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Jasani B, Taniere P, Schildhaus HU, Blighe K, Parry S, Wilkinson D, Atkey N, Clare-Antony S, McCabe C, Quinn C, Dodson A. Global Ring Study to Investigate the Comparability of Total Assay Performance of Commercial Claudin 18 Antibodies for Evaluation in Gastric Cancer. J Transl Med 2024; 104:100284. [PMID: 37949357 DOI: 10.1016/j.labinv.2023.100284] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/23/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023] Open
Abstract
Claudin 18.2 (CLDN18.2), the dominant isoform of CLDN18 in gastric tissues, is a highly specific tight junction protein of the gastric mucosa with variably retained expressions in gastric and gastroesophageal junction cancers. Additionally, CLDN18.2-targeted treatment with zolbetuximab, in combination with chemotherapy, has recently been assessed in 2 phase-III studies of patients with HER2-negative, locally advanced, unresectable, or metastatic gastric or gastroesophageal junction adenocarcinoma. These trials used the investigational VENTANA CLDN18 (43-14A) RxDx immunohistochemistry (IHC) assay on the Ventana BenchMark platform to identify patients eligible for CLDN18.2-targeted treatment. We report the findings of a global ring study evaluating the analytical comparability of concordance of the results of 3 CLDN18 antibodies (Ventana, LSBio, and Novus) stained on 3 IHC-staining platforms (Ventana, Dako, and Leica). A tissue microarray (TMA), comprising 15 gastric cancer cases, was stained by 27 laboratories across 11 countries. Each laboratory stained the TMAs using at least 2 of the 3 evaluated CLDN18 antibodies. Stained TMAs were assessed and scored using an agreed IHC-scoring algorithm, and the results were collated for statistical analysis. The data confirmed a high level of concordance for the VENTANA CLDN18 (43-14A; Ventana platform only) and LSBio antibodies on both the Dako and Leica platforms, with accuracy, precision, sensitivity, and specificity rates all reaching a minimum acceptable ≥85% threshold and good-to-excellent levels of concordance as measured by Cohen's kappa coefficient. The Novus antibody showed the highest level of variability against the reference central laboratory results for the same antibody/platform combinations. It also failed to meet the threshold for accuracy and sensitivity when used on either the Dako or Leica platform. These results demonstrated the reliability of IHC testing for CLDN18 expression in gastric tumor samples when using commercially available platforms with an appropriate methodology and primary antibody selection.
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Affiliation(s)
- Bharat Jasani
- Discovery Life Sciences (DLS) Biomarker Services GmbH, Kassel, Germany
| | - Philippe Taniere
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | | | - Kevin Blighe
- Clinical Bioinformatics Research Ltd, London, UK
| | - Suzanne Parry
- UK National External Quality Assessment Scheme for Immunocytochemistry & In-Situ Hybridisation, London, UK
| | - Dawn Wilkinson
- UK National External Quality Assessment Scheme for Immunocytochemistry & In-Situ Hybridisation, London, UK
| | | | | | | | | | - Andrew Dodson
- UK National External Quality Assessment Scheme for Immunocytochemistry & In-Situ Hybridisation, London, UK
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Baranes K, Hastings N, Rahman S, Poulin N, Tavares JM, Kuan W, Syed N, Kunz M, Blighe K, Belgard TG, Kotter MRN. Transcription factor combinations that define human astrocyte identity encode significant variation of maturity and function. Glia 2023; 71:1870-1889. [PMID: 37029764 PMCID: PMC10952910 DOI: 10.1002/glia.24372] [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: 08/16/2021] [Revised: 03/13/2023] [Accepted: 03/20/2023] [Indexed: 04/09/2023]
Abstract
Increasing evidence indicates that cellular identity can be reduced to the distinct gene regulatory networks controlled by transcription factors (TFs). However, redundancy exists in these states as different combinations of TFs can induce broadly similar cell types. We previously demonstrated that by overcoming gene silencing, it is possible to deterministically reprogram human pluripotent stem cells directly into cell types of various lineages. In the present study we leverage the consistency and precision of our approach to explore four different TF combinations encoding astrocyte identity, based on previously published reports. Analysis of the resulting induced astrocytes (iAs) demonstrated that all four cassettes generate cells with the typical morphology of in vitro astrocytes, which expressed astrocyte-specific markers. The transcriptional profiles of all four iAs clustered tightly together and displayed similarities with mature human astrocytes, although maturity levels differed between cells. Importantly, we found that the TF cassettes induced iAs with distinct differences with regards to their cytokine response and calcium signaling. In vivo transplantation of selected iAs into immunocompromised rat brains demonstrated long term stability and integration. In conclusion, all four TF combinations were able to induce stable astrocyte-like cells that were morphologically similar but showed subtle differences with respect to their transcriptome. These subtle differences translated into distinct differences with regards to cell function, that could be related to maturation state and/or regional identity of the resulting cells. This insight opens an opportunity to precision-engineer cells to meet functional requirements, for example, in the context of therapeutic cell transplantation.
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Affiliation(s)
- Koby Baranes
- Department of Clinical NeurosciencesUniversity of CambridgeCambridgeCB2 0QQUK
- Wellcome‐MRC Cambridge Stem Cell Institute, University of CambridgeCambridgeCB2 0AWUK
| | - Nataly Hastings
- Department of Clinical NeurosciencesUniversity of CambridgeCambridgeCB2 0QQUK
- Wellcome‐MRC Cambridge Stem Cell Institute, University of CambridgeCambridgeCB2 0AWUK
| | - Saifur Rahman
- Department of Clinical NeurosciencesUniversity of CambridgeCambridgeCB2 0QQUK
- Wellcome‐MRC Cambridge Stem Cell Institute, University of CambridgeCambridgeCB2 0AWUK
| | - Noah Poulin
- Department of Clinical NeurosciencesUniversity of CambridgeCambridgeCB2 0QQUK
- Wellcome‐MRC Cambridge Stem Cell Institute, University of CambridgeCambridgeCB2 0AWUK
| | - Joana M. Tavares
- Department of Clinical NeurosciencesUniversity of CambridgeCambridgeCB2 0QQUK
- Wellcome‐MRC Cambridge Stem Cell Institute, University of CambridgeCambridgeCB2 0AWUK
| | - Wei‐Li Kuan
- Department of Clinical NeurosciencesUniversity of CambridgeCambridgeCB2 0QQUK
| | - Najeeb Syed
- The Bioinformatics CROSanfordFlorida32771USA
| | - Meik Kunz
- The Bioinformatics CROSanfordFlorida32771USA
| | | | | | - Mark R. N. Kotter
- Department of Clinical NeurosciencesUniversity of CambridgeCambridgeCB2 0QQUK
- Wellcome‐MRC Cambridge Stem Cell Institute, University of CambridgeCambridgeCB2 0AWUK
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Carlotti E, Murray-Brown W, Blighe K, Caliste M, Astorri E, Sutcliffe N, Tappuni AR, Pitzalis C, Corsiero E, Bombardieri M. High-throughput sequencing of IgH gene in minor salivary glands from Sjögren's syndrome patients reveals dynamic B cell recirculation between ectopic lymphoid structures. Clin Exp Rheumatol 2022; 40:2363-2372. [PMID: 36541240 DOI: 10.55563/clinexprheumatol/82u3cs] [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: 08/01/2022] [Accepted: 10/24/2022] [Indexed: 12/23/2022]
Abstract
OBJECTIVES B cells play a central role in Sjögren's syndrome (SS) whereby autoreactive B-cells populate ectopic germinal centres (GC) in SS salivary glands (SG) and undergo somatic hypermutation (SHM) and class-switch recombination of the immunoglobulin genes. However, the capacity of specific B cell clones to seed ectopic GC in different SG and undergo clonal diversification is unclear. To unravel the dynamics of B cell recirculation among minor SG biopsies, we investigated the immunoglobulin heavy chain (IgH) gene usage and the pattern of SHM using a high-throughput sequencing approach. METHODS We generated ~166,000 reads longer than 350bp and detected 1631 clonotypes across eight samples from four different SS patients, all characterised by the presence of functional ectopic GC as demonstrated by the expression of activation-induced cytidine deaminase. RESULTS A large number of shared clonotypes were observed among paired mSG biopsies from each patient but not across different patients. Lineage tree analysis revealed significant clonal expansion within the mSG with the identification of shared dominant B cell clones suggestive of extensive recirculation across different SG. Several shared clonotypes with high proliferating capacity displayed IgH-VH gene usage common in autoreactive B cells, including VH1-69, which is typical of rheumatoid factor+ B cells representing potential lymphoma precursors. CONCLUSIONS The complex dynamic recirculation of B cells that we observed within ectopic GC responses linked with their ability to independently proliferate, undergo ongoing SHM and Ig class-switching within individual glands may explain the difficulty in achieving consistent eradication of ectopic GCs following B cell depleting agents reported in different studies.
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Affiliation(s)
- Emanuela Carlotti
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London, UK
| | - William Murray-Brown
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London, UK
| | - Kevin Blighe
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London, UK
| | - Mattia Caliste
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London, UK
| | - Elisa Astorri
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London, UK
| | - Nurhan Sutcliffe
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London, UK
| | - Anwar R Tappuni
- Department of Oral Medicine, Queen Mary University of London, UK
| | - Costantino Pitzalis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London, UK
| | - Elisa Corsiero
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London, UK.
| | - Michele Bombardieri
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London, UK.
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Gurudas S, Nugawela M, Prevost AT, Sathish T, Mathur R, Rafferty JM, Blighe K, Rajalakshmi R, Mohan AR, Saravanan J, Majeed A, Mohan V, Owens DR, Robson J, Sivaprasad S. Development and validation of resource-driven risk prediction models for incident chronic kidney disease in type 2 diabetes. Sci Rep 2021; 11:13654. [PMID: 34211028 PMCID: PMC8249456 DOI: 10.1038/s41598-021-93096-w] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 06/14/2021] [Indexed: 12/23/2022] Open
Abstract
Prediction models for population-based screening need, for global usage, to be resource-driven, involving predictors that are affordably resourced. Here, we report the development and validation of three resource-driven risk models to identify people with type 2 diabetes (T2DM) at risk of stage 3 CKD defined by a decline in estimated glomerular filtration rate (eGFR) to below 60 mL/min/1.73m2. The observational study cohort used for model development consisted of data from a primary care dataset of 20,510 multi-ethnic individuals with T2DM from London, UK (2007-2018). Discrimination and calibration of the resulting prediction models developed using cox regression were assessed using the c-statistic and calibration slope, respectively. Models were internally validated using tenfold cross-validation and externally validated on 13,346 primary care individuals from Wales, UK. The simplest model was simplified into a risk score to enable implementation in community-based medicine. The derived full model included demographic, laboratory parameters, medication-use, cardiovascular disease history (CVD) and sight threatening retinopathy status (STDR). Two less resource-intense models were developed by excluding CVD and STDR in the second model and HbA1c and HDL in the third model. All three 5-year risk models had good internal discrimination and calibration (optimism adjusted C-statistics were each 0.85 and calibration slopes 0.999-1.002). In Wales, models achieved excellent discrimination(c-statistics ranged 0.82-0.83). Calibration slopes at 5-years suggested models over-predicted risks, however were successfully updated to accommodate reduced incidence of stage 3 CKD in Wales, which improved their alignment with the observed rates in Wales (E/O ratios near to 1). The risk score demonstrated similar model performance compared to direct evaluation of the cox model. These resource-driven risk prediction models may enable universal screening for Stage 3 CKD to enable targeted early optimisation of risk factors for CKD.
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Affiliation(s)
- Sarega Gurudas
- Institute of Ophthalmology, University College London, London, UK
| | - Manjula Nugawela
- Institute of Ophthalmology, University College London, London, UK
| | - A Toby Prevost
- Nightingale-Saunders Clinical Trials and Epidemiology Unit, King's College London, London, UK
| | | | - Rohini Mathur
- Institute of Applied Data Science, Queen Mary's University London, London, UK
| | | | - Kevin Blighe
- Institute of Ophthalmology, University College London, London, UK
| | | | - Anjana R Mohan
- Madras Diabetes Research Foundation, Dr Mohan's Diabetes Specialities Centre, Chennai, India
| | - Jebarani Saravanan
- Madras Diabetes Research Foundation, Dr Mohan's Diabetes Specialities Centre, Chennai, India
| | - Azeem Majeed
- School of Public, Health Imperial College London, London, UK
| | - Viswanthan Mohan
- Madras Diabetes Research Foundation, Dr Mohan's Diabetes Specialities Centre, Chennai, India
| | | | - John Robson
- Institute of Applied Data Science, Queen Mary's University London, London, UK
| | - Sobha Sivaprasad
- NIHR Moorfields Biomedical Research Centre, University College London, City Road, London, 162EC1V 2PD, UK.
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5
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Robertson LJ, Moore JS, Blighe K, Ng KY, Quinn N, Jennings F, Warnock G, Sharpe P, Clarke M, Maguire K, Rainey S, Price RK, Burns WP, Kowalczyk AM, Awuah A, McNamee SE, Wallace GE, Hunter D, Sager S, Chao Shern C, Nesbit MA, McLaughlin JAD, Moore T. Evaluation of the IgG antibody response to SARS CoV-2 infection and performance of a lateral flow immunoassay: cross-sectional and longitudinal analysis over 11 months. BMJ Open 2021; 11:e048142. [PMID: 34187827 PMCID: PMC8245291 DOI: 10.1136/bmjopen-2020-048142] [Citation(s) in RCA: 9] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/27/2021] [Indexed: 01/14/2023] Open
Abstract
OBJECTIVE To evaluate the dynamics and longevity of the humoral immune response to SARS-CoV-2 infection and assess the performance of professional use of the UK-RTC AbC-19 Rapid Test lateral flow immunoassay (LFIA) for the target condition of SARS-CoV-2 spike protein IgG antibodies. DESIGN Nationwide serological study. SETTING Northern Ireland, UK, May 2020-February 2021. PARTICIPANTS Plasma samples were collected from a diverse cohort of individuals from the general public (n=279), Northern Ireland healthcare workers (n=195), pre-pandemic blood donations and research studies (n=223) and through a convalescent plasma programme (n=183). Plasma donors (n=101) were followed with sequential samples over 11 months post-symptom onset. MAIN OUTCOME MEASURES SARS-CoV-2 antibody levels in plasma samples using Roche Elecsys Anti-SARS-CoV-2 IgG/IgA/IgM, Abbott SARS-CoV-2 IgG and EuroImmun IgG SARS-CoV-2 ELISA immunoassays over time. UK-RTC AbC-19 LFIA sensitivity and specificity, estimated using a three-reference standard system to establish a characterised panel of 330 positive and 488 negative SARS-CoV-2 IgG samples. RESULTS We detected persistence of SARS-CoV-2 IgG antibodies for up to 10 months post-infection, across a minimum of two laboratory immunoassays. On the known positive cohort, the UK-RTC AbC-19 LFIA showed a sensitivity of 97.58% (95.28% to 98.95%) and on known negatives, showed specificity of 99.59% (98.53 % to 99.95%). CONCLUSIONS Through comprehensive analysis of a cohort of pre-pandemic and pandemic individuals, we show detectable levels of IgG antibodies, lasting over 46 weeks when assessed by EuroImmun ELISA, providing insight to antibody levels at later time points post-infection. We show good laboratory validation performance metrics for the AbC-19 rapid test for SARS-CoV-2 spike protein IgG antibody detection in a laboratory-based setting.
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Affiliation(s)
- Louise J Robertson
- Biomedical Sciences Research Institute, Ulster University, Coleraine, UK
| | - Julie S Moore
- Biomedical Sciences Research Institute, Ulster University, Coleraine, UK
| | - Kevin Blighe
- Biomedical Sciences Research Institute, Ulster University, Coleraine, UK
| | - Kok Yew Ng
- Nanotechnology and Integrated Bioengineering Centre, Ulster University-Jordanstown Campus, Newtownabbey, UK
| | - Nigel Quinn
- Clinical Biochemistry Laboratory, Southern Health and Social Care Trust, Portadown, UK
| | - Fergal Jennings
- Clinical Biochemistry Laboratory, Southern Health and Social Care Trust, Portadown, UK
| | - Gary Warnock
- Microbiology Laboratory, Southern Health and Social Care Trust, Portadown, UK
| | - Peter Sharpe
- Clinical Biochemistry Laboratory, Southern Health and Social Care Trust, Portadown, UK
| | - Mark Clarke
- Northern Ireland Blood Transfusion Service, Belfast City Hospital, Belfast, UK
| | - Kathryn Maguire
- Northern Ireland Blood Transfusion Service, Belfast City Hospital, Belfast, UK
| | - Sharon Rainey
- Northern Ireland Blood Transfusion Service, Belfast City Hospital, Belfast, UK
| | - Ruth K Price
- Biomedical Sciences Research Institute, Ulster University, Coleraine, UK
| | - William P Burns
- Nanotechnology and Integrated Bioengineering Centre, Ulster University-Jordanstown Campus, Newtownabbey, UK
| | - Amanda M Kowalczyk
- Biomedical Sciences Research Institute, Ulster University, Coleraine, UK
| | - Agnes Awuah
- Biomedical Sciences Research Institute, Ulster University, Coleraine, UK
| | - Sara E McNamee
- Nanotechnology and Integrated Bioengineering Centre, Ulster University-Jordanstown Campus, Newtownabbey, UK
| | - Gayle E Wallace
- Royal Victoria Hospital, Belfast Health and Social Care Trust, Belfast, UK
| | - David Hunter
- Royal Victoria Hospital, Belfast Health and Social Care Trust, Belfast, UK
| | - Steve Sager
- Biomedical Sciences Research Institute, Ulster University, Coleraine, UK
| | | | - M Andrew Nesbit
- Biomedical Sciences Research Institute, Ulster University, Coleraine, UK
| | - James A D McLaughlin
- Nanotechnology and Integrated Bioengineering Centre, Ulster University-Jordanstown Campus, Newtownabbey, UK
| | - Tara Moore
- Biomedical Sciences Research Institute, Ulster University, Coleraine, UK
- R&D, Avellino Labs USA, Menlo Park, California, USA
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Opzoomer JW, Timms JA, Blighe K, Mourikis TP, Chapuis N, Bekoe R, Kareemaghay S, Nocerino P, Apollonio B, Ramsay AG, Tavassoli M, Harrison C, Ciccarelli F, Parker P, Fontenay M, Barber PR, Arnold JN, Kordasti S. ImmunoCluster provides a computational framework for the nonspecialist to profile high-dimensional cytometry data. eLife 2021; 10:e62915. [PMID: 33929322 PMCID: PMC8112868 DOI: 10.7554/elife.62915] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 09/08/2020] [Accepted: 04/22/2021] [Indexed: 01/04/2023] Open
Abstract
High-dimensional cytometry is an innovative tool for immune monitoring in health and disease, and it has provided novel insight into the underlying biology as well as biomarkers for a variety of diseases. However, the analysis of large multiparametric datasets usually requires specialist computational knowledge. Here, we describe ImmunoCluster (https://github.com/kordastilab/ImmunoCluster), an R package for immune profiling cellular heterogeneity in high-dimensional liquid and imaging mass cytometry, and flow cytometry data, designed to facilitate computational analysis by a nonspecialist. The analysis framework implemented within ImmunoCluster is readily scalable to millions of cells and provides a variety of visualization and analytical approaches, as well as a rich array of plotting tools that can be tailored to users' needs. The protocol consists of three core computational stages: (1) data import and quality control; (2) dimensionality reduction and unsupervised clustering; and (3) annotation and differential testing, all contained within an R-based open-source framework.
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Affiliation(s)
- James W Opzoomer
- School of Cancer and Pharmaceutical Sciences, King’s College London, Faculty of Life Sciences and Medicine, Guy’s HospitalLondonUnited Kingdom
| | - Jessica A Timms
- School of Cancer and Pharmaceutical Sciences, King’s College London, Faculty of Life Sciences and Medicine, Guy’s HospitalLondonUnited Kingdom
| | - Kevin Blighe
- School of Cancer and Pharmaceutical Sciences, King’s College London, Faculty of Life Sciences and Medicine, Guy’s HospitalLondonUnited Kingdom
| | - Thanos P Mourikis
- School of Cancer and Pharmaceutical Sciences, King’s College London, Faculty of Life Sciences and Medicine, Guy’s HospitalLondonUnited Kingdom
| | - Nicolas Chapuis
- Institut Cochin, Institut National de la Santé et de la Recherche Médicale U1016, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, Université Paris DescartesParisFrance
| | - Richard Bekoe
- UCL Cancer Institute, Paul O'Gorman Building, University College LondonLondonUnited Kingdom
| | - Sedigeh Kareemaghay
- Centre for Host Microbiome Interaction, FoDOCS, King’s College, Guy’s HospitalLondonUnited Kingdom
| | - Paola Nocerino
- School of Cancer and Pharmaceutical Sciences, King’s College London, Faculty of Life Sciences and Medicine, Guy’s HospitalLondonUnited Kingdom
| | - Benedetta Apollonio
- School of Cancer and Pharmaceutical Sciences, King’s College London, Faculty of Life Sciences and Medicine, Guy’s HospitalLondonUnited Kingdom
| | - Alan G Ramsay
- School of Cancer and Pharmaceutical Sciences, King’s College London, Faculty of Life Sciences and Medicine, Guy’s HospitalLondonUnited Kingdom
| | - Mahvash Tavassoli
- Centre for Host Microbiome Interaction, FoDOCS, King’s College, Guy’s HospitalLondonUnited Kingdom
| | - Claire Harrison
- School of Cancer and Pharmaceutical Sciences, King’s College London, Faculty of Life Sciences and Medicine, Guy’s HospitalLondonUnited Kingdom
- Haematology Department, Guy’s HospitalLondonUnited Kingdom
| | - Francesca Ciccarelli
- School of Cancer and Pharmaceutical Sciences, King’s College London, Faculty of Life Sciences and Medicine, Guy’s HospitalLondonUnited Kingdom
- Cancer Systems Biology Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Peter Parker
- School of Cancer and Pharmaceutical Sciences, King’s College London, Faculty of Life Sciences and Medicine, Guy’s HospitalLondonUnited Kingdom
- Francis Crick InstituteLondonUnited Kingdom
| | - Michaela Fontenay
- Institut Cochin, Institut National de la Santé et de la Recherche Médicale U1016, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, Université Paris DescartesParisFrance
| | - Paul R Barber
- School of Cancer and Pharmaceutical Sciences, King’s College London, Faculty of Life Sciences and Medicine, Guy’s HospitalLondonUnited Kingdom
- UCL Cancer Institute, Paul O'Gorman Building, University College LondonLondonUnited Kingdom
| | - James N Arnold
- School of Cancer and Pharmaceutical Sciences, King’s College London, Faculty of Life Sciences and Medicine, Guy’s HospitalLondonUnited Kingdom
| | - Shahram Kordasti
- School of Cancer and Pharmaceutical Sciences, King’s College London, Faculty of Life Sciences and Medicine, Guy’s HospitalLondonUnited Kingdom
- Haematology Department, Guy’s HospitalLondonUnited Kingdom
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Saavedra-García P, Roman-Trufero M, Al-Sadah HA, Blighe K, López-Jiménez E, Christoforou M, Penfold L, Capece D, Xiong X, Miao Y, Parzych K, Caputo VS, Siskos AP, Encheva V, Liu Z, Thiel D, Kaiser MF, Piazza P, Chaidos A, Karadimitris A, Franzoso G, Snijders AP, Keun HC, Oyarzún DA, Barahona M, Auner HW. Systems level profiling of chemotherapy-induced stress resolution in cancer cells reveals druggable trade-offs. Proc Natl Acad Sci U S A 2021; 118:e2018229118. [PMID: 33883278 PMCID: PMC8092411 DOI: 10.1073/pnas.2018229118] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cancer cells can survive chemotherapy-induced stress, but how they recover from it is not known. Using a temporal multiomics approach, we delineate the global mechanisms of proteotoxic stress resolution in multiple myeloma cells recovering from proteasome inhibition. Our observations define layered and protracted programs for stress resolution that encompass extensive changes across the transcriptome, proteome, and metabolome. Cellular recovery from proteasome inhibition involved protracted and dynamic changes of glucose and lipid metabolism and suppression of mitochondrial function. We demonstrate that recovering cells are more vulnerable to specific insults than acutely stressed cells and identify the general control nonderepressable 2 (GCN2)-driven cellular response to amino acid scarcity as a key recovery-associated vulnerability. Using a transcriptome analysis pipeline, we further show that GCN2 is also a stress-independent bona fide target in transcriptional signature-defined subsets of solid cancers that share molecular characteristics. Thus, identifying cellular trade-offs tied to the resolution of chemotherapy-induced stress in tumor cells may reveal new therapeutic targets and routes for cancer therapy optimization.
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Affiliation(s)
- Paula Saavedra-García
- Cancer Cell Protein Metabolism, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
| | - Monica Roman-Trufero
- Cancer Cell Protein Metabolism, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
| | - Hibah A Al-Sadah
- Cancer Cell Protein Metabolism, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
| | - Kevin Blighe
- Clinical Bioinformatics Research, London W1B 3HH, United Kingdom
| | - Elena López-Jiménez
- Cancer Cell Protein Metabolism, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
| | - Marilena Christoforou
- Cancer Cell Protein Metabolism, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
| | - Lucy Penfold
- Cancer Cell Protein Metabolism, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
- Cellular Stress, MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom
| | - Daria Capece
- Centre for Molecular Immunology and Inflammation, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
| | - Xiaobei Xiong
- Cancer Cell Protein Metabolism, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
| | - Yirun Miao
- Cancer Cell Protein Metabolism, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
| | - Katarzyna Parzych
- Cancer Cell Protein Metabolism, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
| | - Valentina S Caputo
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
| | - Alexandros P Siskos
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, United Kingdom
| | - Vesela Encheva
- Proteomics Platform, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Zijing Liu
- Department of Mathematics, Imperial College London, London SW7 2AZ, United Kingdom
- Department of Brain Sciences, Imperial College London, London W12 0NN, United Kingdom
- UK Dementia Research Institute at Imperial College, London W12 0NN, United Kingdom
| | - Denise Thiel
- Department of Mathematics, Imperial College London, London SW7 2AZ, United Kingdom
| | - Martin F Kaiser
- Myeloma Molecular Therapy, The Institute of Cancer Research, Sutton SW7 3RP, United Kingdom
| | - Paolo Piazza
- Imperial BRC Genomics Facility, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, United Kingdom
| | - Aristeidis Chaidos
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
| | - Anastasios Karadimitris
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
| | - Guido Franzoso
- Centre for Molecular Immunology and Inflammation, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom
| | - Ambrosius P Snijders
- Proteomics Platform, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Hector C Keun
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, United Kingdom
| | - Diego A Oyarzún
- School of Informatics, The University of Edinburgh, Edinburgh EH8 9AB, United Kingdom
- School of Biological Sciences, The University of Edinburgh, Edinburgh EH8 9AB, United Kingdom
| | - Mauricio Barahona
- Department of Mathematics, Imperial College London, London SW7 2AZ, United Kingdom
| | - Holger W Auner
- Cancer Cell Protein Metabolism, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, United Kingdom;
- The Hugh and Josseline Langmuir Centre for Myeloma Research, Imperial College London, London W12 0NN, United Kingdom
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8
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Stebbing J, Zhang H, Xu Y, Lit LC, Green AR, Grothey A, Lombardo Y, Periyasamy M, Blighe K, Zhang W, Shaw JA, Ellis IO, Lenz HJ, Giamas G. Correction to: KSR1 regulates BRCA1 degradation and inhibits breast cancer growth. Oncogene 2021; 40:3473. [PMID: 33888869 DOI: 10.1038/s41388-021-01759-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- J Stebbing
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial College Centre for Translational and Experimental Medicine, Hammersmith Hospital Campus, London, UK
| | - H Zhang
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial College Centre for Translational and Experimental Medicine, Hammersmith Hospital Campus, London, UK
| | - Y Xu
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial College Centre for Translational and Experimental Medicine, Hammersmith Hospital Campus, London, UK
| | - L C Lit
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial College Centre for Translational and Experimental Medicine, Hammersmith Hospital Campus, London, UK.,Faculty of Medicine, Department of Physiology, University of Malaya, Kuala, Lumpur, Malaysia
| | - A R Green
- Department of Cellular Pathology, Queen's Medical Centre, Nottingham University Hospital NHS Trust, Nottingham, UK
| | - A Grothey
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial College Centre for Translational and Experimental Medicine, Hammersmith Hospital Campus, London, UK
| | - Y Lombardo
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial College Centre for Translational and Experimental Medicine, Hammersmith Hospital Campus, London, UK
| | - M Periyasamy
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial College Centre for Translational and Experimental Medicine, Hammersmith Hospital Campus, London, UK
| | - K Blighe
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester, UK
| | - W Zhang
- Division of Medical Oncology, University of Southern California, Norris Comprehensive Cancer Centre, Keck School of Medicine, Los Angeles, CA, USA
| | - J A Shaw
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester, UK
| | - I O Ellis
- Faculty of Medicine, Department of Physiology, University of Malaya, Kuala, Lumpur, Malaysia
| | - H J Lenz
- Division of Medical Oncology, University of Southern California, Norris Comprehensive Cancer Centre, Keck School of Medicine, Los Angeles, CA, USA
| | - G Giamas
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial College Centre for Translational and Experimental Medicine, Hammersmith Hospital Campus, London, UK.
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9
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Brennan PF, McNeil AJ, Jing M, Awuah A, Moore JS, Mailey J, Finlay DD, Blighe K, McLaughlin JAD, Nesbit MA, Trucco E, Moore TCB, Spence MS. Assessment of the conjunctival microcirculation for patients presenting with acute myocardial infarction compared to healthy controls. Sci Rep 2021; 11:7660. [PMID: 33828174 PMCID: PMC8027463 DOI: 10.1038/s41598-021-87315-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/23/2021] [Indexed: 11/25/2022] Open
Abstract
Microcirculatory dysfunction occurs early in cardiovascular disease (CVD) development. Acute myocardial infarction (MI) is a late consequence of CVD. The conjunctival microcirculation is readily-accessible for quantitative assessment and has not previously been studied in MI patients. We compared the conjunctival microcirculation of acute MI patients and age/sex-matched healthy controls to determine if there were differences in microcirculatory parameters. We acquired images using an iPhone 6s and slit-lamp biomicroscope. Parameters measured included diameter, axial velocity, wall shear rate and blood volume flow. Results are for all vessels as they were not sub-classified into arterioles or venules. The conjunctival microcirculation was assessed in 56 controls and 59 inpatients with a presenting diagnosis of MI. Mean vessel diameter for the controls was 21.41 ± 7.57 μm compared to 22.32 ± 7.66 μm for the MI patients (p < 0.001). Axial velocity for the controls was 0.53 ± 0.15 mm/s compared to 0.49 ± 0.17 mm/s for the MI patients (p < 0.001). Wall shear rate was higher for controls than MI patients (162 ± 93 s-1 vs 145 ± 88 s-1, p < 0.001). Blood volume flow did not differ significantly for the controls and MI patients (153 ± 124 pl/s vs 154 ± 125 pl/s, p = 0.84). This pilot iPhone and slit-lamp assessment of the conjunctival microcirculation found lower axial velocity and wall shear rate in patients with acute MI. Further study is required to correlate these findings further and assess long-term outcomes in this patient group with a severe CVD phenotype.
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Affiliation(s)
- Paul F Brennan
- Department of Cardiology, Royal Victoria Hospital, Belfast Health and Social Care Trust, Belfast, UK.
- Biomedical Sciences Research Institute, Ulster University, Coleraine, UK.
| | - Andrew J McNeil
- Biomedical Sciences Research Institute, Ulster University, Coleraine, UK
| | - Min Jing
- Nanotechnology and Integrated Bioengineering Centre (NIBEC), Ulster University, Jordanstown, UK
| | - Agnes Awuah
- Biomedical Sciences Research Institute, Ulster University, Coleraine, UK
| | - Julie S Moore
- Biomedical Sciences Research Institute, Ulster University, Coleraine, UK
| | - Jonathan Mailey
- Department of Cardiology, Royal Victoria Hospital, Belfast Health and Social Care Trust, Belfast, UK
| | - Dewar D Finlay
- Nanotechnology and Integrated Bioengineering Centre (NIBEC), Ulster University, Jordanstown, UK
| | - Kevin Blighe
- Biomedical Sciences Research Institute, Ulster University, Coleraine, UK
| | - James A D McLaughlin
- Nanotechnology and Integrated Bioengineering Centre (NIBEC), Ulster University, Jordanstown, UK
| | - M Andrew Nesbit
- Biomedical Sciences Research Institute, Ulster University, Coleraine, UK
| | - Emanuele Trucco
- VAMPIRE project, Computing (SSEN), University of Dundee, Dundee, UK
| | - Tara C B Moore
- Biomedical Sciences Research Institute, Ulster University, Coleraine, UK
| | - Mark S Spence
- Department of Cardiology, Royal Victoria Hospital, Belfast Health and Social Care Trust, Belfast, UK
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10
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Mencias M, Levene M, Blighe K, Bax BE. Circulating miRNAs as Biomarkers for Mitochondrial Neuro-Gastrointestinal Encephalomyopathy. Int J Mol Sci 2021; 22:ijms22073681. [PMID: 33916195 PMCID: PMC8037498 DOI: 10.3390/ijms22073681] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/25/2021] [Accepted: 03/27/2021] [Indexed: 02/05/2023] Open
Abstract
Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is an ultra-rare disease for which there are currently no validated outcome measures for assessing therapeutic intervention efficacy. The aim of this study was to identify a plasma and/or serum microRNA (miRNA) biomarker panel for MNGIE. Sixty-five patients and 65 age and sex matched healthy controls were recruited and assigned to one of four study phases: (i) discovery for sample size determination; (ii) candidate screening; (iii) candidate validation; and (iv) verifying the performance of the validated miRNA panel in four patients treated with erythrocyte-encapsulated thymidine phosphorylase (EE-TP), an enzyme replacement under development for MNGIE. Quantitative PCR (qPCR) was used to profile miRNAs in serum and/or plasma samples collected for the discovery, validation and performance phases, and next generation sequencing (NGS) analysis was applied to serum samples assigned to the candidate screening phase. Forty-one differentially expressed candidate miRNAs were identified in the sera of patients (p < 0.05, log2 fold change > 1). The validation cohort revealed that of those, 27 miRNAs were upregulated in plasma and three miRNAs were upregulated in sera (p < 0.05). Through binary logistic regression analyses, five plasma miRNAs (miR-192-5p, miR-193a-5p, miR-194-5p, miR-215-5p and miR-34a-5p) and three serum miRNAs (miR-192-5p, miR-194-5p and miR-34a-5p) were shown to robustly distinguish MNGIE from healthy controls. Reduced longitudinal miRNA expression of miR-34a-5p was observed in all four patients treated with EE-TP and coincided with biochemical and clinical improvements. We recommend the inclusion of the plasma exploratory miRNA biomarker panel in future clinical trials of investigational therapies for MNGIE; it may have prognostic value for assessing clinical status.
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Affiliation(s)
- Mark Mencias
- Molecular and Clinical Sciences, St. George’s, University of London, London SW17 0RE, UK; (M.M.); (M.L.)
| | - Michelle Levene
- Molecular and Clinical Sciences, St. George’s, University of London, London SW17 0RE, UK; (M.M.); (M.L.)
| | - Kevin Blighe
- Clinical Bioinformatics Research Ltd., London W1B 3HH, UK;
| | - Bridget E. Bax
- Molecular and Clinical Sciences, St. George’s, University of London, London SW17 0RE, UK; (M.M.); (M.L.)
- Correspondence: ; Tel.: +44-(0)208-266-6836
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11
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Nalesso G, Thorup AS, Eldridge SE, De Palma A, Kaur A, Peddireddi K, Blighe K, Rana S, Stott B, Vincent TL, Thomas BL, Bertrand J, Sherwood J, Fioravanti A, Pitzalis C, Dell'Accio F. Calcium calmodulin kinase II activity is required for cartilage homeostasis in osteoarthritis. Sci Rep 2021; 11:5682. [PMID: 33707504 PMCID: PMC7952598 DOI: 10.1038/s41598-021-82067-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 09/25/2020] [Accepted: 12/28/2020] [Indexed: 12/16/2022] Open
Abstract
WNT ligands can activate several signalling cascades of pivotal importance during development and regenerative processes. Their de-regulation has been associated with the onset of different diseases. Here we investigated the role of the WNT/Calcium Calmodulin Kinase II (CaMKII) pathway in osteoarthritis. We identified Heme Oxygenase I (HMOX1) and Sox-9 as specific markers of the WNT/CaMKII signalling in articular chondrocytes through a microarray analysis. We showed that the expression of the activated form of CaMKII, phospho-CaMKII, was increased in human and murine osteoarthritis and the expression of HMOX1 was accordingly reduced, demonstrating the activation of the pathway during disease progression. To elucidate its function, we administered the CaMKII inhibitor KN93 to mice in which osteoarthritis was induced by resection of the anterior horn of the medial meniscus and of the medial collateral ligament in the knee joint. Pharmacological blockade of CaMKII exacerbated cartilage damage and bone remodelling. Finally, we showed that CaMKII inhibition in articular chondrocytes upregulated the expression of matrix remodelling enzymes alone and in combination with Interleukin 1. These results suggest an important homeostatic role of the WNT/CaMKII signalling in osteoarthritis which could be exploited in the future for therapeutic purposes.
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Affiliation(s)
- Giovanna Nalesso
- Department of Veterinary Pre-Clinical Sciences, School of Veterinary Medicine, University of Surrey, Daphne Jackson Road, Guildford, GU2 7AL, UK.
| | - Anne-Sophie Thorup
- Barts and the London School of Medicine and Dentistry, William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Suzanne Elizabeth Eldridge
- Barts and the London School of Medicine and Dentistry, William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Anna De Palma
- Department of Veterinary Pre-Clinical Sciences, School of Veterinary Medicine, University of Surrey, Daphne Jackson Road, Guildford, GU2 7AL, UK
| | - Amanpreet Kaur
- Barts and the London School of Medicine and Dentistry, William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Kiran Peddireddi
- MRC Clinical Trials Unit, Institute of Clinical Trials and Methodology, UCL, London, UK
| | | | | | - Bryony Stott
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | | | - Bethan Lynne Thomas
- Barts and the London School of Medicine and Dentistry, William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Jessica Bertrand
- Department of Orthopaedic Surgery, Otto-von-Guericke University, Magdeburg, Germany
| | - Joanna Sherwood
- Institute of Musculoskeletal Medicine, University Hospital Münster, Münster, Germany
| | - Antonella Fioravanti
- Rheumatology Unit, Azienda Ospedaliera Universitaria Senese, Policlinico Le Scotte, Siena, Italy
| | - Costantino Pitzalis
- Barts and the London School of Medicine and Dentistry, William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Francesco Dell'Accio
- Barts and the London School of Medicine and Dentistry, William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.
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12
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Safdar LB, Umer MJ, Almas F, Uddin S, Safdar QTA, Blighe K, Quraishi UM. Identification of genetic factors controlling phosphorus utilization efficiency in wheat by genome-wide association study with principal component analysis. Gene 2020; 768:145301. [PMID: 33181261 DOI: 10.1016/j.gene.2020.145301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 09/06/2020] [Accepted: 11/04/2020] [Indexed: 11/30/2022]
Abstract
Despite the economic importance of P utilization efficiency, information on genetic factors underlying this trait remains elusive. To address that, we performed a genome-wide association study in a spring wheat diversity panel ranging from landraces to elite varieties. We evaluated the phenotype variation for P utilization efficiency in controlled conditions and genotype variation using wheat 90 K SNP array. Phenotype variables were transformed into a smaller set of uncorrelated principal components that captured the most important variation data. We identified two significant loci associated with both P utilization efficiency and the 1st principal component on chromosomes 3A and 4A: qPE1-3A and qPE2-4A. Annotation of genes at these loci revealed 53 wheat genes, among which 6 were identified in significantly enriched pathways. The expression pattern of these 6 genes indicated that TraesCS4A02G481800, involved in pyruvate metabolism and TCA cycle, had a significantly higher expression in the P efficient variety under limited P conditions. Further characterization of these loci and candidate genes can help stimulate P utilization efficiency in wheat.
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Affiliation(s)
- Luqman Bin Safdar
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
| | - Muhammad Jawad Umer
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Fakhrah Almas
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Siraj Uddin
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; Plant Breeding Institute, Faculty of Agriculture & Environment, University of Sydney, Australia
| | | | - Kevin Blighe
- Institute of Ophthalmology, 11-43 Bath Street, University College London, London, UK
| | - Umar Masood Quraishi
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
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13
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Arbore G, Ong VH, Costantini B, Denton CP, Abraham D, Placais L, Blighe K, Mitchell L, Ellis R, Heck S, Nocerino P, Woodruff TM, Kordasti S, Kemper C, Hourcade DE. Deep phenotyping detects a pathological CD4 + T-cell complosome signature in systemic sclerosis. Cell Mol Immunol 2020; 17:1010-1013. [PMID: 31974397 PMCID: PMC7608471 DOI: 10.1038/s41423-019-0360-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 11/09/2022] Open
Affiliation(s)
- Giuseppina Arbore
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milano, Italy
| | - Voon H Ong
- Centre for Rheumatology and Connective Tissue Diseases, UCL Division of Medicine, London, UK
| | - Benedetta Costantini
- Systems Cancer Immunology Lab, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| | - Christopher P Denton
- Centre for Rheumatology and Connective Tissue Diseases, UCL Division of Medicine, London, UK
| | - David Abraham
- Centre for Rheumatology and Connective Tissue Diseases, UCL Division of Medicine, London, UK
| | - Leo Placais
- Complement and Inflammation Research Section, NIH, NHLBI, Bethesda, MD, USA
| | - Kevin Blighe
- Systems Cancer Immunology Lab, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| | - Lynne Mitchell
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Richard Ellis
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Susanne Heck
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Paola Nocerino
- Systems Cancer Immunology Lab, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| | - Trent M Woodruff
- School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Shahram Kordasti
- Systems Cancer Immunology Lab, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King's College London, London, UK.
- Haematology Department, Guy's Hospital, London, UK.
| | - Claudia Kemper
- Complement and Inflammation Research Section, NIH, NHLBI, Bethesda, MD, USA.
- School of Immunology and Microbial Sciences, King's College London, London, UK.
- Institute for Systemic Inflammation Research, University of Lübeck, Lübeck, Germany.
| | - Dennis E Hourcade
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA.
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14
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Lewis MJ, Barnes MR, Blighe K, Goldmann K, Rana S, Hackney JA, Ramamoorthi N, John CR, Watson DS, Kummerfeld SK, Hands R, Riahi S, Rocher-Ros V, Rivellese F, Humby F, Kelly S, Bombardieri M, Ng N, DiCicco M, van der Heijde D, Landewé R, van der Helm-van Mil A, Cauli A, McInnes IB, Buckley CD, Choy E, Taylor PC, Townsend MJ, Pitzalis C. Molecular Portraits of Early Rheumatoid Arthritis Identify Clinical and Treatment Response Phenotypes. Cell Rep 2020; 28:2455-2470.e5. [PMID: 31461658 PMCID: PMC6718830 DOI: 10.1016/j.celrep.2019.07.091] [Citation(s) in RCA: 188] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 05/22/2019] [Accepted: 07/24/2019] [Indexed: 12/31/2022] Open
Abstract
There is a current imperative to unravel the hierarchy of molecular pathways that drive the transition of early to established disease in rheumatoid arthritis (RA). Herein, we report a comprehensive RNA sequencing analysis of the molecular pathways that drive early RA progression in the disease tissue (synovium), comparing matched peripheral blood RNA-seq in a large cohort of early treatment-naive patients, namely, the Pathobiology of Early Arthritis Cohort (PEAC). We developed a data exploration website (https://peac.hpc.qmul.ac.uk/) to dissect gene signatures across synovial and blood compartments, integrated with deep phenotypic profiling. We identified transcriptional subgroups in synovium linked to three distinct pathotypes: fibroblastic pauci-immune pathotype, macrophage-rich diffuse-myeloid pathotype, and a lympho-myeloid pathotype characterized by infiltration of lymphocytes and myeloid cells. This is suggestive of divergent pathogenic pathways or activation disease states. Pro-myeloid inflammatory synovial gene signatures correlated with clinical response to initial drug therapy, whereas plasma cell genes identified a poor prognosis subgroup with progressive structural damage. Deep phenotyping and RNA-seq of early rheumatoid arthritis individuals pre-treatment Synovial plasma cell gene expression predicts future progressive joint damage on X-ray Blood interferon gene signature associates with synovial B and plasma cell infiltration Interactive website enables RNA-seq and clinical data to be fully explored
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Affiliation(s)
- Myles J Lewis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Michael R Barnes
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; Alan Turing Institute, British Library, London NW1 2DB, UK
| | - Kevin Blighe
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Katriona Goldmann
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Sharmila Rana
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Jason A Hackney
- Bioinformatics and Computational Biology, Genentech Research & Early Development, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Nandhini Ramamoorthi
- Biomarker Discovery OMNI, Genentech Research & Early Development, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Christopher R John
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - David S Watson
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; Alan Turing Institute, British Library, London NW1 2DB, UK; Oxford Internet Institute, University of Oxford, Oxford OX1 3JS, UK
| | - Sarah K Kummerfeld
- Bioinformatics and Computational Biology, Genentech Research & Early Development, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Rebecca Hands
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Sudeh Riahi
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Vidalba Rocher-Ros
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Felice Rivellese
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Frances Humby
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Stephen Kelly
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Michele Bombardieri
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Nora Ng
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Maria DiCicco
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | | | - Robert Landewé
- Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, the Netherlands
| | | | - Alberto Cauli
- Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy
| | - Iain B McInnes
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK
| | - Christopher D Buckley
- Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK; Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences and the Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Ernest Choy
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Peter C Taylor
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences and the Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Michael J Townsend
- Biomarker Discovery OMNI, Genentech Research & Early Development, 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Costantino Pitzalis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
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15
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Christie KA, Robertson LJ, Conway C, Blighe K, DeDionisio LA, Chao-Shern C, Kowalczyk AM, Marshall J, Turnbull D, Nesbit MA, Moore CBT. Mutation-Independent Allele-Specific Editing by CRISPR-Cas9, a Novel Approach to Treat Autosomal Dominant Disease. Mol Ther 2020; 28:1846-1857. [PMID: 32416058 PMCID: PMC7403340 DOI: 10.1016/j.ymthe.2020.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 02/14/2020] [Accepted: 05/01/2020] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas9 provides a tool to treat autosomal dominant disease by non-homologous end joining (NHEJ) gene disruption of the mutant allele. In order to discriminate between wild-type and mutant alleles, Streptococcus pyogenes Cas9 (SpCas9) must be able to detect a single nucleotide change. Allele-specific editing can be achieved by using either a guide-specific approach, in which the missense mutation is found within the guide sequence, or a protospacer-adjacent motif (PAM)-specific approach, in which the missense mutation generates a novel PAM. While both approaches have been shown to offer allele specificity in certain contexts, in cases where numerous missense mutations are associated with a particular disease, such as TGFBI (transforming growth factor β-induced) corneal dystrophies, it is neither possible nor realistic to target each mutation individually. In this study, we demonstrate allele-specific CRISPR gene editing independent of the disease-causing mutation that is capable of achieving complete allele discrimination, and we propose it as a targeting approach for autosomal dominant disease. Our approach utilizes natural variants in the target region that contain a PAM on one allele that lies in cis with the causative mutation, removing the constraints of a mutation-dependent approach. Our innovative patient-specific guide design approach takes into account the patient's individual genetic make-up, allowing on- and off-target activity to be assessed in a personalized manner.
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Affiliation(s)
- Kathleen A Christie
- Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK
| | - Louise J Robertson
- Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK
| | - Caroline Conway
- Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK
| | - Kevin Blighe
- Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK
| | | | - Connie Chao-Shern
- Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK; Avellino Laboratories, Menlo Park, CA 94025, USA
| | - Amanda M Kowalczyk
- Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK
| | - John Marshall
- Department of Genetics, UCL Institute of Ophthalmology, London EC1V 9EL, UK
| | - Doug Turnbull
- Genomics and Cell Characterization Core Facility, University of Oregon, OR 97403, USA
| | - M Andrew Nesbit
- Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK
| | - C B Tara Moore
- Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK; Avellino Laboratories, Menlo Park, CA 94025, USA.
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16
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Hosseinkhan N, Honardoost M, Blighe K, Moore CBT, Khamseh ME. Comprehensive transcriptomic analysis of papillary thyroid cancer: potential biomarkers associated with tumor progression. J Endocrinol Invest 2020; 43:911-923. [PMID: 31965517 DOI: 10.1007/s40618-019-01175-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 12/23/2019] [Indexed: 12/23/2022]
Abstract
PURPOSE Identification of stage-specific prognostic/predictive biomarkers in papillary thyroid carcinoma (PTC) could lead to its more efficient clinical management. The main objective of this study was to characterize the stage-specific deregulation in genes and miRNA expression in PTC to identify potential prognostic biomarkers. METHODS 495 RNASeq and 499 miRNASeq PTC samples (stage I-IV) as well as, respectively, 56 and 57 normal samples were retrieved from The Cancer Genome Atlas (TCGA). Differential expression analysis was performed using DESeq 2 to identify deregulation of genes and miRNAs between sequential stages. To identify the minority of patients who progress to higher stages, we performed clustering analysis on stage I RNASeq data. An independent PTC RNASeq data set (BioProject accession PRJEB11591) was also used for the validation of the results. RESULTS LTF and PLA2R1 were identified as two promising biomarkers down-regulated in a subgroup of stage I (both in TCGA and in the validation data set) and in the majority of stage IV of PTC (in TCGA data set). hsa-miR-205, hsa-miR-509-2, hsa-miR-514-1 and hsa-miR-514-2 were also detected as up-regulated miRNAs in both PTC patients with stage I and stage III. Hierarchical clustering of stage I samples showed substantial heterogeneity in the expression pattern of PTC indicating the necessity of categorizing stage I patients based on the expressional alterations of specific biomarkers. CONCLUSION Stage I PTC patients showed large amount of expressional heterogeneity. Therefore, risk stratification based on the expressional alterations of candidate biomarkers could be an important step toward personalized management of these patients.
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Affiliation(s)
- N Hosseinkhan
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran
| | - M Honardoost
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran
| | - K Blighe
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland
| | - C B T Moore
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland
| | - M E Khamseh
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran.
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17
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Ghorani E, Reading JL, Henry JY, Massy MRD, Rosenthal R, Turati V, Joshi K, Furness AJS, Ben Aissa A, Saini SK, Ramskov S, Georgiou A, Sunderland MW, Wong YNS, Mucha MVD, Day W, Galvez-Cancino F, Becker PD, Uddin I, Oakes T, Ismail M, Ronel T, Woolston A, Jamal-Hanjani M, Veeriah S, Birkbak NJ, Wilson GA, Litchfield K, Conde L, Guerra-Assunção JA, Blighe K, Biswas D, Salgado R, Lund T, Bakir MA, Moore DA, Hiley CT, Loi S, Sun Y, Yuan Y, AbdulJabbar K, Turajilic S, Herrero J, Enver T, Hadrup SR, Hackshaw A, Peggs KS, McGranahan N, Chain B, Swanton C, Quezada SA. The T cell differentiation landscape is shaped by tumour mutations in lung cancer. Nat Cancer 2020; 1:546-561. [PMID: 32803172 PMCID: PMC7115931 DOI: 10.1038/s43018-020-0066-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/20/2020] [Indexed: 01/06/2023]
Abstract
Tumour mutational burden (TMB) predicts immunotherapy outcome in non-small cell lung cancer (NSCLC), consistent with immune recognition of tumour neoantigens. However, persistent antigen exposure is detrimental for T cell function. How TMB affects CD4 and CD8 T cell differentiation in untreated tumours, and whether this affects patient outcomes is unknown. Here we paired high-dimensional flow cytometry, exome, single-cell and bulk RNA sequencing from patients with resected, untreated NSCLC to examine these relationships. TMB was associated with compartment-wide T cell differentiation skewing, characterized by loss of TCF7-expressing progenitor-like CD4 T cells, and an increased abundance of dysfunctional CD8 and CD4 T cell subsets, with significant phenotypic and transcriptional similarity to neoantigen-reactive CD8 T cells. A gene signature of redistribution from progenitor-like to dysfunctional states associated with poor survival in lung and other cancer cohorts. Single-cell characterization of these populations informs potential strategies for therapeutic manipulation in NSCLC.
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Affiliation(s)
- Ehsan Ghorani
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - James L Reading
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Jake Y Henry
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Marc Robert de Massy
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Rachel Rosenthal
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Virginia Turati
- Department of Cancer Biology, University College London Cancer Institute, London, UK
| | - Kroopa Joshi
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Andrew J S Furness
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Assma Ben Aissa
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sunil Kumar Saini
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Sofie Ramskov
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Andrew Georgiou
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mariana Werner Sunderland
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Yien Ning Sophia Wong
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Maria Vila De Mucha
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - William Day
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Felipe Galvez-Cancino
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Pablo D Becker
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Imran Uddin
- Division of Infection and Immunity, University College London, London, UK
| | - Theres Oakes
- Division of Infection and Immunity, University College London, London, UK
| | - Mazlina Ismail
- Division of Infection and Immunity, University College London, London, UK
| | - Tahel Ronel
- Division of Infection and Immunity, University College London, London, UK
| | - Annemarie Woolston
- Division of Infection and Immunity, University College London, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Lucia Conde
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | | | - Kevin Blighe
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Dhruva Biswas
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | | | - Tom Lund
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - David A Moore
- Department of Pathology, University College London Cancer Institute, London, UK
| | - Crispin T Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Sherene Loi
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | - Yuxin Sun
- Division of Infection and Immunity, University College London, London, UK
| | - Yinyin Yuan
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Khalid AbdulJabbar
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Samra Turajilic
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Tariq Enver
- Department of Cancer Biology, University College London Cancer Institute, London, UK
| | - Sine R Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Allan Hackshaw
- Cancer Research UK and University College London Cancer Trials Centre, London, UK
| | - Karl S Peggs
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, UK
- Department of Computer Sciences, University College London, London, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- University College London Hospitals, London, UK.
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
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18
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Kachroo P, Kelly RS, Mirzakhani H, Lee-Sarwar K, Chawes BL, Blighe K, Davaasambuu G, Bisgaard H, Litonjua AA, Weiss ST, Lasky-Su J. Fish oil supplementation during pregnancy is protective against asthma/wheeze in offspring. J Allergy Clin Immunol Pract 2020; 8:388-391.e2. [PMID: 31226448 PMCID: PMC7087445 DOI: 10.1016/j.jaip.2019.05.054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 05/21/2019] [Accepted: 05/31/2019] [Indexed: 11/16/2022]
Abstract
The trial was approved by the Institutional Review Boards of the participating institutions and at Brigham and Women’s Hospital and is registered with NCT00920621 ). Written informed consent was obtained from all women at recruitment.
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Affiliation(s)
- Priyadarshini Kachroo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Rachel S Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Hooman Mirzakhani
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Kathleen Lee-Sarwar
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Bo L Chawes
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Gentofte, Denmark
| | - Kevin Blighe
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Ganmaa Davaasambuu
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, Mass
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Gentofte, Denmark
| | - Augusto A Litonjua
- Division of Pediatric Pulmonary Medicine, Department of Pediatrics, University of Rochester Medical Center, Rochester, NY
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Partners Center for Personalized Medicine, Partners Health Care, Boston, Mass
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass.
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19
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Pucino V, Certo M, Bulusu V, Cucchi D, Goldmann K, Pontarini E, Haas R, Smith J, Headland SE, Blighe K, Ruscica M, Humby F, Lewis MJ, Kamphorst JJ, Bombardieri M, Pitzalis C, Mauro C. Lactate Buildup at the Site of Chronic Inflammation Promotes Disease by Inducing CD4 + T Cell Metabolic Rewiring. Cell Metab 2019; 30:1055-1074.e8. [PMID: 31708446 PMCID: PMC6899510 DOI: 10.1016/j.cmet.2019.10.004] [Citation(s) in RCA: 247] [Impact Index Per Article: 49.4] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 06/21/2019] [Accepted: 10/12/2019] [Indexed: 02/06/2023]
Abstract
Accumulation of lactate in the tissue microenvironment is a feature of both inflammatory disease and cancer. Here, we assess the response of immune cells to lactate in the context of chronic inflammation. We report that lactate accumulation in the inflamed tissue contributes to the upregulation of the lactate transporter SLC5A12 by human CD4+ T cells. SLC5A12-mediated lactate uptake into CD4+ T cells induces a reshaping of their effector phenotype, resulting in increased IL17 production via nuclear PKM2/STAT3 and enhanced fatty acid synthesis. It also leads to CD4+ T cell retention in the inflamed tissue as a consequence of reduced glycolysis and enhanced fatty acid synthesis. Furthermore, antibody-mediated blockade of SLC5A12 ameliorates the disease severity in a murine model of arthritis. Finally, we propose that lactate/SLC5A12-induced metabolic reprogramming is a distinctive feature of lymphoid synovitis in rheumatoid arthritis patients and a potential therapeutic target in chronic inflammatory disorders.
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Affiliation(s)
- Valentina Pucino
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK; William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Michelangelo Certo
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK; William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Vinay Bulusu
- Cancer Research UK Beatson Institute, Glasgow, UK; Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Danilo Cucchi
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Katriona Goldmann
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Elena Pontarini
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Robert Haas
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Joanne Smith
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Sarah E Headland
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Kevin Blighe
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Massimiliano Ruscica
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Frances Humby
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Myles J Lewis
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Jurre J Kamphorst
- Cancer Research UK Beatson Institute, Glasgow, UK; Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Michele Bombardieri
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Costantino Pitzalis
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Claudio Mauro
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK; William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK; Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK; Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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20
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Kelly RS, Chawes BL, Guo F, Zhang L, Blighe K, Litonjua AA, Raby BA, Levy BD, Rago D, Stokholm J, Bønnelykke K, Bisgaard H, Zhou X, Lasky-Su JA, Weiss ST. The role of the 17q21 genotype in the prevention of early childhood asthma and recurrent wheeze by vitamin D. Eur Respir J 2019; 54:13993003.00761-2019. [PMID: 31439681 DOI: 10.1183/13993003.00761-2019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/18/2019] [Indexed: 02/05/2023]
Abstract
Evidence suggests vitamin D has preventive potential in asthma; however, not all children benefit from this intervention. This study aimed to investigate whether variation in the functional 17q21 single nucleotide polymorphism rs12936231 affects the preventive potential of vitamin D against asthma.A combined secondary analysis of two randomised controlled trials of prenatal vitamin D supplementation for the prevention of asthma in offspring (Vitamin D Antenatal Asthma Reduction Trial (VDAART) and Copenhagen Prospective Studies on Asthma in Childhood 2010 (COPSAC2010)) was performed, stratifying by genotype and integrating metabolite data to explore underlying mechanisms.The protective effect of vitamin D on asthma/wheeze was evident among children with the low-risk rs12936231 GG genotype (hazard ratio (HR) 0.49, 95% CI 0.26-0.94, p=0.032) but not the high-risk CC genotype (HR 1.08, 95% CI 0.69-1.69, p=0.751). In VDAART, in the GG genotype vitamin D supplementation was associated with increased plasma levels of sphingolipids, including sphingosine-1-phosphate (β 0.022, 95% CI 0.001-0.044, p=0.038), but this was not evident with the CC genotype, known to be associated with increased expression of ORMDL3 in bronchial epithelial cells. Sphingolipid levels were associated with decreased risk of asthma/wheeze, and there was evidence of interactions between sphingolipid levels, vitamin D and genotype (p-interactionvitaminD*genotype*sphingosine-1-phosphate=0.035). In a cellular model, there was a significant difference in the induction of sphingosine-1-phosphate by vitamin D between a control human bronchial epithelial cell line and a cell line overexpressing ORMDL3 (p=0.002).Results suggest prenatal vitamin D supplementation may reduce the risk of early childhood asthma/wheeze via alterations of sphingolipid metabolism dependent on the 17q21 genotype.
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Affiliation(s)
- Rachel S Kelly
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Co-first authors
| | - Bo L Chawes
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.,Co-first authors
| | - Feng Guo
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Li Zhang
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Dept of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu, PR China
| | - Kevin Blighe
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Augusto A Litonjua
- Pulmonary Division, Dept of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Benjamin A Raby
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Bruce D Levy
- Harvard Medical School, Boston, MA, USA.,Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Daniela Rago
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Stokholm
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Jessica A Lasky-Su
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Co-senior authors
| | - Scott T Weiss
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA .,Harvard Medical School, Boston, MA, USA.,Co-senior authors
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21
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Blighe K, DeDionisio L, Christie KA, Chawes B, Shareef S, Kakouli-Duarte T, Chao-Shern C, Harding V, Kelly RS, Castellano L, Stebbing J, Lasky-Su JA, Nesbit MA, Moore CBT. Gene editing in the context of an increasingly complex genome. BMC Genomics 2018; 19:595. [PMID: 30086710 PMCID: PMC6081867 DOI: 10.1186/s12864-018-4963-8] [Citation(s) in RCA: 8] [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: 06/26/2017] [Accepted: 07/26/2018] [Indexed: 12/15/2022] Open
Abstract
The reporting of the first draft of the human genome in 2000 brought with it much hope for the future in what was felt as a paradigm shift toward improved health outcomes. Indeed, we have now mapped the majority of variation across human populations with landmark projects such as 1000 Genomes; in cancer, we have catalogued mutations across the primary carcinomas; whilst, for other diseases, we have identified the genetic variants with strongest association. Despite this, we are still awaiting the genetic revolution in healthcare to materialise and translate itself into the health benefits for which we had hoped. A major problem we face relates to our underestimation of the complexity of the genome, and that of biological mechanisms, generally. Fixation on DNA sequence alone and a 'rigid' mode of thinking about the genome has meant that the folding and structure of the DNA molecule -and how these relate to regulation- have been underappreciated. Projects like ENCODE have additionally taught us that regulation at the level of RNA is just as important as that at the spatiotemporal level of chromatin.In this review, we chart the course of the major advances in the biomedical sciences in the era pre- and post the release of the first draft sequence of the human genome, taking a focus on technology and how its development has influenced these. We additionally focus on gene editing via CRISPR/Cas9 as a key technique, in particular its use in the context of complex biological mechanisms. Our aim is to shift the mode of thinking about the genome to that which encompasses a greater appreciation of the folding of the DNA molecule, DNA- RNA/protein interactions, and how these regulate expression and elaborate disease mechanisms.Through the composition of our work, we recognise that technological improvement is conducive to a greater understanding of biological processes and life within the cell. We believe we now have the technology at our disposal that permits a better understanding of disease mechanisms, achievable through integrative data analyses. Finally, only with greater understanding of disease mechanisms can techniques such as gene editing be faithfully conducted.
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Affiliation(s)
- K Blighe
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, USA.
- Department of Cancer Studies and Molecular Medicine, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, UK.
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, WC1E 6DD, London, UK.
| | - L DeDionisio
- Avellino Laboratories, Menlo Park, CA, 94025, USA
| | - K A Christie
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, Northern Ireland, BT52 1SA, UK
| | - B Chawes
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - S Shareef
- University of Raparin, Ranya, Kurdistan Region, Iraq
| | - T Kakouli-Duarte
- Institute of Technology Carlow, Department of Science and Health, Kilkenny Road, Carlow, Ireland
| | - C Chao-Shern
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, Northern Ireland, BT52 1SA, UK
- Avellino Laboratories, Menlo Park, CA, 94025, USA
| | - V Harding
- Imperial College London, Division of Cancer, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - R S Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, USA
| | - L Castellano
- Imperial College London, Division of Cancer, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
- JMS Building, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - J Stebbing
- Imperial College London, Division of Cancer, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - J A Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, USA
| | - M A Nesbit
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, Northern Ireland, BT52 1SA, UK
| | - C B T Moore
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, Northern Ireland, BT52 1SA, UK.
- Avellino Laboratories, Menlo Park, CA, 94025, USA.
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Kelly RS, Chawes BL, Blighe K, Virkud YV, Croteau-Chonka DC, McGeachie MJ, Clish CB, Bullock K, Celedón JC, Weiss ST, Lasky-Su JA. An Integrative Transcriptomic and Metabolomic Study of Lung Function in Children With Asthma. Chest 2018; 154:335-348. [PMID: 29908154 DOI: 10.1016/j.chest.2018.05.038] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 04/17/2018] [Accepted: 05/01/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Single omic analyses have provided some insight into the basis of lung function in children with asthma, but the underlying biologic pathways are still poorly understood. METHODS Weighted gene coexpression network analysis (WGCNA) was used to identify modules of coregulated gene transcripts and metabolites in blood among 325 children with asthma from the Genetic Epidemiology of Asthma in Costa Rica study. The biology of modules associated with lung function as measured by FEV1, the FEV1/FVC ratio, bronchodilator response, and airway responsiveness to methacholine was explored. Significantly correlated gene-metabolite module pairs were then identified, and their constituent features were analyzed for biologic pathway enrichments. RESULTS WGCNA clustered 25,060 gene probes and 8,185 metabolite features into eight gene modules and eight metabolite modules, where four and six, respectively, were associated with lung function (P ≤ .05). The gene modules were enriched for immune, mitotic, and metabolic processes and asthma-associated microRNA targets. The metabolite modules were enriched for lipid and amino acid metabolism. Integration of correlated gene-metabolite modules expanded the single omic findings, linking the FEV1/FVC ratio with ORMDL3 and dysregulated lipid metabolism. This finding was replicated in an independent population. CONCLUSIONS The results of this hypothesis-generating study suggest a mechanistic basis for multiple asthma genes, including ORMDL3, and a role for lipid metabolism. They demonstrate that integrating multiple omic technologies may provide a more informative picture of asthmatic lung function biology than single omic analyses.
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Affiliation(s)
- Rachel S Kelly
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA.
| | - Bo L Chawes
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Kevin Blighe
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Yamini V Virkud
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Division of Pulmonary Medicine, Allergy and Immunology, Children's Hospital of Pittsburgh of the University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, PA
| | - Damien C Croteau-Chonka
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Michael J McGeachie
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | | | | | - Juan C Celedón
- Division of Allergy and Immunology, Department of Pediatrics, Massachusetts General Hospital, Boston, MA
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Jessica A Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
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Guttery DS, Blighe K, Polymeros K, Symonds RP, Macip S, Moss EL. Racial differences in endometrial cancer molecular portraits in The Cancer Genome Atlas. Oncotarget 2018; 9:17093-17103. [PMID: 29682207 PMCID: PMC5908308 DOI: 10.18632/oncotarget.24907] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [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: 01/15/2018] [Accepted: 03/10/2018] [Indexed: 12/11/2022] Open
Abstract
Endometrial cancer (EC) is now the most prevalent gynaecological malignancy in the Western world. Black or African American women (BoAA) have double the mortality of Caucasian women, and their tumours tend to be of higher grade. Despite these disparities, little is known regarding the mutational landscape of EC between races. Hence, we wished to investigate the molecular features of ECs within The Cancer Genome Atlas (TCGA) dataset by racial groupings. In total 374 Caucasian, 109 BoAA and 20 Asian patients were included in the analysis. Asian women were diagnosed at younger age, 54.2 years versus 64.5 years for Caucasian and 64.9 years for BoAA women (OR 3.432; p=0.011); BoAA women were more likely to have serous type tumors (OR 2.061; p=0.008). No difference in overall survival was evident. The most frequently mutated gene in Caucasian and Asian tumours was PTEN (63% and 85%), unlike BoAA cases where it was TP53 (49%). Mutation and somatic copy number alteration (SCNA) analysis revealed an enrichment of TP53 mutations in BoAAs; whereas POLE and RPL22 mutations were more frequent in Caucasians. Major recurrent SCNA racial differences were observed at chromosomes 3p, 8, 10, and 16, which clustered BoAA tumors into 4 distinct groups and Caucasian tumors into 5 groups. There was a significantly higher frequency of somatic mutations in DNA mismatch repair genes in Asian tumours, in particular PMS2 (p=0.0036). In conclusion, inherent racial disparities appear to be present in the molecular profile of EC, which could have potential implications on clinical management.
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Affiliation(s)
- David S Guttery
- Leicester Cancer Research Centre, University of Leicester, Robert Kilpatrick Building, Leicester Royal Infirmary, Leicester, UK
| | - Kevin Blighe
- Leicester Cancer Research Centre, University of Leicester, Robert Kilpatrick Building, Leicester Royal Infirmary, Leicester, UK
| | - Konstantinos Polymeros
- Leicester Cancer Research Centre, University of Leicester, Robert Kilpatrick Building, Leicester Royal Infirmary, Leicester, UK.,Department of Gynaecological Oncology, University Hospitals of Leicester NHS Trust, Leicester General Hospital, Leicester, UK.,Mechanisms of Cancer and Ageing Lab, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - R Paul Symonds
- Leicester Cancer Research Centre, University of Leicester, Robert Kilpatrick Building, Leicester Royal Infirmary, Leicester, UK
| | - Salvador Macip
- Mechanisms of Cancer and Ageing Lab, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Esther L Moss
- Leicester Cancer Research Centre, University of Leicester, Robert Kilpatrick Building, Leicester Royal Infirmary, Leicester, UK.,Department of Gynaecological Oncology, University Hospitals of Leicester NHS Trust, Leicester General Hospital, Leicester, UK
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Blighe K, Chawes BL, Kelly RS, Mirzakhani H, McGeachie M, Litonjua AA, Weiss ST, Lasky-Su JA. Vitamin D prenatal programming of childhood metabolomics profiles at age 3 y. Am J Clin Nutr 2017; 106:1092-1099. [PMID: 28835366 PMCID: PMC5611786 DOI: 10.3945/ajcn.117.158220] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [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: 04/06/2017] [Accepted: 07/18/2017] [Indexed: 12/28/2022] Open
Abstract
Background: Vitamin D deficiency is implicated in a range of common complex diseases that may be prevented by gestational vitamin D repletion. Understanding the metabolic mechanisms related to in utero vitamin D exposure may therefore shed light on complex disease susceptibility.Objective: The goal was to analyze the programming role of in utero vitamin D exposure on children's metabolomics profiles.Design: First, unsupervised clustering was done with plasma metabolomics profiles from a case-control subset of 245 children aged 3 y with and without asthma from the Vitamin D Antenatal Asthma Reduction Trial (VDAART), in which pregnant women were randomly assigned to vitamin D supplementation or placebo. Thereafter, we analyzed the influence of maternal pre- and postsupplement vitamin D concentrations on cluster membership. Finally, we used the metabolites driving the clustering of children to identify the dominant metabolic pathways that were influential in each cluster.Results: We identified 3 clusters of children characterized by 1) high concentrations of fatty acids and amines and low maternal postsupplement vitamin D (mean ± SD; 27.5 ± 11.0 ng/mL), 2) high concentrations of amines, moderate concentrations of fatty acids, and normal maternal postsupplement vitamin D (34.0 ± 14.1 ng/mL), and 3) low concentrations of fatty acids, amines, and normal maternal postsupplement vitamin D (35.2 ± 15.9 ng/mL). Adjusting for sample storage time, maternal age and education, and both child asthma and vitamin D concentration at age 3 y did not modify the association between maternal postsupplement vitamin D and cluster membership (P = 0.0014). Maternal presupplement vitamin D did not influence cluster membership, whereas the combination of pre- and postsupplement concentrations did (P = 0.03).Conclusions: Young children can be clustered into distinct biologically meaningful groups by their metabolomics profiles. The clusters differed in concentrations of inflammatory mediators, and cluster membership was influenced by in utero vitamin D exposure, suggesting a prenatal programming role of vitamin D on the child's metabolome. This trial was registered at clinicaltrials.gov as NCT00920621.
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Affiliation(s)
- Kevin Blighe
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA; and
| | - Bo L Chawes
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA; and,Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Rachel S Kelly
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA; and
| | - Hooman Mirzakhani
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA; and
| | - Michael McGeachie
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA; and
| | - Augusto A Litonjua
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA; and
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA; and
| | - Jessica A Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; and
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25
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Kelly RS, Giorgio RT, Chawes BL, Palacios NI, Gray KJ, Mirzakhani H, Wu A, Blighe K, Weiss ST, Lasky-Su J. Applications of Metabolomics in the Study and Management of Preeclampsia; A Review of the Literature. Metabolomics 2017; 13:86. [PMID: 30473646 PMCID: PMC6247796 DOI: 10.1007/s11306-017-1225-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 06/05/2017] [Indexed: 12/12/2022]
Abstract
Introduction Preeclampsia represents a major public health burden worldwide, but predictive and diagnostic biomarkers are lacking. Metabolomics is emerging as a valuable approach to generating novel biomarkers whilst increasing the mechanistic understanding of this complex condition. Objectives To summarize the published literature on the use of metabolomics as a tool to study preeclampsia. Methods PubMed and Web of Science were searched for articles that performed metabolomic profiling of human biosamples using either Mass-spectrometry or Nuclear Magnetic Resonance based approaches and which included preeclampsia as a primary endpoint. Results Twenty-eight studies investigating the metabolome of preeclampsia in a variety of biospecimens were identified. Individual metabolite and metabolite profiles were reported to have discriminatory ability to distinguish preeclamptic from normal pregnancies, both prior to and post diagnosis. Lipids and carnitines were among the most commonly reported metabolites. Further work and validation studies are required to demonstrate the utility of such metabolites as preeclampsia biomarkers. Conclusion Metabolomic-based biomarkers of preeclampsia have yet to be integrated into routine clinical practice. However, metabolomic profiling is becoming increasingly popular in the study of preeclampsia and is likely to be a valuable tool to better understand the pathophysiology of this disorder and to better classify its subtypes, particularly when integrated with other omic data.
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Affiliation(s)
- Rachel S Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital Harvard Medical School, Boston MA 02115, USA
| | - Rachel T Giorgio
- Channing Division of Network Medicine, Brigham and Women's Hospital Harvard Medical School, Boston MA 02115, USA
| | - Bo L Chawes
- Channing Division of Network Medicine, Brigham and Women's Hospital Harvard Medical School, Boston MA 02115, USA
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Natalia I Palacios
- Department of Public Health University of Massachusetts, Lowell, Lowell MA
- Department of Nutrition, Harvard School of Public Health, Boston MA
| | - Kathryn J Gray
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Hoooman Mirzakhani
- Channing Division of Network Medicine, Brigham and Women's Hospital Harvard Medical School, Boston MA 02115, USA
| | - Ann Wu
- Boston Children's Hospital
| | - Kevin Blighe
- Channing Division of Network Medicine, Brigham and Women's Hospital Harvard Medical School, Boston MA 02115, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital Harvard Medical School, Boston MA 02115, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital Harvard Medical School, Boston MA 02115, USA
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26
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Boulianne B, Robinson ME, May PC, Castellano L, Blighe K, Thomas J, Reid A, Müschen M, Apperley JF, Stebbing J, Feldhahn N. Lineage-Specific Genes Are Prominent DNA Damage Hotspots during Leukemic Transformation of B Cell Precursors. Cell Rep 2017; 18:1687-1698. [PMID: 28199841 PMCID: PMC5318656 DOI: 10.1016/j.celrep.2017.01.057] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 04/22/2016] [Revised: 11/29/2016] [Accepted: 01/23/2017] [Indexed: 02/07/2023] Open
Abstract
In human leukemia, lineage-specific genes represent predominant targets of deletion, with lymphoid-specific genes frequently affected in lymphoid leukemia and myeloid-specific genes in myeloid leukemia. To investigate the basis of lineage-specific alterations, we analyzed global DNA damage in primary B cell precursors expressing leukemia-inducing oncogenes by ChIP-seq. We identified more than 1,000 sensitive regions, of which B lineage-specific genes constitute the most prominent targets. Identified hotspots at B lineage genes relate to DNA-DSBs, affect genes that harbor genomic lesions in human leukemia, and associate with ectopic deletion in successfully transformed cells. Furthermore, we show that most identified regions overlap with gene bodies of highly expressed genes and that induction of a myeloid lineage phenotype in transformed B cell precursors promotes de novo DNA damage at myeloid loci. Hence, we demonstrate that lineage-specific transcription predisposes lineage-specific genes in transformed B cell precursors to DNA damage, which is likely to promote the frequent alteration of lineage-specific genes in human leukemia.
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Affiliation(s)
- Bryant Boulianne
- Centre for Haematology, Department of Medicine, Imperial College London, W12 0NN London, UK
| | - Mark E Robinson
- Centre for Haematology, Department of Medicine, Imperial College London, W12 0NN London, UK; Division of Cancer, Department of Surgery and Cancer, Imperial College London, W12 0NN London, UK
| | - Philippa C May
- Centre for Haematology, Department of Medicine, Imperial College London, W12 0NN London, UK; Molecular Pathology, Imperial College Healthcare NHS Trust, W12 0NN London, UK
| | - Leandro Castellano
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, W12 0NN London, UK
| | - Kevin Blighe
- Centre for Haematology, Department of Medicine, Imperial College London, W12 0NN London, UK; Division of Cancer, Department of Surgery and Cancer, Imperial College London, W12 0NN London, UK
| | - Jennifer Thomas
- Centre for Haematology, Department of Medicine, Imperial College London, W12 0NN London, UK; Division of Cancer, Department of Surgery and Cancer, Imperial College London, W12 0NN London, UK
| | - Alistair Reid
- Centre for Haematology, Department of Medicine, Imperial College London, W12 0NN London, UK; Molecular Pathology, Imperial College Healthcare NHS Trust, W12 0NN London, UK
| | - Markus Müschen
- Department of Systems Biology, Beckman Research Institute and City of Hope Comprehensive Cancer Center, Pasadena, CA 91016, USA
| | - Jane F Apperley
- Centre for Haematology, Department of Medicine, Imperial College London, W12 0NN London, UK
| | - Justin Stebbing
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, W12 0NN London, UK
| | - Niklas Feldhahn
- Centre for Haematology, Department of Medicine, Imperial College London, W12 0NN London, UK.
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Mahto A, Humby F, Gregoriadou S, Ng N, Blighe K, Zou L, Lewis M, Bombardieri M, Kelly S, Pitzalis C. OP0263 Synovial B-Cell Gene Signature Predicts Response To Rituximab Therapy. Ann Rheum Dis 2016. [DOI: 10.1136/annrheumdis-2016-eular.5428] [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: 11/04/2022]
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Humby F, Dicicco M, Kelly S, Bombardieri M, Hands R, Rocher V, Zou L, Myles L, Blighe K, Ng N, Ramamoorthi N, Hackney J, Zuckerman N, Townsend M, Landewe R, Van der Helm van Mihl A, van der Heijde D, Buckely C, Taylor P, McInnes I, Pitzalis C. OP0240 Synovial Lymphocytic Aggregates Associate with Highly Active RA and Predict Erosive Disease Progression at 12 Months: Results from The Pathobiology of Early Arthritis Cohort. Ann Rheum Dis 2016. [DOI: 10.1136/annrheumdis-2016-eular.3229] [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: 11/04/2022]
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29
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Nerviani A, DiCicco M, Humby F, Kelly S, Zou L, Lewis M, Hands R, Rocher V, Blighe K, Bombardieri M, Pitzalis C. FRI0157 A Baseline Prediction Model for Response To Certolizumab-Pegol: Role of Synovial Histopathology. Ann Rheum Dis 2016. [DOI: 10.1136/annrheumdis-2016-eular.4218] [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: 11/04/2022]
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Stebbing J, Zhang H, Xu Y, Lit LC, Green AR, Grothey A, Lombardo Y, Periyasamy M, Blighe K, Zhang W, Shaw JA, Ellis IO, Lenz HJ, Giamas G. KSR1 regulates BRCA1 degradation and inhibits breast cancer growth. Oncogene 2015; 34:2103-14. [PMID: 24909178 DOI: 10.1038/onc.2014.129] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 04/02/2014] [Accepted: 04/12/2014] [Indexed: 12/16/2022]
Abstract
Kinase suppressor of Ras-1 (KSR1) facilitates signal transduction in Ras-dependent cancers, including pancreatic and lung carcinomas but its role in breast cancer has not been well studied. Here, we demonstrate for the first time it functions as a tumor suppressor in breast cancer in contrast to data in other tumors. Breast cancer patients (n>1000) with high KSR1 showed better disease-free and overall survival, results also supported by Oncomine analyses, microarray data (n=2878) and genomic data from paired tumor and cell-free DNA samples revealing loss of heterozygosity. KSR1 expression is associated with high breast cancer 1, early onset (BRCA1), high BRCA1-associated ring domain 1 (BARD1) and checkpoint kinase 1 (Chk1) levels. Phospho-profiling of major components of the canonical Ras-RAF-mitogen-activated protein kinases pathway showed no significant changes after KSR1 overexpression or silencing. Moreover, KSR1 stably transfected cells formed fewer and smaller size colonies compared to the parental ones, while in vivo mouse model also demonstrated that the growth of xenograft tumors overexpressing KSR1 was inhibited. The tumor suppressive action of KSR1 is BRCA1 dependent shown by 3D-matrigel and soft agar assays. KSR1 stabilizes BRCA1 protein levels by reducing BRCA1 ubiquitination through increasing BARD1 abundance. These data link these proteins in a continuum with clinical relevance and position KSR1 in the major oncoprotein pathways in breast tumorigenesis.
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Affiliation(s)
- J Stebbing
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial College Centre for Translational and Experimental Medicine, Hammersmith Hospital Campus, London, UK
| | - H Zhang
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial College Centre for Translational and Experimental Medicine, Hammersmith Hospital Campus, London, UK
| | - Y Xu
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial College Centre for Translational and Experimental Medicine, Hammersmith Hospital Campus, London, UK
| | - L C Lit
- 1] Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial College Centre for Translational and Experimental Medicine, Hammersmith Hospital Campus, London, UK [2] Faculty of Medicine, Department of Physiology, University of Malaya, Kuala, Lumpur, Malaysia
| | - A R Green
- Department of Cellular Pathology, Queen's Medical Centre, Nottingham University Hospital NHS Trust, Nottingham, UK
| | - A Grothey
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial College Centre for Translational and Experimental Medicine, Hammersmith Hospital Campus, London, UK
| | - Y Lombardo
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial College Centre for Translational and Experimental Medicine, Hammersmith Hospital Campus, London, UK
| | - M Periyasamy
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial College Centre for Translational and Experimental Medicine, Hammersmith Hospital Campus, London, UK
| | - K Blighe
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester, UK
| | - W Zhang
- Division of Medical Oncology, University of Southern California, Norris Comprehensive Cancer Centre, Keck School of Medicine, Los Angeles, CA, USA
| | - J A Shaw
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester, UK
| | - I O Ellis
- Faculty of Medicine, Department of Physiology, University of Malaya, Kuala, Lumpur, Malaysia
| | - H J Lenz
- Division of Medical Oncology, University of Southern California, Norris Comprehensive Cancer Centre, Keck School of Medicine, Los Angeles, CA, USA
| | - G Giamas
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial College Centre for Translational and Experimental Medicine, Hammersmith Hospital Campus, London, UK
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Blighe K, Kenny L, Patel N, Guttery DS, Page K, Gronau JH, Golshani C, Stebbing J, Coombes RC, Shaw JA. Whole genome sequence analysis suggests intratumoral heterogeneity in dissemination of breast cancer to lymph nodes. PLoS One 2014; 9:e115346. [PMID: 25546409 PMCID: PMC4278903 DOI: 10.1371/journal.pone.0115346] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 11/22/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Intratumoral heterogeneity may help drive resistance to targeted therapies in cancer. In breast cancer, the presence of nodal metastases is a key indicator of poorer overall survival. The aim of this study was to identify somatic genetic alterations in early dissemination of breast cancer by whole genome next generation sequencing (NGS) of a primary breast tumor, a matched locally-involved axillary lymph node and healthy normal DNA from blood. METHODS Whole genome NGS was performed on 12 µg (range 11.1-13.3 µg) of DNA isolated from fresh-frozen primary breast tumor, axillary lymph node and peripheral blood following the DNA nanoball sequencing protocol. Single nucleotide variants, insertions, deletions, and substitutions were identified through a bioinformatic pipeline and compared to CIN25, a key set of genes associated with tumor metastasis. RESULTS Whole genome sequencing revealed overlapping variants between the tumor and node, but also variants that were unique to each. Novel mutations unique to the node included those found in two CIN25 targets, TGIF2 and CCNB2, which are related to transcription cyclin activity and chromosomal stability, respectively, and a unique frameshift in PDS5B, which is required for accurate sister chromatid segregation during cell division. We also identified dominant clonal variants that progressed from tumor to node, including SNVs in TP53 and ARAP3, which mediates rearrangements to the cytoskeleton and cell shape, and an insertion in TOP2A, the expression of which is significantly associated with tumor proliferation and can segregate breast cancers by outcome. CONCLUSION This case study provides preliminary evidence that primary tumor and early nodal metastasis have largely overlapping somatic genetic alterations. There were very few mutations unique to the involved node. However, significant conclusions regarding early dissemination needs analysis of a larger number of patient samples.
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Affiliation(s)
- Kevin Blighe
- Department of Cancer Studies and Molecular Medicine, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, United Kingdom
| | - Laura Kenny
- Division of Cancer, Imperial College, Hammersmith Hospital Campus, London, W12 0NN, United Kingdom
| | - Naina Patel
- Division of Cancer, Imperial College, Hammersmith Hospital Campus, London, W12 0NN, United Kingdom
| | - David S. Guttery
- Department of Cancer Studies and Molecular Medicine, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, United Kingdom
| | - Karen Page
- Department of Cancer Studies and Molecular Medicine, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, United Kingdom
| | - Julian H. Gronau
- Division of Cancer, Imperial College, Hammersmith Hospital Campus, London, W12 0NN, United Kingdom
| | - Cyrus Golshani
- Division of Cancer, Imperial College, Hammersmith Hospital Campus, London, W12 0NN, United Kingdom
| | - Justin Stebbing
- Division of Cancer, Imperial College, Hammersmith Hospital Campus, London, W12 0NN, United Kingdom
| | - R. Charles Coombes
- Division of Cancer, Imperial College, Hammersmith Hospital Campus, London, W12 0NN, United Kingdom
| | - Jacqueline A. Shaw
- Department of Cancer Studies and Molecular Medicine, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, United Kingdom
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Page K, Guttery DS, Zahra N, Primrose L, Elshaw SR, Pringle JH, Blighe K, Marchese SD, Hills A, Woodley L, Stebbing J, Coombes RC, Shaw JA. Influence of plasma processing on recovery and analysis of circulating nucleic acids. PLoS One 2013; 8:e77963. [PMID: 24205045 PMCID: PMC3799744 DOI: 10.1371/journal.pone.0077963] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 09/06/2013] [Indexed: 12/20/2022] Open
Abstract
Circulating nucleic acids (CNAs) are under investigation as a liquid biopsy in cancer. However there is wide variation in blood processing and methods for isolation of circulating free DNA (cfDNA) and microRNAs (miRNAs). Here we compare the extraction efficiency and reproducibility of 4 commercially available kits for cfDNA and 3 for miRNA using spike-in of reference templates. We also compare the effects of increasing time between venepuncture and centrifugation and differential centrifugation force on recovery of CNAs. cfDNA was quantified by TaqMan qPCR and targeted deep sequencing. miRNA profiles were assessed with TaqMan low-density arrays and assays. The QIAamp(®) DNA Blood Mini and Circulating nucleic acid kits gave the highest recovery of cfDNA and efficient recovery (>90%) of a 564bp spike-in. Moreover, targeted sequencing revealed overlapping cfDNA profiles and variant depth, including detection of HER2 gene amplification, using the Ion AmpliSeq™Cancer Hotspot Panel v2. Highest yields of miRNA and the synthetic Arabidopsis thaliana miR-159a spike-in were obtained using the miRNeasy Serum/Plasma kit, with saturation above 200 µl of plasma. miRNA profiles showed significant variation with increasing time before centrifugation (p<0.001) and increasing centrifugation force, with depletion of platelet associated miRNAs, whereas cfDNA was unaffected. However, sample replicates showed excellent reproducibility on TaqMan low density arrays (ρ = 0.96, p<0.0001). We also successfully generated miRNA profiles for plasma samples stored > 12 years, highlighting the potential for analysis of stored sample biobanks. In the era of the liquid biopsy, standardisation of methods is required to minimise variation, particularly for miRNA.
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Affiliation(s)
- Karen Page
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester Royal Infirmary, Leicester, United Kingdom
| | - David S. Guttery
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester Royal Infirmary, Leicester, United Kingdom
| | - Nathalie Zahra
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester Royal Infirmary, Leicester, United Kingdom
| | - Lindsay Primrose
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester Royal Infirmary, Leicester, United Kingdom
| | - Shona R. Elshaw
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester Royal Infirmary, Leicester, United Kingdom
| | - J. Howard Pringle
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester Royal Infirmary, Leicester, United Kingdom
| | - Kevin Blighe
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester Royal Infirmary, Leicester, United Kingdom
| | | | - Allison Hills
- Division of Cancer, ICTEM, Hammersmith Campus, London, United Kingdom
| | - Laura Woodley
- Division of Cancer, ICTEM, Hammersmith Campus, London, United Kingdom
| | - Justin Stebbing
- Division of Cancer, ICTEM, Hammersmith Campus, London, United Kingdom
| | | | - Jacqueline A. Shaw
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester Royal Infirmary, Leicester, United Kingdom
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Stebbing J, Filipovic A, Lit LC, Blighe K, Grothey A, Xu Y, Miki Y, Chow LW, Coombes RC, Sasano H, Shaw JA, Giamas G. LMTK3 is implicated in endocrine resistance via multiple signaling pathways. Oncogene 2013; 32:3371-80. [PMID: 22869149 DOI: 10.1038/onc.2012.343] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [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: 06/04/2012] [Revised: 06/20/2012] [Accepted: 06/21/2012] [Indexed: 02/07/2023]
Abstract
Resistance to endocrine therapy in breast cancer is common. With the aim of discovering new molecular targets for breast cancer therapy, we have recently identified LMTK3 as a regulator of the estrogen receptor-alpha (ERα) and wished to understand its role in endocrine resistance. We find that inhibition of LMTK3 in a xenograft tamoxifen (Tam)-resistant (BT474) breast cancer mouse model results in re-sensitization to Tam as demonstrated by a reduction in tumor volume. A whole genome microarray analysis, using a BT474 cell line, reveals genes significantly modulated (positively or negatively) after LMTK3 silencing, including some that are known to be implicated in Tam resistance, notably c-MYC, HSPB8 and SIAH2. We show that LMTK3 is able to increase the levels of HSPB8 at a transcriptional and translational level thereby protecting MCF7 cells from Tam-induced cell death, by reducing autophagy. Finally, high LMTK3 levels at baseline in tumors are predictive for endocrine resistance; therapy does not lead to alteration in levels, whereas in patient's plasma samples, acquired LMTK3 gene amplification (copy number variation) was associated with relapse while receiving Tam. In aggregate, these data support a role for LMTK3 in both innate (intrinsic) and acquired (adaptive) endocrine resistance in breast cancer.
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Affiliation(s)
- J Stebbing
- Department of Surgery and Cancer, Division of Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, UK
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Abstract
Breast cancer treatment is improving due to the introduction of new drugs, guided by molecular testing of the primary tumour for mutations/oncogenic drivers (e.g. HER2 gene amplification). However, tumour tissue is not always available for molecular analysis, intra-tumoural heterogeneity is common and the "cancer genome" is known to evolve with time, particularly following treatment as resistance develops. After resection, those patients with only residual micrometastases are likely to be cured but those with radiologically detectable overt disease are not. Thus, the discovery of blood test(s) that could (1) alert clinicians to early primary or recurrent disease and (2) monitor response to treatment could impact significantly on mortality. Towards this, we and others have focused on molecular profiling of circulating nucleic acids isolated from plasma, both cell-free DNA (cfDNA) and microRNAs, and the relationship of these to circulating tumour cells (CTCs). This review considers the utility of each as circulating biomarkers in breast cancer with particular emphasis on the bioinformatic tools available to support molecular profiling.
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Affiliation(s)
- David S Guttery
- Department of Cancer Studies and Molecular Medicine, Leicester Royal Infirmary, Leicester, UK.
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Shaw JA, Page K, Blighe K, Hava N, Guttery D, Ward B, Brown J, Ruangpratheep C, Stebbing J, Payne R, Palmieri C, Cleator S, Walker RA, Coombes RC. Genomic analysis of circulating cell-free DNA infers breast cancer dormancy. Genome Res 2012; 22:220-31. [PMID: 21990379 PMCID: PMC3266030 DOI: 10.1101/gr.123497.111] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [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: 04/20/2011] [Accepted: 08/16/2011] [Indexed: 11/24/2022]
Abstract
Biomarkers in breast cancer to monitor minimal residual disease have remained elusive. We hypothesized that genomic analysis of circulating free DNA (cfDNA) isolated from plasma may form the basis for a means of detecting and monitoring breast cancer. We profiled 251 genomes using Affymetrix SNP 6.0 arrays to determine copy number variations (CNVs) and loss of heterozygosity (LOH), comparing 138 cfDNA samples with matched primary tumor and normal leukocyte DNA in 65 breast cancer patients and eight healthy female controls. Concordance of SNP genotype calls in paired cfDNA and leukocyte DNA samples distinguished between breast cancer patients and healthy female controls (P < 0.0001) and between preoperative patients and patients on follow-up who had surgery and treatment (P = 0.0016). Principal component analyses of cfDNA SNP/copy number results also separated presurgical breast cancer patients from the healthy controls, suggesting specific CNVs in cfDNA have clinical significance. We identified focal high-level DNA amplification in paired tumor and cfDNA clustered in a number of chromosome arms, some of which harbor genes with oncogenic potential, including USP17L2 (DUB3), BRF1, MTA1, and JAG2. Remarkably, in 50 patients on follow-up, specific CNVs were detected in cfDNA, mirroring the primary tumor, up to 12 yr after diagnosis despite no other evidence of disease. These data demonstrate the potential of SNP/CNV analysis of cfDNA to distinguish between patients with breast cancer and healthy controls during routine follow-up. The genomic profiles of cfDNA infer dormancy/minimal residual disease in the majority of patients on follow-up.
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Affiliation(s)
- Jacqueline A Shaw
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester LE2 7LX, United Kingdom.
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Payne RE, Hava NL, Page K, Blighe K, Ward B, Slade M, Brown J, Guttery DS, Zaidi SAA, Stebbing J, Jacob J, Yagüe E, Shaw JA, Coombes RC. The presence of disseminated tumour cells in the bone marrow is inversely related to circulating free DNA in plasma in breast cancer dormancy. Br J Cancer 2012; 106:375-82. [PMID: 22166803 PMCID: PMC3261674 DOI: 10.1038/bjc.2011.537] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 09/29/2011] [Accepted: 11/10/2011] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The aim of this study was to gain insight into breast cancer dormancy by examining different measures of minimal residual disease (MRD) over time in relation to known prognostic factors. METHODS Sixty-four primary breast cancer patients on follow-up (a median of 8.3 years post surgery) who were disease free had sequential bone marrow aspirates and blood samples taken for the measurement of disseminated tumour cells (DTCs), circulating tumour cells (CTCs) by CellSearch and qPCR measurement of overlapping (96-bp and 291-bp) amplicons in circulating free DNA (cfDNA). RESULTS The presence of CTCs was correlated with the presence of DTCs measured by immunocytochemistry (P=0.01) but both were infrequently detected. Increasing cfDNA concentration correlated with ER, HER2 and triple-negative tumours and high tumour grade, and the 291-bp amplicon was inversely correlated with DTCs measured by CK19 qRT-PCR (P=0.047). CONCLUSION Our results show that breast cancer patients have evidence of MRD for many years after diagnosis despite there being no overt evidence of disease. The inverse relationship between bone marrow CK19 mRNA and the 291-bp amplicon in cfDNA suggests that an inverse relationship between a measure of cell viability in the bone marrow (DTCs) and cell death in the plasma occurs during the dormancy phase of breast cancer.
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Affiliation(s)
- R E Payne
- Division of Cancer, Imperial College, MRC Cyclotron Building, Imperial College Healthcare NHS Trust, Hammersmith Hospital, Du Cane Road, London W12 ONN, UK
| | - N L Hava
- Division of Cancer, Imperial College, MRC Cyclotron Building, Imperial College Healthcare NHS Trust, Hammersmith Hospital, Du Cane Road, London W12 ONN, UK
| | - K Page
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Robert Kilpatrick Building, PO Box 65, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - K Blighe
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Robert Kilpatrick Building, PO Box 65, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - B Ward
- Department of Medical Oncology, Charing Cross Hospital, London W6 8RF, UK
| | - M Slade
- Division of Cancer, Imperial College, MRC Cyclotron Building, Imperial College Healthcare NHS Trust, Hammersmith Hospital, Du Cane Road, London W12 ONN, UK
| | - J Brown
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Robert Kilpatrick Building, PO Box 65, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - D S Guttery
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Robert Kilpatrick Building, PO Box 65, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - S A A Zaidi
- Division of Cancer, Imperial College, MRC Cyclotron Building, Imperial College Healthcare NHS Trust, Hammersmith Hospital, Du Cane Road, London W12 ONN, UK
| | - J Stebbing
- Division of Cancer, Imperial College, MRC Cyclotron Building, Imperial College Healthcare NHS Trust, Hammersmith Hospital, Du Cane Road, London W12 ONN, UK
| | - J Jacob
- Division of Cancer, Imperial College, MRC Cyclotron Building, Imperial College Healthcare NHS Trust, Hammersmith Hospital, Du Cane Road, London W12 ONN, UK
| | - E Yagüe
- Division of Cancer, Imperial College, MRC Cyclotron Building, Imperial College Healthcare NHS Trust, Hammersmith Hospital, Du Cane Road, London W12 ONN, UK
| | - J A Shaw
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Robert Kilpatrick Building, PO Box 65, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - R C Coombes
- Division of Cancer, Imperial College, MRC Cyclotron Building, Imperial College Healthcare NHS Trust, Hammersmith Hospital, Du Cane Road, London W12 ONN, UK
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Shaw JA, Page K, Blighe K, Hava N, Guttery D, Ward B, Brown J, Ruangpratheep C, Payne R, Palmieri C, Cleator S, Walker R, Coombes C. A molecular portrait of circulating free DNA of patients with breast cancer: High-resolution analysis using SNP 6.0 arrays. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.555] [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: 11/20/2022] Open
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Page K, Hava N, Ward B, Brown J, Guttery DS, Ruangpratheep C, Blighe K, Sharma A, Walker RA, Coombes RC, Shaw JA. Detection of HER2 amplification in circulating free DNA in patients with breast cancer. Br J Cancer 2011; 104:1342-8. [PMID: 21427727 PMCID: PMC3078598 DOI: 10.1038/bjc.2011.89] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [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: 12/27/2022] Open
Abstract
BACKGROUND Human epidermal growth factor receptor 2 (HER2) is amplified and overexpressed in 20-25% of breast cancers. This study investigated circulating free DNA (cfDNA) for detection of HER2 gene amplification in patients with breast cancer. METHODS Circulating free DNA was extracted from plasma of unselected patients with primary breast cancer (22 before surgery and 68 following treatment), 30 metastatic patients and 98 female controls using the QIAamp Blood DNA Mini Kit (Qiagen). The ratio of HER2 to an unamplified reference gene (contactin-associated protein 1 (CNTNAP1)) was measured in cfDNA samples by quantitative PCR (qPCR) using SK-BR-3 cell line DNA as a positive control. RESULTS We validated the qPCR assay with DNA extracted from 23 HER2 3+ and 40 HER2-negative tumour tissue samples; the results agreed for 60 of 63 (95.2%) tumours. Amplification was detected in cfDNA for 8 of 68 patients following primary breast cancer treatment and 5 of 30 metastatic patients, but was undetected in 22 patients with primary breast cancer and 98 healthy female controls. Of the patients with amplification in cfDNA, 10 had HER2 3+ tumour status by immunohistochemistry. CONCLUSIONS The results demonstrate for the first time the existence of amplified HER2 in cfDNA in the follow-up of breast cancer patients who are otherwise disease free. This approach could potentially provide a marker in patients with HER2-positive breast cancer.
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Affiliation(s)
- K Page
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Robert Kilpatrick Building, PO Box 65, Leicester Royal Infirmary, Leicester LE2 7LX, UK
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