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Hedayat S, Cascione L, Cunningham D, Schirripa M, Lampis A, Hahne JC, Tunariu N, Hong SP, Marchetti S, Khan K, Fontana E, Angerilli V, Delrieux M, Nava Rodrigues D, Procaccio L, Rao S, Watkins D, Starling N, Chau I, Braconi C, Fotiadis N, Begum R, Guppy N, Howell L, Valenti M, Cribbes S, Kolozsvari B, Kirkin V, Lonardi S, Ghidini M, Passalacqua R, Elghadi R, Magnani L, Pinato DJ, Di Maggio F, Ghelardi F, Sottotetti E, Vetere G, Ciraci P, Vlachogiannis G, Pietrantonio F, Cremolini C, Cortellini A, Loupakis F, Fassan M, Valeri N. Circulating microRNA analysis in a prospective co-clinical trial identifies MIR652-3p as a response biomarker and driver of regorafenib resistance mechanisms in colorectal cancer. Clin Cancer Res 2024:734699. [PMID: 38376926 DOI: 10.1158/1078-0432.ccr-23-2748] [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: 10/16/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND The multi-kinase inhibitor regorafenib has demonstrated efficacy in chemo-refractory metastatic colorectal cancer (mCRC) patients. However, lack of predictive biomarkers and concerns over significant toxicities hamper the use of regorafenib in clinical practice. METHODS Serial liquid biopsies were obtained at baseline and monthly until disease progression in chemo-refractory mCRC patients treated with regorafenib in a phase II clinical trial (PROSPECT-R n=40; NCT03010722) and in a multicentric validation cohort (n=241). Tissue biopsies collected at baseline, after 2 months and at progression in the PROSPECT-R trial were used to establish Patient-Derived Organoids (PDOs) and for molecular analyses. MicroRNA profiling was performed on baseline bloods using the NanoString nCounter platform and results were validated by digital droplet PCR and/or In Situ Hybridization in paired liquid and tissue biopsies. PDOs co-cultures and PDO-xenotransplants were generated for functional analyses. RESULTS Large-scale microRNA expression analysis in longitudinal matched liquid and tissue biopsies from the PROSPECT-R trial identified MIR652-3p as a biomarker of clinical benefit to regorafenib. These findings were confirmed in an independent validation cohort and in a "control" group of 100 patients treated with lonsurf. Using ex vivo co-culture assays paired with single-cell RNA-sequencing of PDO established pre- and post-treatment, we modelled regorafenib response observed in vivo and in patients, and showed that MIR652-3p controls resistance to regorafenib by impairing regorafenib-induced lethal autophagy and by orchestrating the switch from neo-angiogenesis to vessel co-option. CONCLUSIONS Our results identify MIR652-3p as potential biomarker and as a driver of cell and non-cell autonomous mechanisms of resistance to regorafenib.
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Affiliation(s)
| | - Luciano Cascione
- IOR - Institute of Oncology Research, Bellinzona, Ticino, Switzerland
| | | | - Marta Schirripa
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States
| | - Andrea Lampis
- Institute of Cancer Research, Sutton, United Kingdom
| | - Jens C Hahne
- Institute of Cancer Research, Sutton, United Kingdom
| | | | - Sung Pil Hong
- Yonsei University College of Medicine, Seoul, Korea (South), Republic of
| | | | - Khurum Khan
- Institute of Cancer Research, Sutton, United Kingdom
| | - Elisa Fontana
- Sarah Cannon Research Institute, London, London, United Kingdom
| | | | - Mia Delrieux
- Institute of Cancer Research, Sutton, United Kingdom
| | | | | | - Sheela Rao
- Royal Marsden NHS Foundation Trust, Sutton, Surrey, United Kingdom
| | | | | | - Ian Chau
- Royal Marsden Hospital, Sutton, Surrey, United Kingdom
| | | | | | - Ruwaida Begum
- Royal Marsden NHS Foundation Trust, London and Surrey, United Kingdom
| | - Naomi Guppy
- Institute of Cancer Research, London, United Kingdom
| | - Louise Howell
- Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | | | | | | | | | - Sara Lonardi
- Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
| | | | | | | | - Luca Magnani
- Institute of Cancer Research, London, United Kingdom
| | | | | | | | | | | | - Paolo Ciraci
- Azienda Ospedaliera Universitaria Pisana, Pisa, Italy
| | | | | | | | | | | | | | - Nicola Valeri
- Institute of Cancer Research, Sutton, London, United Kingdom
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2
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Bland P, Saville H, Wai PT, Curnow L, Muirhead G, Nieminuszczy J, Ravindran N, John MB, Hedayat S, Barker HE, Wright J, Yu L, Mavrommati I, Read A, Peck B, Allen M, Gazinska P, Pemberton HN, Gulati A, Nash S, Noor F, Guppy N, Roxanis I, Pratt G, Oldreive C, Stankovic T, Barlow S, Kalirai H, Coupland SE, Broderick R, Alsafadi S, Houy A, Stern MH, Pettit S, Choudhary JS, Haider S, Niedzwiedz W, Lord CJ, Natrajan R. SF3B1 hotspot mutations confer sensitivity to PARP inhibition by eliciting a defective replication stress response. Nat Genet 2023; 55:1311-1323. [PMID: 37524790 PMCID: PMC10412459 DOI: 10.1038/s41588-023-01460-5] [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: 03/09/2023] [Accepted: 06/26/2023] [Indexed: 08/02/2023]
Abstract
SF3B1 hotspot mutations are associated with a poor prognosis in several tumor types and lead to global disruption of canonical splicing. Through synthetic lethal drug screens, we identify that SF3B1 mutant (SF3B1MUT) cells are selectively sensitive to poly (ADP-ribose) polymerase inhibitors (PARPi), independent of hotspot mutation and tumor site. SF3B1MUT cells display a defective response to PARPi-induced replication stress that occurs via downregulation of the cyclin-dependent kinase 2 interacting protein (CINP), leading to increased replication fork origin firing and loss of phosphorylated CHK1 (pCHK1; S317) induction. This results in subsequent failure to resolve DNA replication intermediates and G2/M cell cycle arrest. These defects are rescued through CINP overexpression, or further targeted by a combination of ataxia-telangiectasia mutated and PARP inhibition. In vivo, PARPi produce profound antitumor effects in multiple SF3B1MUT cancer models and eliminate distant metastases. These data provide the rationale for testing the clinical efficacy of PARPi in a biomarker-driven, homologous recombination proficient, patient population.
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Affiliation(s)
- Philip Bland
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Harry Saville
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Patty T Wai
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Lucinda Curnow
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Gareth Muirhead
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Nivedita Ravindran
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Marie Beatrix John
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Somaieh Hedayat
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Holly E Barker
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - James Wright
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Lu Yu
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Ioanna Mavrommati
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Abigail Read
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Barrie Peck
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Translational Cancer Metabolism Team, Centre for Tumour Biology, Barts Cancer Institute, Cancer Research UK Centre of Excellence, Queen Mary University of London, Charterhouse Square, London, UK
| | - Mark Allen
- Biological Services Unit, The Institute of Cancer Research, London, UK
| | - Patrycja Gazinska
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Helen N Pemberton
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Aditi Gulati
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Sarah Nash
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Farzana Noor
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Naomi Guppy
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Ioannis Roxanis
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Guy Pratt
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Ceri Oldreive
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Tatjana Stankovic
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Samantha Barlow
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Helen Kalirai
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Sarah E Coupland
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Ronan Broderick
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Samar Alsafadi
- Inserm U830, PSL University, Institut Curie, Paris, France
| | - Alexandre Houy
- Inserm U830, PSL University, Institut Curie, Paris, France
| | | | - Stephen Pettit
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Jyoti S Choudhary
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, 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 Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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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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4
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Khalique S, Nash S, Mansfield D, Wampfler J, Attygale A, Vroobel K, Kemp H, Buus R, Cottom H, Roxanis I, Jones T, von Loga K, Begum D, Guppy N, Ramagiri P, Fenwick K, Matthews N, Hubank MJF, Lord CJ, Haider S, Melcher A, Banerjee S, Natrajan R. Quantitative Assessment and Prognostic Associations of the Immune Landscape in Ovarian Clear Cell Carcinoma. Cancers (Basel) 2021; 13:3854. [PMID: 34359755 PMCID: PMC8345766 DOI: 10.3390/cancers13153854] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022] Open
Abstract
Ovarian clear cell carcinoma (OCCC) is a rare subtype of epithelial ovarian cancer characterised by a high frequency of loss-of-function ARID1A mutations and a poor response to chemotherapy. Despite their generally low mutational burden, an intratumoural T cell response has been reported in a subset of OCCC, with ARID1A purported to be a biomarker for the response to the immune checkpoint blockade independent of micro-satellite instability (MSI). However, assessment of the different immune cell types and spatial distribution specifically within OCCC patients has not been described to date. Here, we characterised the immune landscape of OCCC by profiling a cohort of 33 microsatellite stable OCCCs at the genomic, gene expression and histological level using targeted sequencing, gene expression profiling using the NanoString targeted immune panel, and multiplex immunofluorescence to assess the spatial distribution and abundance of immune cell populations at the protein level. Analysis of these tumours and subsequent independent validation identified an immune-related gene expression signature associated with risk of recurrence of OCCC. Whilst histological quantification of tumour-infiltrating lymphocytes (TIL, Salgado scoring) showed no association with the risk of recurrence or ARID1A mutational status, the characterisation of TILs via multiplexed immunofluorescence identified spatial differences in immunosuppressive cell populations in OCCC. Tumour-associated macrophages (TAM) and regulatory T cells were excluded from the vicinity of tumour cells in low-risk patients, suggesting that high-risk patients have a more immunosuppressive microenvironment. We also found that TAMs and cytotoxic T cells were also excluded from the vicinity of tumour cells in ARID1A-mutated OCCCs compared to ARID1A wild-type tumours, suggesting that the exclusion of these immune effectors could determine the host response of ARID1A-mutant OCCCs to therapy. Overall, our study has provided new insights into the immune landscape and prognostic associations in OCCC and suggest that tailored immunotherapeutic approaches may be warranted for different subgroups of OCCC patients.
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Affiliation(s)
- Saira Khalique
- Division of Brest Cancer, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (S.K.); (S.N.); (H.K.); (R.B.); (H.C.); (I.R.); (N.G.); (C.J.L.); (S.H.)
| | - Sarah Nash
- Division of Brest Cancer, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (S.K.); (S.N.); (H.K.); (R.B.); (H.C.); (I.R.); (N.G.); (C.J.L.); (S.H.)
| | - David Mansfield
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London SW3 6JB, UK; (D.M.); (A.M.)
| | - Julian Wampfler
- Gynaecology Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; (J.W.); (A.A.); (K.V.)
| | - Ayoma Attygale
- Gynaecology Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; (J.W.); (A.A.); (K.V.)
- Department of Histopathology, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Katherine Vroobel
- Gynaecology Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; (J.W.); (A.A.); (K.V.)
- Department of Histopathology, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Harriet Kemp
- Division of Brest Cancer, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (S.K.); (S.N.); (H.K.); (R.B.); (H.C.); (I.R.); (N.G.); (C.J.L.); (S.H.)
| | - Richard Buus
- Division of Brest Cancer, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (S.K.); (S.N.); (H.K.); (R.B.); (H.C.); (I.R.); (N.G.); (C.J.L.); (S.H.)
| | - Hannah Cottom
- Division of Brest Cancer, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (S.K.); (S.N.); (H.K.); (R.B.); (H.C.); (I.R.); (N.G.); (C.J.L.); (S.H.)
| | - Ioannis Roxanis
- Division of Brest Cancer, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (S.K.); (S.N.); (H.K.); (R.B.); (H.C.); (I.R.); (N.G.); (C.J.L.); (S.H.)
| | - Thomas Jones
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK; (T.J.); (M.J.F.H.)
| | - Katharina von Loga
- Biomedical Research Centre, The Royal Marsden NHS Foundation Trust, London SM2 5PT, UK; (K.v.L.); (D.B.)
| | - Dipa Begum
- Biomedical Research Centre, The Royal Marsden NHS Foundation Trust, London SM2 5PT, UK; (K.v.L.); (D.B.)
| | - Naomi Guppy
- Division of Brest Cancer, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (S.K.); (S.N.); (H.K.); (R.B.); (H.C.); (I.R.); (N.G.); (C.J.L.); (S.H.)
| | - Pradeep Ramagiri
- Tumour Profiling Unit, The Institute of Cancer Research, London SW3 6JB, UK; (P.R.); (K.F.); (N.M.)
| | - Kerry Fenwick
- Tumour Profiling Unit, The Institute of Cancer Research, London SW3 6JB, UK; (P.R.); (K.F.); (N.M.)
| | - Nik Matthews
- Tumour Profiling Unit, The Institute of Cancer Research, London SW3 6JB, UK; (P.R.); (K.F.); (N.M.)
| | - Michael J. F. Hubank
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK; (T.J.); (M.J.F.H.)
| | - Christopher J. Lord
- Division of Brest Cancer, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (S.K.); (S.N.); (H.K.); (R.B.); (H.C.); (I.R.); (N.G.); (C.J.L.); (S.H.)
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - Syed Haider
- Division of Brest Cancer, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (S.K.); (S.N.); (H.K.); (R.B.); (H.C.); (I.R.); (N.G.); (C.J.L.); (S.H.)
| | - Alan Melcher
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London SW3 6JB, UK; (D.M.); (A.M.)
| | - Susana Banerjee
- Gynaecology Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; (J.W.); (A.A.); (K.V.)
- Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK
| | - Rachael Natrajan
- Division of Brest Cancer, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (S.K.); (S.N.); (H.K.); (R.B.); (H.C.); (I.R.); (N.G.); (C.J.L.); (S.H.)
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5
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Garcia LR, Tenev T, Newman R, Haich RO, Liccardi G, John SW, Annibaldi A, Yu L, Pardo M, Young SN, Fitzgibbon C, Fernando W, Guppy N, Kim H, Liang LY, Lucet IS, Kueh A, Roxanis I, Gazinska P, Sims M, Smyth T, Ward G, Bertin J, Beal AM, Geddes B, Choudhary JS, Murphy JM, Aurelia Ball K, Upton JW, Meier P. Ubiquitylation of MLKL at lysine 219 positively regulates necroptosis-induced tissue injury and pathogen clearance. Nat Commun 2021; 12:3364. [PMID: 34099649 PMCID: PMC8184782 DOI: 10.1038/s41467-021-23474-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [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: 08/11/2020] [Accepted: 04/29/2021] [Indexed: 12/19/2022] Open
Abstract
Necroptosis is a lytic, inflammatory form of cell death that not only contributes to pathogen clearance but can also lead to disease pathogenesis. Necroptosis is triggered by RIPK3-mediated phosphorylation of MLKL, which is thought to initiate MLKL oligomerisation, membrane translocation and membrane rupture, although the precise mechanism is incompletely understood. Here, we show that K63-linked ubiquitin chains are attached to MLKL during necroptosis and that ubiquitylation of MLKL at K219 significantly contributes to the cytotoxic potential of phosphorylated MLKL. The K219R MLKL mutation protects animals from necroptosis-induced skin damage and renders cells resistant to pathogen-induced necroptosis. Mechanistically, we show that ubiquitylation of MLKL at K219 is required for higher-order assembly of MLKL at membranes, facilitating its rupture and necroptosis. We demonstrate that K219 ubiquitylation licenses MLKL activity to induce lytic cell death, suggesting that necroptotic clearance of pathogens as well as MLKL-dependent pathologies are influenced by the ubiquitin-signalling system.
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Affiliation(s)
- Laura Ramos Garcia
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - Tencho Tenev
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Richard Newman
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Rachel O Haich
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Gianmaria Liccardi
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Institute of Biochemistry I, Medical Faculty, Joseph-Stelzmann-Str. 44, University of Cologne, Cologne, Germany
| | - Sidonie Wicky John
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Alessandro Annibaldi
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Lu Yu
- Functional Proteomics Group, The Institute of Cancer Research, London, UK
| | - Mercedes Pardo
- Functional Proteomics Group, The Institute of Cancer Research, London, UK
| | - Samuel N Young
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Cheree Fitzgibbon
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Winnie Fernando
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Naomi Guppy
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Hyojin Kim
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Lung-Yu Liang
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Isabelle S Lucet
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Andrew Kueh
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Ioannis Roxanis
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Patrycja Gazinska
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | | | | | - John Bertin
- Innate Immunity Research Unit, GlaxoSmithKline, Collegeville, PA, USA
- Immunology and Inflammation Research Therapeutic Area at Sanofi, Cambridge, MA, USA
| | - Allison M Beal
- Innate Immunity Research Unit, GlaxoSmithKline, Collegeville, PA, USA
| | - Brad Geddes
- Innate Immunity Research Unit, GlaxoSmithKline, Collegeville, PA, USA
| | - Jyoti S Choudhary
- Functional Proteomics Group, The Institute of Cancer Research, London, UK
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - K Aurelia Ball
- Department of Chemistry, Skidmore College, Saratoga Springs, NY, USA
| | - Jason W Upton
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Pascal Meier
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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6
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Tsang SM, Kim H, Oliemuller E, Newman R, Boateng NA, Guppy N, Howard BA. Sox11 regulates mammary tumour-initiating and metastatic capacity in Brca1-deficient mouse mammary tumour cells. Dis Model Mech 2021; 14:261799. [PMID: 33969421 PMCID: PMC8188883 DOI: 10.1242/dmm.046037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
Little is known about the role of Sox11 in the regulation of mammary progenitor cells. Sox11 is expressed by mammary bud epithelial cells during embryonic mammary gland development and is not detected in mammary epithelial cells after birth. As Sox11 is an oncofetal gene, we investigated the effects of reducing Sox11 levels in embryonic mammary progenitor cells and found that Sox11 regulates proliferative state, stem cell activity and lineage marker expression. We also investigated the effect of reducing Sox11 levels in two transplantable Brca1-deficient oestrogen receptor-negative mouse mammary tumour cell lines, to assess whether Sox11 regulates similar functions in tumour progenitor cells. When Sox11 levels were reduced in one Brca1-deficient mammary tumour cell line that expressed both epithelial and mesenchymal markers, similar effects on proliferation, stem cell activity and expression of lineage markers to those seen in the embryonic mammary progenitor cells were observed. Orthotopic grafting of mammary tumour cells with reduced Sox11 levels led to alterations in tumour-initiating capacity, latency, expression of lineage markers and metastatic burden. Our results support a model in which tumours expressing higher levels of Sox11 have more stem and tumour-initiating cells, and are less proliferative, whereas tumours expressing lower levels of Sox11 become more proliferative and capable of morphogenetic/metastatic growth, similar to what occurs during embryonic mammary developmental progression. Summary:Brca1−/− mammary tumours expressing Sox11 at high levels have more stem- and tumour-initiating cells, and are less proliferative, whereas tumours expressing Sox11 at lower levels become more proliferative and are capable of morphogenetic/metastatic growth.
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Affiliation(s)
- Siu Man Tsang
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Hyojin Kim
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Erik Oliemuller
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Richard Newman
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Naa-Anyima Boateng
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Naomi Guppy
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Beatrice A Howard
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
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7
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Narayanan PL, Raza SEA, Hall AH, Marks JR, King L, West RB, Hernandez L, Guppy N, Dowsett M, Gusterson B, Maley C, Hwang ES, Yuan Y. Unmasking the immune microecology of ductal carcinoma in situ with deep learning. NPJ Breast Cancer 2021; 7:19. [PMID: 33649333 PMCID: PMC7921670 DOI: 10.1038/s41523-020-00205-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023] Open
Abstract
Despite increasing evidence supporting the clinical relevance of tumour infiltrating lymphocytes (TILs) in invasive breast cancer, TIL spatial variability within ductal carcinoma in situ (DCIS) samples and its association with progression are not well understood. To characterise tissue spatial architecture and the microenvironment of DCIS, we designed and validated a new deep learning pipeline, UNMaSk. Following automated detection of individual DCIS ducts using a new method IM-Net, we applied spatial tessellation to create virtual boundaries for each duct. To study local TIL infiltration for each duct, DRDIN was developed for mapping the distribution of TILs. In a dataset comprising grade 2-3 pure DCIS and DCIS adjacent to invasive cancer (adjacent DCIS), we found that pure DCIS cases had more TILs compared to adjacent DCIS. However, the colocalisation of TILs with DCIS ducts was significantly lower in pure DCIS compared to adjacent DCIS, which may suggest a more inflamed tissue ecology local to DCIS ducts in adjacent DCIS cases. Our study demonstrates that technological developments in deep convolutional neural networks and digital pathology can enable an automated morphological and microenvironmental analysis of DCIS, providing a new way to study differential immune ecology for individual ducts and identify new markers of progression.
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Affiliation(s)
- Priya Lakshmi Narayanan
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.
- Division of Molecular Pathology, Institute of Cancer Research, London, UK.
| | - Shan E Ahmed Raza
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Allison H Hall
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Jeffrey R Marks
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Lorraine King
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Robert B West
- Department of Pathology, Surgical Pathology, Stanford, CA, USA
| | - Lucia Hernandez
- Department of Anatomic Pathology, Hospital Universitario, 12 de Octubre, Madrid, Spain
| | - Naomi Guppy
- Breast Cancer Now Histopathology Core, Institute of Cancer Research, London, UK
- UCL Advanced Diagnostics, University College London, London, UK
| | - Mitch Dowsett
- The Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, UK
- Academic Department of Biochemistry, Royal Marsden Hospital, London, UK
| | - Barry Gusterson
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Carlo Maley
- Biodesign Center for Personalized Diagnostics and School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - E Shelley Hwang
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Yinyin Yuan
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.
- Division of Molecular Pathology, Institute of Cancer Research, London, UK.
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8
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Peck B, Bland P, Mavrommati I, Muirhead G, Cottom H, Wai PT, Maguire SL, Barker HE, Morrison E, Kriplani D, Yu L, Gibson A, Falgari G, Brennan K, Farnie G, Buus R, Marlow R, Novo D, Knight E, Guppy N, Kolarevic D, Susnjar S, Milijic NM, Naidoo K, Gazinska P, Roxanis I, Pancholi S, Martin LA, Holgersen EM, Cheang MCU, Noor F, Postel-Vinay S, Quinn G, McDade S, Krasny L, Huang P, Daley F, Wallberg F, Choudhary JS, Haider S, Tutt AN, Natrajan R. 3D Functional Genomics Screens Identify CREBBP as a Targetable Driver in Aggressive Triple-Negative Breast Cancer. Cancer Res 2021; 81:847-859. [PMID: 33509944 PMCID: PMC7611219 DOI: 10.1158/0008-5472.can-20-1822] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 05/29/2020] [Revised: 10/12/2020] [Accepted: 11/25/2020] [Indexed: 11/16/2022]
Abstract
Triple-negative breast cancers (TNBC) are resistant to standard-of-care chemotherapy and lack known targetable driver gene alterations. Identification of novel drivers could aid the discovery of new treatment strategies for this hard-to-treat patient population, yet studies using high-throughput and accurate models to define the functions of driver genes in TNBC to date have been limited. Here, we employed unbiased functional genomics screening of the 200 most frequently mutated genes in breast cancer, using spheroid cultures to model in vivo-like conditions, and identified the histone acetyltransferase CREBBP as a novel tumor suppressor in TNBC. CREBBP protein expression in patient tumor samples was absent in 8% of TNBCs and at a high frequency in other tumors, including squamous lung cancer, where CREBBP-inactivating mutations are common. In TNBC, CREBBP alterations were associated with higher genomic heterogeneity and poorer patient survival and resulted in upregulation and dependency on a FOXM1 proliferative program. Targeting FOXM1-driven proliferation indirectly with clinical CDK4/6 inhibitors (CDK4/6i) selectively impaired growth in spheroids, cell line xenografts, and patient-derived models from multiple tumor types with CREBBP mutations or loss of protein expression. In conclusion, we have identified CREBBP as a novel driver in aggressive TNBC and identified an associated genetic vulnerability in tumor cells with alterations in CREBBP and provide a preclinical rationale for assessing CREBBP alterations as a biomarker of CDK4/6i response in a new patient population. SIGNIFICANCE: This study demonstrates that CREBBP genomic alterations drive aggressive TNBC, lung cancer, and lymphomas and may be selectively treated with clinical CDK4/6 inhibitors.
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Affiliation(s)
- Barrie Peck
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Philip Bland
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Ioanna Mavrommati
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Gareth Muirhead
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Hannah Cottom
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Patty T Wai
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Sarah L Maguire
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Holly E Barker
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Stem Cells and Cancer, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Eamonn Morrison
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Divya Kriplani
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Lu Yu
- Division of Cancer Biology, The Institute of Cancer Research, London, England, United Kingdom
| | - Amy Gibson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Giulia Falgari
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Keith Brennan
- Faculty of Life Sciences, University of Manchester, Manchester, England, United Kingdom
| | - Gillian Farnie
- SGC Oxford, University of Oxford, Oxford, England, United Kingdom
| | - Richard Buus
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Rebecca Marlow
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Breast Cancer Now Research Unit, King's College London, London, England, United Kingdom
| | - Daniela Novo
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Eleanor Knight
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Naomi Guppy
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Daniela Kolarevic
- The Royal Marsden NHS Foundation Trust, London, England, United Kingdom
| | - Snezana Susnjar
- Department of Medical Oncology, The Institute of Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Natasa Medic Milijic
- Department of Pathology and Cytology, The Institute of Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Kalnisha Naidoo
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Patrycja Gazinska
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Ioannis Roxanis
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Sunil Pancholi
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Lesley-Ann Martin
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Erle M Holgersen
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Maggie C U Cheang
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, England, United Kingdom
| | - Farzana Noor
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Sophie Postel-Vinay
- Department of Drug Development (DITEP), Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- UMR981, ATIP-Avenir team, INSERM, Villejuif, France
| | - Gerard Quinn
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Simon McDade
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Lukas Krasny
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Paul Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
| | - Frances Daley
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Fredrik Wallberg
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Jyoti S Choudhary
- Division of Cancer Biology, The Institute of Cancer Research, London, England, United Kingdom
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
| | - Andrew N Tutt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom
- Breast Cancer Now Research Unit, King's College London, London, England, United Kingdom
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, England, United Kingdom.
- Division of Molecular Pathology, The Institute of Cancer Research, London, England, United Kingdom
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9
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Busacca S, O'Regan L, Singh A, Sharkey AJ, Dawson AG, Dzialo J, Parsons A, Kumar N, Schunselaar LM, Guppy N, Nakas A, Sheaff M, Mansfield AS, Janes SM, Baas P, Fry AM, Fennell DA. BRCA1/MAD2L1 Deficiency Disrupts the Spindle Assembly Checkpoint to Confer Vinorelbine Resistance in Mesothelioma. Mol Cancer Ther 2020; 20:379-388. [PMID: 33158996 DOI: 10.1158/1535-7163.mct-20-0363] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 05/04/2020] [Revised: 09/02/2020] [Accepted: 10/27/2020] [Indexed: 11/16/2022]
Abstract
Mesothelioma is a universally lethal cancer lacking effective therapy. The spindle poison vinorelbine exhibits clinical activity in the relapsed setting, and in preclinical models requires BRCA1 to initiate apoptosis. However, the mechanisms underlying this regulation and the clinical implications have not been explored. Here, we show that BRCA1 silencing abrogated vinorelbine-induced cell-cycle arrest, recruitment of BUBR1 to kinetochores, and apoptosis. BRCA1 silencing led to codepletion of MAD2L1 at the mRNA and protein levels consistent with its status as a transcriptional target of BRCA1 Silencing of MAD2L1 phenocopied BRCA1 and was sufficient to confer resistance to vinorelbine. This was recapitulated in cell lines selected for resistance to vinorelbine, which acquired loss of both BRCA1 and MAD2L1 expression. Following ex vivo vinorelbine in 20 primary tumor explants, apoptotic response rate was 59% in BRCA1/MAD2L1-positive explants compared with 0% in BRCA1/MAD2L1-negative explants. In 48 patients, BRCA1 and/or MAD2L1 loss of expression was not prognostic; however, in a subset of patients treated with vinorelbine, survival was shorter for patients lacking BRCA1/MAD2L1 expression compared with double-positive patients (5.9 vs. 36.7 months, P = 0.03). Our data implicate BRCA1/MAD2L1 loss as a putative predictive marker of resistance to vinorelbine in mesothelioma and warrant prospective clinical evaluation.
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Affiliation(s)
- Sara Busacca
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | - Laura O'Regan
- Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Anita Singh
- Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Annabel J Sharkey
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | - Alan G Dawson
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
- Department of Thoracic Surgery, Glenfield Hospital, University Hospitals of Leicester, Leicester, United Kingdom
| | - Joanna Dzialo
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | - Aimee Parsons
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | - Neelam Kumar
- University College London, UCL Respiratory, London, United Kingdom
| | - Laurel M Schunselaar
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Naomi Guppy
- University College London Advanced Diagnostics, London, United Kingdom
| | - Apostolos Nakas
- Department of Thoracic Surgery, Glenfield Hospital, University Hospitals of Leicester, Leicester, United Kingdom
| | - Michael Sheaff
- Department of Histopathology, Barts Health NHS Trust, London, United Kingdom
| | - Aaron S Mansfield
- Department of Oncology, Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota
| | - Sam M Janes
- University College London, UCL Respiratory, London, United Kingdom
| | - Paul Baas
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Andrew M Fry
- Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Dean A Fennell
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom.
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10
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Smith HG, Jamal K, Dayal JHS, Tenev T, Kyula‐Currie J, Guppy N, Gazinska P, Roulstone V, Liccardi G, Davies E, Roxanis I, Melcher AA, Hayes AJ, Inman GJ, Harrington KJ, Meier P. RIPK1-mediated immunogenic cell death promotes anti-tumour immunity against soft-tissue sarcoma. EMBO Mol Med 2020; 12:e10979. [PMID: 32419365 PMCID: PMC7278545 DOI: 10.15252/emmm.201910979] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 06/11/2019] [Revised: 04/15/2020] [Accepted: 04/20/2020] [Indexed: 11/09/2022] Open
Abstract
Drugs that mobilise the immune system against cancer are dramatically improving care for many people. Dying cancer cells play an active role in inducing anti-tumour immunity but not every form of death can elicit an immune response. Moreover, resistance to apoptosis is a major problem in cancer treatment and disease control. While the term "immunogenic cell death" is not fully defined, activation of receptor-interacting serine/threonine-protein kinase 1 (RIPK1) can induce a type of death that mobilises the immune system against cancer. However, no clinical treatment protocols have yet been established that would harness the immunogenic potential of RIPK1. Here, we report the first pre-clinical application of an in vivo treatment protocol for soft-tissue sarcoma that directly engages RIPK1-mediated immunogenic cell death. We find that RIPK1-mediated cell death significantly improves local disease control, increases activation of CD8+ T cells as well as NK cells, and enhances the survival benefit of immune checkpoint blockade. Our findings warrant a clinical trial to assess the survival benefit of RIPK1-induced cell death in patients with advanced disease at limb extremities.
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Affiliation(s)
- Henry G Smith
- Targeted Therapy TeamThe Institute of Cancer ResearchLondonUK
| | - Kunzah Jamal
- The Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer ResearchLondonUK
| | | | - Tencho Tenev
- The Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer ResearchLondonUK
| | | | - Naomi Guppy
- The Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer ResearchLondonUK
| | - Patrycja Gazinska
- The Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer ResearchLondonUK
| | | | - Gianmaria Liccardi
- The Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer ResearchLondonUK
| | - Emma Davies
- Targeted Therapy TeamThe Institute of Cancer ResearchLondonUK
| | - Ioannis Roxanis
- The Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer ResearchLondonUK
- Cancer Research UK Beatson InstituteGlasgowUK
- Division of Molecular PathologyThe Institute of Cancer ResearchLondonUK
- Royal Free London NHS Foundation TrustLondonUK
| | - Alan A Melcher
- The Translational Immunology TeamThe Institute of Cancer ResearchLondonUK
| | - Andrew J Hayes
- The Sarcoma and Melanoma UnitThe Royal Marsden HospitalLondonUK
| | - Gareth J Inman
- Cancer Research UK Beatson InstituteGlasgowUK
- Institute of Cancer SciencesUniversity of GlasgowGlasgowUK
| | | | - Pascal Meier
- The Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer ResearchLondonUK
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11
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Nagarajan S, Rao SV, Sutton J, Cheeseman D, Dunn S, Papachristou EK, Prada JEG, Couturier DL, Kumar S, Kishore K, Chilamakuri CSR, Glont SE, Goode EA, Brodie C, Guppy N, Natrajan R, Bruna A, Caldas C, Russell A, Siersbæk R, Yusa K, Chernukhin I, Carroll JS. Author Correction: ARID1A influences HDAC1/BRD4 activity, intrinsic proliferative capacity and breast cancer treatment response. Nat Genet 2020; 52:354. [PMID: 32005967 DOI: 10.1038/s41588-020-0582-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
| | - Shalini V Rao
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Joseph Sutton
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Danya Cheeseman
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | | | | | | | - Sanjeev Kumar
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Kamal Kishore
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | | | | | - Cara Brodie
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Naomi Guppy
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Alejandra Bruna
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Carlos Caldas
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Alasdair Russell
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Rasmus Siersbæk
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Kosuke Yusa
- Wellcome Trust Sanger Institute, Hinxton, UK
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Igor Chernukhin
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Jason S Carroll
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK.
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12
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Nagarajan S, Rao SV, Sutton J, Cheeseman D, Dunn S, Papachristou EK, Prada JEG, Couturier DL, Kumar S, Kishore K, Chilamakuri CSR, Glont SE, Archer Goode E, Brodie C, Guppy N, Natrajan R, Bruna A, Caldas C, Russell A, Siersbæk R, Yusa K, Chernukhin I, Carroll JS. ARID1A influences HDAC1/BRD4 activity, intrinsic proliferative capacity and breast cancer treatment response. Nat Genet 2020; 52:187-197. [PMID: 31913353 PMCID: PMC7116647 DOI: 10.1038/s41588-019-0541-5] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [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: 02/01/2019] [Accepted: 11/01/2019] [Indexed: 12/20/2022]
Abstract
Using genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) screens to understand endocrine drug resistance, we discovered ARID1A and other SWI/SNF complex components as the factors most critically required for response to two classes of estrogen receptor-alpha (ER) antagonists. In this context, SWI/SNF-specific gene deletion resulted in drug resistance. Unexpectedly, ARID1A was also the top candidate in regard to response to the bromodomain and extraterminal domain inhibitor JQ1, but in the opposite direction, with loss of ARID1A sensitizing breast cancer cells to bromodomain and extraterminal domain inhibition. We show that ARID1A is a repressor that binds chromatin at ER cis-regulatory elements. However, ARID1A elicits repressive activity in an enhancer-specific, but forkhead box A1-dependent and active, ER-independent manner. Deletion of ARID1A resulted in loss of histone deacetylase 1 binding, increased histone 4 lysine acetylation and subsequent BRD4-driven transcription and growth. ARID1A mutations are more frequent in treatment-resistant disease, and our findings provide mechanistic insight into this process while revealing rational treatment strategies for these patients.
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Affiliation(s)
| | - Shalini V Rao
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Joseph Sutton
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Danya Cheeseman
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | | | | | | | - Sanjeev Kumar
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Kamal Kishore
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | | | | | - Cara Brodie
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Naomi Guppy
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Alejandra Bruna
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Carlos Caldas
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Alasdair Russell
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Rasmus Siersbæk
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Kosuke Yusa
- Wellcome Trust Sanger Institute, Hinxton, UK
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Igor Chernukhin
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Jason S Carroll
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK.
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13
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Kumar N, Alrifai D, Kolluri KK, Sage EK, Ishii Y, Guppy N, Borg E, Falzon M, Nankivell M, Nicholson AG, Janes SM. Retrospective response analysis of BAP1 expression to predict the clinical activity of systemic cytotoxic chemotherapy in mesothelioma. Lung Cancer 2018; 127:164-166. [PMID: 30642545 DOI: 10.1016/j.lungcan.2018.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/02/2018] [Accepted: 12/04/2018] [Indexed: 10/27/2022]
Abstract
Introduction BRCA1 associated protein-1 (BAP1) is a key tumor driver in mesothelioma and a potential biomarker predicting response to several targeted therapies in clinical testing. Whether it also modulates response to cytotoxic chemotherapy is undetermined. This study used retrospective response analysis of BAP1 expression in archival tumor biopsies taken from patients in the MS01 trial (NCT00075699). We aimed to determine if BAP1 expression correlated with overall survival within the three treatment arms in this trial, namely active symptom control (ASC); ASC plus mitomycin, vinblastine and cisplatin (MVP); and ASC plus vinorelbine. Materials and methods We used immunohistochemical analysis of tumor samples from the MS01 trial to identify subgroups with and without nuclear BAP1 expression. We performed correlative analysis of clinical characteristics (age at diagnosis, sex and histological subtype) and overall survival within treatment arms with nuclear BAP1 expression. Results 89 tumor samples from the 409 patients originally in the trial were available for analysis. Of these, 60 samples harbored a positive internal control, in the form of positive staining of inflammatory cells for BAP1, and were carried forward for analysis. Correlative analysis suggested no significant association between loss of nuclear BAP1 expression and age at diagnosis, sex and histological subtype. Kaplan Meier survival analysis revealed a small, though non-significant, overall survival disadvantage associated with BAP1 expression in tumors from patients treated with vinorelbine. Discussion This exploratory analysis suggests BAP1 expression may modify response to vinorelbine in MPM, possibly due to prevention of mitotic microtubule formation. We suggest ongoing and planned clinical studies of vinorelbine in MPM assess BAP1 expression as a predictive biomarker of response.
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Affiliation(s)
- Neelam Kumar
- Lungs for Living Research Centre, UCL Respiratory, Rayne Institute, University Street, London, WC1E 6JF, United Kingdom
| | - Doraid Alrifai
- Lungs for Living Research Centre, UCL Respiratory, Rayne Institute, University Street, London, WC1E 6JF, United Kingdom
| | - Krishna K Kolluri
- Lungs for Living Research Centre, UCL Respiratory, Rayne Institute, University Street, London, WC1E 6JF, United Kingdom
| | - Elizabeth K Sage
- Lungs for Living Research Centre, UCL Respiratory, Rayne Institute, University Street, London, WC1E 6JF, United Kingdom
| | - Yuki Ishii
- Lungs for Living Research Centre, UCL Respiratory, Rayne Institute, University Street, London, WC1E 6JF, United Kingdom
| | - Naomi Guppy
- HSL Advanced Diagnostics, Rockefeller Building, 21 University Street, London, WC1E 6JJ, United Kingdom
| | - Elaine Borg
- Department of Histopathology, University College Hospital, Euston Road, Fitzrovia, London, NW1 2BU, United Kingdom
| | - Mary Falzon
- Department of Histopathology, University College Hospital, Euston Road, Fitzrovia, London, NW1 2BU, United Kingdom
| | - Matthew Nankivell
- MRC Clinical Trials Unit at University College London, 90 High Holborn, London, WC1V 6LJ, United Kingdom
| | - Andrew G Nicholson
- Department of Histopathology, Royal Brompton Hospital, Sydney Street, London, SW3 6NP, United Kingdom
| | - Sam M Janes
- Lungs for Living Research Centre, UCL Respiratory, Rayne Institute, University Street, London, WC1E 6JF, United Kingdom.
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14
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Kolluri KK, Alifrangis C, Kumar N, Ishii Y, Price S, Michaut M, Williams S, Barthorpe S, Lightfoot H, Busacca S, Sharkey A, Yuan Z, Sage EK, Vallath S, Le Quesne J, Tice DA, Alrifai D, von Karstedt S, Montinaro A, Guppy N, Waller DA, Nakas A, Good R, Holmes A, Walczak H, Fennell DA, Garnett M, Iorio F, Wessels L, McDermott U, Janes SM. Loss of functional BAP1 augments sensitivity to TRAIL in cancer cells. eLife 2018; 7:e30224. [PMID: 29345617 PMCID: PMC5773178 DOI: 10.7554/elife.30224] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 07/07/2017] [Accepted: 12/13/2017] [Indexed: 12/29/2022] Open
Abstract
Malignant mesothelioma (MM) is poorly responsive to systemic cytotoxic chemotherapy and invariably fatal. Here we describe a screen of 94 drugs in 15 exome-sequenced MM lines and the discovery of a subset defined by loss of function of the nuclear deubiquitinase BRCA associated protein-1 (BAP1) that demonstrate heightened sensitivity to TRAIL (tumour necrosis factor-related apoptosis-inducing ligand). This association is observed across human early passage MM cultures, mouse xenografts and human tumour explants. We demonstrate that BAP1 deubiquitinase activity and its association with ASXL1 to form the Polycomb repressive deubiquitinase complex (PR-DUB) impacts TRAIL sensitivity implicating transcriptional modulation as an underlying mechanism. Death receptor agonists are well-tolerated anti-cancer agents demonstrating limited therapeutic benefit in trials without a targeting biomarker. We identify BAP1 loss-of-function mutations, which are frequent in MM, as a potential genomic stratification tool for TRAIL sensitivity with immediate and actionable therapeutic implications.
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Affiliation(s)
- Krishna Kalyan Kolluri
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | | | - Neelam Kumar
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | - Yuki Ishii
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | - Stacey Price
- Wellcome Trust Sanger InstituteCambridgeUnited Kingdom
| | | | | | - Syd Barthorpe
- Wellcome Trust Sanger InstituteCambridgeUnited Kingdom
| | | | - Sara Busacca
- CRUK Leicester Centre, Department of Cancer studiesUniversity of LeicesterLeicesterUnited Kingdom
| | - Annabel Sharkey
- CRUK Leicester Centre, Department of Cancer studiesUniversity of LeicesterLeicesterUnited Kingdom
| | - Zhenqiang Yuan
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | - Elizabeth K Sage
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | - Sabarinath Vallath
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | - John Le Quesne
- CRUK Leicester Centre, Department of Cancer studiesUniversity of LeicesterLeicesterUnited Kingdom
| | - David A Tice
- Oncology Research, MedImmune, Inc.GaithersburgUnited States
| | - Doraid Alrifai
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | - Sylvia von Karstedt
- Centre for Cell Death, Cancer and InflammationUCL Cancer Institute, University College LondonLondonUnited Kingdom
| | - Antonella Montinaro
- Centre for Cell Death, Cancer and InflammationUCL Cancer Institute, University College LondonLondonUnited Kingdom
| | - Naomi Guppy
- UCL Advanced DiagnosticsUniversity College LondonLondonUnited Kingdom
| | - David A Waller
- Department of Thoracic SurgeryGlenfield Hospital, University Hospitals of LeicesterLeicesterUnited Kingdom
| | - Apostolos Nakas
- Department of Thoracic SurgeryGlenfield Hospital, University Hospitals of LeicesterLeicesterUnited Kingdom
| | - Robert Good
- UCL School of PharmacyUniversity College LondonLondonUnited Kingdom
| | - Alan Holmes
- UCL School of PharmacyUniversity College LondonLondonUnited Kingdom
| | - Henning Walczak
- Centre for Cell Death, Cancer and InflammationUCL Cancer Institute, University College LondonLondonUnited Kingdom
| | - Dean A Fennell
- CRUK Leicester Centre, Department of Cancer studiesUniversity of LeicesterLeicesterUnited Kingdom
| | | | - Francesco Iorio
- European Molecular Biology LaboratoryEuropean Bioinformatics InstituteCambridgeUnited Kingdom
| | | | | | - Samuel M Janes
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
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Abstract
The Amur tiger (Panthera tigris altaica) is an endangered tiger subspecies. An adult zoo-bred female was found collapsed, and died despite supportive treatment. Hematology and biochemistry showed pancytopenia and hyperglobulinemia, and serum protein electrophoresis revealed a monoclonal band in the β-globulin region. Necropsy demonstrated hemoabdomen, multifocal lytic bone marrow lesions, splenomegaly, and hemorrhagic hepatic nodules, with left medial lobe rupture. There were mutifocal hemorrhages in the subcutis, lung, epicardium, and intestinal mucosa. Histopathology demonstrated plasmacytoid cells infiltrating the bone marrow, liver and spleen, and circulating within blood vessels. On immunohistochemistry, cell infiltrates of the three tissues were positive for λ light chains, bone marrow infiltrates were positive for MUM-1 and bone marrow and spleen infiltrates were positive for CD20. These findings indicate that this animal died of hemoabdomen subsequent to multiple myeloma. This is the first time this disease has been reported in a tiger.
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Affiliation(s)
- Alison M Lee
- Pathobiology Section, UCD School of Veterinary Medicine, University College Dublin, Dublin 4, Ireland
| | - Naomi Guppy
- UCL Advanced Diagnostics, Rockefeller Building, Bloomsbury, London, UK
| | | | - Hanne Jahns
- Pathobiology Section, UCD School of Veterinary Medicine, University College Dublin, Dublin 4, Ireland
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16
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Pollara G, Murray MJ, Heather JM, Byng-Maddick R, Guppy N, Ellis M, Turner CT, Chain BM, Noursadeghi M. Validation of Immune Cell Modules in Multicellular Transcriptomic Data. PLoS One 2017; 12:e0169271. [PMID: 28045996 PMCID: PMC5207692 DOI: 10.1371/journal.pone.0169271] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 06/29/2016] [Accepted: 12/14/2016] [Indexed: 01/16/2023] Open
Abstract
Numerous gene signatures, or modules have been described to evaluate the immune cell composition in transcriptomes of multicellular tissue samples. However, significant diversity in module gene content for specific cell types is associated with heterogeneity in their performance. In order to rank modules that best reflect their purported association, we have generated the modular discrimination index (MDI) score that assesses expression of each module in the target cell type relative to other cells. We demonstrate that MDI scores predict modules that best reflect independently validated differences in cellular composition, and correlate with the covariance between cell numbers and module expression in human blood and tissue samples. Our analyses demonstrate that MDI scores provide an ordinal summary statistic that reliably ranks the accuracy of gene expression modules for deconvolution of cell type abundance in transcriptional data.
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Affiliation(s)
- Gabriele Pollara
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Matthew J. Murray
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - James M. Heather
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Rachel Byng-Maddick
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Naomi Guppy
- UCL Advanced Diagnostics, University College London, London, United Kingdom
| | - Matthew Ellis
- Department of Neurodegenerative Disease, UCL Institute of Neurology, University College London, London, United Kingdom
| | - Carolin T. Turner
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Benjamin M. Chain
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Mahdad Noursadeghi
- Division of Infection & Immunity, University College London, London, United Kingdom
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17
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Kularatne B, Arora R, Elshstein G, Guppy N, Kirkwood A, Meyer T, Kristeleit R. Immunohistochemistry (IHC) evaluation of a novel 4-protein prognostic and predictive biomarker panel in endometrial cancer (EC). Ann Oncol 2016. [DOI: 10.1093/annonc/mdw374.36] [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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18
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Scheipl S, Barnard M, Cottone L, Jorgensen M, Drewry DH, Zuercher WJ, Turlais F, Ye H, Leite AP, Smith JA, Leithner A, Möller P, Brüderlein S, Guppy N, Amary F, Tirabosco R, Strauss SJ, Pillay N, Flanagan AM. EGFR inhibitors identified as a potential treatment for chordoma in a focused compound screen. J Pathol 2016; 239:320-34. [PMID: 27102572 PMCID: PMC4922416 DOI: 10.1002/path.4729] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [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: 11/19/2015] [Revised: 03/11/2016] [Accepted: 04/10/2016] [Indexed: 12/24/2022]
Abstract
Chordoma is a rare malignant bone tumour with a poor prognosis and limited therapeutic options. We undertook a focused compound screen (FCS) against 1097 compounds on three well-characterized chordoma cell lines; 154 compounds were selected from the single concentration screen (1 µm), based on their growth-inhibitory effect. Their half-maximal effective concentration (EC50 ) values were determined in chordoma cells and normal fibroblasts. Twenty-seven of these compounds displayed chordoma selective cell kill and 21/27 (78%) were found to be EGFR/ERBB family inhibitors. EGFR inhibitors in clinical development were then studied on an extended cell line panel of seven chordoma cell lines, four of which were sensitive to EGFR inhibition. Sapitinib (AstraZeneca) emerged as the lead compound, followed by gefitinib (AstraZeneca) and erlotinib (Roche/Genentech). The compounds were shown to induce apoptosis in the sensitive cell lines and suppressed phospho-EGFR and its downstream pathways in a dose-dependent manner. Analysis of substituent patterns suggested that EGFR-inhibitors with small aniline substituents in the 4-position of the quinazoline ring were more effective than inhibitors with large substituents in that position. Sapitinib showed significantly reduced tumour growth in two xenograft mouse models (U-CH1 xenograft and a patient-derived xenograft, SF8894). One of the resistant cell lines (U-CH2) was shown to express high levels of phospho-MET, a known bypass signalling pathway to EGFR. Neither amplifications (EGFR, ERBB2, MET) nor mutations in EGFR, ERBB2, ERBB4, PIK3CA, BRAF, NRAS, KRAS, PTEN, MET or other cancer gene hotspots were detected in the cell lines. Our findings are consistent with the reported (p-)EGFR expression in the majority of clinical samples, and provide evidence for exploring the efficacy of EGFR inhibitors in the treatment of patients with chordoma and studying possible resistance mechanisms to these compounds in vitro and in vivo. © 2016 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Susanne Scheipl
- University College London Cancer Institute, London, UK
- Department of Orthopaedics and Orthopaedic Surgery, Medical University of Graz, Austria
| | - Michelle Barnard
- University College London Cancer Institute, London, UK
- Cancer Research Technology Discovery Laboratories, Cambridge, UK
- CRUK-MedImmune Alliance Laboratory, Cambridge, UK
| | - Lucia Cottone
- University College London Cancer Institute, London, UK
| | | | - David H Drewry
- GlaxoSmithKline, Research Triangle Park, NC, USA
- SGC-UNC, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, NC, USA
| | - William J Zuercher
- GlaxoSmithKline, Research Triangle Park, NC, USA
- SGC-UNC, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, NC, USA
| | - Fabrice Turlais
- Cancer Research Technology Discovery Laboratories, Cambridge, UK
| | - Hongtao Ye
- Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Ana P Leite
- University College London Cancer Institute, London, UK
| | - James A Smith
- Cancer Research Technology Discovery Laboratories, Cambridge, UK
| | - Andreas Leithner
- Department of Orthopaedics and Orthopaedic Surgery, Medical University of Graz, Austria
| | | | | | - Naomi Guppy
- University College London Advanced Diagnostics, London, UK
| | - Fernanda Amary
- Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Roberto Tirabosco
- Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | | | - Nischalan Pillay
- University College London Cancer Institute, London, UK
- Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Adrienne M Flanagan
- University College London Cancer Institute, London, UK
- Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
- University College London Advanced Diagnostics, London, UK
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19
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Abstract
The purpose of this study was to examine the relationship between the pre-retirement life-style of adult men, and both the degree of planning for the retirement years and the decision to retire early. Adult males (N = 360) between 55 and 64 years of age were interviewed about their present leisure life-style and the amount of retirement planning they were doing or had done. In order to determine which demographic, attitudinal and social participation variables predict retirement related behavior, Multiple Classification Analysis (MCA) was used. It was found that socioeconomic status, health, involvement in expressive type organizations, job satisfaction and degree of leisure orientation were associated with pre-retirement attitudes toward retirement.
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