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Yoneyama M, Zormpas-Petridis K, Robinson R, Sobhani F, Provenzano E, Steel H, Lightowlers S, Towns C, Castillo SP, Anbalagan S, Lund T, Wennerberg E, Melcher A, Coles CE, Roxanis I, Yuan Y, Somaiah N. Longitudinal assessment of tumor-infiltrating lymphocytes in primary breast cancer following neoadjuvant radiotherapy. Int J Radiat Oncol Biol Phys 2024:S0360-3016(24)00566-2. [PMID: 38677525 DOI: 10.1016/j.ijrobp.2024.04.065] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 04/16/2024] [Accepted: 04/21/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND Tumor-infiltrating lymphocytes (TILs) have prognostic significance in several cancers, including breast. Despite interest in combining radiotherapy with immunotherapy, little is known about the effect of radiotherapy itself on the tumor-immune microenvironment, including TILs. Here, we interrogated longitudinal dynamics of tumor-infiltrating and systemic lymphocytes in patient samples taken before, during, and after neoadjuvant radiotherapy (NART), from XXX and XXX breast clinical trials. METHODS We manually scored stromal TILs (sTILs) from longitudinal tumor samples using standardized guidelines, as well as deep learning-based scores at cell-level (cTIL) and cell- and tissue-level combination analysis (SuperTIL). In parallel, we interrogated absolute lymphocyte counts from routine blood tests at corresponding timepoints during treatment. Exploratory analyses studied the relationship between TILs and pathological complete response (pCR) and long-term outcomes. RESULTS Patients receiving NART experienced a significant and uniform decrease in sTILs that did not recover at the time of surgery (P < 0.0001). This lymphodepletive effect was also mirrored in peripheral blood. Our "SuperTIL" deep learning score showed good concordance with manual sTILs, and importantly performed comparably to manual scores in predicting pCR from diagnostic biopsies. Analysis suggested an association between baseline sTILs and pCR, as well as sTILs at surgery and relapse, in patients receiving NART. CONCLUSIONS This study provides novel insights into TIL dynamics in the context of NART in breast cancer, and demonstrates the potential for artificial intelligence to assist routine pathology. We have identified trends which warrant further interrogation and have a bearing on future radio-immunotherapy trials.
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Affiliation(s)
- Miki Yoneyama
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - Konstantinos Zormpas-Petridis
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK; Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Ruth Robinson
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK; The Royal Marsden NHS Foundation Trust, London, UK
| | - Faranak Sobhani
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Elena Provenzano
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Harriet Steel
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - Sara Lightowlers
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Department of Oncology, University of Cambridge, Cambridge, UK
| | - Catherine Towns
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Simon P Castillo
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Selvakumar Anbalagan
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - Tom Lund
- Integrated Pathology Unit, The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, London, UK
| | - Erik Wennerberg
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - Alan Melcher
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - Charlotte E Coles
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Department of Oncology, University of Cambridge, Cambridge, UK
| | - Ioannis Roxanis
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Yinyin Yuan
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
| | - Navita Somaiah
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK; The Royal Marsden NHS Foundation Trust, London, UK.
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Harvey-Jones E, Raghunandan M, Robbez-Masson L, Magraner-Pardo L, Alaguthurai T, Yablonovitch A, Yen J, Xiao H, Brough R, Frankum J, Song F, Yeung J, Savy T, Gulati A, Alexander J, Kemp H, Starling C, Konde A, Marlow R, Cheang M, Proszek P, Hubank M, Cai M, Trendell J, Lu R, Liccardo R, Ravindran N, Llop-Guevara A, Rodriguez O, Balmana J, Lukashchuk N, Dorschner M, Drusbosky L, Roxanis I, Serra V, Haider S, Pettitt SJ, Lord CJ, Tutt ANJ. Longitudinal profiling identifies co-occurring BRCA1/2 reversions, TP53BP1, RIF1 and PAXIP1 mutations in PARP inhibitor-resistant advanced breast cancer. Ann Oncol 2024; 35:364-380. [PMID: 38244928 DOI: 10.1016/j.annonc.2024.01.003] [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] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Resistance to therapies that target homologous recombination deficiency (HRD) in breast cancer limits their overall effectiveness. Multiple, preclinically validated, mechanisms of resistance have been proposed, but their existence and relative frequency in clinical disease are unclear, as is how to target resistance. PATIENTS AND METHODS Longitudinal mutation and methylation profiling of circulating tumour (ct)DNA was carried out in 47 patients with metastatic BRCA1-, BRCA2- or PALB2-mutant breast cancer treated with HRD-targeted therapy who developed progressive disease-18 patients had primary resistance and 29 exhibited response followed by resistance. ctDNA isolated at multiple time points in the patient treatment course (before, on-treatment and at progression) was sequenced using a novel >750-gene intron/exon targeted sequencing panel. Where available, matched tumour biopsies were whole exome and RNA sequenced and also used to assess nuclear RAD51. RESULTS BRCA1/2 reversion mutations were present in 60% of patients and were the most prevalent form of resistance. In 10 cases, reversions were detected in ctDNA before clinical progression. Two new reversion-based mechanisms were identified: (i) intragenic BRCA1/2 deletions with intronic breakpoints; and (ii) intragenic BRCA1/2 secondary mutations that formed novel splice acceptor sites, the latter being confirmed by in vitro minigene reporter assays. When seen before commencing subsequent treatment, reversions were associated with significantly shorter time to progression. Tumours with reversions retained HRD mutational signatures but had functional homologous recombination based on RAD51 status. Although less frequent than reversions, nonreversion mechanisms [loss-of-function (LoF) mutations in TP53BP1, RIF1 or PAXIP1] were evident in patients with acquired resistance and occasionally coexisted with reversions, challenging the notion that singular resistance mechanisms emerge in each patient. CONCLUSIONS These observations map the prevalence of candidate drivers of resistance across time in a clinical setting, information with implications for clinical management and trial design in HRD breast cancers.
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Affiliation(s)
- E Harvey-Jones
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK; The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK; The City of London Cancer Research UK Centre at King's College London, UK
| | - M Raghunandan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - L Robbez-Masson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - L Magraner-Pardo
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - T Alaguthurai
- The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK
| | | | - J Yen
- Guardant Health Inc., Redwood City, USA
| | - H Xiao
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - R Brough
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - J Frankum
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - F Song
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - J Yeung
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - T Savy
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - A Gulati
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - J Alexander
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - H Kemp
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - C Starling
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - A Konde
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - R Marlow
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - M Cheang
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - P Proszek
- Clinical Genomics, The Royal Marsden Hospital, London, UK
| | - M Hubank
- Clinical Genomics, The Royal Marsden Hospital, London, UK
| | - M Cai
- Guardant Health Inc., Redwood City, USA
| | - J Trendell
- The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK
| | - R Lu
- The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK
| | - R Liccardo
- The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK
| | - N Ravindran
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - O Rodriguez
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - J Balmana
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | | | | | - I Roxanis
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - V Serra
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - S Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - S J Pettitt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - C J Lord
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - A N J Tutt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK; The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK; The City of London Cancer Research UK Centre at King's College London, UK.
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3
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Dillon MT, Guevara J, Mohammed K, Patin EC, Smith SA, Dean E, Jones GN, Willis SE, Petrone M, Silva C, Thway K, Bunce C, Roxanis I, Nenclares P, Wilkins A, McLaughlin M, Jayme-Laiche A, Benafif S, Nintos G, Kwatra V, Grove L, Mansfield D, Proszek P, Martin P, Moore L, Swales KE, Banerji U, Saunders MP, Spicer J, Forster MD, Harrington KJ. Durable responses to ATR inhibition with ceralasertib in tumors with genomic defects and high inflammation. J Clin Invest 2024; 134:e175369. [PMID: 37934611 PMCID: PMC10786692 DOI: 10.1172/jci175369] [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: 08/31/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUNDPhase 1 study of ATRinhibition alone or with radiation therapy (PATRIOT) was a first-in-human phase I study of the oral ATR (ataxia telangiectasia and Rad3-related) inhibitor ceralasertib (AZD6738) in advanced solid tumors.METHODSThe primary objective was safety. Secondary objectives included assessment of antitumor responses and pharmacokinetic (PK) and pharmacodynamic (PD) studies. Sixty-seven patients received 20-240 mg ceralasertib BD continuously or intermittently (14 of a 28-day cycle).RESULTSIntermittent dosing was better tolerated than continuous, which was associated with dose-limiting hematological toxicity. The recommended phase 2 dose of ceralasertib was 160 mg twice daily for 2 weeks in a 4-weekly cycle. Modulation of target and increased DNA damage were identified in tumor and surrogate PD. There were 5 (8%) confirmed partial responses (PRs) (40-240 mg BD), 34 (52%) stable disease (SD), including 1 unconfirmed PR, and 27 (41%) progressive disease. Durable responses were seen in tumors with loss of AT-rich interactive domain-containing protein 1A (ARID1A) and DNA damage-response defects. Treatment-modulated tumor and systemic immune markers and responding tumors were more immune inflamed than nonresponding.CONCLUSIONCeralasertib monotherapy was tolerated at 160 mg BD intermittently and associated with antitumor activity.TRIAL REGISTRATIONClinicaltrials.gov: NCT02223923, EudraCT: 2013-003994-84.FUNDINGCancer Research UK, AstraZeneca, UK Department of Health (National Institute for Health Research), Rosetrees Trust, Experimental Cancer Medicine Centre.
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Affiliation(s)
- Magnus T. Dillon
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Jeane Guevara
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Kabir Mohammed
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | | | | | - Emma Dean
- Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | | | | | - Marcella Petrone
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Carlos Silva
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Khin Thway
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Catey Bunce
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | | | | | - Anna Wilkins
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | | | - Adoracion Jayme-Laiche
- UCL Cancer Institute and University College London Hospital NHS Foundation Trust, London, United Kingdom
| | - Sarah Benafif
- UCL Cancer Institute and University College London Hospital NHS Foundation Trust, London, United Kingdom
| | - Georgios Nintos
- King’s College London, and Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Vineet Kwatra
- King’s College London, and Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Lorna Grove
- The Institute of Cancer Research, London, United Kingdom
| | | | - Paula Proszek
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Philip Martin
- Oncology R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Luiza Moore
- Oncology R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | | | - Udai Banerji
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | | | - James Spicer
- King’s College London, and Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Martin D. Forster
- UCL Cancer Institute and University College London Hospital NHS Foundation Trust, London, United Kingdom
| | - Kevin J. Harrington
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
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4
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Fitzpatrick A, Iravani M, Mills A, Vicente D, Alaguthurai T, Roxanis I, Turner NC, Haider S, Tutt ANJ, Isacke CM. Genomic profiling and pre-clinical modelling of breast cancer leptomeningeal metastasis reveals acquisition of a lobular-like phenotype. Nat Commun 2023; 14:7408. [PMID: 37973922 PMCID: PMC10654396 DOI: 10.1038/s41467-023-43242-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 01/06/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
Breast cancer leptomeningeal metastasis (BCLM), where tumour cells grow along the lining of the brain and spinal cord, is a devastating development for patients. Investigating this metastatic site is hampered by difficulty in accessing tumour material. Here, we utilise cerebrospinal fluid (CSF) cell-free DNA (cfDNA) and CSF disseminated tumour cells (DTCs) to explore the clonal evolution of BCLM and heterogeneity between leptomeningeal and extracranial metastatic sites. Somatic alterations with potential therapeutic actionability were detected in 81% (17/21) of BCLM cases, with 19% detectable in CSF cfDNA only. BCLM was enriched in genomic aberrations in adherens junction and cytoskeletal genes, revealing a lobular-like breast cancer phenotype. CSF DTCs were cultured in 3D to establish BCLM patient-derived organoids, and used for the successful generation of BCLM in vivo models. These data reveal that BCLM possess a unique genomic aberration profile and highlight potential cellular dependencies in this hard-to-treat form of metastatic disease.
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Affiliation(s)
- Amanda Fitzpatrick
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK
| | - Marjan Iravani
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Adam Mills
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - David Vicente
- 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
| | - Nicholas C Turner
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Andrew N J Tutt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Breast Cancer Now Research Unit, Guy's Hospital, King's College London, London, UK
- Oncology and Haematology Directorate, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Clare M Isacke
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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5
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Tovey H, Sipos O, Parker JS, Hoadley KA, Quist J, Kernaghan S, Kilburn L, Salgado R, Loi S, Kennedy RD, Roxanis I, Gazinska P, Pinder SE, Bliss J, Perou CM, Haider S, Grigoriadis A, Tutt A, Cheang MCU. Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727). Clin Cancer Res 2023; 29:3691-3705. [PMID: 37574209 PMCID: PMC10502473 DOI: 10.1158/1078-0432.ccr-23-0370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/23/2023] [Accepted: 07/24/2023] [Indexed: 08/15/2023]
Abstract
PURPOSE The TNT trial (NCT00532727) showed no evidence of carboplatin superiority over docetaxel in metastatic triple-negative breast cancer (mTNBC), but carboplatin benefit was observed in the germline BRCA1/2 mutation subgroup. Broader response-predictive biomarkers are needed. We explored the predictive ability of DNA damage response (DDR) and immune markers. EXPERIMENTAL DESIGN Tumor-infiltrating lymphocytes were evaluated for 222 of 376 patients. Primary tumors (PT) from 186 TNT participants (13 matched recurrences) were profiled using total RNA sequencing. Four transcriptional DDR-related and 25 immune-related signatures were evaluated. We assessed their association with objective response rate (ORR) and progression-free survival (PFS). Conditional inference forest clustering was applied to integrate multimodal data. The biology of subgroups was characterized by 693 gene expression modules and other markers. RESULTS Transcriptional DDR-related biomarkers were not predictive of ORR to either treatment overall. Changes from PT to recurrence were demonstrated; in chemotherapy-naïve patients, transcriptional DDR markers separated carboplatin responders from nonresponders (P values = 0.017; 0.046). High immune infiltration was associated with docetaxel ORR (interaction P values < 0.05). Six subgroups were identified; the immune-enriched cluster had preferential docetaxel response [62.5% (D) vs. 29.4% (C); P = 0.016]. The immune-depleted cluster had preferential carboplatin response [8.0% (D) vs. 40.0% (C); P = 0.011]. DDR-related subgroups were too small to assess ORR. CONCLUSIONS High immune features predict docetaxel response, and high DDR signature scores predict carboplatin response in treatment-naïve mTNBC. Integrating multimodal DDR and immune-related markers identifies subgroups with differential treatment sensitivity. Treatment options for patients with immune-low and DDR-proficient tumors remains an outstanding need. Caution is needed using PT-derived transcriptional signatures to direct treatment in mTNBC, particularly DDR-related markers following prior chemotherapy.
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Affiliation(s)
- Holly Tovey
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Orsolya Sipos
- Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Joel S. Parker
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Katherine A. Hoadley
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jelmar Quist
- The Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
| | - Sarah Kernaghan
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Lucy Kilburn
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Roberto Salgado
- Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium
| | - Sherene Loi
- Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Ioannis Roxanis
- Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Patrycja Gazinska
- Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London, United Kingdom
- Biobank Research Group, Lukasiewicz Research Network – PORT Polish Center for Technology Development, Wroclaw, Poland
| | - Sarah E. Pinder
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
| | - Judith Bliss
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Charles M. Perou
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Syed Haider
- Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Anita Grigoriadis
- The Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
| | - Andrew Tutt
- Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London, United Kingdom
- The Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
| | - Maggie Chon U. Cheang
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
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6
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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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Graham R, Gazinska P, Zhang B, Khiabany A, Sinha S, Alaguthurai T, Flores-Borja F, Vicencio J, Beuron F, Roxanis I, Matkowski R, Liam-Or R, Tutt A, Ng T, Al-Jamal KT, Zhou Y, Irshad S. Serum-derived extracellular vesicles from breast cancer patients contribute to differential regulation of T-cell-mediated immune-escape mechanisms in breast cancer subtypes. Front Immunol 2023; 14:1204224. [PMID: 37441083 PMCID: PMC10335744 DOI: 10.3389/fimmu.2023.1204224] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/05/2023] [Indexed: 07/15/2023] Open
Abstract
Background Intracellular communication within the tumour is complex and extracellular vesicles (EVs) have been identified as major contributing factors for the cell-to-cell communication in the local and distant tumour environments. Here, we examine the differential effects of breast cancer (BC) subtype-specific patient serum and cell-line derived EVs in the regulation of T cell mediated immune responses. Methods Ultracentrifugation was used to isolate EVs from sera of 63 BC patients, 15 healthy volunteers and 4 human breast cancer cell lines. Longitudinal blood draws for EV isolation for patients on neoadjuvant chemotherapy was also performed. Characterization of EVs was performed by Nanoparticle Tracking Analysis (NTA), transmission electron microscopy (TEM) and immunoblotting. CD63 staining was performed on a tissue microarray of 218 BC patients. In-house bioinformatics algorithms were utilized for the computation of EV associated expression scores within The Cancer Genome Atlas (TCGA) and correlated with tumour infiltrating lymphocyte (TIL) scores. In vitro stimulation of PBMCs with EVs from serum and cell-line derived EVs was performed and changes in the immune phenotypes characterized by flow cytometry. Cytokine profiles were assessed using a 105-plex immunoassay or IL10 ELISA. Results Patients with triple negative breast cancers (TNBCs) exhibited the lowest number of EVs in the sera; whilst the highest was detected in ER+HER2+ cancers; reflected also in the higher level of CD63+ vesicles found within the ER+HER2+ local tumour microenvironment. Transcriptomic analysis of the TCGA data identified that samples assigned with lower EV scores had significantly higher abundance of CD4+ memory activated T cells, T follicular cells and CD8 T cells, plasma, and memory B cells; whilst samples with high EV scores were more enriched for anti-inflammatory M2 macrophages and mast cells. A negative correlation between EV expression scores and stromal TIL counts was also observed. In vitro experiments confirmed that circulating EVs within breast cancer subtypes have functionally differing immunomodulatory capabilities, with EVs from patients with the most aggressive breast cancer subtype (TNBCs) demonstrating the most immune-suppressive phenotype (decreased CD3+HLA-DR+ but increased CD3+PD-L1 T cells, increased CD4+CD127-CD25hi T regulatory cells with associated increase in IL10 cytokine production). In depth assessment of the cytokine modulation triggered by the serum/cell line derived exosomes confirmed differential inflammatory cytokine profiles across differing breast cancer subtypes. Studies using the MDA-231 TNBC breast cancer cell-line derived EVs provided further support that TNBC EVs induced the most immunosuppressive response within PBMCs. Discussion Our study supports further investigations into how tumour derived EVs are a mechanism that cancers can exploit to promote immune suppression; and breast cancer subtypes produce EVs with differing immunomodulatory capabilities. Understanding the intracellular/extracellular pathways implicated in alteration from active to suppressed immune state may provide a promising way forward for restoring immune competence in specific breast cancer patient populations.
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Affiliation(s)
- Rosalind Graham
- Breast Immunology Group, School of Cancer & Pharmaceutical Sciences, King’s College London, London, United Kingdom
| | - Patrycja Gazinska
- Breast Cancer Now Research Unit, King's College London, Guy's Hospital, London, United Kingdom
- Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, United Kingdom
- Biobank Research Group, Lukasiewicz Research Network – PORT Polish Center for Technology Development, Wroclaw, Poland
| | - Birong Zhang
- Systems Immunity University Research Institute and Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Atousa Khiabany
- Breast Immunology Group, School of Cancer & Pharmaceutical Sciences, King’s College London, London, United Kingdom
| | - Shubhankar Sinha
- Breast Immunology Group, School of Cancer & Pharmaceutical Sciences, King’s College London, London, United Kingdom
| | - Thanussuyah Alaguthurai
- Breast Immunology Group, School of Cancer & Pharmaceutical Sciences, King’s College London, London, United Kingdom
- Breast Cancer Now Research Unit, King's College London, Guy's Hospital, London, United Kingdom
| | - Fabian Flores-Borja
- Richard Dimbleby Laboratory of Cancer Research School of Cancer and Pharmaceutical Sciences, King’s College London, London, United Kingdom
| | - Jose Vicencio
- UCL Cancer Institute, Paul O'Gorman Building, University College London, London, United Kingdom
| | - Fabienne Beuron
- Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, United Kingdom
| | - Ioannis Roxanis
- Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, United Kingdom
| | - Rafal Matkowski
- Breast Unit, Lower Silesian Oncology, Pulmunology and Hematology Center, Wroclaw, Poland
- Department of Oncology, Wroclaw Medical University, Wroclaw, Poland
| | - Revadee Liam-Or
- Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Andrew Tutt
- Breast Cancer Now Research Unit, King's College London, Guy's Hospital, London, United Kingdom
- Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, United Kingdom
| | - Tony Ng
- Breast Cancer Now Research Unit, King's College London, Guy's Hospital, London, United Kingdom
- Richard Dimbleby Laboratory of Cancer Research School of Cancer and Pharmaceutical Sciences, King’s College London, London, United Kingdom
- UCL Cancer Institute, Paul O'Gorman Building, University College London, London, United Kingdom
| | - Khuloud T. Al-Jamal
- Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - You Zhou
- Systems Immunity University Research Institute and Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Sheeba Irshad
- Breast Immunology Group, School of Cancer & Pharmaceutical Sciences, King’s College London, London, United Kingdom
- Breast Cancer Now Research Unit, King's College London, Guy's Hospital, London, United Kingdom
- Medical Oncology, Guy's & St Thomas' NHS Trust, London, United Kingdom
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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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Yeung J, Fotiadis N, Diamantopoulos A, Tutt A, Roxanis I, Bandula S. Next generation sequencing and image-guided tissue sampling: a primer for interventional radiologists. J Vasc Interv Radiol 2023:S1051-0443(23)00224-5. [PMID: 36977432 DOI: 10.1016/j.jvir.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 03/06/2023] [Accepted: 03/18/2023] [Indexed: 03/29/2023] Open
Abstract
The discovery of increasing numbers of actionable molecular and gene targets for cancer treatment has driven demand for tissue sampling for next generation sequencing (NGS). Requirements for sequencing can be very specific and inadequate sampling leads to delays in management and decision making. It is important that interventional radiologists are aware of NGS technologies, their common applications, and be cognisant of the factors that contribute to successful sample sequencing. This review summarises the fundamentals of cancer tissue collection and processing for NGS. It elaborates on sequencing technologies and their applications, with the aim of providing readers with a working understanding that can enhance their clinical practice. It then describes imaging, tumour, biopsy and sample collection factors that improve the chances of NGS success. Finally, it discusses future practice, highlighting the problem of under-sampling in both clinical and research settings and the opportunities within interventional radiology to address this.
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Tovey H, Sipos O, Hoadley KA, Parker JS, Quist J, Kernaghan S, Kilburn L, Salgado R, Loi S, Kennedy RD, Roxanis I, Gazinska P, Pinder SE, Bliss J, Perou CM, Haider S, Tutt A, Grigoriadis A, Cheang MCU. Abstract PD9-06: Histopathological and molecular immune landscape and DNA damage response signatures to predict response to carboplatin and docetaxel in TNT trial TNBC cohort. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-pd9-06] [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 The TNT trial (NCT00532727) showed no evidence of carboplatin (C) superiority over docetaxel (D) overall in metastatic triple negative breast cancers (TNBC), but a C benefit was observed in the pre-specified sub-group analysis in patients with a gBRCA1/2 mutation (Tutt et al, Nat Med 2018). Given only ~30% of patients have a gBRCA1/2 mutation, broader predictive biomarkers of response are needed. In this cohort we previously found that DNA Damage Response (DDR) signatures were associated with improved C response in chemotherapy (CT) naïve patients only (Tovey et al, ASCO 2020). Since DDR activities influence tumour immune-microenvironment, we explored the predictive ability of immune cell markers and performed integrative analyses on multi-omics features to identify novel TNBC subgroups. Patients and Methods Tumour infiltrating lymphocytes (TILs) were evaluated on haematoxylin and eosin stained primary tumour (PT) slides for 222/376 TNT patients. Formalin-fixed paraffin-embedded PT tissues from 186/376 TNT patients were successfully profiled using total RNA-sequencing. Matched recurrence (REC) was also sequenced for 13 patients. Twenty-five immune signatures were assessed. Logistic regression and restricted mean progression free survival (PFS) were applied to delineate the relationship of these features with treatment outcomes. Random forest clustering of multi-omics DDR and immune biology markers, including gene expression signatures and mutation/methylation status, was applied to identify subgroups. We further molecularly characterised these clusters through supervised clustering of 693 gene expression “modules” (sets of co-expressed genes), immune cell deconvolution and genomic scars. Results Immune gene expression signatures and TILs were highly correlated. Average immune infiltration based on ConsensusTME was lower in mutated/methylated tumours compared with BRCA1 wildtype tumours (p=0.04). Immune signature score markers decreased from PT to REC, demonstrating a dynamic immune microenvironment. In the overall population and when restricting to prior CT treated patients, high immune infiltration (gene expression based & TILs) was associated with response to D while C response rates were not associated with immune scores (interaction p-values< 0.05). This did not translate to a PFS benefit. Multi-omics clustering identified 6 biological subgroups including immune enriched, immune depleted, DDR deficient and proficient clusters as well as 2 small clusters with no obvious distinguishing features. Immune enriched TNBC were predominantly basal-like immune activated with high B-cell/T-cell diversity. Immune depleted TNBC showed higher activity of proliferation and DDR pathway modules. DDR proficient tumours had low expression of immune markers and enrichment for ESR1/PGR expression, markers of extra cellular formation, cell structure, lipid metabolism and proliferation. The DDR deficient cluster was enriched for proliferation and demonstrated high number of TILs despite no apparent enrichment for gene expression-based immune modules. In the prior CT treated cohort, the immune enriched cluster had preferential response to D (62.5% (D) vs. 29.4% (C); p=0.02). The immune depleted cluster had preferential response to C (8.0% (D) vs. 40.0% (C); p=0.01). Numbers were too small to assess differential response within the other clusters or in the CT naïve cohort. Conclusions Tumours with high immune features have high response to D while those with low immune features have preferential response to C in advanced TNBC. Combining multi-omics markers of DDR deficiency and immune biology can identify clusters of patients with distinct biological profiles and differential treatment specific response rates.
Citation Format: Holly Tovey, Orsolya Sipos, Katherine A Hoadley, Joel S Parker, Jelmar Quist, Sarah Kernaghan, Lucy Kilburn, Roberto Salgado, Sherene Loi, Richard D Kennedy, Ioannis Roxanis, Patrycja Gazinska, Sarah E. Pinder, Judith Bliss, Charles M. Perou, Syed Haider, Andrew Tutt, Anita Grigoriadis, Maggie Chon U Cheang. Histopathological and molecular immune landscape and DNA damage response signatures to predict response to carboplatin and docetaxel in TNT trial TNBC cohort [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 PD9-06.
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Affiliation(s)
- Holly Tovey
- 1Clinical Trials and Statistics Unit, The Institute of Cancer Research, London
| | - Orsolya Sipos
- 2Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London
| | - Katherine A Hoadley
- 3Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Joel S Parker
- 4Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Jelmar Quist
- 5Breast Cancer Now Unit, King’s College London Faculty of Life Sciences and Medicine, London; School of Cancer and Pharmaceutical Sciences, King’s College London Faculty of Life Sciences and Medicine, London
| | - Sarah Kernaghan
- 6Clinical Trials and Statistics Unit, The Institute of Cancer Research, London
| | - Lucy Kilburn
- 7Clinical Trials and Statistics Unit, The Institute of Cancer Research, London
| | - Roberto Salgado
- 8GZA-ZNA-Hospitals, Antwerp, Belgium; Peter Mac Callum Cancer Centre, Melbourne, Australia
| | - Sherene Loi
- 9Peter MacCallum Cancer Centre, Melbourne, Australia, Australia
| | | | - Ioannis Roxanis
- 11Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London
| | - Patrycja Gazinska
- 12Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London; Biobank Research Group, Lukasiewicz Research Network – PORT Polish Center for Technology Development, Wroclaw, Poland
| | - Sarah E. Pinder
- 13School of Cancer and Pharmaceutical Sciences, King’s College London Faculty of Life Sciences and Medicine, London, London, England, United Kingdom
| | - Judith Bliss
- 14Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Charles M. Perou
- 15University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Syed Haider
- 16Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London
| | - Andrew Tutt
- 17Institute of Cancer Research, London, United Kingdom
| | - Anita Grigoriadis
- 18Breast Cancer Now Unit, King’s College London Faculty of Life Sciences and Medicine, London; School of Cancer and Pharmaceutical Sciences, King’s College London Faculty of Life Sciences and Medicine, London
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Gazinska P, Milton C, Iacovacci J, Ward J, Buus R, Alaguthurai T, Graham R, Akarca A, Lips E, Naidoo K, Wesseling J, Marafioti T, Cheang M, Gillett C, Wu Y, Khan A, Melcher A, Salgado R, Dowsett M, Tutt A, Roxanis I, Haider S, Irshad S. Dynamic Changes in the NK-, Neutrophil-, and B-cell Immunophenotypes Relevant in High Metastatic Risk Post Neoadjuvant Chemotherapy-Resistant Early Breast Cancers. Clin Cancer Res 2022; 28:4494-4508. [PMID: 36161312 PMCID: PMC9561554 DOI: 10.1158/1078-0432.ccr-22-0543] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 02/19/2022] [Revised: 05/12/2022] [Accepted: 08/12/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE To identify potential immune targets in post-neoadjuvant chemotherapy (NAC)-resistant triple-negative breast cancer (TNBC) and ER+HER2- breast cancer disease. EXPERIMENTAL DESIGN Following pathology review, 153 patients were identified as having residual cancer burden (RCB) II/III disease (TNBC n = 80; ER+HER2-n = 73). Baseline pre-NAC samples were available for evaluation for 32 of 80 TNBC and 36 of 73 ER+HER2- cases. Bright-field hematoxylin and eosin assessment allowed for tumor-infiltrating lymphocyte (TIL) evaluation in all cases. Multiplexed immunofluorescence was used to identify the abundance and distribution of immune cell subsets. Levels of checkpoints including PD-1/PD-L1 expression were also quantified. Findings were then validated using expression profiling of cancer and immune-related genes. Cytometry by time-of-flight characterized the dynamic changes in circulating immune cells with NAC. RESULTS RCB II/III TNBC and ER+HER2- breast cancer were immunologically "cold" at baseline and end of NAC. Although the distribution of immune cell subsets across subtypes was similar, the mRNA expression profiles were both subtype- and chemotherapy-specific. TNBC RCB II/III disease was enriched with genes related to neutrophil degranulation, and displayed strong interplay across immune and cancer pathways. We observed similarities in the dynamic changes in B-cell biology following NAC irrespective of subtype. However, NAC induced changes in the local and circulating tumor immune microenvironment (TIME) that varied by subtype and response. Specifically, in TNBC residual disease, we observed downregulation of stimulatory (CD40/OX40L) and inhibitory (PD-L1/PD-1) receptor expression and an increase in NK cell populations (especially non-cytolytic, exhausted CD56dimCD16-) within both the local TIME and peripheral white cell populations. CONCLUSIONS This study identifies several potential immunologic pathways in residual disease, which may be targeted to benefit high-risk patients.
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Affiliation(s)
- Patrycja Gazinska
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Charlotte Milton
- School of Cancer and Pharmaceutical Sciences, King's College London, UK
| | - Jacopo Iacovacci
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Joseph Ward
- Targeted Therapy Team, The Institute of Cancer Research, Chester Beatty Laboratories, London, UK
| | - Richard Buus
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Thanussuyah Alaguthurai
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Breast Cancer Now Research Unit, King's College London, London, UK
| | - Rosalind Graham
- School of Cancer and Pharmaceutical Sciences, King's College London, UK
| | - Ayse Akarca
- Department of Cellular Pathology, University College London, London, UK
| | - Esther Lips
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Kalnisha Naidoo
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Jelle Wesseling
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Maggie Cheang
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - Cheryl Gillett
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Yin Wu
- School of Cancer and Pharmaceutical Sciences, King's College London, UK
| | - Aadil Khan
- Targeted Therapy Team, The Institute of Cancer Research, Chester Beatty Laboratories, London, UK
| | - Alan Melcher
- Division of Radiotherapy and Imaging, Institute of Cancer Research, London, UK
| | - Roberto Salgado
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia; Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium
| | - Mitch Dowsett
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - Andrew Tutt
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Breast Cancer Now Research Unit, King's College London, London, UK
- Oncology and Haematology Directorate, Guy's and St Thomas’ NHS Foundation Trust, London, UK
| | - Ioannis Roxanis
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Syed Haider
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Sheeba Irshad
- School of Cancer and Pharmaceutical Sciences, King's College London, UK
- Breast Cancer Now Research Unit, King's College London, London, UK
- Oncology and Haematology Directorate, Guy's and St Thomas’ NHS Foundation Trust, London, UK
- Cancer Research UK (CRUK) Clinician Scientist, London, UK
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Ferro R, Carroll A, Mendes-Pereira A, Reen V, Roxanis I, Annunziato S, Jonkers J, Liv N, Alexander J, Quist J, Pardo M, Roumeliotis T, Choudhary J, Weekes D, Marra P, Natrajan R, Grigoriadis A, Haider S, Lord C, Tutt A. The anion channel GPR89 is a novel oncogene associated with tumour specific dependency in breast cancer. Eur J Cancer 2022. [DOI: 10.1016/s0959-8049(22)00934-0] [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: 11/03/2022]
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13
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El-Sheikh S, Rathbone M, Chaudhary K, Joshi A, Lee J, Muthukumar S, Mylona E, Roxanis I, Rees J. Rates and Outcomes of Breast Lesions of Uncertain Malignant Potential (B3) benchmarked against the National Breast Screening Pathology Audit; Improving Performance in a High Volume Screening Unit. Clin Breast Cancer 2022; 22:381-390. [DOI: 10.1016/j.clbc.2022.02.004] [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] [Received: 12/01/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 11/29/2022]
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14
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Sheldon H, Bridges E, Silva I, Masiero M, Favara DM, Wang D, Leek R, Snell C, Roxanis I, Kreuzer M, Gileadi U, Buffa FM, Banham A, Harris AL. ADGRL4/ELTD1 Expression in Breast Cancer Cells Induces Vascular Normalization and Immune Suppression. Mol Cancer Res 2021; 19:1957-1969. [PMID: 34348993 PMCID: PMC7611948 DOI: 10.1158/1541-7786.mcr-21-0171] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/08/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022]
Abstract
ELTD1/ADGRL4 expression is increased in the vasculature of a number of tumor types and this correlates with a good prognosis. Expression has also been reported in some tumor cells with high expression correlating with a good prognosis in hepatocellular carcinoma (HCC) and a poor prognosis in glioblastoma. Here we show that 35% of primary human breast tumors stain positively for ELTD1, with 9% having high expression that correlates with improved relapse-free survival. Using immunocompetent, syngeneic mouse breast cancer models we found that tumors expressing recombinant murine Eltd1 grew faster than controls, with an enhanced ability to metastasize and promote systemic immune effects. The Eltd1-expressing tumors had larger and better perfused vessels and tumor-endothelial cell interaction led to the release of proangiogenic and immune-modulating factors. M2-like macrophages increased in the stroma along with expression of programmed death-ligand 1 (PD-L1) on tumor and immune cells, to create an immunosuppressive microenvironment that allowed Eltd1-regulated tumor growth in the presence of an NY-ESO-1-specific immune response. Eltd1-positive tumors also responded better to chemotherapy which could explain the relationship to a good prognosis observed in primary human cases. Thus, ELTD1 expression may enhance delivery of therapeutic antibodies to reverse the immunosuppression and increase response to chemotherapy and radiotherapy in this subset of tumors. ELTD1 may be useful as a selection marker for such therapies. IMPLICATIONS: ELTD1 expression in mouse breast tumors creates an immunosuppressive microenvironment and increases vessel size and perfusion. Its expression may enhance the delivery of therapies targeting the immune system.
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Affiliation(s)
- Helen Sheldon
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford, United Kingdom
- Cancer Research UK Molecular Oncology Laboratories, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Esther Bridges
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford, United Kingdom
- Cancer Research UK Molecular Oncology Laboratories, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Ildefonso Silva
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford, United Kingdom
- Cancer Research UK Molecular Oncology Laboratories, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Massimo Masiero
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - David M Favara
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford, United Kingdom
- Cancer Research UK Molecular Oncology Laboratories, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Dian Wang
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Russell Leek
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Cameron Snell
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Ioannis Roxanis
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Mira Kreuzer
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford, United Kingdom
- Cancer Research UK Molecular Oncology Laboratories, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Uzi Gileadi
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Francesca M Buffa
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford, United Kingdom
- Cancer Research UK Molecular Oncology Laboratories, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Alison Banham
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Adrian L Harris
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford, United Kingdom.
- Cancer Research UK Molecular Oncology Laboratories, Department of Oncology, University of Oxford, Oxford, United Kingdom
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15
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Robinson R, Roxanis I, Sobhani F, Zormpas-Petridis K, Steel H, Anbalagan S, Sommer A, Gothard L, Khan A, MacNeill F, Melcher A, Yuan Y, Somaiah N. PO-1085 Longitudinal assessment of immune infiltrate in breast cancer treated with neoadjuvant radiotherapy. Radiother Oncol 2021. [DOI: 10.1016/s0167-8140(21)07536-8] [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: 10/20/2022]
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16
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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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17
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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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18
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Sobhani F, Robinson R, Hamidinekoo A, Roxanis I, Somaiah N, Yuan Y. Artificial intelligence and digital pathology: Opportunities and implications for immuno-oncology. Biochim Biophys Acta Rev Cancer 2021; 1875:188520. [PMID: 33561505 PMCID: PMC9062980 DOI: 10.1016/j.bbcan.2021.188520] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 01/04/2021] [Accepted: 01/30/2021] [Indexed: 02/08/2023]
Abstract
The field of immuno-oncology has expanded rapidly over the past decade, but key questions remain. How does tumour-immune interaction regulate disease progression? How can we prospectively identify patients who will benefit from immunotherapy? Identifying measurable features of the tumour immune-microenvironment which have prognostic or predictive value will be key to making meaningful gains in these areas. Recent developments in deep learning enable big-data analysis of pathological samples. Digital approaches allow data to be acquired, integrated and analysed far beyond what is possible with conventional techniques, and to do so efficiently and at scale. This has the potential to reshape what can be achieved in terms of volume, precision and reliability of output, enabling data for large cohorts to be summarised and compared. This review examines applications of artificial intelligence (AI) to important questions in immuno-oncology (IO). We discuss general considerations that need to be taken into account before AI can be applied in any clinical setting. We describe AI methods that have been applied to the field of IO to date and present several examples of their use.
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Affiliation(s)
- Faranak Sobhani
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK; Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
| | - Ruth Robinson
- Division of Radiotherapy and Imaging, Institute of Cancer Research, The Royal Marsden NHS Foundation Trust, London, UK.
| | - Azam Hamidinekoo
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK; Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
| | - Ioannis Roxanis
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - Navita Somaiah
- Division of Radiotherapy and Imaging, Institute of Cancer Research, The Royal Marsden NHS Foundation Trust, London, UK.
| | - Yinyin Yuan
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK; Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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19
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Wershof E, Park D, Barry DJ, Jenkins RP, Rullan A, Wilkins A, Schlegelmilch K, Roxanis I, Anderson KI, Bates PA, Sahai E. A FIJI macro for quantifying pattern in extracellular matrix. Life Sci Alliance 2021; 4:e202000880. [PMID: 33504622 PMCID: PMC7898596 DOI: 10.26508/lsa.202000880] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 11/24/2022] Open
Abstract
Diverse extracellular matrix patterns are observed in both normal and pathological tissue. However, most current tools for quantitative analysis focus on a single aspect of matrix patterning. Thus, an automated pipeline that simultaneously quantifies a broad range of metrics and enables a comprehensive description of varied matrix patterns is needed. To this end, we have developed an ImageJ plugin called TWOMBLI, which stands for The Workflow Of Matrix BioLogy Informatics. This pipeline includes metrics of matrix alignment, length, branching, end points, gaps, fractal dimension, curvature, and the distribution of fibre thickness. TWOMBLI is designed to be quick, versatile and easy-to-use particularly for non-computational scientists. TWOMBLI can be downloaded from https://github.com/wershofe/TWOMBLI together with detailed documentation and tutorial video. Although developed with the extracellular matrix in mind, TWOMBLI is versatile and can be applied to vascular and cytoskeletal networks. Here we present an overview of the pipeline together with examples from a wide range of contexts where matrix patterns are generated.
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Affiliation(s)
- Esther Wershof
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Danielle Park
- Developmental Signalling Laboratory, The Francis Crick Institute, London, UK
| | - David J Barry
- Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Robert P Jenkins
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
| | - Antonio Rullan
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
| | - Anna Wilkins
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
| | | | - Ioannis Roxanis
- Breast Cancer Research Division, Toby Robins Breast Cancer Now Research Centre, The Institute of Cancer Research, London, UK
| | - Kurt I Anderson
- Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Paul A Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
| | - Erik Sahai
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
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20
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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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21
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Zormpas-Petridis K, Noguera R, Ivankovic DK, Roxanis I, Jamin Y, Yuan Y. SuperHistopath: A Deep Learning Pipeline for Mapping Tumor Heterogeneity on Low-Resolution Whole-Slide Digital Histopathology Images. Front Oncol 2021; 10:586292. [PMID: 33552964 PMCID: PMC7855703 DOI: 10.3389/fonc.2020.586292] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/30/2020] [Indexed: 12/27/2022] Open
Abstract
High computational cost associated with digital pathology image analysis approaches is a challenge towards their translation in routine pathology clinic. Here, we propose a computationally efficient framework (SuperHistopath), designed to map global context features reflecting the rich tumor morphological heterogeneity. SuperHistopath efficiently combines i) a segmentation approach using the linear iterative clustering (SLIC) superpixels algorithm applied directly on the whole-slide images at low resolution (5x magnification) to adhere to region boundaries and form homogeneous spatial units at tissue-level, followed by ii) classification of superpixels using a convolution neural network (CNN). To demonstrate how versatile SuperHistopath was in accomplishing histopathology tasks, we classified tumor tissue, stroma, necrosis, lymphocytes clusters, differentiating regions, fat, hemorrhage and normal tissue, in 127 melanomas, 23 triple-negative breast cancers, and 73 samples from transgenic mouse models of high-risk childhood neuroblastoma with high accuracy (98.8%, 93.1% and 98.3% respectively). Furthermore, SuperHistopath enabled discovery of significant differences in tumor phenotype of neuroblastoma mouse models emulating genomic variants of high-risk disease, and stratification of melanoma patients (high ratio of lymphocyte-to-tumor superpixels (p = 0.015) and low stroma-to-tumor ratio (p = 0.028) were associated with a favorable prognosis). Finally, SuperHistopath is efficient for annotation of ground-truth datasets (as there is no need of boundary delineation), training and application (~5 min for classifying a whole-slide image and as low as ~30 min for network training). These attributes make SuperHistopath particularly attractive for research in rich datasets and could also facilitate its adoption in the clinic to accelerate pathologist workflow with the quantification of phenotypes, predictive/prognosis markers.
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Affiliation(s)
| | - Rosa Noguera
- Department of Pathology, Medical School, University of Valencia-INCLIVA Biomedical Health Research Institute, Valencia, Spain.,Low Prevalence Tumors, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Ioannis Roxanis
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Yann Jamin
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, United Kingdom
| | - Yinyin Yuan
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
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22
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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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23
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Zormpas-Petridis K, Failmezger H, Raza SEA, Roxanis I, Jamin Y, Yuan Y. Superpixel-Based Conditional Random Fields (SuperCRF): Incorporating Global and Local Context for Enhanced Deep Learning in Melanoma Histopathology. Front Oncol 2019; 9:1045. [PMID: 31681583 PMCID: PMC6798642 DOI: 10.3389/fonc.2019.01045] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 06/11/2019] [Accepted: 09/25/2019] [Indexed: 01/08/2023] Open
Abstract
Computational pathology-based cell classification algorithms are revolutionizing the study of the tumor microenvironment and can provide novel predictive/prognosis biomarkers crucial for the delivery of precision oncology. Current algorithms used on hematoxylin and eosin slides are based on individual cell nuclei morphology with limited local context features. Here, we propose a novel multi-resolution hierarchical framework (SuperCRF) inspired by the way pathologists perceive regional tissue architecture to improve cell classification and demonstrate its clinical applications. We develop SuperCRF by training a state-of-art deep learning spatially constrained- convolution neural network (SC-CNN) to detect and classify cells from 105 high-resolution (20×) H&E-stained slides of The Cancer Genome Atlas melanoma dataset and subsequently, a conditional random field (CRF) by combining cellular neighborhood with tumor regional classification from lower resolution images (5, 1.25×) given by a superpixel-based machine learning framework. SuperCRF led to an 11.85% overall improvement in the accuracy of the state-of-art deep learning SC-CNN cell classifier. Consistent with a stroma-mediated immune suppressive microenvironment, SuperCRF demonstrated that (i) a high ratio of lymphocytes to all lymphocytes within the stromal compartment (p = 0.026) and (ii) a high ratio of stromal cells to all cells (p < 0.0001 compared to p = 0.039 for SC-CNN only) are associated with poor survival in patients with melanoma. SuperCRF improves cell classification by introducing global and local context-based information and can be implemented in combination with any single-cell classifier. SuperCRF provides valuable tools to study the tumor microenvironment and identify predictors of survival and response to therapy.
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Affiliation(s)
- Konstantinos Zormpas-Petridis
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Trust, Surrey, United Kingdom
| | - Henrik Failmezger
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Shan E Ahmed Raza
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Ioannis Roxanis
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Yann Jamin
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Trust, Surrey, United Kingdom
| | - Yinyin Yuan
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
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24
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Toss MS, Miligy IM, Gorringe KL, AlKawaz A, Mittal K, Aneja R, Ellis IO, Green AR, Roxanis I, Rakha EA. Geometric characteristics of collagen have independent prognostic significance in breast ductal carcinoma in situ: an image analysis study. Mod Pathol 2019; 32:1473-1485. [PMID: 31175326 DOI: 10.1038/s41379-019-0296-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/01/2019] [Accepted: 05/02/2019] [Indexed: 12/30/2022]
Abstract
Collagen plays a key role in normal and malignant tissue homeostasis. While the prognostic significance of collagen fiber remodeling in invasive breast cancer has been studied, its role in ductal carcinoma in situ (DCIS) remains poorly defined. Using image analysis, we aimed to evaluate the prognostic significance of the geometric characteristics of collagen surrounding DCIS. A large well-characterized cohort of DCIS comprising pure DCIS (n = 610) and DCIS coexisting with invasive carcinoma (n = 180) were histochemically stained for collagen using picrosirius red. ImageJ software was used to assess collagen density, degree of collagen fiber dispersion and directionality in relation to DCIS ducts' boundary. We developed a collagen prognostic index and evaluated its prognostic significance. A poor index was observed in 24% of the pure DCIS and was associated with determinants of high-risk DCIS including higher nuclear grade, comedo type necrosis, hormonal receptor negativity, HER2 positivity and high proliferation index. High collagen prognostic index was associated with the collagen remodeling protein prolyl-4-hydroxlase alpha subunit 2 and the hypoxia-related protein hypoxia inducible factor 1α. DCIS coexisting with invasive breast cancer had a higher collagen prognostic index than pure DCIS ( p < 0.0001). High index was an independent poor prognostic factor for DCIS recurrence for all recurrences (HR = 2.3, p = 0.005) and just invasive recurrences (HR = 3.4, p = 0.003). Interaction between collagen prognostic index and radiotherapy showed that the index was associated with poor outcome even with adjuvant radiotherapy ( p = 0.0001). Collagen reorganization around DCIS is associated with poor outcome and provides a potential predictor for disease progression and resistance to radiotherapy. Mechanistic studies are warranted to decipher the underlying mechanisms.
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Affiliation(s)
- Michael S Toss
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham, Nottingham City Hospital, Nottingham, UK.,Histopathology Department, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
| | - Islam M Miligy
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham, Nottingham City Hospital, Nottingham, UK.,Histopathology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Kylie L Gorringe
- Cancer Genomics Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Abdulbaqi AlKawaz
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham, Nottingham City Hospital, Nottingham, UK.,College of Dentistry, Al Mustansiriya University, Baghdad, Iraq
| | | | - Ritu Aneja
- Georgia State University, Atlanta, GA, USA
| | - Ian O Ellis
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham, Nottingham City Hospital, Nottingham, UK
| | - Andrew R Green
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham, Nottingham City Hospital, Nottingham, UK
| | - Ioannis Roxanis
- Institute of Cancer Research, London, UK.,Royal Free London NHS Foundation Trust, London, UK
| | - Emad A Rakha
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham, Nottingham City Hospital, Nottingham, UK. .,Histopathology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt.
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25
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Lord SR, Cheng WC, Liu D, Gaude E, Haider S, Metcalf T, Patel N, Teoh EJ, Gleeson F, Bradley K, Wigfield S, Zois C, McGowan DR, Ah-See ML, Thompson AM, Sharma A, Bidaut L, Pollak M, Roy PG, Karpe F, James T, English R, Adams RF, Campo L, Ayers L, Snell C, Roxanis I, Frezza C, Fenwick JD, Buffa FM, Harris AL. Integrated Pharmacodynamic Analysis Identifies Two Metabolic Adaption Pathways to Metformin in Breast Cancer. Cell Metab 2018; 28:679-688.e4. [PMID: 30244975 PMCID: PMC6224605 DOI: 10.1016/j.cmet.2018.08.021] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 04/21/2018] [Accepted: 08/24/2018] [Indexed: 12/13/2022]
Abstract
Late-phase clinical trials investigating metformin as a cancer therapy are underway. However, there remains controversy as to the mode of action of metformin in tumors at clinical doses. We conducted a clinical study integrating measurement of markers of systemic metabolism, dynamic FDG-PET-CT, transcriptomics, and metabolomics at paired time points to profile the bioactivity of metformin in primary breast cancer. We show metformin reduces the levels of mitochondrial metabolites, activates multiple mitochondrial metabolic pathways, and increases 18-FDG flux in tumors. Two tumor groups are identified with distinct metabolic responses, an OXPHOS transcriptional response (OTR) group for which there is an increase in OXPHOS gene transcription and an FDG response group with increased 18-FDG uptake. Increase in proliferation, as measured by a validated proliferation signature, suggested that patients in the OTR group were resistant to metformin treatment. We conclude that mitochondrial response to metformin in primary breast cancer may define anti-tumor effect.
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Affiliation(s)
- Simon R Lord
- Department of Oncology, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK; Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford OX3 7LE, UK.
| | - Wei-Chen Cheng
- Department of Oncology, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK
| | - Dan Liu
- Department of Oncology, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK
| | - Edoardo Gaude
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Syed Haider
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Tom Metcalf
- Institute of Translational Medicine, University of Liverpool, Royal Liverpool University Hospital, Liverpool L69 3GA, UK
| | - Neel Patel
- Department of Nuclear Medicine, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford OX3 7LE, UK
| | - Eugene J Teoh
- Department of Oncology, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK; Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Department of Nuclear Medicine, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford OX3 7LE, UK
| | - Fergus Gleeson
- Department of Oncology, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford OX3 7LE, UK; Department of Nuclear Medicine, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford OX3 7LE, UK
| | - Kevin Bradley
- Department of Nuclear Medicine, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford OX3 7LE, UK
| | - Simon Wigfield
- Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Christos Zois
- Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Daniel R McGowan
- Department of Oncology, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK
| | - Mei-Lin Ah-See
- Department of Oncology, Luton and Dunstable Hospital, Luton, UK
| | - Alastair M Thompson
- Department of Breast Surgical Oncology, MD Anderson Cancer Centre, Houston, TX 77030, USA
| | - Anand Sharma
- Department of Oncology, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK; Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Luc Bidaut
- College of Science, University of Lincoln, Lincoln LN6 7TS, UK; Clinical Research Imaging Facility, University of Dundee, Ninewells Hospital, Dundee DD2 1SY, UK
| | - Michael Pollak
- Department of Oncology, McGill University, Montreal, QC H3T 1E2, Canada
| | - Pankaj G Roy
- Breast Surgery Unit, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford OX3 7LE, UK
| | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK
| | - Tim James
- Department of Clinical Biochemistry, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Ruth English
- Oxford Breast Imaging Centre, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - Rosie F Adams
- Oxford Breast Imaging Centre, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - Leticia Campo
- Department of Oncology, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK
| | - Lisa Ayers
- Department of Clinical and Laboratory Immunology, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford OX3 7LE, UK
| | - Cameron Snell
- Department of Anatomical Pathology, Mater Research Institute, Brisbane 4101, Australia
| | - Ioannis Roxanis
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - John D Fenwick
- Institute of Translational Medicine, University of Liverpool, Royal Liverpool University Hospital, Liverpool L69 3GA, UK
| | - Francesca M Buffa
- Department of Oncology, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK
| | - Adrian L Harris
- Department of Oncology, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK; Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford OX3 7LE, UK
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26
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Robbe P, Popitsch N, Knight SJL, Antoniou P, Becq J, He M, Kanapin A, Samsonova A, Vavoulis DV, Ross MT, Kingsbury Z, Cabes M, Ramos SDC, Page S, Dreau H, Ridout K, Jones LJ, Tuff-Lacey A, Henderson S, Mason J, Buffa FM, Verrill C, Maldonado-Perez D, Roxanis I, Collantes E, Browning L, Dhar S, Damato S, Davies S, Caulfield M, Bentley DR, Taylor JC, Turnbull C, Schuh A. Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project. Genet Med 2018; 20:1196-1205. [PMID: 29388947 PMCID: PMC6520241 DOI: 10.1038/gim.2017.241] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [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: 05/19/2017] [Accepted: 11/06/2017] [Indexed: 12/16/2022] Open
Abstract
PURPOSE Fresh-frozen (FF) tissue is the optimal source of DNA for whole-genome sequencing (WGS) of cancer patients. However, it is not always available, limiting the widespread application of WGS in clinical practice. We explored the viability of using formalin-fixed, paraffin-embedded (FFPE) tissues, available routinely for cancer patients, as a source of DNA for clinical WGS. METHODS We conducted a prospective study using DNAs from matched FF, FFPE, and peripheral blood germ-line specimens collected from 52 cancer patients (156 samples) following routine diagnostic protocols. We compared somatic variants detected in FFPE and matching FF samples. RESULTS We found the single-nucleotide variant agreement reached 71% across the genome and somatic copy-number alterations (CNAs) detection from FFPE samples was suboptimal (0.44 median correlation with FF) due to nonuniform coverage. CNA detection was improved significantly with lower reverse crosslinking temperature in FFPE DNA extraction (80 °C or 65 °C depending on the methods). Our final data showed somatic variant detection from FFPE for clinical decision making is possible. We detected 98% of clinically actionable variants (including 30/31 CNAs). CONCLUSION We present the first prospective WGS study of cancer patients using FFPE specimens collected in a routine clinical environment proving WGS can be applied in the clinic.
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Affiliation(s)
- Pauline Robbe
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Niko Popitsch
- Wellcome Trust Centre of Human Genetics, University of Oxford, Old Road Campus Research Building, Oxford, UK
| | - Samantha J L Knight
- Wellcome Trust Centre of Human Genetics, University of Oxford, Old Road Campus Research Building, Oxford, UK
| | - Pavlos Antoniou
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jennifer Becq
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Miao He
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | | | | | - Dimitrios V Vavoulis
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Mark T Ross
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Zoya Kingsbury
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Maite Cabes
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Sara D C Ramos
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Suzanne Page
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Helene Dreau
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Kate Ridout
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Louise J Jones
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Alice Tuff-Lacey
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Shirley Henderson
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Joanne Mason
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Francesca M Buffa
- Computational Biology and Integrative Genomics, Department of Oncology, University of Oxford, Oxford, UK
| | - Clare Verrill
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - David Maldonado-Perez
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Ioannis Roxanis
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Elena Collantes
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Lisa Browning
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Sunanda Dhar
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Stephen Damato
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Susan Davies
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Mark Caulfield
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
- NIHR Biomedical Research Centre at Barts Health NHS Trust, London, UK
| | - David R Bentley
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Jenny C Taylor
- Wellcome Trust Centre of Human Genetics, University of Oxford, Old Road Campus Research Building, Oxford, UK
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
| | - Clare Turnbull
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Anna Schuh
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Oxford Molecular Diagnostics Centre, Department of Oncology, University of Oxford, Oxford, UK
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27
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Roxanis I, Colling R, Kartsonaki C, Green AR, Rakha EA. The significance of tumour microarchitectural features in breast cancer prognosis: a digital image analysis. Breast Cancer Res 2018; 20:11. [PMID: 29402299 PMCID: PMC5799893 DOI: 10.1186/s13058-018-0934-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/10/2018] [Indexed: 12/02/2022] Open
Abstract
Background As only a minor portion of the information present in histological sections is accessible by eye, recognition and quantification of complex patterns and relationships among constituents relies on digital image analysis. In this study, our working hypothesis was that, with the application of digital image analysis technology, visually unquantifiable breast cancer microarchitectural features can be rigorously assessed and tested as prognostic parameters for invasive breast carcinoma of no special type. Methods Digital image analysis was performed using public domain software (ImageJ) on tissue microarrays from a cohort of 696 patients, and validated with a commercial platform (Visiopharm). Quantified features included elements defining tumour microarchitecture, with emphasis on the extent of tumour-stroma interface. The differential prognostic impact of tumour nest microarchitecture in the four immunohistochemical surrogates for molecular classification was analysed. Prognostic parameters included axillary lymph node status, breast cancer-specific survival, and time to distant metastasis. Associations of each feature with prognostic parameters were assessed using logistic regression and Cox proportional models adjusting for age at diagnosis, grade, and tumour size. Results An arrangement in numerous small nests was associated with axillary lymph node involvement. The association was stronger in luminal tumours (odds ratio (OR) = 1.39, p = 0.003 for a 1-SD increase in nest number, OR = 0.75, p = 0.006 for mean nest area). Nest number was also associated with survival (hazard ratio (HR) = 1.15, p = 0.027), but total nest perimeter was the parameter most significantly associated with survival in luminal tumours (HR = 1.26, p = 0.005). In the relatively small cohort of triple-negative tumours, mean circularity showed association with time to distant metastasis (HR = 1.71, p = 0.027) and survival (HR = 1.8, p = 0.02). Conclusions We propose that tumour arrangement in few large nests indicates a decreased metastatic potential. By contrast, organisation in numerous small nests provides the tumour with increased metastatic potential to regional lymph nodes. An outstretched pattern in small nests bestows tumours with a tendency for decreased breast cancer-specific survival. Although further validation studies are required before the argument for routine quantification of microarchitectural features is established, our approach is consistent with the demand for cost-effective methods for triaging breast cancer patients that are more likely to benefit from chemotherapy.
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Affiliation(s)
- I Roxanis
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Headley Way, Headington, Oxford, OX3 9DU, UK. .,Present Address: Institute of Cancer Research, London and Royal Free London NHS Foundation Trust, London, UK.
| | - R Colling
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Headley Way, Headington, Oxford, OX3 9DU, UK
| | - C Kartsonaki
- Nuffield Department of Population Health, University of Oxford, Big Data Institute Building, Old Road Campus, Roosevelt Drive, Oxford, OX3 7LF, UK
| | - A R Green
- Academic Pathology, Division of Cancer and Stem Cells, The University of Nottingham, Room 2-052-S Academic Unit of Oncology, Nottingham City Hospital, Nottingham, NG5 1PB, UK
| | - E A Rakha
- Department of Cellular Pathology, University of Nottingham and Nottingham University Hospitals NHS Trust, City Hospital Campus, Nottingham, NG5 1PB, UK
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28
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Harjes U, Bridges E, Gharpure KM, Roxanis I, Sheldon H, Miranda F, Mangala LS, Pradeep S, Lopez-Berestein G, Ahmed A, Fielding B, Sood AK, Harris AL. Antiangiogenic and tumour inhibitory effects of downregulating tumour endothelial FABP4. Oncogene 2017; 36:912-921. [PMID: 27568980 PMCID: PMC5318662 DOI: 10.1038/onc.2016.256] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 05/15/2016] [Accepted: 06/01/2016] [Indexed: 12/31/2022]
Abstract
Fatty acid binding protein 4 (FABP4) is a fatty acid chaperone, which is induced during adipocyte differentiation. Previously we have shown that FABP4 in endothelial cells is induced by the NOTCH1 signalling pathway, the latter of which is involved in mechanisms of resistance to antiangiogenic tumour therapy. Here, we investigated the role of FABP4 in endothelial fatty acid metabolism and tumour angiogenesis. We analysed the effect of transient FABP4 knockdown in human umbilical vein endothelial cells on fatty acid metabolism, viability and angiogenesis. Through therapeutic delivery of siRNA targeting mouse FABP4, we investigated the effect of endothelial FABP4 knockdown on tumour growth and blood vessel formation. In vitro, siRNA-mediated FABP4 knockdown in endothelial cells led to a marked increase of endothelial fatty acid oxidation, an increase of reactive oxygen species and decreased angiogenesis. In vivo, we found that increased NOTCH1 signalling in tumour xenografts led to increased expression of endothelial FABP4 that decreased when NOTCH1 and VEGFA inhibitors were used in combination. Angiogenesis, growth and metastasis in ovarian tumour xenografts were markedly inhibited by therapeutic siRNA delivery targeting mouse endothelial FABP4. Therapeutic targeting of endothelial FABP4 by siRNA in vivo has antiangiogenic and antitumour effects with minimal toxicity and should be investigated further.
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MESH Headings
- Angiogenesis Inhibitors/metabolism
- Animals
- Apoptosis
- Biomarkers, Tumor/metabolism
- Cell Movement
- Cell Proliferation
- Cystadenocarcinoma, Serous/blood supply
- Cystadenocarcinoma, Serous/metabolism
- Cystadenocarcinoma, Serous/pathology
- Cystadenocarcinoma, Serous/prevention & control
- Fatty Acid-Binding Proteins/antagonists & inhibitors
- Fatty Acid-Binding Proteins/genetics
- Fatty Acid-Binding Proteins/metabolism
- Female
- Follow-Up Studies
- Human Umbilical Vein Endothelial Cells/metabolism
- Human Umbilical Vein Endothelial Cells/pathology
- Humans
- Mice
- Mice, Nude
- Neoplasm Grading
- Neoplasm Invasiveness
- Neovascularization, Pathologic/metabolism
- Neovascularization, Pathologic/pathology
- Neovascularization, Pathologic/prevention & control
- Ovarian Neoplasms/blood supply
- Ovarian Neoplasms/metabolism
- Ovarian Neoplasms/pathology
- Ovarian Neoplasms/prevention & control
- Prognosis
- Prospective Studies
- Receptor, Notch1/metabolism
- Signal Transduction
- Survival Rate
- Tumor Cells, Cultured
- Vascular Endothelial Growth Factor A/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
- U Harjes
- Hypoxia and Growth Factor Group, WIMM, Department of Oncology, University of Oxford, Oxford, UK
| | - E Bridges
- Hypoxia and Growth Factor Group, WIMM, Department of Oncology, University of Oxford, Oxford, UK
| | - K M Gharpure
- Department of Gynecologic Oncology, University of Texas, Austin, TX, USA
| | - I Roxanis
- Department of Cellular Pathology, Oxford University Hospitals and NIHR Biomedical Research Centre Oxford, John Radcliffe Hospital, Oxford, UK
| | - H Sheldon
- Hypoxia and Growth Factor Group, WIMM, Department of Oncology, University of Oxford, Oxford, UK
| | - F Miranda
- Ovarian Cancer Cell Laboratory, WIMM, Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Oxford, UK
| | - L S Mangala
- Department of Gynecologic Oncology, University of Texas, Austin, TX, USA
- Center for RNA Interference and Non-Coding RNA, MD Anderson Cancer Center, Department of Gynecologic Oncology, University of Texas, Austin, TX, USA
| | - S Pradeep
- Department of Gynecologic Oncology, University of Texas, Austin, TX, USA
| | - G Lopez-Berestein
- Center for RNA Interference and Non-Coding RNA, MD Anderson Cancer Center, Department of Gynecologic Oncology, University of Texas, Austin, TX, USA
- Department of Cancer Biology, University of Texas, Austin, TX, USA
| | - A Ahmed
- Ovarian Cancer Cell Laboratory, WIMM, Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Oxford, UK
| | - B Fielding
- Department of Nutritional Sciences, University of Surrey, Surrey, UK
| | - A K Sood
- Department of Gynecologic Oncology, University of Texas, Austin, TX, USA
- Center for RNA Interference and Non-Coding RNA, MD Anderson Cancer Center, Department of Gynecologic Oncology, University of Texas, Austin, TX, USA
- Department of Cancer Biology, University of Texas, Austin, TX, USA
| | - A L Harris
- Hypoxia and Growth Factor Group, WIMM, Department of Oncology, University of Oxford, Oxford, UK
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29
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Lord S, Liu D, Cheng WC, Haider S, Gaude E, Teoh E, Patel N, Metcalf T, McGowan D, Roxanis I, Qifeng Z, Roy P, Gleeson F, Thompson A, Pollak M, Wakelam M, Buffa F, Frezza C, Fenwick J, Harris A. Metformin increases 18F-FDG flux and inhibits fatty acid oxidation at clinical doses in breast cancer: Results of a phase 0 clinical trial. Eur J Surg Oncol 2016. [DOI: 10.1016/j.ejso.2016.07.060] [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: 10/20/2022] Open
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30
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Chen L, Zeng X, Kleibeuker E, Buffa F, Barberis A, Leek RD, Roxanis I, Zhang W, Worth A, Beech JS, Harris AL, Cai S. Paracrine effect of GTP cyclohydrolase and angiopoietin-1 interaction in stromal fibroblasts on tumor Tie2 activation and breast cancer growth. Oncotarget 2016; 7:9353-67. [PMID: 26814432 PMCID: PMC4891045 DOI: 10.18632/oncotarget.6981] [Citation(s) in RCA: 10] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 12/26/2015] [Indexed: 12/19/2022] Open
Abstract
Cancer-associated fibroblasts (CAFs) play a key role in promoting tumor growth, acting through complex paracrine regulation. GTP cyclohydrolase (GTPCH) expression for tetrahydrobiopterin synthesis in tumor stroma is implicated in angiogenesis and tumor development. However, the clinical significance of GTPCH expression in breast cancer is still elusive and how GTPCH regulates stromal fibroblast and tumor cell communication remains unknown. We found that GTPCH was upregulated in breast CAFs and epithelia, and high GTPCH RNA was significantly correlated with larger high grade tumors and worse prognosis. In cocultures, GTPCH expressing fibroblasts stimulated breast cancer cell proliferation and motility, cancer cell Tie2 phosphorylation and consequent downstream pathway activation. GTPCH interacted with Ang-1 in stromal fibroblasts and enhanced Ang-1 expression and function, which in turn phosphorylated tumor Tie2 and induced cell proliferation. In coimplantation xenografts, GTPCH in fibroblasts enhanced tumor growth, upregulating Ang-1 and alpha-smooth muscle actin mainly in fibroblast-like cells. GTPCH inhibition resulted in the attenuation of tumor growth and angiogenesis. GTPCH/Ang-1 interaction in stromal fibroblasts and activation of Tie2 on breast tumor cells could play an important role in supporting breast cancer growth. GTPCH may be an important mechanism of paracrine tumor growth and hence a target for therapy in breast cancer.
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Affiliation(s)
- Liye Chen
- Molecular Oncology Laboratories, Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Xin Zeng
- Molecular Oncology Laboratories, Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
- Current address: Xiamen Institute for Diabetes Research, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Esther Kleibeuker
- Molecular Oncology Laboratories, Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Francesca Buffa
- Molecular Oncology Laboratories, Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Alessandro Barberis
- Molecular Oncology Laboratories, Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Russell D. Leek
- Molecular Oncology Laboratories, Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Ioannis Roxanis
- Department of Cellular Pathology, Oxford University Hospitals and NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Wei Zhang
- Nuffield Department of Obstetrics and Gynaecology, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Andrew Worth
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - John S. Beech
- Gray Institute for Radiation Oncology and Biology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Adrian L. Harris
- Molecular Oncology Laboratories, Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Shijie Cai
- Molecular Oncology Laboratories, Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
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31
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Zois CE, Haider S, Wigfield S, Giatromanolaki A, Sivridis E, Morten K, Roxanis I, Leek R, Buffa F, Koukourakis M, Harris AL. Abstract 2903: Differential regulation of LC3 A and B, GABARAPL 1 and 2 autophagy genes by micro-environmental stress and role in breast cancer survival. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-2903] [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
The microtubule-associated protein light chain 3 MAP1LC3 (LC3) and GABARAPL1 and 2 are the major proteins to monitor autophagy. Here, we analyzed the role of both MAP1LC3, GABARAPL1 and 2 in breast cancer cells and primary human breast cancer. HER2 amplified (BT474, SKBR3, MDA-MB-453), ER positive (MCF7, T47D) and triple negative (MDAMB231) breast cancer cell lines were studied in response to hypoxia, in high [25mM] and low glucose [5mM] treatment. Low glucose increased the basal levels for LC3A-II, LC3B-II and GABARAPL2-II in BT474, MCF7 and MDAMB231 cell lines. SKBR3 cell line had the lowest autophagic protein levels for LC3B-II, and Gabarapl2-II and was the most resistance to the autophagy inhibition mediated using siRNAs to all theseIn hypoxia both LC3B (up to 8 fold) and GABARAPL1 (up to 12 fold) mRNA expression were induced in all cell lines (p<0.001). MAP1LC3A knockdown significantly decrease cell proliferation in BT474, MCF7 and MDAMB231 while GABARAPL2 knockdown additionally decreased baseline cell proliferation in T47D and SKBR3 breast cancer cells (p<0.05, n = 3). Moreover, using the Seahorse, decreased MAP1LC3A and GABARAPL2 expression by siRNA led to cellular bioenergetic changes including increased basal oxygen consumption of the MCF7.
Co-expression analysis of autophagic genes define distinctive clusters of MAP1LC3, GABARAPL 1 and 2 with the hypoxic signature in breast cancer subtypes using the METABRIC series.
The expression levels of the MAP1LC3 and GABARAPL1 and 2 among the breast cancer subtypes and normal tissue showed significant suppession of all of them in cancer compared to normal breast tissue. In conclusion, all the pathways were suppressed at RNA level in cancer compared to normal, baseline levels were not associated with core classification of breast cancer types. These latter data were confirmed in a breast cancer cell line panel, which showed a marked variation in inducibility by environemntal stress and role in survival under low glucose and hypoxia. Thus analysis of induced gene expression in response to stress may be important, or heterogeneity in selection of tumors for anti-autophagy therapy.
Citation Format: Christos E. Zois, Syed Haider, Simon Wigfield, Alexandra Giatromanolaki, Efthimios Sivridis, Karl Morten, Ioannis Roxanis, Russell Leek, Francesca Buffa, Michael Koukourakis, Adrian L. Harris. Differential regulation of LC3 A and B, GABARAPL 1 and 2 autophagy genes by micro-environmental stress and role in breast cancer survival. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2903. doi:10.1158/1538-7445.AM2015-2903
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Affiliation(s)
| | - Syed Haider
- 1University of Oxford, Oxford, United Kingdom
| | | | | | - Efthimios Sivridis
- 2Democritus University of Thrace Medical School, Alexandroupolis, Greece
| | - Karl Morten
- 1University of Oxford, Oxford, United Kingdom
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32
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Leung WY, Roxanis I, Sheldon H, Buffa FM, Li JL, Harris AL, Kong A. Combining lapatinib and pertuzumab to overcome lapatinib resistance due to NRG1-mediated signalling in HER2-amplified breast cancer. Oncotarget 2015; 6:5678-94. [PMID: 25691057 PMCID: PMC4467394 DOI: 10.18632/oncotarget.3296] [Citation(s) in RCA: 27] [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: 11/13/2014] [Accepted: 01/02/2015] [Indexed: 12/24/2022] Open
Abstract
Acquired resistance to lapatinib, an inhibitor of EGFR and HER2 kinases, is common. We found that reactivation of EGFR, HER2 and HER3 occurred within 24 hours of lapatinib treatment after their initial dephosphorylation. This was associated with increased expression of NRG1 in cells treated with lapatinib. Exogenous NRG1 partially rescued breast cancer cells from growth inhibition by lapatinib. In addition, both parental and lapatinib-resistant breast cancer cells were sensitive to SGP1, which inhibits binding of NRG1 and other HER3 ligands. Addition of pertuzumab to lapatinib further inhibited NRG1-induced signalling, which was not fully inhibited by either drug alone. In animal model, a combination of pertuzumab to lapatinib induced a greater tumor regression than either lapatinib or pertuzumab monotherapy. This novel combination treatment may provide a promising strategy in clinical HER2-targeted therapy and may inhibit a subset of lapatinib-resistant breast cancer, although the group of patients that will respond to this therapy requires further stratification.
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MESH Headings
- Animals
- Antibodies, Monoclonal, Humanized/administration & dosage
- Antibodies, Monoclonal, Humanized/pharmacology
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Breast Neoplasms/drug therapy
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Drug Resistance, Neoplasm
- Drug Synergism
- Female
- Humans
- Lapatinib
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Neuregulin-1/metabolism
- Quinazolines/administration & dosage
- Quinazolines/pharmacology
- Random Allocation
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/metabolism
- Signal Transduction
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Wing-yin Leung
- Department of Oncology, Molecular Oncology Laboratories, The Weatherall Institute of Molecular Medicine, University of Oxford, United Kingdom
| | - Ioannis Roxanis
- Department of Cellular Pathology, Oxford University Hospitals and Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Helen Sheldon
- Department of Oncology, Molecular Oncology Laboratories, The Weatherall Institute of Molecular Medicine, University of Oxford, United Kingdom
| | - Francesca M. Buffa
- Department of Oncology, Molecular Oncology Laboratories, The Weatherall Institute of Molecular Medicine, University of Oxford, United Kingdom
| | - Ji-Liang Li
- Department of Oncology, Molecular Oncology Laboratories, The Weatherall Institute of Molecular Medicine, University of Oxford, United Kingdom
| | - Adrian L. Harris
- Department of Oncology, Molecular Oncology Laboratories, The Weatherall Institute of Molecular Medicine, University of Oxford, United Kingdom
| | - Anthony Kong
- Department of Oncology, Molecular Oncology Laboratories, The Weatherall Institute of Molecular Medicine, University of Oxford, United Kingdom
- New address: School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom
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33
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Feldinger K, Generali D, Kramer-Marek G, Gijsen M, Ng TB, Wong JH, Strina C, Cappelletti M, Andreis D, Li JL, Bridges E, Turley H, Leek R, Roxanis I, Capala J, Murphy G, Harris AL, Kong A. ADAM10 mediates trastuzumab resistance and is correlated with survival in HER2 positive breast cancer. Oncotarget 2014; 5:6633-46. [PMID: 24952873 PMCID: PMC4196152 DOI: 10.18632/oncotarget.1955] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [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: 03/08/2014] [Accepted: 05/07/2014] [Indexed: 11/29/2022] Open
Abstract
Trastuzumab prolongs survival in HER2 positive breast cancer patients. However, resistance remains a challenge. We have previously shown that ADAM17 plays a key role in maintaining HER2 phosphorylation during trastuzumab treatment. Beside ADAM17, ADAM10 is the other well characterized ADAM protease responsible for HER ligand shedding. Therefore, we studied the role of ADAM10 in relation to trastuzumab treatment and resistance in HER2 positive breast cancer. ADAM10 expression was assessed in HER2 positive breast cancer cell lines and xenograft mice treated with trastuzumab. Trastuzumab treatment increased ADAM10 levels in HER2 positive breast cancer cells (p ≤ 0.001 in BT474; p ≤ 0.01 in SKBR3) and in vivo (p ≤ 0.0001) compared to control, correlating with a decrease in PKB phosphorylation. ADAM10 inhibition or knockdown enhanced trastuzumab response in naïve and trastuzumab resistant breast cancer cells. Trastuzumab monotherapy upregulated ADAM10 (p ≤ 0.05); and higher pre-treatment ADAM10 levels correlated with decreased clinical response (p ≤ 0.05) at day 21 in HER2 positive breast cancer patients undergoing a trastuzumab treatment window study. Higher ADAM10 levels correlated with poorer relapse-free survival (p ≤ 0.01) in a cohort of HER2 positive breast cancer patients. Our studies implicate a role of ADAM10 in acquired resistance to trastuzumab and establish ADAM10 as a therapeutic target and a potential biomarker for HER2 positive breast cancer patients.
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Affiliation(s)
- Katharina Feldinger
- Human Epidermal Growth Factor Group, Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Daniele Generali
- U.O. Multidisciplinare di Patologia Mammaria, U.S Terapia Molecolare e Farmacogenomica, A.O. Instituti Ospitalieri di Cremona, Cremona, Italy
| | - Gabriela Kramer-Marek
- National Institutes of Health, Radiation Oncology Branch, Bethesda MD, US
- Institute of Cancer Research, Division of Radiotherapy and Imaging, Belmont, Sutton, Surrey, UK (New address)
| | - Merel Gijsen
- Human Epidermal Growth Factor Group, Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Tzi Bun Ng
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Tai Po Road, Sha Tin, Hong Kong
| | - Jack Ho Wong
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Tai Po Road, Sha Tin, Hong Kong
| | - Carla Strina
- U.O. Multidisciplinare di Patologia Mammaria, U.S Terapia Molecolare e Farmacogenomica, A.O. Instituti Ospitalieri di Cremona, Cremona, Italy
| | - Mariarosa Cappelletti
- U.O. Multidisciplinare di Patologia Mammaria, U.S Terapia Molecolare e Farmacogenomica, A.O. Instituti Ospitalieri di Cremona, Cremona, Italy
| | - Daniele Andreis
- U.O. Multidisciplinare di Patologia Mammaria, U.S Terapia Molecolare e Farmacogenomica, A.O. Instituti Ospitalieri di Cremona, Cremona, Italy
| | - Ji-Liang Li
- Growth Factor Group, Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Esther Bridges
- Growth Factor Group, Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Helen Turley
- Growth Factor Group, Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Russell Leek
- Growth Factor Group, Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Ioannis Roxanis
- Department of Cellular Pathology, Oxford University Hospitals and Oxford Biomedical Research Centre, Oxford, UK
| | - Jacek Capala
- National Institutes of Health, Radiation Oncology Branch, Bethesda MD, US
| | - Gillian Murphy
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Adrian L. Harris
- Growth Factor Group, Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Anthony Kong
- Human Epidermal Growth Factor Group, Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
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Canonici A, Gijsen M, Mullooly M, Bennett R, Bouguern N, Pedersen K, O'Brien NA, Roxanis I, Li JL, Bridge E, Finn R, Siamon D, McGowan P, Duffy MJ, O'Donovan N, Crown J, Kong A. Neratinib overcomes trastuzumab resistance in HER2 amplified breast cancer. Oncotarget 2014; 4:1592-605. [PMID: 24009064 PMCID: PMC3858548 DOI: 10.18632/oncotarget.1148] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [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] [Indexed: 01/08/2023] Open
Abstract
Trastuzumab has been shown to improve the survival outcomes of HER2 positive breast cancer patients. However, a significant proportion of HER2-positive patients are either inherently resistant or develop resistance to trastuzumab. We assessed the effects of neratinib, an irreversible panHER inhibitor, in a panel of 36 breast cancer cell lines. We further assessed its effects with or without trastuzumab in several sensitive and resistant breast cancer cells as well as a BT474 xenograft model. We confirmed that neratinib was significantly more active in HER2-amplified than HER2 non-amplified cell lines. Neratinib decreased the activation of the 4 HER receptors and inhibited downstream pathways. However, HER3 and Akt were reactivated at 24 hours, which was prevented by the combination of trastuzumab and neratinib. Neratinib also decreased pHER2 and pHER3 in acquired trastuzumab resistant cells. Neratinib in combination with trastuzumab had a greater growth inhibitory effect than either drug alone in 4 HER2 positive cell lines. Furthermore, trastuzumab in combination with neratinib was growth inhibitory in SKBR3 and BT474 cells which had acquired resistance to trastuzumab as well as in a BT474 xenograft model. Innately trastuzumab resistant cell lines showed sensitivity to neratinib, but the combination did not enhance response compared to neratinib alone. Levels of HER2 and phospho-HER2 showed a direct correlation with sensitivity to neratinib. Our data indicate that neratinib is an effective anti-HER2 therapy and counteracted both innate and acquired trastuzumab resistance in HER2 positive breast cancer. Our results suggest that combined treatment with trastuzumab and neratinib is likely to be more effective than either treatment alone for both trastuzumab-sensitive breast cancer as well as HER2-positive tumors with acquired resistance to trastuzumab.
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Affiliation(s)
- Alexandra Canonici
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, Ireland
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Roxanis I, Makaroni S, Ginieri-Coccossis M, Triantafyllou A, Typaldou M. Quality of life among Greek smokers and nonsmokers. A study in local community workers in Athens suburbia. Tob Induc Dis 2014. [PMCID: PMC4101572 DOI: 10.1186/1617-9625-12-s1-a33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Ioannis Roxanis
- First Department of Psychiatry, Eginition Hospital, Athens University Medical School, Athens, 11528, Greece
| | - Sotiria Makaroni
- Center for the Prevention of Addictions and Psychosocial Health Promotion "PRONOI", Athens, 14500, Greece
| | - Maria Ginieri-Coccossis
- First Department of Psychiatry, Eginition Hospital, Athens University Medical School, Athens, 11528, Greece
| | - Aggeliki Triantafyllou
- Department of Biological Chemistry, Athens University School of Medicine, Athens, 10679, Greece
| | - Maria Typaldou
- First Department of Psychiatry, Eginition Hospital, Athens University Medical School, Athens, 11528, Greece
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Behjati S, Tarpey PS, Sheldon H, Martincorena I, Van Loo P, Gundem G, Wedge DC, Ramakrishna M, Cooke SL, Pillay N, Vollan HKM, Papaemmanuil E, Koss H, Bunney TD, Hardy C, Joseph OR, Martin S, Mudie L, Butler A, Teague JW, Patil M, Steers G, Cao Y, Gumbs C, Ingram D, Lazar AJ, Little L, Mahadeshwar H, Protopopov A, Al Sannaa GA, Seth S, Song X, Tang J, Zhang J, Ravi V, Torres KE, Khatri B, Halai D, Roxanis I, Baumhoer D, Tirabosco R, Amary MF, Boshoff C, McDermott U, Katan M, Stratton MR, Futreal PA, Flanagan AM, Harris A, Campbell PJ. Recurrent PTPRB and PLCG1 mutations in angiosarcoma. Nat Genet 2014; 46:376-379. [PMID: 24633157 PMCID: PMC4032873 DOI: 10.1038/ng.2921] [Citation(s) in RCA: 224] [Impact Index Per Article: 22.4] [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: 12/02/2013] [Accepted: 02/18/2014] [Indexed: 12/14/2022]
Abstract
Angiosarcoma is an aggressive malignancy that arises spontaneously or secondarily to ionizing radiation or chronic lymphoedema. Previous work has identified aberrant angiogenesis, including occasional somatic mutations in angiogenesis signaling genes, as a key driver of angiosarcoma. Here we employed whole-genome, whole-exome and targeted sequencing to study the somatic changes underpinning primary and secondary angiosarcoma. We identified recurrent mutations in two genes, PTPRB and PLCG1, which are intimately linked to angiogenesis. The endothelial phosphatase PTPRB, a negative regulator of vascular growth factor tyrosine kinases, harbored predominantly truncating mutations in 10 of 39 tumors (26%). PLCG1, a signal transducer of tyrosine kinases, encoded a recurrent, likely activating p.Arg707Gln missense variant in 3 of 34 cases (9%). Overall, 15 of 39 tumors (38%) harbored at least one driver mutation in angiogenesis signaling genes. Our findings inform and reinforce current therapeutic efforts to target angiogenesis signaling in angiosarcoma.
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Affiliation(s)
- Sam Behjati
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Hills Road, Cambridge, CB2 2XY, UK
| | - Patrick S Tarpey
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Helen Sheldon
- The Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Inigo Martincorena
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Peter Van Loo
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
- Human Genome Laboratory, Department of Human Genetics, VIB and KU Leuven, B-3000 Leuven, Belgium
| | - Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - David C Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Manasa Ramakrishna
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Susanna L Cooke
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Nischalan Pillay
- Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, HA7 4LP, UK
- University College London Cancer Institute, Huntley Street, London, WC1E 6BT, UK
| | - Hans Kristian M Vollan
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
- Department of Oncology, Oslo University Hospital, N-0310 Oslo, Norway
- The K.G. Jebsen Center for Breast Cancer Research, University of Oslo, N-0424 Oslo, Norway
| | - Elli Papaemmanuil
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Hans Koss
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
- Division of Molecular Structure, MRC-National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Tom D Bunney
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Claire Hardy
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Olivia R Joseph
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Sancha Martin
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Laura Mudie
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Adam Butler
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Jon W Teague
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Meena Patil
- Department of Pathology, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Graham Steers
- Department of Pathology, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Yu Cao
- M. D. Anderson Cancer Center, The University of Texas, 1901 East Road, Houston, Texas 77054, USA
| | - Curtis Gumbs
- M. D. Anderson Cancer Center, The University of Texas, 1901 East Road, Houston, Texas 77054, USA
| | - Davis Ingram
- M. D. Anderson Cancer Center, The University of Texas, 1901 East Road, Houston, Texas 77054, USA
| | - Alexander J Lazar
- M. D. Anderson Cancer Center, The University of Texas, 1901 East Road, Houston, Texas 77054, USA
| | - Latasha Little
- M. D. Anderson Cancer Center, The University of Texas, 1901 East Road, Houston, Texas 77054, USA
| | - Harshad Mahadeshwar
- M. D. Anderson Cancer Center, The University of Texas, 1901 East Road, Houston, Texas 77054, USA
| | - Alexei Protopopov
- M. D. Anderson Cancer Center, The University of Texas, 1901 East Road, Houston, Texas 77054, USA
| | - Ghadah A Al Sannaa
- M. D. Anderson Cancer Center, The University of Texas, 1901 East Road, Houston, Texas 77054, USA
| | - Sahil Seth
- M. D. Anderson Cancer Center, The University of Texas, 1901 East Road, Houston, Texas 77054, USA
| | - Xingzhi Song
- M. D. Anderson Cancer Center, The University of Texas, 1901 East Road, Houston, Texas 77054, USA
| | - Jiabin Tang
- M. D. Anderson Cancer Center, The University of Texas, 1901 East Road, Houston, Texas 77054, USA
| | - Jianhua Zhang
- M. D. Anderson Cancer Center, The University of Texas, 1901 East Road, Houston, Texas 77054, USA
| | - Vinod Ravi
- M. D. Anderson Cancer Center, The University of Texas, 1901 East Road, Houston, Texas 77054, USA
| | - Keila E Torres
- M. D. Anderson Cancer Center, The University of Texas, 1901 East Road, Houston, Texas 77054, USA
| | - Bhavisha Khatri
- Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, HA7 4LP, UK
| | - Dina Halai
- Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, HA7 4LP, UK
| | - Ioannis Roxanis
- Department of Pathology, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Daniel Baumhoer
- Bone Tumour Reference Centre, Institute of Pathology, University Hospital Basel, Basel, Institute for Applied Cancer Science, Switzerland
| | - Roberto Tirabosco
- Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, HA7 4LP, UK
| | - M Fernanda Amary
- Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, HA7 4LP, UK
| | - Chris Boshoff
- University College London Cancer Institute, Huntley Street, London, WC1E 6BT, UK
- Pfizer Oncology, 10555 Science Center Dr, La Jolla, CA, 92121
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Michael R Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - P Andrew Futreal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
- M. D. Anderson Cancer Center, The University of Texas, 1901 East Road, Houston, Texas 77054, USA
| | - Adrienne M Flanagan
- Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, HA7 4LP, UK
- University College London Cancer Institute, Huntley Street, London, WC1E 6BT, UK
| | - Adrian Harris
- The Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Department of Pathology, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
- Department of Haematology, Addenbrooke's Hospital, Cambridge, UK
- Department of Haematology, University of Cambridge, Hills Road, Cambridge, CB2 2XY, UK
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Typaldou GM, Konstantakopoulos G, Roxanis I, Nidos A, Vaidakis N, Papadimitriou GN, Wells A. Assessment of the Greek worry-related metacognitions: the Greek version of the Metacognitions Questionnaire (MCQ-30). Psychiatriki 2014; 25:39-47. [PMID: 24739501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The Metacognitions Questionnaire-30 (MCQ-30), developed by Wells and Cartwright-Hatton (2004), represents a multidimensional measure of metacognitive factors considered to be important in the metacognitive model of psychological disorders. The primary aim of the present study was to examine internal consistency, test-retest reliability, convergent validity and the factor structure of the Greek version of the MCQ-30. Moreover, we investigated the associations of the extracted factors with trait anxiety in a Greek sample. The study sample consisted of 547 non-clinical participants (213 males and 334 females). All participants completed the Greek version of the MCQ-30. A subsample of 157 participants also completed the Trait Anxiety subscale of the State -Trait Anxiety Inventory and the Meta-worry subscale of the Anxious Thought Inventory. Thirty participants were retested with the MCQ-30 over a retest interval ranging from three to five weeks. The results confirmed the dimensionality of the MCQ-30 and five factors were extracted consistent with the original English version: (1) positive beliefs about worry, (2) negative beliefs about worry concerning uncontrollability and danger, (3) cognitive confidence, (4) beliefs about the need to control thoughts and the negative consequences of not controlling them, and (5) cognitive selfconsciousness. The MCQ-30 showed high levels of internal consistency and test-retest reliability. The correlation between MCQ-30 total score and AnTI-MW was strong, indicating high level of convergent validity. Moreover, all correlations between MCQ-30 total and subscale scores and STAI-T were significant apart from the correlation between 'cognitive confidence' and trait anxiety. The Greek sample scored higher in the MCQ-30 and its subscales than the English sample in the original study. Women scored significantly higher than men in the overall MCQ-30 and the "uncontrollability and danger" and "need to control thoughts" subscales, whereas no significant differences between genders had been found in the original study. The assumption that the differences in score levels and the gender effect might reflect cultural differences warrants further investigation. The findings of the present study indicate that the Greek version of the MCQ-30 is a comprehensible and psychometrically adequate instrument, as well as a reliable tool in assessing a range of dimensions of worry-related metacognitions in the Greek population. The Greek version of this scale facilitates crosscultural research in metacognition and wider testing of the metacognitive approach to emotional vulnerability, psychological disturbances and mental disorders.
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Affiliation(s)
- G M Typaldou
- First Department of Psychiatry, Athens University Medical School, Eginition Hospital, Αthens, Greece
| | - G Konstantakopoulos
- First Department of Psychiatry, Athens University Medical School, Eginition Hospital, Αthens, Greece
| | - I Roxanis
- First Department of Psychiatry, Athens University Medical School, Eginition Hospital, Αthens, Greece
| | - A Nidos
- First Department of Psychiatry, Athens University Medical School, Eginition Hospital, Αthens, Greece
| | - N Vaidakis
- First Department of Psychiatry, Athens University Medical School, Eginition Hospital, Αthens, Greece
| | - G N Papadimitriou
- First Department of Psychiatry, Athens University Medical School, Eginition Hospital, Αthens, Greece
| | - A Wells
- Department of Clinical Psychology, University of Manchester, UK
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Hashimoto K, Roxanis I, Generali D, Andreis D, Strina C, Cappelletti M, Macaulay V, Kong A. Abstract P6-05-08: Nuclear HER3 localisation plays a role in trastuzumab resistance in HER2-positive breast cancer. Cancer Res 2013. [DOI: 10.1158/0008-5472.sabcs13-p6-05-08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: HER3 is known to locate in the nucleus. Unlike HER4, nuclear HER3 translocation has not been reported to be due to a proteolytic cleavage process by ADAM17 and gamma-secretase. The mechanisms of nuclear HER3 induction and its role in relation to trastuzumab treatment and resistance for HER2-positive breast cancer is unclear.
Methods: Using nuclear fractionation and confocal microscopy, nuclear HER3 localisation was investigated in response to trastuzumab with or without ADAM17 inhibitor and gamma-secretase inhibitor in a panel of HER2 expressing cell lines. We also correlated nuclear HER3 expression by immunohistochemistry with treatment response in patients who underwent window trastuzumab study as well as the survival outcome in a cohort of HER2-positive breast cancer patients using Kaplan–Meier survival curves with Log-rank test.
Results: HER3 ligand heregulin and trastuzumab was found to induce nuclear HER3 translocation in HER2-positive breast cancer cell lines, including SKBR3. Nuclear HER3 was also enriched in acquired trastuzumab resistant SKBR3 cells (SKBr3-TR). Trastuzumab treatment induced several HER3 fragments and HER3100kD was found to be responsible for nuclear HER3 enrichment by fractionation. This fragment was confirmed to be a specific band of HER3 as shown by HER3 knockdown. Nuclear HER3 was reduced by inhibiting either gamma-secretase or ADAM17 inhibitor. Gamma-secretase or ADAM17 inhibitor reduced HER3100kD in both SKBr3 and SKBr3-TR cells.
In HER2-positive breast cancer patients who underwent window trastuzumab study, baseline nuclear HER3 status was not a predictor of response for trastuzumab monotherapy at day 21. However, nuclear HER3 was enriched after trastuzumab treatment in a poor-responder patient. Total HER3 expression level in cytoplasm positively was correlated with poor response to trastuzumab monotherapy in HER2-positive patients (r = 0.67, p = 0.05). There was no statistically significant difference in disease-free survival between positive and negative nuclear HER3 expression but the number of patients was small (n = 87). Further validation to assess nuclear HER3 expression as a prognostic and predictive biomarker in HER2-positive breast cancer patients undergoing trastuzumab treatment will be assessed in randomized tumour samples from FinHER study.
Conclusion: Heregulin and trastuzumab treatment seems to induce nuclear HER3 translocation in some of the HER2 positive breast cancer cells. This may be due to proteolytic cleavage of HER3 as it is reduced by ADAM17 or gamma-secretase inhibitor. Enriched nuclear localisation of HER3 seems to be one possible mechanism of acquired resistance to trastuzumab in HER2-positive breast cancer.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P6-05-08.
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Affiliation(s)
- K Hashimoto
- Epidermal Growth Factor Receptors Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; IGF Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Cellular Pathology, University of Oxford, Oxford, United Kingdom; Instituti Ospitalieri di Cremona, Cremona, Italy
| | - I Roxanis
- Epidermal Growth Factor Receptors Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; IGF Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Cellular Pathology, University of Oxford, Oxford, United Kingdom; Instituti Ospitalieri di Cremona, Cremona, Italy
| | - D Generali
- Epidermal Growth Factor Receptors Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; IGF Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Cellular Pathology, University of Oxford, Oxford, United Kingdom; Instituti Ospitalieri di Cremona, Cremona, Italy
| | - D Andreis
- Epidermal Growth Factor Receptors Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; IGF Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Cellular Pathology, University of Oxford, Oxford, United Kingdom; Instituti Ospitalieri di Cremona, Cremona, Italy
| | - C Strina
- Epidermal Growth Factor Receptors Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; IGF Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Cellular Pathology, University of Oxford, Oxford, United Kingdom; Instituti Ospitalieri di Cremona, Cremona, Italy
| | - M Cappelletti
- Epidermal Growth Factor Receptors Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; IGF Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Cellular Pathology, University of Oxford, Oxford, United Kingdom; Instituti Ospitalieri di Cremona, Cremona, Italy
| | - V Macaulay
- Epidermal Growth Factor Receptors Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; IGF Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Cellular Pathology, University of Oxford, Oxford, United Kingdom; Instituti Ospitalieri di Cremona, Cremona, Italy
| | - A Kong
- Epidermal Growth Factor Receptors Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; IGF Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Cellular Pathology, University of Oxford, Oxford, United Kingdom; Instituti Ospitalieri di Cremona, Cremona, Italy
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Abstract
By contrast with developmental epithelial-mesenchymal transition (EMT), where epithelial characteristics undergo transformation to a mesenchymal-like phenotype in a coordinated fashion, oncogenic EMT occurs in the context of unpredictable genetic changes present in the tumour cells, as well as an abnormal tumour microenvironment. Therefore, a partial form of EMT has been proposed as variably participating in the establishment of invasive phenotype in different types of breast carcinoma, in keeping with their morphological and phenotypical diversity. A complex network of signalling pathways and transcription factors appears responding to various growth factors and cytokines released by stromal and neoplastic elements, endowing the system with abundant regulatory opportunities. The process of EMT is largely elusive in histopathological preparations, prompting doubts regarding its significance in tumour progression. This might be related to the presumed focal occurrence of EMT in the majority of tumours. Detailed topological studies might facilitate understanding of the orchestration of events taking place in vivo. Even more importantly, clinical correlations can be endeavoured and, in parallel with advancement in molecular pathology, a contribution to taxonomy refinement can be envisaged.
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Affiliation(s)
- Ioannis Roxanis
- Department of Cellular Pathology, Oxford University Hospitals and NIHR Biomedical Research Centre Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford OX3 9DU, UK.
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Gijsen M, Tang P, Leung W, Roxanis I, Kong A. 24P PTPN9 is a Negative Regulator of HER3 Phosphorylation and a Prognostic Biomarker in HER2 Positive Breast Cancer. Ann Oncol 2012. [DOI: 10.1016/s0923-7534(19)65669-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Kramer-Marek G, Gijsen M, Kiesewetter DO, Bennett R, Roxanis I, Zielinski R, Kong A, Capala J. Potential of PET to Predict the Response to Trastuzumab Treatment in an ErbB2-Positive Human Xenograft Tumor Model. J Nucl Med 2012; 53:629-37. [DOI: 10.2967/jnumed.111.096685] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Shiono H, Roxanis I, Zhang W, Sims GP, Meager A, Jacobson LW, Liu JL, Matthews I, Wong YL, Bonifati M, Micklem K, Stott DI, Todd JA, Beeson D, Vincent A, Willcox N. Scenarios for autoimmunization of T and B cells in myasthenia gravis. Ann N Y Acad Sci 2003; 998:237-56. [PMID: 14592881 DOI: 10.1196/annals.1254.026] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [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: 11/12/2022]
Abstract
We have studied responses in thymoma patients to interferon-alpha and to the acetylcholine receptor (AChR) in early-onset myasthenia gravis (EOMG), seeking clues to autoimmunizing mechanisms. Our new evidence implicates a two-step process: (step 1) professional antigen-presenting cells and thymic epithelial cells prime AChR-specific T cells; then (step 2) thymic myoid cells subsequently provoke germinal center formation in EOMG. Our unifying hypothesis proposes that AChR epitopes expressed by neoplastic or hyperplastic thymic epithelial cells aberrantly prime helper T cells, whether generated locally or infiltrating from the circulation. These helper T cells then induce antibody responses against linear epitopes that cross-react with whole AChR and attack myoid cells in the EOMG thymus. The resulting antigen-antibody complexes and the recruitment of professional antigen-presenting cells increase the exposure of thymic cells to the infiltrates and provoke local germinal center formation and determinant spreading. Both these and the consequently enhanced heterogeneity and pathogenicity of the autoantibodies should be minimized by early thymectomy.
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Affiliation(s)
- H Shiono
- Neuroscience Group, Weatherall Institute for Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
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Roxanis I, Micklem K, McConville J, Newsom-Davis J, Willcox N. Thymic myoid cells and germinal center formation in myasthenia gravis; possible roles in pathogenesis. J Neuroimmunol 2002; 125:185-97. [PMID: 11960656 DOI: 10.1016/s0165-5728(02)00038-3] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.8] [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: 11/24/2022]
Abstract
In early-onset myasthenia gravis (EOMG), the thymus usually shows medullary lymph node-type infiltrates, rearranged bands of hyperplastic epithelium and focal fenestrations in the intervening laminin borders. This resemblance to autoimmune target organs may reflect autoantigen expression by rare thymic myoid cells, long ago implicated circumstantially as agents provocateurs. In this quantitative study, they were frequently seen at the laminin fenestrations; if so, germinal centers (GC) were significantly commoner nearby, our most EOMG-specific finding (not seen in a distinct MG patient subset). As autoantibodies became detectable, myoid cell involvement apparently progressed. Our unifying hypothesis--that an early autoantibody attack on myoid cells provokes local GC formation--helps to resolve many puzzles.
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Affiliation(s)
- Ioannis Roxanis
- Neurosciences Group, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
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Roxanis I, Micklem K, Willcox N. True epithelial hyperplasia in the thymus of early-onset myasthenia gravis patients: implications for immunopathogenesis. J Neuroimmunol 2001; 112:163-73. [PMID: 11108945 DOI: 10.1016/s0165-5728(00)00415-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [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: 01/25/2023]
Abstract
The early-onset myasthenia gravis (EOMG) thymus shows characteristic medullary epithelial bands (MEB), greatly expanded perivascular infiltrates and fenestrations of the intervening basement membranes. We now compare epithelial expression of epidermal growth factor receptor (EGFR) and many integrins in EOMG and control samples. The main differences are striking/consistent thickening (in MEB) of what is normally a monolayer of perivascular epithelium, with focal protrusion into the infiltrates. This evidently hyperplastic epithelial subpopulation also strongly expresses EGFR and certain integrins. We suggest that its enhanced interactions with the locally increased extracellular matrix protein deposits may play an important role in autosensitization.
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Affiliation(s)
- I Roxanis
- Neurosciences Group, Institute of Molecular Medicine, John Radcliffe Hospital, Headington, OX3 9DS, Oxford, UK
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Watt SM, Butler LH, Tavian M, Bühring HJ, Rappold I, Simmons PJ, Zannettino AC, Buck D, Fuchs A, Doyonnas R, Chan JY, Levesque JP, Peault B, Roxanis I. Functionally defined CD164 epitopes are expressed on CD34(+) cells throughout ontogeny but display distinct distribution patterns in adult hematopoietic and nonhematopoietic tissues. Blood 2000; 95:3113-24. [PMID: 10807777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
Three distinct classes of epitopes on human CD164 have been identified. Two of these, recognized by the monoclonal antibodies 105A5 and 103B2/9E10, are the CD164 class I and class II functionally defined epitopes, which cooperate to regulate adhesion and proliferation of CD34(+) cell subsets. In this article, we demonstrate that these 2 CD164 epitopes are expressed on CD34(+) cells throughout ontogeny, in particular on CD34(+ )cell clusters associated with the ventral floor of the dorsal aorta in the developing embryo and on CD34(+) hematopoietic precursor cells in fetal liver, cord blood, and adult bone marrow. While higher levels of expression of these CD164 epitopes occur on the more primitive AC133(hi)CD34(hi)CD38(lo/-) cell population, they also occur on most cord blood Lin(-)CD34(lo/-)CD38(lo/- )cells, which are potential precursors for the AC133(hi)CD34(hi)CD38(lo/-) subset. In direct contrast to these common patterns of expression on hematopoietic precursor cells, notable differences in expression of the CD164 epitopes were observed in postnatal lymphoid and nonhematopoietic tissues, with the class I and class II CD164 epitopes generally exhibiting differential and often reciprocal cellular distribution patterns. This is particularly striking in the colon, where infiltrating lymphoid cells are CD164 class I-positive but class II-negative, while epithelia are weakly CD164 class II-positive. Similarly, in certain lymphoid tissues, high endothelial venules and basal and subcapsular epithelia are CD164 class II-positive, while lymphoid cells are CD164 class I-positive. It therefore seems highly likely that these CD164 class I and II epitopes will mediate reciprocal homing functions in these tissue types.
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Affiliation(s)
- S M Watt
- MRC Molecular Haematology Unit and from the Neurosciences Group, Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, England.
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Nagvekar N, Moody AM, Moss P, Roxanis I, Curnow J, Beeson D, Pantic N, Newsom-Davis J, Vincent A, Willcox N. A pathogenetic role for the thymoma in myasthenia gravis. Autosensitization of IL-4- producing T cell clones recognizing extracellular acetylcholine receptor epitopes presented by minority class II isotypes. J Clin Invest 1998; 101:2268-77. [PMID: 9593783 PMCID: PMC508815 DOI: 10.1172/jci2068] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.5] [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: 11/17/2022] Open
Abstract
Myasthenia gravis (MG) is caused by helper T cell-dependent autoantibodies against the muscle acetylcholine receptor (AChR). Thymic epithelial tumors (thymomas) occur in 10% of MG patients, but their autoimmunizing potential is unclear. They express mRNAs encoding AChR alpha and epsilon subunits, and might aberrantly select or sensitize developing thymocytes or recirculating peripheral T cells against AChR epitopes. Alternatively, there could be defective self-tolerance induction in the abundant maturing thymocytes that they usually generate. For the first time, we have isolated and characterized AChR-specific T cell clones from two MG thymomas. They recognize extracellular epitopes (alpha75-90 and alpha149-158) which are processed very efficiently from muscle AChR. Both clones express CD4 and CD8alpha, and have a Th-0 cytokine profile, producing IL-4 as well as IFN-gamma. They are restricted to HLA-DP14 and DR52a; expression of these minority isotypes was strong on professional antigen-presenting cells in the donors' tumors, although it is generally weak in the periphery. The two clones' T cell receptor beta chains are different, but their alpha chain sequences are very similar. These resemblances, and the striking contrasts with T cells previously cloned from non-thymoma patients, show that thymomas generate and actively induce specific T cells rather than merely failing to tolerize them against self antigens.
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Affiliation(s)
- N Nagvekar
- Neuroscience Group, Institute for Molecular Medicine, University of Oxford, OX3 9DS, United Kingdom
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Beeson D, Bond AP, Corlett L, Curnow SJ, Hill ME, Jacobson LW, MacLennan C, Meager A, Moody AM, Moss P, Nagvekar N, Newsom-Davis J, Pantic N, Roxanis I, Spack EG, Vincent A, Willcox N. Thymus, thymoma, and specific T cells in myasthenia gravis. Ann N Y Acad Sci 1998; 841:371-87. [PMID: 9668262 DOI: 10.1111/j.1749-6632.1998.tb10950.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- D Beeson
- Institute of Molecular Medicine, University of Oxford, United Kingdom
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