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Bland P, Saville H, Read A, Wai P, Muirhead G, Curnow L, Nieminuszczy J, Ravindran N, John M, Hedayat S, Barker H, Wright J, Yu L, Mavrommati I, Peck B, Allen M, Gazinska P, Pemberton H, Gulati A, Nash S, Noor F, Guppy N, Roxanis I, Barlow S, Kalirai H, Coupland S, Broderick R, Alsafadi S, Houy A, Stern MH, Pettit S, Choudhary J, Haider S, Niedzwiedz W, Lord C, Natrajan R. Abstract P6-10-05: Mutations in the RNA Splicing Factor SF3B1 drive endocrine therapy resistance and confer a targetable replication stress response defect through PARP inhibition. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-p6-10-05] [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: 03/06/2023]
Abstract
Abstract
Background: Heterozygous hotspot mutations in the RNA splicing factor SF3B1, occur in 3% of unselected breast cancers and are associated with oestrogen receptor (ER+) breast cancer (BC) where they are enriched in metastatic disease and are associated with a poor clinical outcome. SF3B1 mutations drive distinct signatures of alternative splicing through cryptic 3’ splice site selection leading to global transcriptomic and proteomic changes. The functional consequences of the mis-splicing events and resultant genetic vulnerabilities are poorly understood and precision medicine approaches that exploit these characteristics are not clinically available (Table 1).
Methods: To understand the role of SF3B1 mutations in ER+ BC, we generated a series of SF3B1 mutant (SF3B1MUT) isogenic cell lines which were characterised using RNA-sequencing and high content mass-spectrometry proteomic profiling. SF3B1 interactome analysis was also performed using immunoprecipitation of SF3B1 followed by mass-spectrometry. The molecular consequences of aberrant splicing were investigated using a targeted screening approach of 280 genes predicted to be alternatively spliced in SF3B1MUT BC, while high-throughput drug screens were used to identify novel therapeutic options for patients with SF3B1MUT breast cancer using isogenic cells. Hits were validated in vitro and in vivo using cell line and patient derived xenografts.
Results: Transcriptomic and proteomic profiling of SF3B1MUT cells identified global alternative 3’ splice site selection and subsequent proteomic changes induced by the mutations. Investigation of the SF3B1K700E interactome identified an enrichment of SF3B1K700E binding with ER, aberrant splicing of ER target genes, global rewiring of ER chromatin binding and resistance to endocrine therapy. Silencing of the aberrantly spliced candidate genes PPIH, TRIM37, HIGD1A, BRD9, and PHKG2 significantly enhanced the growth of the SF3B1 mutant cells, suggestive of a dose dependent tumour suppressive effect.
Through synthetic-lethal drug screens we found that SF3B1MUT cells are selectively sensitive to PARP inhibitors. SF3B1MUT cells display a defective response to PARPi induced replication stress. Mechanistically, this occurs via defective ATR signalling in SF3B1MUT cells, which upon PARPi exposure leads to increased replication origin firing and loss of pChk1 (S317) induction. The resultant replication stress leads to failure to resolve DNA replication intermediates via the endonuclease MUS81 and cell cycle stalling at the G2/M checkpoint. These defects can be further targeted by ATM, CDK7 or FACT inhibition, when used in combination with PARPi treatment. This SF3B1MUT selective PARPi sensitivity is preserved across multiple cell lines and patient derived tumour models. In vivo, PARPi produce profound anti-tumour effects in multiple SF3B1MUT cancer models and eliminate distant metastases.
Conclusions: Our integrative analysis reveals mechanistic insight into the role of SF3B1 mutations in endocrine therapy response in ER+ breast cancers, where altered SF3B1 induces ER-transcriptional re-programming. We further identified a robust synthetic-lethal relationship of mutant SF3B1 with PARP inhibition that is caused by a defective response to PARPi induced replication stress. Furthermore, we identified several potential selective combination strategies together with PARPi that are selective for SF3B1MUT cells. Together, these data provide the pre-clinical and mechanistic rationale for assessing already-approved PARPi in a biomarker-defined subset of advanced ER+ BC.
Table 1. Identified potential therapies for SF3B1 mutant cancers from this study and the literature
Citation Format: Phil Bland, Harry Saville, Abigail Read, Patty Wai, Gareth Muirhead, Lucinda Curnow, Jadwiga Nieminuszczy, Nivedita Ravindran, Marie John, Somaieh Hedayat, Holly Barker, James Wright, Lu Yu, Ioanna Mavrommati, Barrie Peck, Mark Allen, Patrycja Gazinska, Helen Pemberton, Aditi Gulati, Sarah Nash, Farzana Noor, Naomi Guppy, Ioannis Roxanis, Samantha Barlow, Helen Kalirai, Sarah Coupland, Ronan Broderick, Samar Alsafadi, Alexandre Houy, Marc-Henri Stern, Stephen Pettit, Jyoti Choudhary, Syed Haider, Wojciech Niedzwiedz, Christopher Lord, Rachael Natrajan. Mutations in the RNA Splicing Factor SF3B1 drive endocrine therapy resistance and confer a targetable replication stress response defect through PARP inhibition. [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-10-05.
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Affiliation(s)
- Phil Bland
- 1The Institute of Cancer Research, London, United Kingdom
| | - Harry Saville
- 2The Institute of Cancer Research, London,, United Kingdom
| | - Abigail Read
- 3The Institute of Cancer Research, London, United Kingdom
| | - Patty Wai
- 4The Institute of Cancer Research, London, United Kingdom
| | | | - Lucinda Curnow
- 6The Institute of Cancer Research, London, United Kingdom
| | | | | | - Marie John
- 9The Institute of Cancer Research, United Kingdom
| | | | - Holly Barker
- 11The Institute of Cancer Research, London, Australia
| | - James Wright
- 12The Institute of Cancer Research, London, United Kingdom
| | - Lu Yu
- 13The Institute of Cancer Research, London, United Kingdom
| | | | - Barrie Peck
- 15Barts Cancer Institute, Queen Mary University of London, United Kingdom
| | - Mark Allen
- 16The Institute of Cancer Research, London, United Kingdom
| | | | | | - Aditi Gulati
- 19The Institute of Cancer Research, London, United Kingdom
| | - Sarah Nash
- 20The Institute of Cancer Research, London, United Kingdom
| | - Farzana Noor
- 21The Institute of Cancer Research, London, United Kingdom
| | - Naomi Guppy
- 22The Institute of Cancer Research, London, United Kingdom
| | - Ioannis Roxanis
- 23Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London
| | - Samantha Barlow
- 24Department of Molecular and Clinical Cancer Medicine, University of Liverpool, United Kingdom
| | - Helen Kalirai
- 25Department of Molecular and Clinical Cancer Medicine, United Kingdom
| | - Sarah Coupland
- 26Department of Molecular and Clinical Cancer Medicine, United Kingdom
| | | | | | - Alexandre Houy
- 29Inserm U830, PSL University, Institut Curie, United Kingdom
| | | | - Stephen Pettit
- 31The Institute of Cancer Research, London, United Kingdom
| | | | - Syed Haider
- 33Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London
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Tarantino D, Walker C, Weekes D, Pemberton H, Davidson K, Torga G, Frankum J, Mendes-Pereira AM, Prince C, Ferro R, Brough R, Pettitt SJ, Lord CJ, Grigoriadis A, Nj Tutt A. Functional screening reveals HORMAD1-driven gene dependencies associated with translesion synthesis and replication stress tolerance. Oncogene 2022; 41:3969-3977. [PMID: 35768547 PMCID: PMC9355871 DOI: 10.1038/s41388-022-02369-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 07/29/2021] [Revised: 05/21/2022] [Accepted: 05/30/2022] [Indexed: 11/09/2022]
Abstract
HORMAD1 expression is usually restricted to germline cells, but it becomes mis-expressed in epithelial cells in ~60% of triple-negative breast cancers (TNBCs), where it is associated with elevated genomic instability (1). HORMAD1 expression in TNBC is bimodal with HORMAD1-positive TNBC representing a biologically distinct disease group. Identification of HORMAD1-driven genetic dependencies may uncover novel therapies for this disease group. To study HORMAD1-driven genetic dependencies, we generated a SUM159 cell line model with doxycycline-inducible HORMAD1 that replicated genomic instability phenotypes seen in HORMAD1-positive TNBC (1). Using small interfering RNA screens, we identified candidate genes whose depletion selectively inhibited the cellular growth of HORMAD1-expressing cells. We validated five genes (ATR, BRIP1, POLH, TDP1 and XRCC1), depletion of which led to reduced cellular growth or clonogenic survival in cells expressing HORMAD1. In addition to the translesion synthesis (TLS) polymerase POLH, we identified a HORMAD1-driven dependency upon additional TLS polymerases, namely POLK, REV1, REV3L and REV7. Our data confirms that out-of-context somatic expression of HORMAD1 can lead to genomic instability and reveals that HORMAD1 expression induces dependencies upon replication stress tolerance pathways, such as translesion synthesis. Our data also suggest that HORMAD1 expression could be a patient selection biomarker for agents targeting replication stress.
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Affiliation(s)
- Dalia Tarantino
- Breast Cancer Now Research Unit, King's College London, London, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Callum Walker
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Daniel Weekes
- Breast Cancer Now Research Unit, King's College London, London, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Helen Pemberton
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Kathryn Davidson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Gonzalo Torga
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Jessica Frankum
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Ana M Mendes-Pereira
- Breast Cancer Now Research Unit, King's College London, London, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Cynthia Prince
- Breast Cancer Now Research Unit, King's College London, London, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Riccardo Ferro
- Breast Cancer Now Research Unit, King's College London, London, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Rachel Brough
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Stephen J Pettitt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Christopher J Lord
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Anita Grigoriadis
- Breast Cancer Now Research Unit, King's College London, London, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Andrew Nj Tutt
- Breast Cancer Now Research Unit, King's College London, London, UK.
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK.
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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Goodkin O, Prados F, Vos SB, Pemberton H, Collorone S, Hagens MHJ, Cardoso MJ, Yousry TA, Thornton JS, Sudre CH, Barkhof F. FLAIR-only joint volumetric analysis of brain lesions and atrophy in clinically isolated syndrome (CIS) suggestive of multiple sclerosis. Neuroimage Clin 2020; 29:102542. [PMID: 33418171 PMCID: PMC7804983 DOI: 10.1016/j.nicl.2020.102542] [Citation(s) in RCA: 4] [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] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 12/20/2020] [Indexed: 11/18/2022]
Abstract
Background MRI assessment in multiple sclerosis (MS) focuses on the presence of typical white matter (WM) lesions. Neurodegeneration characterised by brain atrophy is recognised in the research field as an important prognostic factor. It is not routinely reported clinically, in part due to difficulty in achieving reproducible measurements. Automated MRI quantification of WM lesions and brain volume could provide important clinical monitoring data. In general, lesion quantification relies on both T1 and FLAIR input images, while tissue volumetry relies on T1. However, T1-weighted scans are not routinely included in the clinical MS protocol, limiting the utility of automated quantification. Objectives We address an aspect of this important translational challenge by assessing the performance of FLAIR-only lesion and brain segmentation, against a conventional approach requiring multi-contrast acquisition. We explore whether FLAIR-only grey matter (GM) segmentation yields more variability in performance compared with two-channel segmentation; whether this is related to field strength; and whether the results meet a level of clinical acceptability demonstrated by the ability to reproduce established biological associations. Methods We used a multicentre dataset of subjects with a CIS suggestive of MS scanned at 1.5T and 3T in the same week. WM lesions were manually segmented by two raters, ‘manual 1′ guided by consensus reading of CIS-specific lesions and ‘manual 2′ by any WM hyperintensity. An existing brain segmentation method was adapted for FLAIR-only input. Automated segmentation of WM hyperintensity and brain volumes were performed with conventional (T1/T1 + FLAIR) and FLAIR-only methods. Results WM lesion volumes were comparable at 1.5T between ‘manual 2′ and FLAIR-only methods and at 3T between ‘manual 2′, T1 + FLAIR and FLAIR-only methods. For cortical GM volume, linear regression measures between conventional and FLAIR-only segmentation were high (1.5T: α = 1.029, R2 = 0.997, standard error (SE) = 0.007; 3T: α = 1.019, R2 = 0.998, SE = 0.006). Age-associated change in cortical GM volume was a significant covariate in both T1 (p = 0.001) and FLAIR-only (p = 0.005) methods, confirming the expected relationship between age and GM volume for FLAIR-only segmentations. Conclusions FLAIR-only automated segmentation of WM lesions and brain volumes were consistent with results obtained through conventional methods and had the ability to demonstrate biological effects in our study population. Imaging protocol harmonisation and validation with other MS phenotypes could facilitate the integration of automated WM lesion volume and brain atrophy analysis as clinical tools in radiological MS reporting.
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Affiliation(s)
- O Goodkin
- Centre for Medical Image Computing (CMIC), University College London, London, United Kingdom; Neuroradiological Academic Unit, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom.
| | - F Prados
- Centre for Medical Image Computing (CMIC), University College London, London, United Kingdom; Neuroradiological Academic Unit, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom; eHealth Centre, Universitat Oberta de Catalunya, Barcelona, Spain
| | - S B Vos
- Centre for Medical Image Computing (CMIC), University College London, London, United Kingdom; Neuroradiological Academic Unit, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom; Lysholm Department of Neuroradiology, National Hospital for Neurology and Neurosurgery, UCLH NHS Foundation Trust, London, United Kingdom
| | - H Pemberton
- Centre for Medical Image Computing (CMIC), University College London, London, United Kingdom; Neuroradiological Academic Unit, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - S Collorone
- NMR Research Unit, Queen Square Multiple Sclerosis Centre, Department of Neuroinflammation, UCL Institute of Neurology, Faculty of Brain Sciences, University College London (UCL), London, United Kingdom
| | - M H J Hagens
- MS Center Amsterdam, Department of Neurology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - M J Cardoso
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, United Kingdom
| | - T A Yousry
- Neuroradiological Academic Unit, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom; Lysholm Department of Neuroradiology, National Hospital for Neurology and Neurosurgery, UCLH NHS Foundation Trust, London, United Kingdom
| | - J S Thornton
- Neuroradiological Academic Unit, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom; Lysholm Department of Neuroradiology, National Hospital for Neurology and Neurosurgery, UCLH NHS Foundation Trust, London, United Kingdom
| | - C H Sudre
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, United Kingdom; Dementia Research Centre, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - F Barkhof
- Centre for Medical Image Computing (CMIC), University College London, London, United Kingdom; Neuroradiological Academic Unit, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom; Lysholm Department of Neuroradiology, National Hospital for Neurology and Neurosurgery, UCLH NHS Foundation Trust, London, United Kingdom; Radiology & Nuclear Medicine, VU University Medical Center, Amsterdam, Netherlands
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George SL, Lorenzi F, King D, Hartlieb S, Campbell J, Pemberton H, Toprak UH, Barker K, Tall J, da Costa BM, van den Boogaard ML, Dolman MEM, Molenaar JJ, Bryant HE, Westermann F, Lord CJ, Chesler L. Therapeutic vulnerabilities in the DNA damage response for the treatment of ATRX mutant neuroblastoma. EBioMedicine 2020; 59:102971. [PMID: 32846370 PMCID: PMC7452577 DOI: 10.1016/j.ebiom.2020.102971] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [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: 05/22/2020] [Revised: 08/07/2020] [Accepted: 08/07/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In neuroblastoma, genetic alterations in ATRX, define a distinct poor outcome patient subgroup. Despite the need for new therapies, there is a lack of available models and a dearth of pre-clinical research. METHODS To evaluate the impact of ATRX loss of function (LoF) in neuroblastoma, we utilized CRISPR-Cas9 gene editing to generate neuroblastoma cell lines isogenic for ATRX. We used these and other models to identify therapeutically exploitable synthetic lethal vulnerabilities associated with ATRX LoF. FINDINGS In isogenic cell lines, we found that ATRX inactivation results in increased DNA damage, homologous recombination repair (HRR) defects and impaired replication fork processivity. In keeping with this, high-throughput compound screening showed selective sensitivity in ATRX mutant cells to multiple PARP inhibitors and the ATM inhibitor KU60019. ATRX mutant cells also showed selective sensitivity to the DNA damaging agents, sapacitabine and irinotecan. HRR deficiency was also seen in the ATRX deleted CHLA-90 cell line, and significant sensitivity demonstrated to olaparib/irinotecan combination therapy in all ATRX LoF models. In-vivo sensitivity to olaparib/irinotecan was seen in ATRX mutant but not wild-type xenografts. Finally, sustained responses to olaparib/irinotecan therapy were seen in an ATRX deleted neuroblastoma patient derived xenograft. INTERPRETATION ATRX LoF results in specific DNA damage repair defects that can be therapeutically exploited. In ATRX LoF models, preclinical sensitivity is demonstrated to olaparib and irinotecan, a combination that can be rapidly translated into the clinic. FUNDING This work was supported by Christopher's Smile, Neuroblastoma UK, Cancer Research UK, and the Royal Marsden Hospital NIHR BRC.
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Affiliation(s)
- Sally L George
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT United Kingdom.
| | - Federica Lorenzi
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - David King
- Academic Unit of Molecular Oncology, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, United Kingdom
| | - Sabine Hartlieb
- Neuroblastoma Genomics, Hopp Children`s Cancer Center Heidelberg (KiTZ) & German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - James Campbell
- Bioinformatics Core Facility, The Institute of Cancer Research, London, United Kingdom
| | - Helen Pemberton
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research London, SW3 6JB, United Kingdom
| | - Umut H Toprak
- Neuroblastoma Genomics, Hopp Children`s Cancer Center Heidelberg (KiTZ) & German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Karen Barker
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Jennifer Tall
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Barbara Martins da Costa
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | | | - M Emmy M Dolman
- Princess Maxima Center for Pediatric Cancer, Utrecht, The Netherlands
| | - Jan J Molenaar
- Princess Maxima Center for Pediatric Cancer, Utrecht, The Netherlands
| | - Helen E Bryant
- Academic Unit of Molecular Oncology, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, United Kingdom
| | - Frank Westermann
- Neuroblastoma Genomics, Hopp Children`s Cancer Center Heidelberg (KiTZ) & German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christopher J Lord
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research London, SW3 6JB, United Kingdom
| | - Louis Chesler
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT United Kingdom
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Mackay A, Carvalho D, Molinari V, Pemberton H, Temelso S, Burford A, Clarke M, Fofana M, Boult J, Izquierdo E, Taylor K, Bjerke L, Fazal Salom J, Kessler K, Rogers R, Marshall L, Carceller F, Pears J, Moore A, Miele E, Carai A, Mastronuzzi A, Robinson S, Lord C, Olaciregui N, Mora J, Montero Carcaboso A, Hargrave D, Vinci M, Jones C. PDTM-31. DRUG SCREENING LINKED TO MOLECULAR PROFILING IDENTIFIES NOVEL DEPENDENCIES IN PATIENT-DERIVED PRIMARY CULTURES OF PAEDIATRIC HIGH GRADE GLIOMA AND DIPG. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy148.871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Alan Mackay
- The Institute of Cancer Research, Sutton, England, United Kingdom
| | - Diana Carvalho
- The Institute of Cancer Research, Sutton, England, United Kingdom
| | - Valeria Molinari
- The Institute of Cancer Research, Sutton, England, United Kingdom
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jane Pears
- Our Lady Childrens Hospital, Dublin, Irel
| | - Andrew Moore
- Childrens Health Queensland Hospital and Health Service, Brisbane, QLD, Australia
| | | | - Andrea Carai
- Department of Neuroscience and Neurorehabilitation, Neurosurgery Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Angela Mastronuzzi
- Department of Onco-haematology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital-IRCCS, Rome, Italy
| | | | - Chris Lord
- The Institute of Cancer Research, London, England, United Kingdom
| | | | - Jaume Mora
- Hospital San Joan de Deu, Barcelona, Spain
| | | | | | - Maria Vinci
- Department of Onco-haematology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital-IRCCS, Rome, Italy
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Fazal Salom J, Bjerke L, Carvalho D, Boult J, Mackay A, Pemberton H, Molinari V, Clarke M, Vinci M, Carceller F, Marshall L, Moore A, Montero Carcaboso A, Lord C, Robinson S, Hargrave D, Jones C. PDTM-33. ATRX LOSS CONFERS ENHANCED SENSITIVITY TO COMBINED PARP INHIBITION AND RADIOTHERAPY IN PAEDIATRIC GLIOBLASTOMA MODELS. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy148.873] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | | | | | - Alan Mackay
- The Institute of Cancer Research, Sutton, England, United Kingdom
| | | | - Valeria Molinari
- The Institute of Cancer Research, Sutton, England, United Kingdom
| | | | - Maria Vinci
- Department of Onco-haematology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital-IRCCS, Rome, Italy
| | | | | | - Andrew Moore
- The University of Queensland, Brisbane, QLD, Australia
| | | | - Chris Lord
- The Institute of Cancer Research, London, England, United Kingdom
| | | | - Darren Hargrave
- Great Ormond Street Hospital, London, England, United Kingdom
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Bjerke L, Mackay A, Carvalho D, Pemberton H, Molinari V, Vinci M, Carceller F, Marshall L, Moore A, Montero Carcaboso A, Lord C, Hargrave D, Jones C. PDTM-34. TARGETING H3.3G34R/V RE-WIRING OF THE EPIGENOME IN PAEDIATRIC GLIOBLASTOMA OF CHILDREN AND YOUNG ADULTS. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy148.874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Alan Mackay
- The Institute of Cancer Research, Sutton, England, United Kingdom
| | - Diana Carvalho
- The Institute of Cancer Research, Sutton, England, United Kingdom
| | | | - Valeria Molinari
- The Institute of Cancer Research, Sutton, England, United Kingdom
| | - Maria Vinci
- Department of Onco-haematology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital-IRCCS, Rome, Italy
| | | | | | - Andrew Moore
- The University of Queensland, Brisbane, QLD, Australia
| | | | - Chris Lord
- The Institute of Cancer Research, London, England, United Kingdom
| | - Darren Hargrave
- Great Ormond Street Hospital, London, England, United Kingdom
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Tarantino D, Walker C, Weekes D, Pemberton H, Frankum J, Brough R, Lord CJ, Grigoriadis A, Tutt A. Abstract 344: A high-throughput functional screen reveals synthetic lethal interactions associated with replication stress in HORMAD1-expressing triple-negative breast cancers. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-344] [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
HORMAD1, expression of which is usually restricted to germline cells, is expressed in ~60% of triple-negative breast cancers (TNBCs) where it is associated with higher levels of allelic imbalance. In experimental systems, HORMAD1 also drives Homologous Recombination (HR) deficiency, PARP inhibitor and cisplatin sensitivity. To provide further insights into the role of HORMAD1 in TNBC, we generated a doxycycline-inducible HORMAD1 expression system in the copy number stable, HORMAD1-negative, TNBC cell line SUM159. Clonal, HORMAD1-positive, populations were established which displayed increased levels of genomic instability and reduced levels of homologous recombination. To identify synthetic lethal therapeutic targets associated with HORMAD1 expression in TNBC, we performed an RNAi library screen, in which the viability of HORMAD1-expressing SUM159 clonal cell populations was assessed following the targeted depletion of 1743 genes. Candidate synthetic lethal (SL) genes were validated in a secondary screen using 3 additional HORMAD1-expressing SUM159 clones. The primary siRNA screen identified 63 genes which were SL with elevated HORMAD1 expression, including XRCC1, TDP1, Pol η, BRIP1 and ATR - genes with a known function in mitigating replication stress. DNA polymerase η (POLH) is a Y-family DNA polymerase involved in translesion synthesis (TLS), a DNA damage tolerance pathway employed by proliferating cells to bypass replication fork stalling DNA lesions and to prevent replication fork collapse. We hypothesised that HORMAD1 expression leads to Pol η localisation to replication factories, to mediate lesion bypass. Consistent with this, we found an enrichment in Pol η and monoubiquitylated-PCNA in the chromatin fraction of HORMAD1-expressing SUM159 cells, suggesting that Pol η and TLS might buffer the effect of elevated HORMAD1 expression in TNBC. Our data suggest that HORMAD1 expression in mitotic cells leads to a dependency on pathways implicated in preventing or resolving replication stress, such as TLS, and suggests that vulnerabilities associated with specific DNA repair processes could be used to target HORMAD1-positive TNBCs.
Citation Format: Dalia Tarantino, Callum Walker, Daniel Weekes, Helen Pemberton, Jessica Frankum, Rachel Brough, Christopher J. Lord, Anita Grigoriadis, Andrew Tutt. A high-throughput functional screen reveals synthetic lethal interactions associated with replication stress in HORMAD1-expressing triple-negative breast cancers [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 344.
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Affiliation(s)
- Dalia Tarantino
- 1Breast Cancer Now Research Unit, King's College London, London, United Kingdom
| | - Callum Walker
- 2Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Daniel Weekes
- 1Breast Cancer Now Research Unit, King's College London, London, United Kingdom
| | - Helen Pemberton
- 2Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Jessica Frankum
- 2Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Rachel Brough
- 2Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Christopher J. Lord
- 2Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Anita Grigoriadis
- 1Breast Cancer Now Research Unit, King's College London, London, United Kingdom
| | - Andrew Tutt
- 1Breast Cancer Now Research Unit, King's College London, London, United Kingdom
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Mackay A, Molinari V, Carvalho D, Pemberton H, Temelso S, Burford A, Clarke M, Fofana M, Boult J, Izquierdo E, Taylor K, Bjerke L, Salom JF, Kessler K, Rogers R, Chandler C, Zebian B, Martin A, Stapleton S, Hettige S, Marshall L, Carceller F, Mandeville H, Vaidya S, Bridges L, Al-Sarraj S, Pears J, Mastronuzzi A, Carai A, del Bufalo F, de Torres C, Sunol M, Cruz O, Mora J, Moore A, Robinson S, Lord C, Carcaboso AM, Vinci M, Jones C. HGG-23. DRUG SCREENING LINKED TO MOLECULAR PROFILING IDENTIFIES NOVEL DEPENDENCIES IN PATIENT-DERIVED PRIMARY CULTURES OF PAEDIATRIC HIGH GRADE GLIOMA AND DIPG. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jane Pears
- Our Lady Children’s Hospital, Dublin, Irel
| | | | | | | | | | | | | | - Jaume Mora
- Hospital San Joan de Deu, Barcelona, Spain
| | - Andrew Moore
- Queensland Children’s Tumour Bank, Brisbane, Australia
| | | | | | | | - Maria Vinci
- Ospedale Pediatrico Cambio Gesu, Rome, Italy
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Fazal-Salom J, Vinci M, Carvalho D, Pemberton H, Pettitt SJ, Lord CJ, Mackay A, Bjerke L, Jones C. Abstract 1932: Mutations in ATRX increase genetic instability and sensitivity to PARP inhibitors in paediatric glioblastoma cells. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1932] [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
Paediatric glioblastomas (pGBM) are amongst the most common causes of cancer-related deaths in children, and are defined by highly recurrent mutations in H3 histones. Mutations affecting the chromatin remodeling protein ATRX have been reported in 30% of pGBM cases, and are strongly associated with the alternative lengthening of telomeres (ALT) phenotype, but their precise interaction with histone mutations and their role in tumorigenesis remain unclear.
We collected sequence data from 262 published and 64 unpublished cases of pGBM and identified somatic ATRX mutations in 54/326 (17%) of cases. ATRX mutations are mainly loss of function mutations, with the majority of frameshift mutations (37/54, 68,5%) found upstream of the helicase domain resulting in truncation of the main functional domain of ATRX. Missense mutations (16/54, 29,6%) reside almost exclusively in the helicase domain (11/54, 20,4%), whereas nonsense mutations are a less common event (7/54, 13%) but present in both the helicase (4/7, 57,1%) and ADD domains (3/7, 42,9%). ATRX mutations commonly co-segregate with H3.3 G34 (16/54) and TP53 (42/54) mutations, and define a subgroup of patients with a longer overall survival (16 months median overall survival in mutant ATRX cases versus 11 months in wild-type ATRX cases, COXPH p = 0.079), though with a greater number of somatic mutations (MWU p = 0.023) and copy number alterations (MWU p = 0.0011) than wild-type cases.
We screened a series of 21 primary patient-derived pGBM cell cultures for histone and ATRX mutation status in addition to ATRX protein expression and ALT, and subjected the panel to a high-throughput in vitro cell viability screen of >400 chemotherapeutics and small molecules. We identified a specific genetic dependency for ATRX mutation and sensitivity to distinct PARP inhibitor chemotypes, including olaparib and rucaparib (PARP catalytic inhibitors), and talazoparib (PARP trapper inhibitor). These data were validated using CRISPR-Cas9-engineered ATRX knockout, targeting either the ADD or helicase domain, in SF188 pGBM cells. Gene editing was confirmed by IonTorrent sequencing and Western blot. ATRX mutant clones were also more sensitive to drugs targeting DNA damage response pathways such as bleomycin and sapacitabine.
Gene expression analysis of ATRX mutant pGBM samples confirmed an intact homologous recombination pathway and overexpression of PARP1, suggesting an underlying mechanism distinct from that observed in BRCA-mutant breast and ovarian cancers.
Ongoing work is aimed at unravelling the specific pathways involved, and evaluating the utility of PARP inhibition in orthotopic pGBM xenografts in vivo. These data suggest a synthetic lethality for PARP inhibitors in ATRX-deficient pGBM cells, and may represent a novel therapeutic strategy for these highly aggressive tumours in children.
Citation Format: Janat Fazal-Salom, Mara Vinci, Diana Carvalho, Helen Pemberton, Stephen J. Pettitt, Christopher J. Lord, Alan Mackay, Lynn Bjerke, Chris Jones. Mutations in ATRX increase genetic instability and sensitivity to PARP inhibitors in paediatric glioblastoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1932. doi:10.1158/1538-7445.AM2017-1932
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Affiliation(s)
| | - Mara Vinci
- Institute of Cancer Research, London, United Kingdom
| | | | | | | | | | - Alan Mackay
- Institute of Cancer Research, London, United Kingdom
| | - Lynn Bjerke
- Institute of Cancer Research, London, United Kingdom
| | - Chris Jones
- Institute of Cancer Research, London, United Kingdom
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Khalique S, Williamson CT, Pemberton H, Wai PT, Menon M, Brough R, Leonidou A, Peck B, Banerjee S, Natrajan RC, Lord CJ. Abstract NTOC-093: SYNTHETIC LETHAL APPROACHES TO TARGET ARID1A DEFICIENT OVARIAN CANCERS. Clin Cancer Res 2017. [DOI: 10.1158/1557-3265.ovcasymp16-ntoc-093] [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
Epithelial ovarian cancer (EOC) remains the most lethal gynaecological malignancy in the Western world. Ovarian clear cell carcinoma (OCCC), a distinct histological subtype, has a notably poor prognosis in the advanced setting compared to patients with high-grade serous ovarian cancer (HGSOC). Understanding why these patients have a poor outcome may be due to the underlying genetic drivers and their response to treatment. Dysregulation of the SWI/SNF complex is one of the most commonly occurring defects in solid cancers. Mutations in ARID1A (AT-rich interactive domain-containing protein 1A), a gene that encodes for BAF250A, forming part of the SWI/SNF chromatin remodeling complex, rarely occur in HGSOC but are common in ovarian clear cell carcinomas. The vast majority of these are loss of function frameshift or nonsense mutations, resulting in loss of protein function. In addition, loss of ARID1A expression in tumour specimens has been associated with a shorter progression free survival and chemoresistance in ovarian clear cell carcinoma (OCCC).
Despite the understanding that ARID1A defects are associated with tumourigenesis, targeted therapy approaches that exploit this deficiency have not as yet been developed. Our aims were to identify ways of targeting ARID1A deficient tumours by performing a large-scale functional genomics screen to identify actionable synthetic lethal effects. Using a high-throughput combination drug screen with a plate library of 80 compounds and a phase 1 compound, in isogenic ARID1A null and wild type HCT116 cells, we have identified candidate therapeutic approaches to targeting ARID1A mutant tumours that could be assessed in proof of concept clinical trials. We have undertaken subsequent high throughput drug screens in isogenic ARID1A null and wild type MCF10A cells that in we have identified a series of novel synthetic lethal effects. Assessment of this combinatorial approach in in vivo models of ARID1A mutant cancers is now underway. In conclusion, we have identified clinically actionable combinatorial approaches that may provide additional therapeutic benefit for ARID1A deficient patients.
Citation Format: Saira Khalique, Chris T. Williamson, Helen Pemberton, Patty T. Wai, Malini Menon, Rachel Brough, Andri Leonidou, Barrie Peck, Susana Banerjee, Rachael C. Natrajan and Christopher J. Lord,. SYNTHETIC LETHAL APPROACHES TO TARGET ARID1A DEFICIENT OVARIAN CANCERS [abstract]. In: Proceedings of the 11th Biennial Ovarian Cancer Research Symposium; Sep 12-13, 2016; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(11 Suppl):Abstract nr NTOC-093.
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Fazal-Salom J, Vinci M, Carvalho D, Pemberton H, Pettit S, Lord C, Mackay A, Bjerke L, Jones C. HGG-07. MUTATIONS IN ATRX INCREASE GENETIC INSTABILITY AND SENSITIVITY TO PARP INHIBITORS IN PAEDIATRIC GLIOBLASTOMA CELLS. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox083.096] [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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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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Vinci M, Burford A, Molinari V, Popov S, Taylor KR, Pemberton H, Lord CJ, Gutteridge A, Forshew T, Marshall LV, Qin EY, Ingram WJ, Moore AS, Ng HK, Trabelsi S, Brahim DHB, Zacharoulis S, Vaidya S, Mandeville HC, Bridges LR, Martin AJ, Al-Sarraj S, Chandler C, Sunol M, Mora J, de Torres C, Cruz O, Carcaboso AM, Monje M, Mackay A, Jones C. HG-97PAEDIATRIC GBM AND DIPG SUBCLONES CO-OPERATE TO PROMOTE TUMORIGENESIS. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now073.93] [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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Mateo J, Carreira S, Sandhu S, Miranda S, Mossop H, Perez-Lopez R, Nava Rodrigues D, Robinson D, Omlin A, Tunariu N, Boysen G, Porta N, Flohr P, Gillman A, Figueiredo I, Paulding C, Seed G, Jain S, Ralph C, Protheroe A, Hussain S, Jones R, Elliott T, McGovern U, Bianchini D, Goodall J, Zafeiriou Z, Williamson CT, Ferraldeschi R, Riisnaes R, Ebbs B, Fowler G, Roda D, Yuan W, Wu YM, Cao X, Brough R, Pemberton H, A'Hern R, Swain A, Kunju LP, Eeles R, Attard G, Lord CJ, Ashworth A, Rubin MA, Knudsen KE, Feng FY, Chinnaiyan AM, Hall E, de Bono JS. DNA-Repair Defects and Olaparib in Metastatic Prostate Cancer. N Engl J Med 2015; 373:1697-708. [PMID: 26510020 PMCID: PMC5228595 DOI: 10.1056/nejmoa1506859] [Citation(s) in RCA: 1601] [Impact Index Per Article: 177.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Prostate cancer is a heterogeneous disease, but current treatments are not based on molecular stratification. We hypothesized that metastatic, castration-resistant prostate cancers with DNA-repair defects would respond to poly(adenosine diphosphate [ADP]-ribose) polymerase (PARP) inhibition with olaparib. METHODS We conducted a phase 2 trial in which patients with metastatic, castration-resistant prostate cancer were treated with olaparib tablets at a dose of 400 mg twice a day. The primary end point was the response rate, defined either as an objective response according to Response Evaluation Criteria in Solid Tumors, version 1.1, or as a reduction of at least 50% in the prostate-specific antigen level or a confirmed reduction in the circulating tumor-cell count from 5 or more cells per 7.5 ml of blood to less than 5 cells per 7.5 ml. Targeted next-generation sequencing, exome and transcriptome analysis, and digital polymerase-chain-reaction testing were performed on samples from mandated tumor biopsies. RESULTS Overall, 50 patients were enrolled; all had received prior treatment with docetaxel, 49 (98%) had received abiraterone or enzalutamide, and 29 (58%) had received cabazitaxel. Sixteen of 49 patients who could be evaluated had a response (33%; 95% confidence interval, 20 to 48), with 12 patients receiving the study treatment for more than 6 months. Next-generation sequencing identified homozygous deletions, deleterious mutations, or both in DNA-repair genes--including BRCA1/2, ATM, Fanconi's anemia genes, and CHEK2--in 16 of 49 patients who could be evaluated (33%). Of these 16 patients, 14 (88%) had a response to olaparib, including all 7 patients with BRCA2 loss (4 with biallelic somatic loss, and 3 with germline mutations) and 4 of 5 with ATM aberrations. The specificity of the biomarker suite was 94%. Anemia (in 10 of the 50 patients [20%]) and fatigue (in 6 [12%]) were the most common grade 3 or 4 adverse events, findings that are consistent with previous studies of olaparib. CONCLUSIONS Treatment with the PARP inhibitor olaparib in patients whose prostate cancers were no longer responding to standard treatments and who had defects in DNA-repair genes led to a high response rate. (Funded by Cancer Research UK and others; ClinicalTrials.gov number, NCT01682772; Cancer Research UK number, CRUK/11/029.).
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Affiliation(s)
- Joaquin Mateo
- From the Institute of Cancer Research (J.M., S.C., S.S., S.M., H.M., R.P.-L., D.N.R., A.O., N.T., G.B., N.P., P.F., A.G., I.F., C.P., G.S., D.B., J.G., Z.Z., C.T.W., R.F., R.R., B.E., G.F., D. Roda, W.Y., R.B., H.P., R.A., A.S., R.E., G.A., C.J.L., A.A., E.H., J.S.B.), the Royal Marsden NHS Foundation Trust (J.M., S.S., R.P.-L., A.O., N.T., D.B., Z.Z., R.F., D. Roda, R.E., G.A., J.S.B.), and University College London Hospital (U.M.), London, Queen's University, Belfast (S.J.), University of Leeds, Leeds (C.R.), Churchill Hospital, Oxford (A.P.), University of Liverpool, Liverpool (S.H.), Beatson West of Scotland Cancer Centre, Glasgow (R.J.), and Christie Hospital, Manchester (T.E.) - all in the United Kingdom; the University of Michigan, Ann Arbor (D. Robinson, Y.-M.W., X.C., L.P.K., F.Y.F., A.M.C.); Weill Cornell Medical College, New York (M.A.R.); and Thomas Jefferson University, Philadelphia (K.E.K.)
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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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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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O'Loghlen A, Martin N, Krusche B, Pemberton H, Alonso MM, Chandler H, Brookes S, Parrinello S, Peters G, Gil J. The nuclear receptor NR2E1/TLX controls senescence. Oncogene 2014; 34:4069-4077. [PMID: 25328137 PMCID: PMC4305339 DOI: 10.1038/onc.2014.335] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [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: 06/10/2014] [Revised: 08/13/2014] [Accepted: 09/04/2014] [Indexed: 12/25/2022]
Abstract
The nuclear receptor NR2E1 (also known as TLX or tailless) controls the self-renewal of neural stem cells (NSCs) and has been implied as an oncogene which initiates brain tumors including glioblastomas. Despite NR2E1 regulating targets like p21(CIP1) or PTEN we still lack a full explanation for its role in NSC self-renewal and tumorigenesis. We know that polycomb repressive complexes also control stem cell self-renewal and tumorigenesis, but so far, no formal connection has been established between NR2E1 and PRCs. In a screen for transcription factors regulating the expression of the polycomb protein CBX7, we identified NR2E1 as one of its more prominent regulators. NR2E1 binds at the CBX7 promoter, inducing its expression. Notably CBX7 represses NR2E1 as part of a regulatory loop. Ectopic NR2E1 expression inhibits cellular senescence, extending cellular lifespan in fibroblasts via CBX7-mediated regulation of p16(INK4a) and direct repression of p21(CIP1). In addition NR2E1 expression also counteracts oncogene-induced senescence. The importance of NR2E1 to restrain senescence is highlighted through the process of knocking down its expression, which causes premature senescence in human fibroblasts and epithelial cells. We also confirmed that NR2E1 regulates CBX7 and restrains senescence in NSCs. Finally, we observed that the expression of NR2E1 directly correlates with that of CBX7 in human glioblastoma multiforme. Overall we identified control of senescence and regulation of polycomb action as two possible mechanisms that can join those so far invoked to explain the role of NR2E1 in control of NSC self-renewal and cancer.
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Affiliation(s)
- Ana O'Loghlen
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK.,Molecular Oncology Laboratory, CRUK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3PX, UK
| | - Nadine Martin
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Benjamin Krusche
- Cell Interactions and Cancer Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Helen Pemberton
- Molecular Oncology Laboratory, CRUK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3PX, UK
| | - Marta M Alonso
- Department of Medical Oncology, University Hospital of Navarra, Pamplona, Spain
| | - Hollie Chandler
- Molecular Oncology Laboratory, CRUK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3PX, UK
| | - Sharon Brookes
- Molecular Oncology Laboratory, CRUK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3PX, UK
| | - Simona Parrinello
- Cell Interactions and Cancer Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Gordon Peters
- Molecular Oncology Laboratory, CRUK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3PX, UK
| | - Jesús Gil
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, 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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Kim D, Pemberton H, Stratford AL, Buelaert K, Watkinson JC, Lopes V, Franklyn JA, McCabe CJ. Pituitary tumour transforming gene (PTTG) induces genetic instability in thyroid cells. Oncogene 2005; 24:4861-6. [PMID: 15897900 DOI: 10.1038/sj.onc.1208659] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cancer reflects the progressive accumulation of genetic alterations and subsequent genetic instability of cells. Cytogenetic studies have demonstrated the importance of aneuploidy in differentiated thyroid cancer development. The pituitary tumour transforming gene (PTTG), also known as securin, is a mitotic checkpoint protein which inhibits sister chromatid separation during mitosis. PTTG is highly expressed in many cancers and overexpression of PTTG induces aneuploidy in vitro. Using fluorescent intersimple sequence repeat PCR (FISSR-PCR), we investigated the relationship between PTTG expression and the degree of genetic instability in normal and tumorous thyroid samples. The genomic instability index (GI index) was 6.7-72.7% higher in cancers than normal thyroid tissues. Follicular thyroid tumours exhibited greater genetic instability than papillary tumours (27.6% (n=9) versus 14.5% (n=10), P=0.03). We also demonstrated a strong relationship between PTTG expression and the degree of genetic instability in thyroid cancers (R2=0.80, P=0.007). To further investigate PTTG's role in genetic instability, we transfected FTC133 thyroid follicular cells and observed increased genetic instability in cells overexpressing PTTG compared with vector-only-transfected controls (n=3, GI Index VO=29.7+/-5.2 versus PTTG=63.7+/-6.4, P=0.013). Further, we observed a dose response in genetic instability and PTTG expression (GI Index low dose (0.5 microg DNA/ six-well plate) PTTG=15.3%+/-1.7 versus high dose (3 microg DNA) PTTG=50.8%+/-3.3, P=0.006). Overall, we describe the first use of FISSR-PCR in human cancers, and demonstrate that PTTG expression correlates with genetic instability in vivo, and induces genetic instability in vitro. We conclude that PTTG may be an important gene in the mutator phenotype development in thyroid cancer.
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Affiliation(s)
- Dae Kim
- Division of Medical Sciences, 2nd Floor IBR, University of Birmingham, Edgbaston, Birmingham B12 5TT, UK.
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Bussolati B, Ahmed A, Pemberton H, Landis RC, Di Carlo F, Haskard DO, Mason JC. Bifunctional role for VEGF-induced heme oxygenase-1 in vivo: induction of angiogenesis and inhibition of leukocytic infiltration. Blood 2004; 103:761-6. [PMID: 14525760 DOI: 10.1182/blood-2003-06-1974] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
AbstractHeme-oxygenases (HOs) catalyze the conversion of heme into carbon monoxide and biliverdin. HO-1 is induced during hypoxia, ischemia/reperfusion, and inflammation, providing cytoprotection and inhibiting leukocyte migration to inflammatory sites. Although in vitro studies have suggested an additional role for HO-1 in angiogenesis, the relevance of this in vivo remains unknown. We investigated the involvement of HO-1 in angiogenesis in vitro and in vivo. Vascular endothelial growth factor (VEGF) induced prolonged HO-1 expression and activity in human endothelial cells and HO-1 inhibition abrogated VEGF-driven angiogenesis. Two murine models of angiogenesis were used: (1) angiogenesis initiated by addition of VEGF to Matrigel and (2) a lipopolysaccharide (LPS)–induced model of inflammatory angiogenesis in which angiogenesis is secondary to leukocyte invasion. Pharmacologic inhibition of HO-1 induced marked leukocytic infiltration that enhanced VEGF-induced angiogenesis. However, in the presence of an anti-CD18 monoclonal antibody (mAb) to block leukocyte migration, VEGF-induced angiogenesis was significantly inhibited by HO-1 antagonists. Furthermore, in the LPS-induced model of inflammatory angiogenesis, induction of HO-1 with cobalt protoporphyrin significantly inhibited leukocyte invasion into LPS-conditioned Matrigel and thus prevented the subsequent angiogenesis. We therefore propose that during chronic inflammation HO-1 has 2 roles: first, an anti-inflammatory action inhibiting leukocyte infiltration; and second, promotion of VEGF-driven noninflammatory angiogenesis that facilitates tissue repair.
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Affiliation(s)
- Benedetta Bussolati
- Department of Reproductive and Vascular Biology, The Medical School, University of Birmingham, Edgbaston, Birmingham, B12 2TG, United Kingdom.
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Pemberton H. Peculiar Electrical Phenomena. Science 1909; 29:143. [PMID: 17730303 DOI: 10.1126/science.29.734.143] [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: 11/02/2022]
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Pemberton H. ENGINEERING CHEMISTRY. A MANUAL OF QUANTITATIVE CHEMICAL ANALYSIS, FOR THE USE OF STUDENTS, CHEMISTS, AND ENGINEERS. J Am Chem Soc 1901. [DOI: 10.1021/ja02030a013] [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: 11/30/2022]
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Pemberton H. An Apparatus for Heating Substances in Glass Tubes under Pressure. Sci Am 1891. [DOI: 10.1038/scientificamerican05231891-12838asupp] [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: 11/09/2022]
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