sud, Faculté de médicine, Le Kremlin Bicêtre, Paris, France
| | - Christopher J. Lord
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre and
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Sophie Postel-Vinay
- Université Paris Saclay, Université Paris-Sud, Faculté de médicine, Le Kremlin Bicêtre, Paris, France
- ATIP-Avenir group, Inserm U981, Gustave Roussy, Villejuif, France
- Département d’Innovations Thérapeutiques et Essais Précoces (DITEP), Gustave Roussy, Villejuif, France
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Ryan CJ, Bajrami I, Lord CJ. Synthetic Lethality and Cancer - Penetrance as the Major Barrier. Trends Cancer 2018; 4:671-683. [PMID: 30292351 DOI: 10.1016/j.trecan.2018.08.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 12/20/2022]
Abstract
Synthetic lethality has long been proposed as an approach for targeting genetic defects in tumours. Despite a decade of screening efforts, relatively few robust synthetic lethal targets have been identified. Improved genetic perturbation techniques, including CRISPR/Cas9 gene editing, have resulted in renewed enthusiasm for searching for synthetic lethal effects in cancer. An implicit assumption behind this enthusiasm is that the lack of reproducibly identified targets can be attributed to limitations of RNAi technologies. We argue here that a bigger hurdle is that most synthetic lethal interactions (SLIs) are not highly penetrant, in other words they are not robust to the extensive molecular heterogeneity seen in tumours. We outline strategies for identifying and prioritising SLIs that are most likely to be highly penetrant.
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Affiliation(s)
- Colm J Ryan
- School of Computer Science and Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Ilirjana Bajrami
- Breast Cancer Now Toby Robins Research Centre and Cancer Research UK (CRUK) Gene Function Laboratory, Institute of Cancer Research (ICR), London SW3 6JB, UK.
| | - Christopher J Lord
- Breast Cancer Now Toby Robins Research Centre and Cancer Research UK (CRUK) Gene Function Laboratory, Institute of Cancer Research (ICR), London SW3 6JB, UK.
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Holme H, Gulati A, Brough R, Fleuren EDG, Bajrami I, Campbell J, Chong IY, Costa-Cabral S, Elliott R, Fenton T, Frankum J, Jones SE, Menon M, Miller R, Pemberton HN, Postel-Vinay S, Rafiq R, Selfe JL, von Kriegsheim A, Munoz AG, Rodriguez J, Shipley J, van der Graaf WTA, Williamson CT, Ryan CJ, Pettitt S, Ashworth A, Strauss SJ, Lord CJ. Author Correction: Chemosensitivity profiling of osteosarcoma tumour cell lines identifies a model of BRCAness. Sci Rep 2018; 8:12771. [PMID: 30131505 PMCID: PMC6104100 DOI: 10.1038/s41598-018-30922-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
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Affiliation(s)
- Harriett Holme
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Aditi Gulati
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rachel Brough
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Emmy D G Fleuren
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
- Clinical and Translational Sarcoma Research, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Ilirjana Bajrami
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - James Campbell
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Irene Y Chong
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
- The Royal Marsden NHS Foundation Trust, Fulham Road, London, SW3 6JJ, UK
| | - Sara Costa-Cabral
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Richard Elliott
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Tim Fenton
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Jessica Frankum
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Samuel E Jones
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Malini Menon
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rowan Miller
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Helen N Pemberton
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Sophie Postel-Vinay
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rumana Rafiq
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Joanna L Selfe
- Sarcoma Molecular Pathology Laboratory, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Alex von Kriegsheim
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | | | - Javier Rodriguez
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
| | - Janet Shipley
- Sarcoma Molecular Pathology Laboratory, The Institute of Cancer Research, London, SM2 5NG, UK
| | | | - Chris T Williamson
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Colm J Ryan
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
| | - Stephen Pettitt
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Alan Ashworth
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
- UCSF Helen Diller Family Comprehensive Cancer Centre, San Francisco, California, 94158, USA.
| | - Sandra J Strauss
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK.
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
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Holme H, Gulati A, Brough R, Fleuren EDG, Bajrami I, Campbell J, Chong IY, Costa-Cabral S, Elliott R, Fenton T, Frankum J, Jones SE, Menon M, Miller R, Pemberton HN, Postel-Vinay S, Rafiq R, Selfe JL, von Kriegsheim A, Munoz AG, Rodriguez J, Shipley J, van der Graaf WTA, Williamson CT, Ryan CJ, Pettitt S, Ashworth A, Strauss SJ, Lord CJ. Chemosensitivity profiling of osteosarcoma tumour cell lines identifies a model of BRCAness. Sci Rep 2018; 8:10614. [PMID: 30006631 PMCID: PMC6045584 DOI: 10.1038/s41598-018-29043-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/02/2018] [Indexed: 11/22/2022] Open
Abstract
Osteosarcoma (OS) is an aggressive sarcoma, where novel treatment approaches are required. Genomic studies suggest that a subset of OS, including OS tumour cell lines (TCLs), exhibit genomic loss of heterozygosity (LOH) patterns reminiscent of BRCA1 or BRCA2 mutant tumours. This raises the possibility that PARP inhibitors (PARPi), used to treat BRCA1/2 mutant cancers, could be used to target OS. Using high-throughput drug sensitivity screening we generated chemosensitivity profiles for 79 small molecule inhibitors, including three clinical PARPi. Drug screening was performed in 88 tumour cell lines, including 18 OS TCLs. This identified known sensitivity effects in OS TCLs, such as sensitivity to FGFR inhibitors. When compared to BRCA1/2 mutant TCLs, OS TCLs, with the exception of LM7, were PARPi resistant, including those with previously determined BRCAness LoH profiles. Post-screen validation experiments confirmed PARPi sensitivity in LM7 cells as well as a defect in the ability to form nuclear RAD51 foci in response to DNA damage. LM7 provides one OS model for the study of PARPi sensitivity through a potential defect in RAD51-mediated DNA repair. The drug sensitivity dataset we generated in 88 TCLs could also serve as a resource for the study of drug sensitivity effects in OS.
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Affiliation(s)
- Harriett Holme
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Aditi Gulati
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rachel Brough
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Emmy D G Fleuren
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
- Clinical and Translational Sarcoma Research, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Ilirjana Bajrami
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - James Campbell
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Irene Y Chong
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
- The Royal Marsden NHS Foundation Trust, Fulham Road, London, SW3 6JJ, UK
| | - Sara Costa-Cabral
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Richard Elliott
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Tim Fenton
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Jessica Frankum
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Samuel E Jones
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Malini Menon
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rowan Miller
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Helen N Pemberton
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Sophie Postel-Vinay
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rumana Rafiq
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Joanna L Selfe
- Sarcoma Molecular Pathology Laboratory, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Alex von Kriegsheim
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | | | - Javier Rodriguez
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
| | - Janet Shipley
- Sarcoma Molecular Pathology Laboratory, The Institute of Cancer Research, London, SM2 5NG, UK
| | | | - Chris T Williamson
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Colm J Ryan
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
| | - Stephen Pettitt
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Alan Ashworth
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
- UCSF Helen Diller Family Comprehensive Cancer Centre, San Francisco, California, 94158, USA.
| | - Sandra J Strauss
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK.
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
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Bajrami I, Marlow R, Ven MVD, Brough R, Pemberton HN, Frankum J, Song FF, Rafiq R, Konde A, Menon M, Campbell J, Gulati A, Kumar R, Pettitt SJ, Gurden MD, Cardenosa ML, Chong I, Gazinska P, Wallberg F, Sawyer EJ, Martin LA, Dowsett M, Linardopoulos S, Ryan C, Derksen PW, Jonkers J, Tutt AN, Ashworth A, Lord CJ. Abstract 2986: E-cadherin/ROS1 inhibitor synthetic lethality in breast cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-2986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The E-cadherin (CDH1) tumour suppressor gene encodes a calcium-dependent cell-cell adhesion glycoprotein, which has roles in maintaining cell polarity, differentiation, cell migration and survival. E-cadherin dysfunction is a feature common to many epithelial tumours, with the highest incidence occurring in diffuse gastric cancer (50%) and lobular breast cancer (63%) and can occur via CDH1 mutation, deletion or epigenetic silencing. Although E-cadherin dysfunction is relatively common, precision medicine approaches that exploit this pathogenic alteration are not yet available. Using genetic and small-molecule perturbation screens in breast tumour cells with CRISPR-Cas9 engineered CDH1 mutations, we identified a synthetic lethal interaction between E-cadherin deficiency and inhibition of the tyrosine kinase ROS1. Using data from large-scale genetic screens in molecularly diverse breast tumour cell lines, we found that the E-cadherin/ROS1 synthetic lethality was not only robust in the face of considerable molecular heterogeneity but was also elicited with clinical ROS1 inhibitors including foretinib and crizotinib. ROS1 inhibitors induced mitotic abnormalities and multinucleation in E-cadherin defective cells, phenotypes that were associated with a defect in cytokinesis and aberrant p120-catenin phosphorylation and localisation. In vivo, ROS1 inhibitors produced profound anti-tumour effects in multiple, distinct, models of E-cadherin defective breast cancer. This data therefore provides the pre-clinical rationale for assessing ROS1 inhibitors such as the licensed drug crizotinib in appropriately stratified patients.
Citation Format: Ilirjana Bajrami, Rebecca Marlow, Marieke van de Ven, Rachel Brough, Helen N. Pemberton, Jessica Frankum, Fei Fei Song, Rumana Rafiq, Asha Konde, Malini Menon, James Campbell, Aditi Gulati, Rahul Kumar, Stephen J. Pettitt, Mark D. Gurden, Marta Llorca Cardenosa, Irene Chong, Patrycja Gazinska, Fredrik Wallberg, Elinor J. Sawyer, Lesley-Ann Martin, Mitch Dowsett, Spiros Linardopoulos, Colm Ryan, Patrick W. Derksen, Jos Jonkers, Andrew N.J. Tutt, Alan Ashworth, Christopher J. Lord. E-cadherin/ROS1 inhibitor synthetic lethality in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2986.
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Affiliation(s)
| | | | | | - Rachel Brough
- 1The Institute of Cancer Research, London, United Kingdom
| | | | | | - Fei Fei Song
- 1The Institute of Cancer Research, London, United Kingdom
| | - Rumana Rafiq
- 1The Institute of Cancer Research, London, United Kingdom
| | - Asha Konde
- 1The Institute of Cancer Research, London, United Kingdom
| | - Malini Menon
- 1The Institute of Cancer Research, London, United Kingdom
| | - James Campbell
- 1The Institute of Cancer Research, London, United Kingdom
| | - Aditi Gulati
- 1The Institute of Cancer Research, London, United Kingdom
| | - Rahul Kumar
- 1The Institute of Cancer Research, London, United Kingdom
| | | | - Mark D. Gurden
- 1The Institute of Cancer Research, London, United Kingdom
| | | | - Irene Chong
- 1The Institute of Cancer Research, London, United Kingdom
| | | | | | | | | | - Mitch Dowsett
- 1The Institute of Cancer Research, London, United Kingdom
| | | | - Colm Ryan
- 4University College Dublin, Dublin, Ireland
| | | | - Jos Jonkers
- 3The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Alan Ashworth
- 6UCSF Helen Diller Family Comprehensive Cancer Centre, San Francisco, CA
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Bajrami I, Marlow R, van de Ven M, Brough R, Pemberton HN, Frankum J, Song F, Rafiq R, Konde A, Krastev DB, Menon M, Campbell J, Gulati A, Kumar R, Pettitt SJ, Gurden MD, Cardenosa ML, Chong I, Gazinska P, Wallberg F, Sawyer EJ, Martin LA, Dowsett M, Linardopoulos S, Natrajan R, Ryan CJ, Derksen PWB, Jonkers J, Tutt ANJ, Ashworth A, Lord CJ. E-Cadherin/ROS1 Inhibitor Synthetic Lethality in Breast Cancer. Cancer Discov 2018; 8:498-515. [PMID: 29610289 PMCID: PMC6296442 DOI: 10.1158/2159-8290.cd-17-0603] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 12/12/2017] [Accepted: 01/23/2018] [Indexed: 12/22/2022]
Abstract
The cell adhesion glycoprotein E-cadherin (CDH1) is commonly inactivated in breast tumors. Precision medicine approaches that exploit this characteristic are not available. Using perturbation screens in breast tumor cells with CRISPR/Cas9-engineered CDH1 mutations, we identified synthetic lethality between E-cadherin deficiency and inhibition of the tyrosine kinase ROS1. Data from large-scale genetic screens in molecularly diverse breast tumor cell lines established that the E-cadherin/ROS1 synthetic lethality was not only robust in the face of considerable molecular heterogeneity but was also elicited with clinical ROS1 inhibitors, including foretinib and crizotinib. ROS1 inhibitors induced mitotic abnormalities and multinucleation in E-cadherin-defective cells, phenotypes associated with a defect in cytokinesis and aberrant p120 catenin phosphorylation and localization. In vivo, ROS1 inhibitors produced profound antitumor effects in multiple models of E-cadherin-defective breast cancer. These data therefore provide the preclinical rationale for assessing ROS1 inhibitors, such as the licensed drug crizotinib, in appropriately stratified patients.Significance: E-cadherin defects are common in breast cancer but are currently not targeted with a precision medicine approach. Our preclinical data indicate that licensed ROS1 inhibitors, including crizotinib, should be repurposed to target E-cadherin-defective breast cancers, thus providing the rationale for the assessment of these agents in molecularly stratified phase II clinical trials. Cancer Discov; 8(4); 498-515. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 371.
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Affiliation(s)
- Ilirjana Bajrami
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Rebecca Marlow
- The Breast Cancer Now Research Unit, King's College London, London, United Kingdom
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging (MCCA) Preclinical Intervention Unit, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Rachel Brough
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Helen N Pemberton
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Jessica Frankum
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Feifei Song
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Rumana Rafiq
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Asha Konde
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Dragomir B Krastev
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Malini Menon
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - James Campbell
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Aditi Gulati
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Rahul Kumar
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Stephen J Pettitt
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Mark D Gurden
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Marta Llorca Cardenosa
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Biomedical Research Institute INCLIVA, Hospital Clinico Universitario Valencia, University of Valencia, Spain
| | - Irene Chong
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Patrycja Gazinska
- The Breast Cancer Now Research Unit, King's College London, London, United Kingdom
| | - Fredrik Wallberg
- FACS Core Facility, The Institute of Cancer Research, London, United Kingdom
| | - Elinor J Sawyer
- Division of Cancer Studies, Guy's Hospital, King's College London, London, United Kingdom
| | - Lesley-Ann Martin
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Mitch Dowsett
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Spiros Linardopoulos
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Colm J Ryan
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Patrick W B Derksen
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology and Cancer Genomics Netherlands, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Andrew N J Tutt
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- The Breast Cancer Now Research Unit, King's College London, London, United Kingdom
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California.
| | - Christopher J Lord
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom.
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
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Ryan CJ, Kennedy S, Bajrami I, Matallanas D, Lord CJ. A Compendium of Co-regulated Protein Complexes in Breast Cancer Reveals Collateral Loss Events. Cell Syst 2017; 5:399-409.e5. [PMID: 29032073 PMCID: PMC5660599 DOI: 10.1016/j.cels.2017.09.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 07/31/2017] [Accepted: 09/18/2017] [Indexed: 12/19/2022]
Abstract
Protein complexes are responsible for the bulk of activities within the cell, but how their behavior and abundance varies across tumors remains poorly understood. By combining proteomic profiles of breast tumors with a large-scale protein-protein interaction network, we have identified a set of 285 high-confidence protein complexes whose subunits have highly correlated protein abundance across tumor samples. We used this set to identify complexes that are reproducibly under- or overexpressed in specific breast cancer subtypes. We found that mutation or deletion of one subunit of a co-regulated complex was often associated with a collateral reduction in protein expression of additional complex members. This collateral loss phenomenon was typically evident from proteomic, but not transcriptomic, profiles, suggesting post-transcriptional control. Mutation of the tumor suppressor E-cadherin (CDH1) was associated with a collateral loss of members of the adherens junction complex, an effect we validated using an engineered model of E-cadherin loss.
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Affiliation(s)
- Colm J Ryan
- School of Computer Science, University College Dublin, Dublin 4, Ireland; Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland.
| | - Susan Kennedy
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Ilirjana Bajrami
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - David Matallanas
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Christopher J Lord
- The Breast Cancer Now Toby Robins Breast Cancer Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
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Pettitt SJ, Krastev DB, Pemberton HN, Fontebasso Y, Frankum J, Rehman FL, Brough R, Song F, Bajrami I, Rafiq R, Wallberg F, Kozarewa I, Fenwick K, Armisen-Garrido J, Swain A, Gulati A, Campbell J, Ashworth A, Lord CJ. Genome-wide barcoded transposon screen for cancer drug sensitivity in haploid mouse embryonic stem cells. Sci Data 2017; 4:170020. [PMID: 28248920 PMCID: PMC5332012 DOI: 10.1038/sdata.2017.20] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 01/05/2017] [Indexed: 12/21/2022] Open
Abstract
We describe a screen for cellular response to drugs that makes use of haploid embryonic stem cells. We generated ten libraries of mutants with piggyBac gene trap transposon integrations, totalling approximately 100,000 mutant clones. Random barcode sequences were inserted into the transposon vector to allow the number of cells bearing each insertion to be measured by amplifying and sequencing the barcodes. These barcodes were associated with their integration sites by inverse PCR. We exposed these libraries to commonly used cancer drugs and profiled changes in barcode abundance by Ion Torrent sequencing in order to identify mutations that conferred sensitivity. Drugs tested included conventional chemotherapeutics as well as targeted inhibitors of topoisomerases, poly(ADP-ribose) polymerase (PARP), Hsp90 and WEE1.
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Affiliation(s)
- Stephen J. Pettitt
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Dragomir B. Krastev
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Helen N. Pemberton
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Yari Fontebasso
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Jessica Frankum
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Farah L. Rehman
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Rachel Brough
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Feifei Song
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Ilirjana Bajrami
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Rumana Rafiq
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Fredrik Wallberg
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Iwanka Kozarewa
- Tumour Profiling Unit, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Kerry Fenwick
- Tumour Profiling Unit, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Javier Armisen-Garrido
- Tumour Profiling Unit, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Amanda Swain
- Tumour Profiling Unit, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Aditi Gulati
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - James Campbell
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Alan Ashworth
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Christopher J. Lord
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
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17
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Abstract
When the BRCA1 and BRCA2 tumour suppressor genes were identified in the early 1990s, the immediate implications of mapping, cloning and delineating the sequence of these genes were that individuals in families with a BRCA gene mutation could be tested for the presence of a mutation and their risk of developing cancer could be predicted. Over time though, the discovery of BRCA1 and BRCA2 has had a much greater influence than many might have imagined. In this review, we discuss how the discovery of BRCA1 and BRCA2 has not only provided an understanding of the molecular processes that drive tumourigenesis but also reignited an interest in therapeutically exploiting loss-of-function alterations in tumour suppressor genes.
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Affiliation(s)
| | - Ilirjana Bajrami
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer Research, London, UK
| | | | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer Research, London, UK
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18
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Miller RE, Brough R, Bajrami I, Williamson CT, McDade S, Campbell J, Kigozi A, Rafiq R, Pemberton H, Natrajan R, Joel J, Astley H, Mahoney C, Moore JD, Torrance C, Gordan JD, Webber JT, Levin RS, Shokat KM, Bandyopadhyay S, Lord CJ, Ashworth A. Synthetic Lethal Targeting of ARID1A-Mutant Ovarian Clear Cell Tumors with Dasatinib. Mol Cancer Ther 2016; 15:1472-84. [PMID: 27364904 DOI: 10.1158/1535-7163.mct-15-0554] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 04/06/2016] [Indexed: 11/16/2022]
Abstract
New targeted approaches to ovarian clear cell carcinomas (OCCC) are needed, given the limited treatment options in this disease and the poor response to standard chemotherapy. Using a series of high-throughput cell-based drug screens in OCCC tumor cell models, we have identified a synthetic lethal (SL) interaction between the kinase inhibitor dasatinib and a key driver in OCCC, ARID1A mutation. Imposing ARID1A deficiency upon a variety of human or mouse cells induced dasatinib sensitivity, both in vitro and in vivo, suggesting that this is a robust synthetic lethal interaction. The sensitivity of ARID1A-deficient cells to dasatinib was associated with G1-S cell-cycle arrest and was dependent upon both p21 and Rb. Using focused siRNA screens and kinase profiling, we showed that ARID1A-mutant OCCC tumor cells are addicted to the dasatinib target YES1. This suggests that dasatinib merits investigation for the treatment of patients with ARID1A-mutant OCCC. Mol Cancer Ther; 15(7); 1472-84. ©2016 AACR.
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Affiliation(s)
- Rowan E Miller
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Rachel Brough
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Ilirjana Bajrami
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Chris T Williamson
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Simon McDade
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, United Kingdom
| | - James Campbell
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Asha Kigozi
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Rumana Rafiq
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Helen Pemberton
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Rachel Natrajan
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Josephine Joel
- Horizon Discovery, Waterbeach, Cambridge, United Kingdom
| | - Holly Astley
- Horizon Discovery, Waterbeach, Cambridge, United Kingdom
| | - Claire Mahoney
- Horizon Discovery, Waterbeach, Cambridge, United Kingdom
| | | | - Chris Torrance
- Horizon Discovery, Waterbeach, Cambridge, United Kingdom
| | - John D Gordan
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - James T Webber
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Rebecca S Levin
- Cellular and Molecular Pharmacology University of California, San Francisco, San Francisco, California
| | - Kevan M Shokat
- Cellular and Molecular Pharmacology University of California, San Francisco, San Francisco, California. Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California
| | - Sourav Bandyopadhyay
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Christopher J Lord
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom.
| | - Alan Ashworth
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom.
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19
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Campbell J, Ryan CJ, Brough R, Bajrami I, Pemberton HN, Chong IY, Costa-Cabral S, Frankum J, Gulati A, Holme H, Miller R, Postel-Vinay S, Rafiq R, Wei W, Williamson CT, Quigley DA, Tym J, Al-Lazikani B, Fenton T, Natrajan R, Strauss SJ, Ashworth A, Lord CJ. Large-Scale Profiling of Kinase Dependencies in Cancer Cell Lines. Cell Rep 2016; 14:2490-501. [PMID: 26947069 PMCID: PMC4802229 DOI: 10.1016/j.celrep.2016.02.023] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/07/2015] [Accepted: 02/01/2016] [Indexed: 12/27/2022] Open
Abstract
One approach to identifying cancer-specific vulnerabilities and therapeutic targets is to profile genetic dependencies in cancer cell lines. Here, we describe data from a series of siRNA screens that identify the kinase genetic dependencies in 117 cancer cell lines from ten cancer types. By integrating the siRNA screen data with molecular profiling data, including exome sequencing data, we show how vulnerabilities/genetic dependencies that are associated with mutations in specific cancer driver genes can be identified. By integrating additional data sets into this analysis, including protein-protein interaction data, we also demonstrate that the genetic dependencies associated with many cancer driver genes form dense connections on functional interaction networks. We demonstrate the utility of this resource by using it to predict the drug sensitivity of genetically or histologically defined subsets of tumor cell lines, including an increased sensitivity of osteosarcoma cell lines to FGFR inhibitors and SMAD4 mutant tumor cells to mitotic inhibitors.
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MESH Headings
- Cell Line, Tumor
- Gene Expression Profiling
- Humans
- Mutation
- Neoplasms/enzymology
- Neoplasms/genetics
- Neoplasms/pathology
- Protein Kinases/chemistry
- Protein Kinases/genetics
- Protein Kinases/metabolism
- RNA Interference
- RNA, Small Interfering/metabolism
- Receptor, ErbB-2/antagonists & inhibitors
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/metabolism
- Receptor, Fibroblast Growth Factor, Type 1/antagonists & inhibitors
- Receptor, Fibroblast Growth Factor, Type 1/genetics
- Receptor, Fibroblast Growth Factor, Type 1/metabolism
- Smad4 Protein/antagonists & inhibitors
- Smad4 Protein/genetics
- Smad4 Protein/metabolism
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Affiliation(s)
- James Campbell
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - Colm J Ryan
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
| | - Rachel Brough
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - Ilirjana Bajrami
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - Helen N Pemberton
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - Irene Y Chong
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK; Royal Marsden Hospital, London SW3 6JJ, UK
| | - Sara Costa-Cabral
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - Jessica Frankum
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - Aditi Gulati
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - Harriet Holme
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK; UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Rowan Miller
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK; UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Sophie Postel-Vinay
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK; Gustave Roussy Cancer Campus, 94805 Villejuif, France
| | - Rumana Rafiq
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - Wenbin Wei
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - Chris T Williamson
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - David A Quigley
- UCSF Helen Diller Family Comprehensive Cancer Centre, San Francisco, CA 94158, USA
| | - Joe Tym
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, Sutton SM2 5NG, UK
| | - Bissan Al-Lazikani
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, Sutton SM2 5NG, UK
| | - Timothy Fenton
- UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Rachael Natrajan
- Functional Genomics Laboratory, The Breast Cancer Now Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Sandra J Strauss
- UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Alan Ashworth
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK.
| | - Christopher J Lord
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK.
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20
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Aarts M, Bajrami I, Herrera-Abreu MT, Elliott R, Brough R, Ashworth A, Lord CJ, Turner NC. Functional Genetic Screen Identifies Increased Sensitivity to WEE1 Inhibition in Cells with Defects in Fanconi Anemia and HR Pathways. Mol Cancer Ther 2015; 14:865-76. [PMID: 25673822 PMCID: PMC6485454 DOI: 10.1158/1535-7163.mct-14-0845] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 02/04/2015] [Indexed: 01/11/2023]
Abstract
WEE1 kinase regulates CDK1 and CDK2 activity to facilitate DNA replication during S-phase and to prevent unscheduled entry into mitosis. WEE1 inhibitors synergize with DNA-damaging agents that arrest cells in S-phase by triggering direct mitotic entry without completing DNA synthesis, resulting in catastrophic chromosome fragmentation and apoptosis. Here, we investigated how WEE1 inhibition could be best exploited for cancer therapy by performing a functional genetic screen to identify novel determinants of sensitivity to WEE1 inhibition. Inhibition of kinases that regulate CDK activity, CHK1 and MYT1, synergized with WEE1 inhibition through both increased replication stress and forced mitotic entry of S-phase cells. Loss of multiple components of the Fanconi anemia (FA) and homologous recombination (HR) pathways, in particular DNA helicases, sensitized to WEE1 inhibition. Silencing of FA/HR genes resulted in excessive replication stress and nucleotide depletion following WEE1 inhibition, which ultimately led to increased unscheduled mitotic entry. Our results suggest that cancers with defects in FA and HR pathways may be targeted by WEE1 inhibition, providing a basis for a novel synthetic lethal strategy for cancers harboring FA/HR defects.
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Affiliation(s)
- Marieke Aarts
- CRUK Gene Function Laboratory, Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Ilirjana Bajrami
- CRUK Gene Function Laboratory, Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Maria T Herrera-Abreu
- CRUK Gene Function Laboratory, Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Richard Elliott
- CRUK Gene Function Laboratory, Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Rachel Brough
- CRUK Gene Function Laboratory, Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Alan Ashworth
- CRUK Gene Function Laboratory, Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Christopher J Lord
- CRUK Gene Function Laboratory, Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Nicholas C Turner
- CRUK Gene Function Laboratory, Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom. Breast Unit, Royal Marsden Hospital, London, United Kingdom.
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21
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Miller R, Bajrami I, Brough R, Konde A, Campbell J, Rafiq R, Ashworth A, Lord C. 318 Novel therapeutic targets for ARID1A mutant ovarian clear cell carcinoma (OCCC). Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)70444-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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22
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Bajrami I, Pettitt S, Brough R, Pemberton H, Kastrev D, Fontebasso Y, Frankum J, Campbell J, Ashworth A, Lord C. 147 An integrated approach for identifying E-cadherin synthetic lethality networks. Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)70273-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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23
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Pettitt S, Krastev D, Pemberton H, Fontebasso Y, Bajrami I, Kozarewa I, Frankum J, Rafiq R, Campbell J, Brough R, Ashworth A, Lord C. 88 Genome-wide drug sensitivity screens in haploid mouse embryonic stem cells. Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)70214-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Gao S, Bajrami I, Verrill C, Kigozi A, Ouaret D, Aleksic T, Asher R, Han C, Allen P, Bailey D, Feller S, Kashima T, Athanasou N, Blay JY, Schmitz S, Machiels JP, Upile N, Jones TM, Thalmann G, Ashraf SQ, Wilding JL, Bodmer WF, Middleton MR, Ashworth A, Lord CJ, Macaulay VM. Dsh homolog DVL3 mediates resistance to IGFIR inhibition by regulating IGF-RAS signaling. Cancer Res 2014; 74:5866-77. [PMID: 25168481 DOI: 10.1158/0008-5472.can-14-0806] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Drugs that inhibit insulin-like growth factor 1 (IGFI) receptor IGFIR were encouraging in early trials, but predictive biomarkers were lacking and the drugs provided insufficient benefit in unselected patients. In this study, we used genetic screening and downstream validation to identify the WNT pathway element DVL3 as a mediator of resistance to IGFIR inhibition. Sensitivity to IGFIR inhibition was enhanced specifically in vitro and in vivo by genetic or pharmacologic blockade of DVL3. In breast and prostate cancer cells, sensitization tracked with enhanced MEK-ERK activation and relied upon MEK activity and DVL3 expression. Mechanistic investigations showed that DVL3 is present in an adaptor complex that links IGFIR to RAS, which includes Shc, growth factor receptor-bound-2 (Grb2), son-of-sevenless (SOS), and the tumor suppressor DAB2. Dual DVL and DAB2 blockade synergized in activating ERKs and sensitizing cells to IGFIR inhibition, suggesting a nonredundant role for DVL3 in the Shc-Grb2-SOS complex. Clinically, tumors that responded to IGFIR inhibition contained relatively lower levels of DVL3 protein than resistant tumors, and DVL3 levels in tumors correlated inversely with progression-free survival in patients treated with IGFIR antibodies. Because IGFIR does not contain activating mutations analogous to EGFR variants associated with response to EGFR inhibitors, we suggest that IGF signaling achieves an equivalent integration at the postreceptor level through adaptor protein complexes, influencing cellular dependence on the IGF axis and identifying a patient population with potential to benefit from IGFIR inhibition.
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Affiliation(s)
- Shan Gao
- Department of Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Ilirjana Bajrami
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Clare Verrill
- Department of Cellular Pathology and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Asha Kigozi
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Djamila Ouaret
- Department of Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Tamara Aleksic
- Department of Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Ruth Asher
- Department of Cellular Pathology and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Cheng Han
- Department of Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Paul Allen
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Deborah Bailey
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Stephan Feller
- Department of Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Takeshi Kashima
- Department of Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Nicholas Athanasou
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, Department of Pathology, Nuffield Orthopaedic Centre, Oxford, United Kingdom
| | - Jean-Yves Blay
- University Claude Bernard Lyon I, Centre Léon Bérard, Department of Medicine, Lyon, France
| | - Sandra Schmitz
- Service d'oncologie médicale, Cliniques universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Jean-Pascal Machiels
- Service d'oncologie médicale, Cliniques universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Nav Upile
- Liverpool CR-UK Centre, Department of Molecular and Clinical Cancer Medicine, Royal Liverpool University Hospital, Liverpool, United Kingdom
| | - Terry M Jones
- Liverpool CR-UK Centre, Department of Molecular and Clinical Cancer Medicine, Royal Liverpool University Hospital, Liverpool, United Kingdom
| | | | - Shazad Q Ashraf
- Department of Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Jennifer L Wilding
- Department of Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Walter F Bodmer
- Department of Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Mark R Middleton
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Trust, Churchill Hospital, Oxford, Liverpool, United Kingdom
| | - Alan Ashworth
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Christopher J Lord
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Valentine M Macaulay
- Department of Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom. Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Trust, Churchill Hospital, Oxford, Liverpool, United Kingdom.
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25
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Hewish M, Fontebasso Y, Martin SA, Elliott R, Perks KL, Konde A, Bajrami I, Weverwijk AV, Cunningham D, Lord CJ, Ashworth A. Abstract 2931: Cancer cells deficient in DNA mismatch repair (MMR) are selectively sensitive to inhibition of the DNA dependent protein kinase (DNA-PK). Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-2931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Many solid tumors, including a significant proportion of colorectal, endometrial, gastric and urothelial tract cancers, are functionally deficient in MMR. This results in an altered clinicopathological phenotype. With the objective of identifying potential MMR-deficient (dMMR) synthetic lethal vulnerabilities, we performed a large scale screen of drugs which included a library of kinase inhibitors.
Using a pair of isogenic colorectal cancer (CRC) cell lines, deficient and proficient for MLH1, we identified that exposure to an inhibitor of the catalytic subunit of DNA-PK (Ku-57788) was associated with a reduction in cell viability in MLH1-deficient cells at nanomolar concentrations. Validation studies demonstrated a ten-fold difference in sensitivity in clonogenic assays and a significant correlation between MMR status and Ku-57788 across a panel of cancer cell lines. Inhibition of expression of DNA-PK using RNA interference reproduced the dMMR selectivity. The dMMR phenotype was associated with a reduction in cellular proliferation, leading to apoptosis. Given the role of MMR in the repair of oxidative damage, we assayed levels of 8-oxo-dG, a marker of oxidatively damaged DNA, and observed increased levels in dMMR cells. Upregulation of the anti-oxidant response was observed on exposure to Ku-57788, whilst addition of antioxidants to culture media resulted in complete abrogation of dMMR selectivity. We assessed the effect of combining Ku-57788 with standard chemotherapeutics used in CRC and observed a supra-additive effect with irinotecan. In vivo, treatment of CD1 nude mice with a DNA-PK inhibitor was associated with a reduction in growth of MLH1-deficient cancer cell line xenografts with no effect observed in MLH1-proficiency.
We report for the first time that inhibition of DNA-PKcs using small molecule inhibitors, either as a single agent or in combination with chemotherapeutics, may be a potential therapeutic strategy for the treatment of cancers deficient in DNA MMR.
Citation Format: Madeleine Hewish, Yari Fontebasso, Sarah A. Martin, Richard Elliott, Kerry L. Perks, Asha Konde, Ilirjana Bajrami, Antoinette Van Weverwijk, David Cunningham, Christopher J. Lord, Alan Ashworth. Cancer cells deficient in DNA mismatch repair (MMR) are selectively sensitive to inhibition of the DNA dependent protein kinase (DNA-PK). [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2931. doi:10.1158/1538-7445.AM2014-2931
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Affiliation(s)
| | | | | | | | | | - Asha Konde
- 1Institute of Cancer Research, London, United Kingdom
| | | | | | | | | | - Alan Ashworth
- 1Institute of Cancer Research, London, United Kingdom
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Chong I, Cunningham D, Campbell J, Bajrami I, Brough R, Frankum J, Lord C, Ashworth A. Druggable Genetic Dependencies for Molecularly Defined Subgroups of Oesophageal Cancer Identified From High-Throughput Functional Profiling. Ann Oncol 2014. [DOI: 10.1093/annonc/mdu164.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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27
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Natrajan R, Wilkerson PM, Marchiò C, Piscuoglio S, Ng CKY, Wai P, Lambros MB, Samartzis EP, Dedes KJ, Frankum J, Bajrami I, Kopec A, Mackay A, A'hern R, Fenwick K, Kozarewa I, Hakas J, Mitsopoulos C, Hardisson D, Lord CJ, Kumar-Sinha C, Ashworth A, Weigelt B, Sapino A, Chinnaiyan AM, Maher CA, Reis-Filho JS. Characterization of the genomic features and expressed fusion genes in micropapillary carcinomas of the breast. J Pathol 2014; 232:553-65. [PMID: 24395524 PMCID: PMC4013428 DOI: 10.1002/path.4325] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 12/04/2013] [Accepted: 12/29/2013] [Indexed: 12/30/2022]
Abstract
Micropapillary carcinoma (MPC) is a rare histological special type of breast cancer, characterized by an aggressive clinical behaviour and a pattern of copy number aberrations (CNAs) distinct from that of grade- and oestrogen receptor (ER)-matched invasive carcinomas of no special type (IC-NSTs). The aims of this study were to determine whether MPCs are underpinned by a recurrent fusion gene(s) or mutations in 273 genes recurrently mutated in breast cancer. Sixteen MPCs were subjected to microarray-based comparative genomic hybridization (aCGH) analysis and Sequenom OncoCarta mutation analysis. Eight and five MPCs were subjected to targeted capture and RNA sequencing, respectively. aCGH analysis confirmed our previous observations about the repertoire of CNAs of MPCs. Sequencing analysis revealed a spectrum of mutations similar to those of luminal B IC-NSTs, and recurrent mutations affecting mitogen-activated protein kinase family genes and NBPF10. RNA-sequencing analysis identified 17 high-confidence fusion genes, eight of which were validated and two of which were in-frame. No recurrent fusions were identified in an independent series of MPCs and IC-NSTs. Forced expression of in-frame fusion genes (SLC2A1-FAF1 and BCAS4-AURKA) resulted in increased viability of breast cancer cells. In addition, genomic disruption of CDK12 caused by out-of-frame rearrangements was found in one MPC and in 13% of HER2-positive breast cancers, identified through a re-analysis of publicly available massively parallel sequencing data. In vitro analyses revealed that CDK12 gene disruption results in sensitivity to PARP inhibition, and forced expression of wild-type CDK12 in a CDK12-null cell line model resulted in relative resistance to PARP inhibition. Our findings demonstrate that MPCs are neither defined by highly recurrent mutations in the 273 genes tested, nor underpinned by a recurrent fusion gene. Although seemingly private genetic events, some of the fusion transcripts found in MPCs may play a role in maintenance of a malignant phenotype and potentially offer therapeutic opportunities.
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Affiliation(s)
- Rachael Natrajan
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer ResearchLondon, UK
| | - Paul M Wilkerson
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer ResearchLondon, UK
| | | | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan-Kettering Cancer CenterNew York, NY, USA
| | - Charlotte KY Ng
- Department of Pathology, Memorial Sloan-Kettering Cancer CenterNew York, NY, USA
| | - Patty Wai
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer ResearchLondon, UK
| | - Maryou B Lambros
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer ResearchLondon, UK
| | | | | | - Jessica Frankum
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer ResearchLondon, UK
| | - Ilirjana Bajrami
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer ResearchLondon, UK
| | - Alicja Kopec
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer ResearchLondon, UK
| | - Alan Mackay
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer ResearchLondon, UK
| | - Roger A'hern
- Cancer Research UK Clinical Trials Unit, The Institute of Cancer ResearchSutton, UK
| | - Kerry Fenwick
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer ResearchLondon, UK
| | - Iwanka Kozarewa
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer ResearchLondon, UK
| | - Jarle Hakas
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer ResearchLondon, UK
| | - Costas Mitsopoulos
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer ResearchLondon, UK
| | - David Hardisson
- Department of Pathology, Hospital Universitario La Paz, Universidad Autonoma de Madrid, Hospital La Paz Institute for Health Research (IdiPAZ)Madrid, Spain
| | - Christopher J Lord
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer ResearchLondon, UK
| | - Chandan Kumar-Sinha
- Michigan Center for Translational Pathology (MCTP), Department of Pathology, University of MichiganAnn Arbor, MI, USA
| | - Alan Ashworth
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer ResearchLondon, UK
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan-Kettering Cancer CenterNew York, NY, USA
| | - Anna Sapino
- Department of Medical Sciences, University of TurinTurin, Italy
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology (MCTP), Department of Pathology, University of MichiganAnn Arbor, MI, USA
| | - Christopher A Maher
- Washington University Genome Institute, Washington UniversitySt Louis, MO, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan-Kettering Cancer CenterNew York, NY, USA
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Postel-Vinay S, Bajrami I, Friboulet L, Elliott R, Fontebasso Y, Dorvault N, Olaussen KA, André F, Soria JC, Lord CJ, Ashworth A. A high-throughput screen identifies PARP1/2 inhibitors as a potential therapy for ERCC1-deficient non-small cell lung cancer. Oncogene 2013; 32:5377-87. [PMID: 23934192 DOI: 10.1038/onc.2013.311] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 06/08/2013] [Accepted: 06/10/2013] [Indexed: 12/29/2022]
Abstract
Excision repair cross-complementation group 1 (ERCC1) is a DNA repair enzyme that is frequently defective in non-small cell lung cancer (NSCLC). Although low ERCC1 expression correlates with platinum sensitivity, the clinical effectiveness of platinum therapy is limited, highlighting the need for alternative treatment strategies. To discover new mechanism-based therapeutic strategies for ERCC1-defective tumours, we performed high-throughput drug screens in an isogenic NSCLC model of ERCC1 deficiency and dissected the mechanism underlying ERCC1-selective effects by studying molecular biomarkers of tumour cell response. The high-throughput screens identified multiple clinical poly (ADP-ribose) polymerase 1 and 2 (PARP1/2) inhibitors, such as olaparib (AZD-2281), niraparib (MK-4827) and BMN 673, as being selective for ERCC1 deficiency. We observed that ERCC1-deficient cells displayed a significant delay in double-strand break repair associated with a profound and prolonged G₂/M arrest following PARP1/2 inhibitor treatment. Importantly, we found that ERCC1 isoform 202, which has recently been shown to mediate platinum sensitivity, also modulated PARP1/2 sensitivity. A PARP1/2 inhibitor-synthetic lethal siRNA screen revealed that ERCC1 deficiency was epistatic with homologous recombination deficiency. However, ERCC1-deficient cells did not display a defect in RAD51 foci formation, suggesting that ERCC1 might be required to process PARP1/2 inhibitor-induced DNA lesions before DNA strand invasion. PARP1 silencing restored PARP1/2 inhibitor resistance in ERCC1-deficient cells but had no effect in ERCC1-proficient cells, supporting the hypothesis that PARP1 might be required for the ERCC1 selectivity of PARP1/2 inhibitors. This study suggests that PARP1/2 inhibitors as a monotherapy could represent a novel therapeutic strategy for NSCLC patients with ERCC1-deficient tumours.
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Affiliation(s)
- S Postel-Vinay
- 1] The Breakthrough Breast Cancer Research Centre and CRUK Gene Function Laboratory, Institute of Cancer Research, London, UK [2] Département de médecine-Unité INSERM 981, Institut Gustave Roussy, Villejuif, France
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29
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Bajrami I, Frankum JR, Konde A, Miller RE, Rehman FL, Brough R, Campbell J, Sims D, Rafiq R, Hooper S, Chen L, Kozarewa I, Assiotis I, Fenwick K, Natrajan R, Lord CJ, Ashworth A. Genome-wide profiling of genetic synthetic lethality identifies CDK12 as a novel determinant of PARP1/2 inhibitor sensitivity. Cancer Res 2013; 74:287-97. [PMID: 24240700 DOI: 10.1158/0008-5472.can-13-2541] [Citation(s) in RCA: 262] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Small-molecule inhibitors of PARP1/2, such as olaparib, have been proposed to serve as a synthetic lethal therapy for cancers that harbor BRCA1 or BRCA2 mutations. Indeed, in clinical trials, PARP1/2 inhibitors elicit sustained antitumor responses in patients with germline BRCA gene mutations. In hypothesizing that additional genetic determinants might direct use of these drugs, we conducted a genome-wide synthetic lethal screen for candidate olaparib sensitivity genes. In support of this hypothesis, the set of identified genes included known determinants of olaparib sensitivity, such as BRCA1, RAD51, and Fanconi's anemia susceptibility genes. In addition, the set included genes implicated in established networks of DNA repair, DNA cohesion, and chromatin remodeling, none of which were known previously to confer sensitivity to PARP1/2 inhibition. Notably, integration of the list of candidate sensitivity genes with data from tumor DNA sequencing studies identified CDK12 deficiency as a clinically relevant biomarker of PARP1/2 inhibitor sensitivity. In models of high-grade serous ovarian cancer (HGS-OVCa), CDK12 attenuation was sufficient to confer sensitivity to PARP1/2 inhibition, suppression of DNA repair via homologous recombination, and reduced expression of BRCA1. As one of only nine genes known to be significantly mutated in HGS-OVCa, CDK12 has properties that should confirm interest in its use as a biomarker, particularly in ongoing clinical trials of PARP1/2 inhibitors and other agents that trigger replication fork arrest.
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Affiliation(s)
- Ilirjana Bajrami
- Authors' Affiliations: The CRUK Gene Function Laboratory, Functional Genomics Laboratory, Breakthrough Breast Cancer Research Centre, and Tumour Profiling Unit, The Institute of Cancer Research, London, United Kingdom
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30
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Shen Y, Rehman FL, Feng Y, Boshuizen J, Bajrami I, Elliott R, Wang B, Lord CJ, Post LE, Ashworth A. BMN 673, a novel and highly potent PARP1/2 inhibitor for the treatment of human cancers with DNA repair deficiency. Clin Cancer Res 2013; 19:5003-15. [PMID: 23881923 PMCID: PMC6485449 DOI: 10.1158/1078-0432.ccr-13-1391] [Citation(s) in RCA: 367] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE PARP1/2 inhibitors are a class of anticancer agents that target tumor-specific defects in DNA repair. Here, we describe BMN 673, a novel, highly potent PARP1/2 inhibitor with favorable metabolic stability, oral bioavailability, and pharmacokinetic properties. EXPERIMENTAL DESIGN Potency and selectivity of BMN 673 was determined by biochemical assays. Anticancer activity either as a single-agent or in combination with other antitumor agents was evaluated both in vitro and in xenograft cancer models. RESULTS BMN 673 is a potent PARP1/2 inhibitor (PARP1 IC50 = 0.57 nmol/L), but it does not inhibit other enzymes that we have tested. BMN 673 exhibits selective antitumor cytotoxicity and elicits DNA repair biomarkers at much lower concentrations than earlier generation PARP1/2 inhibitors (such as olaparib, rucaparib, and veliparib). In vitro, BMN 673 selectively targeted tumor cells with BRCA1, BRCA2, or PTEN gene defects with 20- to more than 200-fold greater potency than existing PARP1/2 inhibitors. BMN 673 is readily orally bioavailable, with more than 40% absolute oral bioavailability in rats when dosed in carboxylmethyl cellulose. Oral administration of BMN 673 elicited remarkable antitumor activity in vivo; xenografted tumors that carry defects in DNA repair due to BRCA mutations or PTEN deficiency were profoundly sensitive to oral BMN 673 treatment at well-tolerated doses in mice. Synergistic or additive antitumor effects were also found when BMN 673 was combined with temozolomide, SN38, or platinum drugs. CONCLUSION BMN 673 is currently in early-phase clinical development and represents a promising PARP1/2 inhibitor with potentially advantageous features in its drug class.
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Affiliation(s)
- Yuqiao Shen
- BioMarin Pharmaceutical Inc., 105 Digital Drive, Novato, CA 94949, USA
| | - Farah L Rehman
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK
| | - Ying Feng
- BioMarin Pharmaceutical Inc., 105 Digital Drive, Novato, CA 94949, USA
| | - Julia Boshuizen
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK
| | - Ilirjana Bajrami
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK
| | - Richard Elliott
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK
| | - Bing Wang
- BioMarin Pharmaceutical Inc., 105 Digital Drive, Novato, CA 94949, USA
| | - Christopher J. Lord
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK
| | - Leonard E. Post
- BioMarin Pharmaceutical Inc., 105 Digital Drive, Novato, CA 94949, USA
| | - Alan Ashworth
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK
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31
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Neijenhuis S, Bajrami I, Miller R, Lord CJ, Ashworth A. Identification of miRNA modulators to PARP inhibitor response. DNA Repair (Amst) 2013; 12:394-402. [PMID: 23570906 DOI: 10.1016/j.dnarep.2013.02.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 02/08/2013] [Accepted: 02/11/2013] [Indexed: 02/02/2023]
Abstract
Based on the principle of synthetic lethality, PARP inhibitors have been shown to be very effective in killing cells deficient in homologous recombination (HR), such as those bearing mutations in BRCA1/2. However, questions regarding their wider use persist and other determinants of responsiveness to PARP inhibitor remain to be fully explored. MicroRNAs (miRNAs) are small non-coding RNAs, which serve as post-transcriptional regulators of gene expression and are involved in a wide variety of cellular processes, including the DNA damage response (DDR). However, little is known about whether miRNAs might influence sensitivity to PARP inhibitors. To investigate this, we performed a high throughput miRNA mimetic screen, which identified several miRNAs whose over-expression results in sensitization to the clinical PARP inhibitor olaparib. In particular, our findings indicate that hsa-miR-107 and hsa-miR-222 regulate the DDR and sensitise tumour cells to olaparib by repressing expression of RAD51, thus impairing DSB repair by HR. Moreover, elevated expression of hsa-miR-107 has been observed in a subset of ovarian clear cell carcinomas, which correlates with PARP inhibitor sensitivity and reduced RAD51 expression. Taken together, these observations raise the possibility that these miRNAs could be used as biomarkers to identify patients that may benefit from treatment with PARP inhibitors.
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Affiliation(s)
- Sari Neijenhuis
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK
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32
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Bjerke L, Mackay A, Nandhabalan M, Burford A, Jury A, Popov S, Bax DA, Carvalho D, Taylor KR, Vinci M, Bajrami I, McGonnell IM, Lord CJ, Reis RM, Hargrave D, Ashworth A, Workman P, Jones C. Histone H3.3. mutations drive pediatric glioblastoma through upregulation of MYCN. Cancer Discov 2013; 3:512-9. [PMID: 23539269 PMCID: PMC3763966 DOI: 10.1158/2159-8290.cd-12-0426] [Citation(s) in RCA: 221] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED Children and young adults with glioblastoma (GBM) have a median survival rate of only 12 to 15 months, and these GBMs are clinically and biologically distinct from histologically similar cancers in older adults. They are defined by highly specific mutations in the gene encoding the histone H3.3 variant H3F3A , occurring either at or close to key residues marked by methylation for regulation of transcription—K27 and G34. Here, we show that the cerebral hemisphere-specific G34 mutation drives a distinct expression signature through differential genomic binding of the K36 trimethylation mark (H3K36me3). The transcriptional program induced recapitulates that of the developing forebrain, and involves numerous markers of stem-cell maintenance, cell-fate decisions, and self-renewal.Critically, H3F3A G34 mutations cause profound upregulation of MYCN , a potent oncogene that is causative of GBMs when expressed in the correct developmental context. This driving aberration is selectively targetable in this patient population through inhibiting kinases responsible for stabilization of the protein. SIGNIFICANCE We provide the mechanistic explanation for how the fi rst histone gene mutation inhuman disease biology acts to deliver MYCN, a potent tumorigenic initiator, into a stem-cell compartment of the developing forebrain, selectively giving rise to incurable cerebral hemispheric GBM. Using synthetic lethal approaches to these mutant tumor cells provides a rational way to develop novel and highly selective treatment strategies
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Affiliation(s)
- Lynn Bjerke
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Alan Mackay
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Meera Nandhabalan
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Anna Burford
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Alexa Jury
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Sergey Popov
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Dorine A Bax
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Diana Carvalho
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
- University of Coimbra, Portugal
- ICVS, University of Minho, Braga, Portugal
| | - Kathryn R Taylor
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Maria Vinci
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Ilirjana Bajrami
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | | | - Christopher J Lord
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Rui M Reis
- ICVS, University of Minho, Braga, Portugal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos SP, Brazil
| | | | - Alan Ashworth
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Paul Workman
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Chris Jones
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
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Pettitt SJ, Rehman FL, Bajrami I, Pemberton H, Brough R, Kozarewa I, Lord CJ, Ashworth A. Abstract A36: A transposon-based genetic screen in haploid mouse embryonic stem cells identifies Parp1 as a major mediator of olaparib toxicity. Mol Cancer Ther 2013. [DOI: 10.1158/1535-7163.pms-a36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Haploid embryonic stem cells have recently been isolated from activated mouse oocytes. Due to the ease of random gene disruption in haploid cells, these have great promise for forward genetic screens. We have used the piggyBac transposon, a highly active insertional mutagen, to generate stable libraries of mutants in these cells. These libraries comprise at least 200,000 mutants. We have exposed these libraries to several drugs to generate resistant clones. Mapping the transposon integration sites in these clones can identify genes required for toxicity of the drugs to normal cells. In a proof of principle screen we isolated clones resistant to 6-thioguanine that had insertions in components of the DNA mismatch repair pathway, which is known to be required for toxicity of this purine analogue.
In a screen for mutants resistant to the poly-(ADP-ribose) polymerase (PARP) 1/2 inhibitor olaparib, we identified two mutants with different insertions in Parp1 that were more than 100-fold resistant to olaparib than wild type cells. These mutants lacked Parp1 protein expression and radiation-induced poly-(ADP-ribose) formation and were also resistant to other PARP inhibitors. Removal of the transposon by re-expressing transposase in the cells resulted in reversion of the phenotype. Knockdown of PARP1 by siRNA in human cell lines also led to olaparib resistance. The finding that PARP1 itself is required for toxicity of olaparib supports the hypothesis that PARP1 is a component of the toxic lesion. There were several other resistant mutants isolated in the screen, but no other genes had multiple resistant clones with insertions. Removal of the transposon did not revert the phenotype in these clones, suggesting that they arose from background mutations in cell culture. Interestingly many of these clones also lacked Parp1 protein expression, suggesting that inactivation of Parp1 may also be the mechanism of resistance. Therefore Parp1 may be the major determinant of olaparib toxicity to wild type cells.
Conditional gene targeting technology is well-established in diploid embryonic stem cells. By combining targeted mutation in a cancer gene with random transposon mutagenesis, it may also be possible to use this screening system to identify synthetic lethal interactions. We have successfully used gene targeting to modify these cells (at the Hprt locus) and are developing strategies to monitor the loss of mutants from a pooled culture by high throughput sequencing of transposon integration sites.
Citation Format: Stephen J. Pettitt, Farah L. Rehman, Ilirjana Bajrami, Helen Pemberton, Rachel Brough, Iwanka Kozarewa, Christopher J. Lord, Alan Ashworth. A transposon-based genetic screen in haploid mouse embryonic stem cells identifies Parp1 as a major mediator of olaparib toxicity. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr A36.
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Affiliation(s)
| | | | | | | | - Rachel Brough
- Institute of Cancer Research, London, United Kingdom
| | | | | | - Alan Ashworth
- Institute of Cancer Research, London, United Kingdom
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Fenton T, Brough R, Williams L, Bajrami I, Ashworth A, Lord C, Boshoff C. Abstract B28: Screening for kinase dependencies in HPV-associated cancer. Mol Cancer Ther 2013. [DOI: 10.1158/1535-7163.pms-b28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Human papillomavirus (HPV) is the primary causative agent in cervical cancer, a number of other anogenital cancers and a growing subset of head and neck squamous cell carcinomas (HNSCC). HPV-driven tumour cells exhibit a dependence upon the continued expression of two viral oncogenes, E6 and E7, which act primarily by promoting degradation of the p53 and pRb tumour suppressors. While pharmacological targeting of E6 and E7 has proven difficult, we hypothesized that tumour cells expressing these oncogenes may in turn become dependent upon the activity of specific cellular proteins. Since protein kinases have proven readily targetable using small molecule drugs, we screened a kinome-wide siRNA library against a panel of HPV-negative and HPV-positive HNSCC and cervical cancer cell lines to identify kinases specifically required in HPV-positive cancer cells.
Citation Format: Tim Fenton, Rachel Brough, Luke Williams, Ilirjana Bajrami, Alan Ashworth, Chris Lord, Chris Boshoff. Screening for kinase dependencies in HPV-associated cancer. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr B28.
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Affiliation(s)
- Tim Fenton
- 1UCL Cancer Institute, London, United Kingdom,
| | - Rachel Brough
- 2The Institute of Cancer Research, London, United Kingdom
| | | | | | - Alan Ashworth
- 2The Institute of Cancer Research, London, United Kingdom
| | - Chris Lord
- 2The Institute of Cancer Research, London, United Kingdom
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35
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Pettitt SJ, Rehman FL, Bajrami I, Brough R, Wallberg F, Kozarewa I, Fenwick K, Assiotis I, Chen L, Campbell J, Lord CJ, Ashworth A. A genetic screen using the PiggyBac transposon in haploid cells identifies Parp1 as a mediator of olaparib toxicity. PLoS One 2013; 8:e61520. [PMID: 23634208 PMCID: PMC3636235 DOI: 10.1371/journal.pone.0061520] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 03/10/2013] [Indexed: 12/23/2022] Open
Abstract
Genetic perturbation screens have the potential to dissect a wide range of cellular phenotypes. Such screens have historically been difficult in diploid mammalian cells. The recent derivation of haploid embryonic stem cells provides an opportunity to cause loss of function mutants with a random mutagen in a mammalian cell with a normal genetic background. We describe an approach to genetic screens that exploits the highly active piggyBac transposon in haploid mammalian cells. As an example of haploid transposon (HTP) screening, we apply this approach to identifying determinants of cancer drug toxicity and resistance. In a screen for 6-thioguanine resistance we recovered components of the DNA mismatch repair pathway, a known requirement for toxicity. In a further screen for resistance to the clinical poly(ADP-ribose) polymerase (PARP) inhibitor olaparib we recovered multiple Parp1 mutants. Our results show that olaparib toxicity to normal cells is mediated predominantly via Parp1, and suggest that the clinical side effects of olaparib may be on target. The transposon mutant libraries are stable and can be readily reused to screen other drugs. The screening protocol described has several advantages over other methods such as RNA interference: it is rapid and low cost, and mutations can be easily reverted to establish causality.
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Affiliation(s)
- Stephen J. Pettitt
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Farah L. Rehman
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Ilirjana Bajrami
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Rachel Brough
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Fredrik Wallberg
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Iwanka Kozarewa
- Tumour Profiling Unit, The Institute of Cancer Research, London, United Kingdom
| | - Kerry Fenwick
- Tumour Profiling Unit, The Institute of Cancer Research, London, United Kingdom
| | - Ioannis Assiotis
- Tumour Profiling Unit, The Institute of Cancer Research, London, United Kingdom
| | - Lina Chen
- Tumour Profiling Unit, The Institute of Cancer Research, London, United Kingdom
| | - James Campbell
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
- Tumour Profiling Unit, The Institute of Cancer Research, London, United Kingdom
| | - Christopher J. Lord
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Alan Ashworth
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
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Postel-Vinay SC, Bajrami I, Friboulet L, Aarts M, Fontebasso Y, Andre F, Olaussen K, Soria JC, Lord C, Ashworth A. Abstract 617: High-throughput screens identify PARP inhibition as being synthetically lethal with ERCC1 deficiency in non-small cell lung cancer cell lines. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Non-small cell lung cancer (NSCLC) harbors frequent DNA-repair defects that represent therapeutic opportunities. Notably, Excision Repair Cross-Complementation group 1 (ERCC1) deficiency has been described in a subset of tumors and correlated with platinum sensitivity. The use of mechanism-based approaches, such as synthetic lethality, could allow targeting more selectively such DNA repair defects, with reduced systemic toxicity.
Methods: To identify ERCC1-selective synthetic lethal interactions, we adopted an integrated functional and molecular profiling approach. An isogenic model of ERCC1-deficient NSCLC cells, consisting of one parental ERCC1-proficient cell line and 3 ERCC1-deficient clones, was functionally profiled by high throughput drug sensitivity screening using a library containing commonly used oncology agents as well as a large number of in-development targeted agents. This was integrated with data from molecular profiling, including high throughput siRNA screens.
Results: The comparison of functional viability profiles for ERCC1-deficient models enabled the identification of synthetic lethal effects that could represent therapeutic opportunities for ERCC1-deficient tumors. Notably, ERCC1-deficient cells showed increased sensitivity to several PARP inhibitors, representing promising preliminary results that could be translated in the clinical setting. Mechanistic studies revealed a significant delay in double-strand break repair associated with a G2/M arrest following PARP inhibitor treatment in the ERCC1-deficient population only. Further in vitro work is providing deeper insight into the mechanisms underlying this PARP inhibitors sensitivity and in vivo work is underway.
Conclusions: ERCC1-deficiency sensitizes human NSCLC cell lines to PARP inhibitors. In vitro and in vivo revalidations of these results and now underway to further dissect the molecular mechanisms responsible for these ERCC1-deficient selective effects, which could represent therapeutic opportunities.
Citation Format: Sophie C. Postel-Vinay, Ilirjana Bajrami, Luc Friboulet, Marieke Aarts, Yari Fontebasso, Fabrice Andre, Ken Olaussen, Jean-Charles Soria, Chris Lord, Alan Ashworth. High-throughput screens identify PARP inhibition as being synthetically lethal with ERCC1 deficiency in non-small cell lung cancer cell lines. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 617. doi:10.1158/1538-7445.AM2013-617
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Affiliation(s)
| | | | | | | | | | | | | | | | - Chris Lord
- 2Institute of Cancer Research, United Kingdom
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Bie L, Ju Y, Jin Z, Donovan L, Birks S, Grunewald L, Zmuda F, Pilkington G, Kaul A, Chen YH, Dahiya S, Emnett R, Gianino S, Gutmann D, Poschl J, Bianchi E, Bockstaller M, Neumann P, Schuller U, Gevorgian A, Morozova E, Kazantsev I, Iukhta T, Safonova S, Punanov Y, Zheludkova O, Afanasyev B, Buss M, Remke M, Gandhi K, Kool M, Northcott P, Pfister S, Taylor M, Castellino R, Thompson J, Margraf L, Donahue D, Head H, Murray J, Burger P, Wortham M, Reitman Z, He Y, Bigner D, Yan H, Lee C, Triscott J, Foster C, Manoranjan B, Pambid MR, Fotovati A, Berns R, Venugopal C, O'Halloran K, Narendran A, Northcott P, Taylor MD, Singh SK, Singhal A, Rassekh R, Maxwell CA, Dunham C, Dunn SE, Pambid MR, Berns R, Hu K, Adomat H, Moniri M, Chin MY, Hessein M, Zisman N, Maurer N, Dunham C, Guns E, Dunn S, Koks C, De Vleeschouwer S, Graf N, Van Gool S, D'Asti E, Huang A, Korshunov A, Pfister S, Rak J, Gump W, Moriarty T, Gump W, Skjei K, Karkare S, Castelo-Branco P, Choufani S, Mack S, Gallagher D, Zhang C, Merino D, Wasserman J, Kool M, Jones DT, Croul S, Kreitzer F, Largaespada D, Conklin B, Taylor M, Weiss W, Garzia L, Morrissy S, Zayne K, Wu X, Dirks P, Hawkins C, Dick J, Stein L, Collier L, Largaespada D, Dupuy A, Taylor M, Rampazzo G, Moraes L, Paniago M, Oliveira I, Hitzler J, Silva N, Cappellano A, Cavalheiro S, Alves MT, Cerutti J, Toledo S, Liu Z, Zhao X, Mao H, Baxter P, Wang JCY, Huang Y, Yu L, Su J, Adekunle A, Perlaky L, Hurwitz M, Hurwitz R, Lau C, Chintagumpala M, Blaney S, Baruchel S, Li XN, Zhang J, Hariono S, Hashizume R, Fan Q, James CD, Weiss WA, Nicolaides T, Madsen PJ, Slaunwhite ES, Dirks PB, Ma JF, Henn RE, Hanno AG, Boucher KL, Storm PB, Resnick AC, Lourdusamy A, Rogers H, Ward J, Rahman R, Malkin D, Gilbertson R, Grundy R, Lourdusamy A, Rogers H, Ward J, Rahman R, Gilbertson R, Grundy R, Karajannis M, Fisher M, Pfister S, Milla S, Cohen K, Legault G, Wisoff J, Harter D, Merkelson A, Bloom M, Dhall G, Jones D, Korshunov A, Taylor MD, Pfister S, Eberhart C, Sievert A, Resnick A, Zagzag D, Allen J, Hankinson T, Gump J, Serrano-Almeida C, Torok M, Weksberg R, Handler M, Liu A, Foreman N, Garancher A, Rocques N, Miquel C, Sainte-Rose C, Delattre O, Bourdeaut F, Eychene A, Tabori U, Pouponnot C, Danielpour M, Levy R, Antonuk CD, Rodriguez J, Aravena JM, Kim GB, Gate D, Bannykh S, Svendsen C, Huang X, Town T, Breunig J, Amakye D, Robinson D, Rose K, Cho YJ, Ligon KL, Sharp T, Ando Y, Geoerger B, He Y, Doz F, Ashley D, Hargrave D, Casanova M, Tawbi H, Heath J, Bouffet E, Brandes AA, Chisholm J, Rodon J, Dubuc AM, Thomas A, Mita A, MacDonald T, Kieran M, Eisenstat D, Song X, Danielpour M, Levy R, Antonuk CD, Rodriguez J, Hashizume R, Aravena JM, Kim GB, Gate D, Bannykh S, Svendsen C, Town T, Breunig J, Morrissy AS, Mayoh C, Lo A, Zhang W, Thiessen N, Tse K, Moore R, Mungall A, Wu X, Van Meter TE, Cho YJ, Collins VP, MacDonald TJ, Li XN, Stehbens S, Fernandez-Lopez A, Malkin D, Marra MA, Taylor MD, Karajannis M, Legault G, Hagiwara M, Vega E, Merkelson A, Wisoff J, Younger S, Golfinos J, Roland JT, Allen J, Antonuk CD, Levy R, Kim GB, Town T, Danielpour M, Breunig J, Pak E, Barshow S, Zhao X, Ponomaryov T, Segal R, Levy R, Antonuk CD, Aravena JM, Kim GB, Svendsen C, Town T, Danielpour M, Zhu S, Breunig J, Chi S, Cohen K, Fisher M, Biegel J, Bowers D, Fangusaro J, Manley P, Janss A, Zimmerman MA, Wu X, Kieran M, Sayour E, Pham C, Sanchez-Perez L, Snyder D, Flores C, Kemeny H, Xie W, Cui X, Bigner D, Taylor MD, Sampson J, Mitchell D, Bandopadhayay P, Nguyen B, Masoud S, Vue N, Gholamin S, Yu F, Schubert S, Bergthold G, Weiss WA, Mitra S, Qi J, Bradner J, Kieran M, Beroukhim R, Cho YJ, Reddick W, Glass J, Ji Q, Paulus E, James CD, Gajjar A, Ogg R, Vanner R, Remke M, Aviv T, Lee L, Zhu X, Clarke I, Taylor M, Dirks P, Shuman MA, Hamilton R, Pollack I, Calligaris D, Liu X, Feldman D, Thompson C, Ide J, Buhrlage S, Gray N, Kieran M, Jan YN, Stiles C, Agar N, Remke M, Cavalli FMG, Northcott PA, Kool M, Pfister SM, Taylor MD, Project MAGIC, Rakopoulos P, Jan LY, Pajovic S, Buczkowicz P, Morrison A, Bouffet E, Bartels U, Becher O, Hawkins C, Truffaux N, Puget S, Philippe C, Gump W, Castel D, Taylor K, Mackay A, Le Dret L, Saulnier P, Calmon R, Boddaert N, Blauwblomme T, Sainte-Rose C, Jones C, Mutchnick I, Grill J, Liu X, Ebling M, Ide J, Wang L, Davis E, Marchionni M, Stuart D, Alberta J, Kieran M, Li KKW, Stiles C, Agar N, Remke M, Cavalli FMG, Northcott PA, Kool M, Pfister SM, Taylor MD, Project MAGIC, Tien AC, Pang JCS, Griveau A, Rowitch D, Ramkissoon L, Horowitz P, Craig J, Ramkissoon S, Rich B, Bergthold G, Tabori U, Taha H, Ng HK, Bowers D, Hawkins C, Packer R, Eberhart C, Goumnerova L, Chan J, Santagata S, Pomeroy S, Ligon A, Kieran M, Jackson S, Beroukhim R, Ligon K, Kuan CT, Chandramohan V, Keir S, Pastan I, Bigner D, Zhou Z, Ho S, Voss H, Patay Z, Souweidane M, Salloum R, DeWire M, Fouladi M, Goldman S, Chow L, Hummel T, Dorris K, Miles L, Sutton M, Howarth R, Stevenson C, Leach J, Griesinger A, Donson A, Hoffman L, Birks D, Amani V, Handler M, Foreman N, Sangar MC, Pai A, Pedro K, Ditzler SH, Girard E, Olson J, Gustafson WC, Meyerowitz J, Nekritz E, Charron E, Matthay K, Hertz N, Onar-Thomas A, Shokat K, Weiss W, Hanaford A, Raabe E, Eberhart C, Griesinger A, Donson A, Hoffman L, Amani V, Birks D, Gajjar A, Handler M, Mulcahy-Levy J, Foreman N, Olow AK, Dasgupta T, Yang X, Mueller S, Hashizume R, Kolkowitz I, Weiss W, Broniscer A, Resnick AC, Sievert AJ, Nicolaides T, Prados MD, Berger MS, Gupta N, James CD, Haas-Kogan DA, Flores C, Pham C, Dietl SM, Snyder D, Sanchez-Perez L, Bigner D, Sampson J, Mitchell D, Prakash V, Batanian J, Guzman M, Geller T, Pham CD, Wolfl M, Pei Y, Flores C, Snyder D, Bigner DD, Sampson JH, Wechsler-Reya RJ, Mitchell DA, Van Ommeren R, Venugopal C, Manoranjan B, Beilhack A, McFarlane N, Hallett R, Hassell J, Dunn S, Singh S, Dasgupta T, Olow A, Yang X, Hashizume R, Mueller S, Riedel S, Nicolaides T, Kolkowitz I, Weiss W, Prados M, Gupta N, James CD, Haas-Kogan D, Zhao H, Li L, Picotte K, Monoranu C, Stewart R, Modzelewska K, Boer E, Picard D, Huang A, Radiloff D, Lee C, Dunn S, Hutt M, Nazarian J, Dietl S, Price A, Lim KJ, Warren K, Chang H, Eberhart CG, Raabe EH, Persson A, Huang M, Chandler-Militello D, Li N, Vince GH, Berger M, James D, Goldman S, Weiss W, Lindquist R, Tate M, Rowitch D, Alvarez-Buylla A, Hoffman L, Donson A, Eyrich M, Birks D, Griesinger A, Amani V, Handler M, Foreman N, Meijer L, Walker D, Grundy R, O'Dowd S, Jaspan T, Schlegel PG, Dineen R, Fotovati A, Radiloff D, Coute N, Triscott J, Chen J, Yip S, Louis D, Toyota B, Hukin J, Weitzel D, Rassekh SR, Singhal A, Dunham C, Dunn S, Ahsan S, Hanaford A, Taylor I, Eberhart C, Raabe E, Sun YG, Ashcraft K, Stiles C, Han L, Zhang K, Chen L, Shi Z, Pu P, Dong L, Kang C, Cordero F, Lewis P, Liu C, Hoeman C, Schroeder K, Allis CD, Becher O, Gururangan S, Grant G, Driscoll T, Archer G, Herndon J, Friedman H, Li W, Kurtzberg J, Bigner D, Sampson J, Mitchell D, Yadavilli S, Kambhampati M, Becher O, MacDonald T, Bellamkonds R, Packer R, Buckley A, Nazarian J, DeWire M, Fouladi M, Stewart C, Wetmore C, Hawkins C, Jacobs C, Yuan Y, Goldman S, Fisher P, Rodriguez R, Rytting M, Bouffet E, Khakoo Y, Hwang E, Foreman N, Gilbert M, Gilbertson R, Gajjar A, Saratsis A, Yadavilli S, Wetzel W, Snyder K, Kambhampati M, Hall J, Raabe E, Warren K, Packer R, Nazarian J, Thompson J, Griesinger A, Foreman N, Spazojevic I, Rush S, Levy JM, Hutt M, Karajannis MA, Shah S, Eberhart CG, Raabe E, Rodriguez FJ, Gump J, Donson A, Tovmasyan A, Birks D, Handler M, Foreman N, Hankinson T, Torchia J, Khuong-Quang DA, Ho KC, Picard D, Letourneau L, Chan T, Peters K, Golbourn B, Morrissy S, Birks D, Faria C, Foreman N, Taylor M, Rutka J, Pfister S, Bouffet E, Hawkins C, Batinic-Haberle I, Majewski J, Kim SK, Jabado N, Huang A, Ladner T, Tomycz L, Watchmaker J, Yang T, Kaufman L, Pearson M, Dewhirst M, Ogg RJ, Scoggins MA, Zou P, Taherbhoy S, Jones MM, Li Y, Glass JO, Merchant TE, Reddick WE, Conklin HM, Gholamin S, Gajjar A, Khan A, Kumar A, Tye GW, Broaddus WC, Van Meter TE, Shih DJH, Northcott PA, Remke M, Korshunov A, Mitra S, Jones DTW, Kool M, Pfister SM, Taylor MD, Mille F, Levesque M, Remke M, Korshunov A, Izzi L, Kool M, Richard C, Northcott PA, Taylor MD, Pfister SM, Charron F, Yu F, Masoud S, Nguyen B, Vue N, Schubert S, Tolliday N, Kong DS, Sengupta S, Weeraratne D, Schreiber S, Cho YJ, Birks D, Jones K, Griesinger A, Amani V, Handler M, Vibhakar R, Achrol A, Foreman N, Brown R, Rangan K, Finlay J, Olch A, Freyer D, Bluml S, Gate D, Danielpour M, Rodriguez J, Shae JJ, Kim GB, Levy R, Bannykh S, Breunig JJ, Town T, Monje-Deisseroth M, Cho YJ, Weissman I, Cheshier S, Buczkowicz P, Rakopoulos P, Bouffet E, Morrison A, Bartels U, Becher O, Hawkins C, Dey A, Kenney A, Van Gool S, Pauwels F, De Vleeschouwer S, Barszczyk M, Buczkowicz P, Castelo-Branco P, Mack S, Nethery-Brokx K, Morrison A, Taylor M, Dirks P, Tabori U, Hawkins C, Chandramohan V, Keir ST, Bao X, Pastan IH, Kuan CT, Bigner DD, Bender S, Jones D, Kool M, Sturm D, Korshunov A, Lichter P, Pfister SM, Chen M, Lu J, Wang J, Keir S, Zhang M, Zhao S, Mook R, Barak L, Lyerly HK, Chen W, Ramachandran C, Nair S, Escalon E, Khatib Z, Quirrin KW, Melnick S, Kievit F, Stephen Z, Wang K, Silber J, Ellenbogen R, Zhang M, Hutzen B, Studebaker A, Bratasz A, Powell K, Raffel C, Guo C, Chang CC, Wortham M, Chen L, Kernagis D, Qin X, Cho YW, Chi JT, Grant G, McLendon R, Yan H, Ge K, Papadopoulos N, Bigner D, He Y, Cristiano B, Venkataraman S, Birks DK, Alimova I, Harris PS, Dubuc A, Taylor MD, Foreman NK, Vibhakar R, Ichimura K, Fukushima S, Totoki Y, Suzuki T, Mukasa A, Saito N, Kumabe T, Tominaga T, Kobayashi K, Nagane M, Iuchi T, Mizoguchi M, Sasaki T, Tamura K, Sugiyama K, Narita Y, Shibui S, Matsutani M, Shibata T, Nishikawa R, Northcott P, Zichner T, Jones D, Kool M, Jager N, Feychting M, Lannering B, Tynes T, Wesenberg F, Hauser P, Ra YS, Zitterbart K, Jabado N, Chan J, Fults D, Mueller S, Grajkowska W, Lichter P, Korbel J, Pfister S, Kool M, Jones DTW, Jaeger N, Northcott PA, Pugh T, Hovestadt V, Markant SL, Esparza LA, Bourdeaut F, Remke M, Taylor MD, Cho YJ, Pomeroy SL, Schueller U, Korshunov A, Eils R, Wechsler-Reya RJ, Lichter P, Pfister SM, Keir S, Pegram C, Lipp E, Rasheed A, Chandramohan V, Kuan CT, Kwatra M, Yan H, Bigner D, Chornenkyy Y, Buczkowicz P, Agnihotri S, Becher O, Hawkins C, Rogers H, Mayne C, Kilday JP, Coyle B, Grundy R, Sun T, Warrington N, Luo J, Brooks M, Dahiya S, Sengupta R, Rubin J, Erdreich-Epstein A, Robison N, Ren X, Zhou H, Ji L, Margo A, Jones D, Pfister S, Kool M, Sposto R, Asgharzadeh S, Clifford S, Gustafsson G, Ellison D, Figarella-Branger D, Doz F, Rutkowski S, Lannering B, Pietsch T, Broniscer A, Tatevossian R, Sabin N, Klimo P, Dalton J, Lee R, Gajjar A, Ellison D, Garzia L, Dubuc A, Pitcher G, Northcott P, Mariampillai A, Chan T, Skowron P, Wu X, Yao Y, Hawkins C, Peacock J, Zayne K, Croul S, Rutka J, Kenney A, Huang A, Yang V, Baylin S, Salter M, Taylor M, Ward S, Sengupta R, Rubin J, Garzia L, Morrissy S, Skowron P, Jelveh S, Lindsay P, Largaespada D, Collier L, Dupuy A, Hill R, Taylor M, Lulla RR, Laskowski J, Fangusaro J, DiPatri AJ, Alden T, Vanin EF, Tomita T, Goldman S, Soares MB, Rajagopal MU, Lau LS, Hathout Y, Gordish-Dressman H, Rood B, Datar V, Bochare S, Singh A, Khatau S, Fangusaro J, Goldman S, Lulla R, Rajaram V, Gopalakrishnan V, Morfouace M, Shelat A, Jaccus M, Freeman B, Zindy F, Robinson G, Guy K, Stewart C, Gajjar A, Roussel M, Krebs S, Chow K, Yi Z, Brawley V, Ahmed N, Gottschalk S, Lerner R, Harness J, Yoshida Y, Santos R, Torre JDL, Nicolaides T, Ozawa T, James D, Petritsch C, Vitte J, Chareyre F, Stemmer-Rachamimov A, Giovannini M, Hashizume R, Yu-Jen L, Tom M, Ihara Y, Huang X, Waldman T, Mueller S, Gupta N, James D, Shevtsov M, Yakovleva L, Nikolaev B, Dobrodumov A, Onokhin K, Bychkova N, Mikhrina A, Khachatryan W, Guzhova I, Martynova M, Bystrova O, Ischenko A, 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Scheinemann K, Gunnarsson T, Hassell J, Taylor M, Lee C, Triscott J, Foster C, Dunham C, Hawkins C, Dunn S, Singh S, McCrea HJ, Bander E, Venn RA, Reiner AS, Iorgulescu JB, Puchi LA, Schaefer PM, Cederquist G, Greenfield JP, Tsoli M, Luk P, Dilda P, Hogg P, Haber M, Ziegler D, Mack S, Agnihotri S, Witt H, Shih D, Wang X, Ramaswamy V, Zayne K, Bertrand K, Massimi L, Grajkowska W, Lach B, Gupta N, Weiss W, Guha A, Zadeh G, Rutka J, Korshunov A, Pfister S, Taylor M, Mack S, Witt H, Jager N, Zuyderduyn S, Nethery-Brokx K, Garzia L, Zayne K, Wang X, Barszczyk M, Wani K, Bouffet E, Weiss W, Hawkins C, Rutka J, Bader G, Aldape K, Dirks P, Pfister S, Korshunov A, Taylor M, Engler J, Robinson A, Wade A, Molinaro A, Phillips J, Ramaswamy V, Remke M, Bouffet E, Faria C, Shih D, Gururangan S, McLendon R, Schuller U, Ligon K, Pomeroy S, Jabado N, Dunn S, Fouladi M, Rutka J, Hawkins C, Tabori U, Packer R, Pfister S, Korshunov A, Taylor M, Faria C, Dubuc A, Golbourn B, Diaz R, Agnihotri S, Sabha N, Luck A, Leadly M, Reynaud D, Wu X, Remke M, Ramaswamy V, Northcott P, Pfister S, Croul S, Kool M, Korshunov A, Smith C, Taylor M, Rutka J, Pietsch T, Doerner E, Muehlen AZ, Velez-Char N, Warmuth-Metz M, Kortmann R, von Hoff K, Friedrich C, Rutkowski S, von Bueren A, Lu YJ, James CD, Hashizume R, Mueller S, Phillips J, Gupta N, Sturm D, Northcott PA, Jones DTW, Korshunov A, Picard D, Lichter P, Huang A, Pfister SM, Kool M, Ward J, Teague C, Shriyan B, Grundy R, Rahman R, Taylor K, Mackay A, Morozova O, Butterfield Y, Truffaux N, Philippe C, Vinci M, de Torres C, Cruz O, Mora J, Hargrave D, Puget S, Yip S, Jones C, Grill J, Smith S, Ward J, Tan C, Grundy R, Rahman R, Bjerke L, Mackay A, Nandhabalan M, Burford A, Jury A, Popov S, Bax D, Carvalho D, Taylor K, Vinci M, Bajrami I, McGonnell I, Lord C, Reis R, Hargrave D, Ashworth A, Workman P, Jones C, Carvalho D, Mackay A, Burford A, Bjerke L, Chen L, Kozarewa I, Lord C, Ashworth A, Hargrave D, Reis R, Jones C, Marigil M, Jauregui PJ, Alonso M, Chan TS, Hawkins C, Picard D, Henkin J, Huang A, Trubicka J, Kucharczyk M, Pelc M, Chrzanowska K, Ciara E, Perek-Polnik M, Grajkowska W, Piekutowska-Abramczuk D, Jurkiewicz D, Luczak S, Borucka-Mankiewicz M, Kowalski P, Krajewska-Walasek M, de Mola RML, Laskowski J, Fangusaro J, Costa FF, Vanin EF, Goldman S, Soares MB, Lulla RR, Mann A, Venugopal C, Vora P, Singh M, van Ommeren R, McFarlane N, Manoranjan B, Qazi M, Scheinemann K, MacDonald P, Delaney K, Whitton A, Dunn S, Singh S, Sievert A, Lang SS, Boucher K, Madsen P, Slaunwhite E, Choudhari N, Kellet M, Storm P, Resnick A, Agnihotri S, Burrell K, Fernandez N, Golbourn B, Clarke I, Barszczyk M, Sabha N, Dirks P, Jones C, Rutka J, Zadeh G, Hawkins C, Murphy B, Obad S, Bihannic L, Ayrault O, Zindy F, Kauppinen S, Roussel M, Golbourn B, Agnihotri S, Cairns R, Mischel P, Aldape K, Hawkins C, Zadeh G, Rutka J, Rush S, Donson A, Kleinschmidt-DeMasters B, Bemis L, Birks D, Chan M, Smith A, Handler M, Foreman N, Gronych J, Jones DTW, Zuckermann M, Hutter S, Korshunov A, Kool M, Ryzhova M, Reifenberger G, Pfister SM, Lichter P, Jones DTW, Hovestadt V, Picelli S, Wang W, Northcott PA, Kool M, Jager N, Reifenberger G, Rutkowski S, Pietsch T, Sultan M, Yaspo ML, Landgraf P, Eils R, Korshunov A, Zapatka M, Pfister SM, Radlwimmer B, Lichter P, Huang Y, Mao H, Wang Y, Kogiso M, Zhao X, Baxter P, Man C, Wang Z, Zhou Y, Li XN, Chung AH, Crabtree D, Schroeder K, Becher OJ, Panosyan E, Wang Y, Lasky J, Liu Z, Zhao X, Wang Y, Mao H, Huang Y, Kogiso M, Baxter P, Adesina A, Su J, Picard D, Huang A, Perlaky L, Chintagumpala M, Lau C, Blaney S, Li XN, Huang M, Persson A, Swartling F, Moriarity B. Abstracts. Neuro Oncol 2013. [DOI: 10.1093/neuonc/not047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Chong IYS, Hooper SD, Cunningham D, Elliott R, Chen L, Campbell J, Bajrami I, Kozarewa I, Wetterskog D, Wilkerson PM, Lambros MB, Rao S, Starling N, Chau I, Lord CJ, Ashworth A. Association of high-throughput RNAi and drug screening with candidate novel therapeutic targets in esophageal carcinoma. J Clin Oncol 2013. [DOI: 10.1200/jco.2013.31.4_suppl.31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
31 Background: Oesophageal cancer is the sixth most commonly diagnosed cancer worldwide and carries a poor prognosis. Targeted therapeutic strategies have relied on the identification of genes which are amplified and overexpressed but the discrimination between genes which drive cancer and those that are coincidental has not yet been fully achieved. Methods: We carried out a functional genetic screen of 714 kinases in 18 tumour cell line models of oesophageal adenocarcinoma (EAC) and squamous cell carcinoma (SCC) to identify genes critical to the survival of specific oesophageal subtypes. High throughput drug screening of 80 compounds, largely comprising those used in clinical trials or in routine clinical practice, was undertaken in parallel to reveal druggable targets and to validate functional screening results. Results: We show proof of principle that the integration of functional and drug profiling results with molecular profiling data is a valid approach for identifying druggable targets by correlating the effects of ERBB2, EGFR and CDK6 gene knockdown with sensitivity to drugs targeting their respective proteins. We have characterised new genetic dependencies for EAC involving TGF beta signalling and the JAK/STAT pathway. Decreased cell viability associated with silencing of ACVR2 and ACVR1C (activin receptors involved in TGF beta signalling) was consistent with sensitivity to nilotinib, a cABL inhibitor that modulates TGF beta signalling. Furthermore, decreased cell viability in EAC models was observed with silencing of JAK2. This strongly correlated with sensitivity to PF-04691502 and BEZ 235, both potent inhibitors of PI3K/mTOR which signal downstream of JAK2. We have validated novel sensitivity to small molecule tankyrase inhibitors in a subgroup of oesophageal models, suggesting that a subset of Wnt dependent oesophageal cancers could be targeted with these agents. Conclusions: The molecular and functional genetics of oesophageal cancer is poorly understood. By generating functional viability and drug sensitivity data for a panel of oesophageal tumour cell lines, we have identified new genetic dependencies and candidate drug targets for this aggressive disease.
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Affiliation(s)
- Irene Yu-Shing Chong
- The Institute of Cancer Research and The Royal Marsden Hospital, London, United Kingdom
| | - Sean D. Hooper
- The Institute of Cancer Research, London, United Kingdom
| | | | | | - Lina Chen
- The Institute of Cancer Research, London, United Kingdom
| | - James Campbell
- The Institute of Cancer Research, London, United Kingdom
| | | | | | | | | | | | - Sheela Rao
- The Royal Marsden Hospital, Sutton, United Kingdom
| | | | - Ian Chau
- The Royal Marsden Hospital, Sutton, United Kingdom
| | | | - Alan Ashworth
- The Institute of Cancer Research, London, United Kingdom
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Shiu KK, Wetterskog D, Mackay A, Natrajan R, Lambros M, Sims D, Bajrami I, Brough R, Frankum J, Sharpe R, Marchio C, Horlings H, Reyal F, van der Vijver M, Turner N, Reis-Filho JS, Lord CJ, Ashworth A. Integrative molecular and functional profiling of ERBB2-amplified breast cancers identifies new genetic dependencies. Oncogene 2013; 33:619-31. [PMID: 23334330 DOI: 10.1038/onc.2012.625] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 11/04/2012] [Accepted: 11/14/2012] [Indexed: 12/30/2022]
Abstract
Overexpression of the receptor tyrosine kinase ERBB2 (also known as HER2) occurs in around 15% of breast cancers and is driven by amplification of the ERBB2 gene. ERBB2 amplification is a marker of poor prognosis, and although anti-ERBB2-targeted therapies have shown significant clinical benefit, de novo and acquired resistance remains an important problem. Genomic profiling has demonstrated that ERBB2+ve breast cancers are distinguished from ER+ve and 'triple-negative' breast cancers by harbouring not only the ERBB2 amplification on 17q12, but also a number of co-amplified genes on 17q12 and amplification events on other chromosomes. Some of these genes may have important roles in influencing clinical outcome, and could represent genetic dependencies in ERBB2+ve cancers and therefore potential therapeutic targets. Here, we describe an integrated genomic, gene expression and functional analysis to determine whether the genes present within amplicons are critical for the survival of ERBB2+ve breast tumour cells. We show that only a fraction of the ERBB2-amplified breast tumour lines are truly addicted to the ERBB2 oncogene at the mRNA level and display a heterogeneous set of additional genetic dependencies. These include an addiction to the transcription factor gene TFAP2C when it is amplified and overexpressed, suggesting that TFAP2C represents a genetic dependency in some ERBB2+ve breast cancer cells.
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Affiliation(s)
- K-K Shiu
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - D Wetterskog
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - A Mackay
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - R Natrajan
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - M Lambros
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - D Sims
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - I Bajrami
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - R Brough
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - J Frankum
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - R Sharpe
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - C Marchio
- Department of Biomedical Sciences and Human Oncology, University of Turin, Turin, Italy
| | - H Horlings
- Department of Pathology, Academic Medical Centre, Amsterdam, The Netherlands
| | - F Reyal
- Department of Pathology, Academic Medical Centre, Amsterdam, The Netherlands
| | - M van der Vijver
- Department of Pathology, Academic Medical Centre, Amsterdam, The Netherlands
| | - N Turner
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - J S Reis-Filho
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - C J Lord
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - A Ashworth
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
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Ruark E, Snape K, Humburg P, Loveday C, Bajrami I, Brough R, Rodrigues DN, Renwick A, Seal S, Ramsay E, Duarte SDV, Rivas MA, Warren-Perry M, Zachariou A, Campion-Flora A, Hanks S, Murray A, Pour NA, Douglas J, Gregory L, Rimmer A, Walker NM, Yang TP, Adlard JW, Barwell J, Berg J, Brady AF, Brewer C, Brice G, Chapman C, Cook J, Davidson R, Donaldson A, Douglas F, Eccles D, Evans DG, Greenhalgh L, Henderson A, Izatt L, Kumar A, Lalloo F, Miedzybrodzka Z, Morrison PJ, Paterson J, Porteous M, Rogers MT, Shanley S, Walker L, Gore M, Houlston R, Brown MA, Caufield MJ, Deloukas P, McCarthy MI, Todd JA, Turnbull C, Reis-Filho JS, Ashworth A, Antoniou AC, Lord CJ, Donnelly P, Rahman N. Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer. Nature 2013; 493:406-10. [PMID: 23242139 PMCID: PMC3759028 DOI: 10.1038/nature11725] [Citation(s) in RCA: 191] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 10/26/2012] [Indexed: 02/06/2023]
Abstract
Improved sequencing technologies offer unprecedented opportunities for investigating the role of rare genetic variation in common disease. However, there are considerable challenges with respect to study design, data analysis and replication. Using pooled next-generation sequencing of 507 genes implicated in the repair of DNA in 1,150 samples, an analytical strategy focused on protein-truncating variants (PTVs) and a large-scale sequencing case-control replication experiment in 13,642 individuals, here we show that rare PTVs in the p53-inducible protein phosphatase PPM1D are associated with predisposition to breast cancer and ovarian cancer. PPM1D PTV mutations were present in 25 out of 7,781 cases versus 1 out of 5,861 controls (P = 1.12 × 10(-5)), including 18 mutations in 6,912 individuals with breast cancer (P = 2.42 × 10(-4)) and 12 mutations in 1,121 individuals with ovarian cancer (P = 3.10 × 10(-9)). Notably, all of the identified PPM1D PTVs were mosaic in lymphocyte DNA and clustered within a 370-base-pair region in the final exon of the gene, carboxy-terminal to the phosphatase catalytic domain. Functional studies demonstrate that the mutations result in enhanced suppression of p53 in response to ionizing radiation exposure, suggesting that the mutant alleles encode hyperactive PPM1D isoforms. Thus, although the mutations cause premature protein truncation, they do not result in the simple loss-of-function effect typically associated with this class of variant, but instead probably have a gain-of-function effect. Our results have implications for the detection and management of breast and ovarian cancer risk. More generally, these data provide new insights into the role of rare and of mosaic genetic variants in common conditions, and the use of sequencing in their identification.
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Affiliation(s)
- Elise Ruark
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Katie Snape
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Peter Humburg
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Chey Loveday
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Ilirjana Bajrami
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rachel Brough
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Daniel Nava Rodrigues
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Anthony Renwick
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Sheila Seal
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Emma Ramsay
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | | | - Manuel A. Rivas
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7LD, UK
| | - Margaret Warren-Perry
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Anna Zachariou
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Adriana Campion-Flora
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Sandra Hanks
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Anne Murray
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Naser Ansari Pour
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Jenny Douglas
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Lorna Gregory
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Andrew Rimmer
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Neil M. Walker
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | - Tsun-Po Yang
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Julian W. Adlard
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, LS7 4SA, UK
| | - Julian Barwell
- Leicestershire Genetics Centre, University Hospitals of Leicester NHS Trust, LE1 5WW, UK
| | - Jonathan Berg
- Human genetics, Division of Medical Sciences, University of Dundee, DD1 9SY, UK
| | - Angela F. Brady
- NW Thames Regional Genetics Service, Kennedy Galton Centre, London, HA1 3UJ, UK
| | - Carole Brewer
- Peninsula Regional Genetics Service, Royal Devon & Exeter Hospital, Exeter, EX1 2ED, UK
| | - Glen Brice
- SW Thames Regional Genetics Service, St George’s Hospital, London, SW17 0RE, UK
| | - Cyril Chapman
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital, Birmingham, B15 2TG, UK
| | - Jackie Cook
- Sheffield Regional Genetics Service, Sheffield Children’s NHS Foundation Trust, S10 2TH, UK
| | - Rosemarie Davidson
- West of Scotland Regional Genetics Service, Laboratory Medicine, Southern General Hospital, Glasgow, G51 4TF, UK
| | - Alan Donaldson
- South Western Regional Genetics Service, University Hospitals of Bristol NHS Foundation Trust, BS2 8EG, UK
| | - Fiona Douglas
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 3BZ, UK
| | - Diana Eccles
- Faculty of Medicine, University of Southampton, Southampton University Hospitals NHS Trust, SO16 5YA, UK
| | - D. Gareth Evans
- Genetic Medicine, Manchester Academic Health Science Centre, St. Mary’s Hospital, Manchester M13 9WL, UK
| | - Lynn Greenhalgh
- Merseyside and Cheshire Clinical Genetics Service, Liverpool Women’s NHS Foundation Trust, Liverpool, L8 7SS, UK
| | - Alex Henderson
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 3BZ, UK
| | - Louise Izatt
- SE Thames Regional Genetics Service, Guy’s and St Thomas NHS Foundation Trust, London, SE1 9RT, UK
| | - Ajith Kumar
- NE Thames Regional Genetics Service, Great Ormond St Hospital, London, WC1N 3JH, UK
| | - Fiona Lalloo
- University Dept of Medical Genetics & Regional Genetics Service, St Mary’s Hospital, Manchester, M13 9WL, UK
| | - Zosia Miedzybrodzka
- University of Aberdeen and North of Scotland Clinical Genetics Service, Aberdeen Royal Infirmary, AB25 2ZA, UK
| | - Patrick J. Morrison
- Northern Ireland Regional Genetics Service, Belfast HSC Trust, Department of Medical Genetics, Queen’s University Belfast, BT9 7AB, UK
| | - Joan Paterson
- East Anglian Regional Genetics Service, Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ, UK
| | - Mary Porteous
- South East of Scotland Clinical Genetics Service, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Mark T. Rogers
- All Wales Medical Genetics Service, University Hospital of Wales, Cardiff, CF14 4XW, UK
| | - Susan Shanley
- Dept of Cancer Genetics, Royal Marsden NHS Foundation Trust, Sutton, SM2 5PT, UK
| | - Lisa Walker
- Oxford Regional Genetics Service, Oxford University Hospitals NHS Trust, Oxford, OX3 7LJ, UK
| | - Martin Gore
- Dept of Gynaecologic Oncology, Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Richard Houlston
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Matthew A. Brown
- University of Queensland Diamantina Institute, University of Queensland, Princess Alexandra Hospital, Woolloongabba, Brisbane, 4102, Australia
| | - Mark J. Caufield
- Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Panagiotis Deloukas
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Mark I. McCarthy
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Medicine, University of Oxford, Churchill Hospital, Oxford, OX3 7LI, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, OX3 7LI, UK
| | - John A. Todd
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | | | | | - Clare Turnbull
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
- Dept of Cancer Genetics, Royal Marsden NHS Foundation Trust, Sutton, SM2 5PT, UK
| | - Jorge S. Reis-Filho
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Alan Ashworth
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Christopher J. Lord
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Peter Donnelly
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Department of Statistics, University of Oxford, Oxford, OX1 3TG, UK
| | - Nazneen Rahman
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
- Dept of Cancer Genetics, Royal Marsden NHS Foundation Trust, Sutton, SM2 5PT, UK
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Miller R, Brough R, Bajrami I, Kaye S, Banerjee S, Lord C, Ashworth A. 105 Functional Profiling of Clear Cell Ovarian Cancer. Eur J Cancer 2012. [DOI: 10.1016/s0959-8049(12)71903-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Bajrami I, Kigozi A, Van Weverwijk A, Brough R, Frankum J, Lord CJ, Ashworth A. Synthetic lethality of PARP and NAMPT inhibition in triple-negative breast cancer cells. EMBO Mol Med 2012; 4:1087-96. [PMID: 22933245 PMCID: PMC3491838 DOI: 10.1002/emmm.201201250] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 06/28/2012] [Accepted: 07/10/2012] [Indexed: 12/28/2022] Open
Abstract
PARP inhibitors have been proposed as a potential targeted therapy for patients with triple-negative (ER-, PR-, HER2-negative) breast cancers. However, it is as yet unclear as to whether single agent or combination therapy using PARP inhibitors would be most beneficial. To better understand the mechanisms that determine the response to PARP inhibitors, we investigated whether enzymes involved in metabolism of the PARP substrate, β-NAD(+) , might alter the response to a clinical PARP inhibitor. Using an olaparib sensitization screen in a triple-negative (TN) breast cancer model, we identified nicotinamide phosphoribosyltransferase (NAMPT) as a non-redundant modifier of olaparib response. NAMPT is a rate-limiting enzyme involved in the generation of the PARP substrate β-NAD(+) and the suppression of β-NAD(+) levels by NAMPT inhibition most likely explains these observations. Importantly, the combination of a NAMPT small molecule inhibitor, FK866, with olaparib inhibited TN breast tumour growth in vivo to a greater extent than either single agent alone suggesting that assessing NAMPT/PARP inhibitor combinations for the treatment of TN breast cancer may be warranted.
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Affiliation(s)
- Ilirjana Bajrami
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
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Leonard A, Wolff J, Sengupta R, Marassa J, Piwnica-Worms D, Rubin J, Pollack I, Jakacki R, Butterfield L, Okada H, Fangusaro J, Warren KE, Mullins C, Jurgen P, Julia S, Friedrich CC, Keir S, Saling J, Roskoski M, Friedman H, Bigner D, Moertel C, Olin M, Dahlheimer T, Gustafson M, Sumstad D, McKenna D, Low W, Nascene D, Dietz A, Ohlfest J, Sturm D, Witt H, Hovestadt V, Quan DAK, Jones DTW, Konermann C, Pfaff E, Korshunov A, Rizhova M, Milde T, Witt O, Zapatka M, Collins VP, Kool M, Reifenberger G, Lichter P, Lindroth AM, Plass C, Jabado N, Pfister SM, Pizer B, Salehzadeh A, Brodbelt A, Mallucci C, Brassesco M, Pezuk J, Morales A, de Oliveira J, Roberto G, Umezawa K, Valera E, Rego E, Scrideli C, Tone L, Veringa SJE, Van Vuurden DG, Wesseling P, Vandertop WP, Noske DP, Wurdinger T, Kaspers GJL, Hulleman E, Wright K, Broniscer A, Bendel A, Bowers D, Crawford J, Fisher P, Hassall T, Armstrong G, Baker J, Qaddoumi I, Robinson G, Wetmore C, Klimo P, Boop F, Onar-Thomas A, Ellison D, Gajjar A, Cruz O, de Torres C, Sunol M, Rodriguez E, Alonso L, Parareda A, Cardesa T, Salvador H, Celis V, Guillen A, Garcia G, Muchart J, Trampal C, Martin ML, Rebollo M, Mora J, Piotrowski A, Kowalska A, Coyle P, Smith S, Rogers H, Macarthur D, Grundy R, Puccetti D, Salamat S, Kennedy T, Fangusaro J, Patel N, Bradley K, Casey K, Iskandar B, Nakano Y, Okada K, Osugi Y, Yamasaki K, Fujisaki H, Fukushima H, Inoue T, Matsusaka Y, Sakamoto H, Hara J, De Vleeschouwer S, Ardon H, Van Calenbergh F, Sciot R, Wilms G, Van Loon J, Goffin J, Van Gool S, Puccetti D, Salamat S, Rusinak D, Patel N, Bradley K, Casey K, Knight P, Onel K, Wargowski D, Stettner A, Iskandar B, Al-Ghafari A, Punjaruk W, Coyle B, Kerr I, Xipell E, Rodriguez M, Gonzalez-Huarriz M, Tunon MT, Zazpe I, Tejada-Solis S, Diez-Valle R, Fueyo J, Gomez-Manzano C, Alonso MM, Pastakia D, McCully C, Murphy R, Bacher J, Thomas M, Steffen-Smith E, Saleem K, Waldbridge S, Widemann B, Warren K, Miele E, Buttarelli F, Arcella A, Begalli F, Po A, Baldi C, Carissimo G, Antonelli M, Donofrio V, Morra I, Nozza P, Gulino A, Giangaspero F, Ferretti E, Elens I, De Vleeschouwer S, Pauwels F, Van Gool S, Fritzell S, Eberstal S, Sanden E, Visse E, Darabi A, Siesjo P, McDonald P, Wrogemann J, Krawitz S, Del Bigio M, Eisenstat D, Wolff J, Kwiecien R, Pietsch T, Faldum A, Kortmann RD, Warmuth-Metz M, Rutkowski S, Slavc I, Kramm CM, Uparkar U, Geyer R, Ermoian R, Ellenbogen R, Leary S, Triscott J, Hu K, Fotovati A, Yip S, Kast R, Toyota B, Dunn S, Hegde M, Corder A, Chow K, Mukherjee M, Ashoori A, Brawley V, Heslop H, Gottschalk S, Yvon E, Ahmed N, Wong TT, Yang FY, Lu M, Liang HF, Wang HE, Liu RS, Teng MC, Yen CC, Agnihotri S, Ternamian C, Jones C, Zadeh G, Rutka J, Hawkins C, Filipek I, Drogosiewicz M, Perek-Polnik M, Swieszkowska E, Baginska BD, Jurkiewicz E, Perek D, Kuehn A, Falkenstein F, Wolff J, Kwiecien R, Pietsch T, Gnekow A, Kramm C, Brooks MD, Jackson E, Piwnica-Worms D, Mitra RD, Rubin JB, Liu XY, Korshunov A, Schwartzentruber J, Jones DTW, Pfaff E, Sturm D, Fontebasso AM, Quang DAK, Albrecht S, Kool M, Dong Z, Siegel P, Von Diemling A, Faury D, Tabori U, Lichter P, Plass C, Majewski J, Pfister SM, Jabado N, Lulla R, Echevarria M, Alden T, DiPatri A, Tomita T, Goldman S, Fangusaro J, Qaddoumi I, Lin T, Merchant TE, Kocak M, Panandiker AP, Armstrong GT, Wetmore C, Gajjar A, Broniscer A, Gielen GH, Muehlen AZ, Kramm C, Pietsch T, Hubert C, Ding Y, Toledo C, Paddison P, Olson J, Nandhabalan M, Bjerke L, Bax D, Carvalho D, Bajrami I, Ashworth A, Lord C, Hargrave D, Reis R, Workman P, Jones C, Little S, Popov S, Jury A, Burford A, Doey L, Al-Sarraj S, Jurgensmeier J, Jones C, Carvalho D, Bjerke L, Bax D, Chen L, Kozarewa I, Baker S, Grundy R, Ashworth A, Lord C, Hargrave D, Reis R, Jones C, Bjerke L, Perryman L, Burford A, Bax D, Jury A, Popov S, Box G, Raynaud F, Hargrave D, Eccles S, Jones C, Viana-Pereira M, Pereira M, Burford A, Jury A, Popov S, Perryman L, Bax D, Forshew T, Tatevossian R, Sheer D, Pimental J, Pires M, Reis R, Jones C, Sarkar C, Jha P, Patrick IRP, Somasundaram K, Pathak P, Sharma MC, Suri V, Suri A, Gerges N, Haque T, Nantel A, Faury D, Jabado N, Lee C, Fotovati A, Triscott J, Chen J, Venugopal C, Singhal A, Dunham C, Kerr J, Verreault M, Yip S, Wakimoto H, Jones C, Jayanthan A, Narendran A, Singh S, Dunn S, Giraud G, Holm S, Gustavsson B, Van Gool S, Kizyma R, Kizyma Z, Dvornyak L, Kotsay B, Epari S, Sharma P, Gurav M, Gupta T, Shetty P, Moiyadi A, Kane S, Jalali R. HIGH GRADE GLIOMAS. Neuro Oncol 2012; 14:i56-i68. [PMCID: PMC3483348 DOI: 10.1093/neuonc/nos102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023] Open
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Miller R, Brough R, Bajrami I, Kaye SB, Lord CJ, Ashworth A. Functional profiling of clear cell ovarian cancer. J Clin Oncol 2012. [DOI: 10.1200/jco.2012.30.15_suppl.5035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
5035 Background: Clear cell ovarian cancer represents up to 15% of epithelial ovarian cancers. In comparison to other subtypes, clear cell ovarian carcinomas have a poorer prognosis and are relatively resistant to standard platinum based chemotherapy. Recently, loss of function mutations in the tumour suppressor gene ARID1A were identified in up to 50% of ovarian clear cell carcinomas. We have adopted an integral functional and molecular profiling approach as a route to identify new genetic dependencies and therapeutic targets for this disease. Methods: Clear cell ovarian cancer cell lines were functionally profiled using high throughput screening with chemical and siRNA libraries. This has been integrated with molecular profiling data generated from exome and transcriptome sequencing to aid the discovery of novel targets. Results: Using functional screens we have now identified critical gene dependencies and potential therapeutics in a series of clear cell ovarian cancer models. The comparison of functional viability profiles for models characterized by ARID1A loss of function mutations is now enabling an analysis of synthetic lethal effects that could be used to target clear cell ovarian cancers carrying these mutations. Conclusions: The work undertaken so far provides the framework for the discovery of therapeutic targets for clear cell ovarian cancer using an integrated approach. Revalidation of these preliminary results is now underway to characterize new genetic dependencies for this disease.
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Affiliation(s)
- Rowan Miller
- The Institute of Cancer Research, London, United Kingdom
| | - Rachel Brough
- The Institute of Cancer Research, London, United Kingdom
| | | | | | | | - Alan Ashworth
- The Institute of Cancer Research, London, United Kingdom
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Neijenhuis S, Bajrami I, Campbell J, Lord CJ, Ashworth A. Abstract B201: Identification of miRNA modulators to PARP inhibitor response. Mol Cancer Ther 2011. [DOI: 10.1158/1535-7163.targ-11-b201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Many pre-clinical and clinical studies have shown that inhibitors of the DNA repair protein PARP can have potentiating effects when combined with DNA damaging treatment modalities such as IR and temozolomide. Moreover, PARP inhibitors can be used as an efficient single agent in treatment of tumors carrying homologous recombination (HR) gene defects such as BRCA1 and BRCA2.
Genetic screens have previously been used to identify additional genetic deficiencies, which render tumor cells sensitive to PARP inhibitors. As yet, the contribution of microRNAs (miRNAs) to PARP inhibitor sensitivity has not been comprehensively studied. In this study our aim was to identify miRNA determinants of PARP inhibitor sensitivity and resistance, and in doing so potentially refine the eventual clinical use of these agents.
The human genome encodes over 1000 well annotated miRNAs. We used a high throughput method of miRNA mimetic screening to identify novel modulators of PARP inhibitor response. The assay involved transfecting cells with a library of approximately 900 miRNA mimics in a 384-well plate format. 48 hours after transfection half of the cells were treated with PARP inhibitor Olaparib and the other half with the drug vehicle. We identified several miRNA mimetics that modulate the response to Olaprib. Hits were validated by long-term survival assays as well as by analyses of DNA damage foci.
We used several strategies to determine the target genes of our hits. We performed westerns, qRT-PCR, luciferase reporter assays and immunoprecipitation assays and demonstrated several miRNAs involved in regulating the HR repair pathway.
Genes that modulate the response to PARP inhibitors are often implicitly involved in controlling DNA repair by HR and thus frequently found to be mutated in cancers. Our future work will focus upon whether the miRNAs identified in our screen drive HR dysfunction in human tumors and could be used as biomarkers to direct the use of therapy.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr B201.
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Affiliation(s)
| | | | | | | | - Alan Ashworth
- 1Institute of Cancer Research, London, United Kingdom
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Brough R, Frankum JR, Sims D, Mackay A, Mendes-Pereira AM, Bajrami I, Costa-Cabral S, Rafiq R, Ahmad AS, Cerone MA, Natrajan R, Sharpe R, Shiu KK, Wetterskog D, Dedes KJ, Lambros MB, Rawjee T, Linardopoulos S, Reis-Filho JS, Turner NC, Lord CJ, Ashworth A. Functional viability profiles of breast cancer. Cancer Discov 2011; 1:260-73. [PMID: 21984977 DOI: 10.1158/2159-8290.cd-11-0107] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED The design of targeted therapeutic strategies for cancer has largely been driven by the identification of tumor-specific genetic changes. However, the large number of genetic alterations present in tumor cells means that it is difficult to discriminate between genes that are critical for maintaining the disease state and those that are merely coincidental. Even when critical genes can be identified, directly targeting these is often challenging, meaning that alternative strategies such as exploiting synthetic lethality may be beneficial. To address these issues, we have carried out a functional genetic screen in >30 commonly used models of breast cancer to identify genes critical to the growth of specific breast cancer subtypes. In particular, we describe potential new therapeutic targets for PTEN-mutated cancers and for estrogen receptor-positive breast cancers. We also show that large-scale functional profiling allows the classification of breast cancers into subgroups distinct from established subtypes. SIGNIFICANCE Despite the wealth of molecular profiling data that describe breast tumors and breast tumor cell models, our understanding of the fundamental genetic dependencies in this disease is relatively poor. Using high-throughput RNA interference screening of a series of pharmacologically tractable genes, we have generated comprehensive functional viability profiles for a wide panel of commonly used breast tumor cell models. Analysis of these profiles identifies a series of novel genetic dependencies, including that of PTEN-null breast tumor cells upon mitotic checkpoint kinases, and provides a framework upon which additional dependencies and candidate therapeutic targets may be identified.
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Affiliation(s)
- Rachel Brough
- The Breakthrough Breast Cancer Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, United Kingdom
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