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Stewart BJ, Ferdinand JR, Young MD, Mitchell TJ, Loudon KW, Riding AM, Richoz N, Frazer GL, Staniforth JUL, Braga FAV, Botting RA, Popescu DM, Vento-Tormo R, Stephenson E, Cagan A, Farndon SJ, Polanski K, Efremova M, Green K, Velasco-Herrera MDC, Guzzo C, Collord G, Mamanova L, Aho T, Armitage JN, Riddick ACP, Mushtaq I, Farrell S, Rampling D, Nicholson J, Filby A, Burge J, Lisgo S, Lindsay S, Bajenoff M, Warren AY, Stewart GD, Sebire N, Coleman N, Haniffa M, Teichmann SA, Behjati S, Clatworthy MR. Spatiotemporal immune zonation of the human kidney. Science 2019; 365:1461-1466. [PMID: 31604275 PMCID: PMC7343525 DOI: 10.1126/science.aat5031] [Citation(s) in RCA: 228] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 01/31/2019] [Accepted: 09/04/2019] [Indexed: 11/02/2022]
Abstract
Tissue-resident immune cells are important for organ homeostasis and defense. The epithelium may contribute to these functions directly or by cross-talk with immune cells. We used single-cell RNA sequencing to resolve the spatiotemporal immune topology of the human kidney. We reveal anatomically defined expression patterns of immune genes within the epithelial compartment, with antimicrobial peptide transcripts evident in pelvic epithelium in the mature, but not fetal, kidney. A network of tissue-resident myeloid and lymphoid immune cells was evident in both fetal and mature kidney, with postnatal acquisition of transcriptional programs that promote infection-defense capabilities. Epithelial-immune cross-talk orchestrated localization of antibacterial macrophages and neutrophils to the regions of the kidney most susceptible to infection. Overall, our study provides a global overview of how the immune landscape of the human kidney is zonated to counter the dominant immunological challenge.
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Affiliation(s)
- Benjamin J Stewart
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - John R Ferdinand
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
| | - Matthew D Young
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Thomas J Mitchell
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Surgery, University of Cambridge, CB2 0QQ, UK
| | - Kevin W Loudon
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Alexandra M Riding
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Nathan Richoz
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
| | - Gordon L Frazer
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
| | - Joy UL Staniforth
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
| | | | - Rachel A Botting
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Dorin-Mirel Popescu
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Emily Stephenson
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Alex Cagan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Sarah J Farndon
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3JH, UK
- UCL Great Ormond Street Hospital Institute of Child Health, London WC1N 1E, UK
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Mirjana Efremova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Kile Green
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | | | - Charlotte Guzzo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Grace Collord
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Tevita Aho
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - James N Armitage
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Antony CP Riddick
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Imran Mushtaq
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3JH, UK
| | - Stephen Farrell
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Dyanne Rampling
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3JH, UK
| | - James Nicholson
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Andrew Filby
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Johanna Burge
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Steven Lisgo
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Susan Lindsay
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Marc Bajenoff
- Centre d’Immunologie de Marseille-Luminy, Marseille, France
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Grant D Stewart
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Department of Surgery, University of Cambridge, CB2 0QQ, UK
| | - Neil Sebire
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3JH, UK
- UCL Great Ormond Street Hospital Institute of Child Health, London WC1N 1E, UK
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Department of Dermatology and NIHR Newcastle Biomedical research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
| | - Sam Behjati
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
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2
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Syafruddin SE, Rodrigues P, Vojtasova E, Patel SA, Zaini MN, Burge J, Warren AY, Stewart GD, Eisen T, Bihary D, Samarajiwa SA, Vanharanta S. A KLF6-driven transcriptional network links lipid homeostasis and tumour growth in renal carcinoma. Nat Commun 2019; 10:1152. [PMID: 30858363 PMCID: PMC6411998 DOI: 10.1038/s41467-019-09116-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 02/15/2019] [Indexed: 12/17/2022] Open
Abstract
Transcriptional networks are critical for the establishment of tissue-specific cellular states in health and disease, including cancer. Yet, the transcriptional circuits that control carcinogenesis remain poorly understood. Here we report that Kruppel like factor 6 (KLF6), a transcription factor of the zinc finger family, regulates lipid homeostasis in clear cell renal cell carcinoma (ccRCC). We show that KLF6 supports the expression of lipid metabolism genes and promotes the expression of PDGFB, which activates mTOR signalling and the downstream lipid metabolism regulators SREBF1 and SREBF2. KLF6 expression is driven by a robust super enhancer that integrates signals from multiple pathways, including the ccRCC-initiating VHL-HIF2A pathway. These results suggest an underlying mechanism for high mTOR activity in ccRCC cells. More generally, the link between super enhancer-driven transcriptional networks and essential metabolic pathways may provide clues to the mechanisms that maintain the stability of cell identity-defining transcriptional programmes in cancer. Super enhancers are frequently involved in the dysregulation of gene expression in cancer. Here, in kidney cancer, a super enhancer is shown to drive the expression of KLF6, which alters the expression of lipid metabolism genes and promotes tumorigenesis.
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Affiliation(s)
- Saiful E Syafruddin
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK.,UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur, 56000, Malaysia
| | - Paulo Rodrigues
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Erika Vojtasova
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Saroor A Patel
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - M Nazhif Zaini
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Johanna Burge
- Academic Urology Group, Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Grant D Stewart
- Academic Urology Group, Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Tim Eisen
- Department of Oncology, University of Cambridge, Cambridge, CB2 0XZ, UK.,Department of Oncology, Addenbrooke's Hospital, Cambridge University Health Partners, Cambridge, CB2 0QQ, UK.,Oncology Early Clinical Development, AstraZeneca, Cambridge, SG8 6EH, UK
| | - Dóra Bihary
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Shamith A Samarajiwa
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Sakari Vanharanta
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK.
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3
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Mouliere F, Chandrananda D, Piskorz AM, Moore EK, Morris J, Ahlborn LB, Mair R, Goranova T, Marass F, Heider K, Wan JCM, Supernat A, Hudecova I, Gounaris I, Ros S, Jimenez-Linan M, Garcia-Corbacho J, Patel K, Østrup O, Murphy S, Eldridge MD, Gale D, Stewart GD, Burge J, Cooper WN, van der Heijden MS, Massie CE, Watts C, Corrie P, Pacey S, Brindle KM, Baird RD, Mau-Sørensen M, Parkinson CA, Smith CG, Brenton JD, Rosenfeld N. Enhanced detection of circulating tumor DNA by fragment size analysis. Sci Transl Med 2018; 10:eaat4921. [PMID: 30404863 PMCID: PMC6483061 DOI: 10.1126/scitranslmed.aat4921] [Citation(s) in RCA: 555] [Impact Index Per Article: 92.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 10/17/2018] [Indexed: 12/13/2022]
Abstract
Existing methods to improve detection of circulating tumor DNA (ctDNA) have focused on genomic alterations but have rarely considered the biological properties of plasma cell-free DNA (cfDNA). We hypothesized that differences in fragment lengths of circulating DNA could be exploited to enhance sensitivity for detecting the presence of ctDNA and for noninvasive genomic analysis of cancer. We surveyed ctDNA fragment sizes in 344 plasma samples from 200 patients with cancer using low-pass whole-genome sequencing (0.4×). To establish the size distribution of mutant ctDNA, tumor-guided personalized deep sequencing was performed in 19 patients. We detected enrichment of ctDNA in fragment sizes between 90 and 150 bp and developed methods for in vitro and in silico size selection of these fragments. Selecting fragments between 90 and 150 bp improved detection of tumor DNA, with more than twofold median enrichment in >95% of cases and more than fourfold enrichment in >10% of cases. Analysis of size-selected cfDNA identified clinically actionable mutations and copy number alterations that were otherwise not detected. Identification of plasma samples from patients with advanced cancer was improved by predictive models integrating fragment length and copy number analysis of cfDNA, with area under the curve (AUC) >0.99 compared to AUC <0.80 without fragmentation features. Increased identification of cfDNA from patients with glioma, renal, and pancreatic cancer was achieved with AUC > 0.91 compared to AUC < 0.5 without fragmentation features. Fragment size analysis and selective sequencing of specific fragment sizes can boost ctDNA detection and could complement or provide an alternative to deeper sequencing of cfDNA.
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Affiliation(s)
- Florent Mouliere
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Dineika Chandrananda
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Anna M Piskorz
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Elizabeth K Moore
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK
| | - James Morris
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Lise Barlebo Ahlborn
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark
- Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark
| | - Richard Mair
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Division of Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, CB2 0QQ Cambridge, UK
| | - Teodora Goranova
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Francesco Marass
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Katrin Heider
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Jonathan C M Wan
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Anna Supernat
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Department of Medical Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, 80-211 Gdańsk, Poland
| | - Irena Hudecova
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Ioannis Gounaris
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK
| | - Susana Ros
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Mercedes Jimenez-Linan
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK
| | - Javier Garcia-Corbacho
- Clinical Trials Unit, Clinic Institute of Haematological and Oncological Diseases, Hospital Clinic de Barcelona, 170 08036 Barcelona, Spain
| | - Keval Patel
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Olga Østrup
- Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark
| | - Suzanne Murphy
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Matthew D Eldridge
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Davina Gale
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Grant D Stewart
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK
- Academic Urology Group, Department of Surgery, University of Cambridge, CB2 0QQ Cambridge, UK
| | - Johanna Burge
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Academic Urology Group, Department of Surgery, University of Cambridge, CB2 0QQ Cambridge, UK
| | - Wendy N Cooper
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - Michiel S van der Heijden
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Charles E Massie
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Department of Oncology, University of Cambridge, CB2 0XZ Cambridge, UK
| | - Colin Watts
- Institute of Cancer Genomics Science, University of Birmingham, B15 2TT Birmingham, UK
| | - Pippa Corrie
- Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK
| | - Simon Pacey
- Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK
- Department of Oncology, University of Cambridge, CB2 0XZ Cambridge, UK
| | - Kevin M Brindle
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Department of Biochemistry, University of Cambridge, CB2 1QW Cambridge, UK
| | - Richard D Baird
- Early Phase Clinical Trials and Breast Cancer Research Teams, Cancer Research UK Cambridge Centre, CB2 0QQ Cambridge, UK
| | - Morten Mau-Sørensen
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark
| | - Christine A Parkinson
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, CB2 0XZ Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, CB2 0QQ Cambridge, UK
| | - Christopher G Smith
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, CB2 0XZ Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, CB2 0QQ Cambridge, UK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK
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4
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Young MD, Mitchell TJ, Vieira Braga FA, Tran MGB, Stewart BJ, Ferdinand JR, Collord G, Botting RA, Popescu DM, Loudon KW, Vento-Tormo R, Stephenson E, Cagan A, Farndon SJ, Del Castillo Velasco-Herrera M, Guzzo C, Richoz N, Mamanova L, Aho T, Armitage JN, Riddick ACP, Mushtaq I, Farrell S, Rampling D, Nicholson J, Filby A, Burge J, Lisgo S, Maxwell PH, Lindsay S, Warren AY, Stewart GD, Sebire N, Coleman N, Haniffa M, Teichmann SA, Clatworthy M, Behjati S. Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors. Science 2018; 361:594-599. [PMID: 30093597 PMCID: PMC6104812 DOI: 10.1126/science.aat1699] [Citation(s) in RCA: 426] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 07/02/2018] [Indexed: 12/20/2022]
Abstract
Messenger RNA encodes cellular function and phenotype. In the context of human cancer, it defines the identities of malignant cells and the diversity of tumor tissue. We studied 72,501 single-cell transcriptomes of human renal tumors and normal tissue from fetal, pediatric, and adult kidneys. We matched childhood Wilms tumor with specific fetal cell types, thus providing evidence for the hypothesis that Wilms tumor cells are aberrant fetal cells. In adult renal cell carcinoma, we identified a canonical cancer transcriptome that matched a little-known subtype of proximal convoluted tubular cell. Analyses of the tumor composition defined cancer-associated normal cells and delineated a complex vascular endothelial growth factor (VEGF) signaling circuit. Our findings reveal the precise cellular identities and compositions of human kidney tumors.
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Affiliation(s)
| | - Thomas J Mitchell
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | | | - Maxine G B Tran
- UCL Division of Surgery and Interventional Science, Royal Free Hospital, London NW3 2PS, UK
- Specialist Centre for Kidney Cancer, Royal Free Hospital, London NW3 2PS, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | - John R Ferdinand
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | - Grace Collord
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Rachel A Botting
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Dorin-Mirel Popescu
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Kevin W Loudon
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | | | - Emily Stephenson
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Alex Cagan
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Sarah J Farndon
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
- UCL Great Ormond Street Hospital Institute of Child Health, London WC1N 1E, UK
| | | | | | - Nathan Richoz
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | | | - Tevita Aho
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - James N Armitage
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | | | - Imran Mushtaq
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Stephen Farrell
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Dyanne Rampling
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - James Nicholson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Andrew Filby
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Johanna Burge
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Steven Lisgo
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Patrick H Maxwell
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Susan Lindsay
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Grant D Stewart
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Neil Sebire
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
- UCL Great Ormond Street Hospital Institute of Child Health, London WC1N 1E, UK
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
- Department of Dermatology, Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | | | - Menna Clatworthy
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK.
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
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5
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Rodrigues P, Patel SA, Harewood L, Olan I, Vojtasova E, Syafruddin SE, Zaini MN, Richardson EK, Burge J, Warren AY, Stewart GD, Saeb-Parsy K, Samarajiwa SA, Vanharanta S. NF-κB-Dependent Lymphoid Enhancer Co-option Promotes Renal Carcinoma Metastasis. Cancer Discov 2018; 8:850-865. [PMID: 29875134 PMCID: PMC6031301 DOI: 10.1158/2159-8290.cd-17-1211] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 03/26/2018] [Accepted: 05/01/2018] [Indexed: 01/10/2023]
Abstract
Metastases, the spread of cancer cells to distant organs, cause the majority of cancer-related deaths. Few metastasis-specific driver mutations have been identified, suggesting aberrant gene regulation as a source of metastatic traits. However, how metastatic gene expression programs arise is poorly understood. Here, using human-derived metastasis models of renal cancer, we identify transcriptional enhancers that promote metastatic carcinoma progression. Specific enhancers and enhancer clusters are activated in metastatic cancer cell populations, and the associated gene expression patterns are predictive of poor patient outcome in clinical samples. We find that the renal cancer metastasis-associated enhancer complement consists of multiple coactivated tissue-specific enhancer modules. Specifically, we identify and functionally characterize a coregulatory enhancer cluster, activated by the renal cancer driver HIF2A and an NF-κB-driven lymphoid element, as a mediator of metastasis in vivo We conclude that oncogenic pathways can acquire metastatic phenotypes through cross-lineage co-option of physiologic epigenetic enhancer states.Significance: Renal cancer is associated with significant mortality due to metastasis. We show that in metastatic renal cancer, functionally important metastasis genes are activated via co-option of gene regulatory enhancer modules from distant developmental lineages, thus providing clues to the origins of metastatic cancer. Cancer Discov; 8(7); 850-65. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 781.
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Affiliation(s)
- Paulo Rodrigues
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Saroor A Patel
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Louise Harewood
- Cancer Research UK/Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Ioana Olan
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Erika Vojtasova
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Saiful E Syafruddin
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Jalan Yaa'cob Latiff, Bandar Tun Razak, Kuala Lumpur, Malaysia
| | - M Nazhif Zaini
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Emma K Richardson
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Johanna Burge
- Academic Urology Group, Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Grant D Stewart
- Academic Urology Group, Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Shamith A Samarajiwa
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Sakari Vanharanta
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom.
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Suetterlin K, Sud R, Burge J, McCall S, Fialho D, Haworth A, Sweeney M, Houlden H, Schorge S, Matthews E, Hanna M, Mannikko R. Large scale validation of functional expression of ClC-1 variants in genetic counselling of myotonia congenital. Neuromuscul Disord 2017. [DOI: 10.1016/j.nmd.2017.06.260] [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: 11/24/2022]
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7
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Suetterlin K, Sud R, Burge J, McCall S, Fialho D, Haworth A, Sweeney M, Houlden H, Schorge S, Matthews E, Hanna M, Männikkö R. Improving genetic diagnosis and counselling for patients with myotoniacongenita. Neuromuscul Disord 2017. [DOI: 10.1016/s0960-8966(17)30320-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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8
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Thomas BC, Kay JD, Menon S, Vowler SL, Dawson SN, Bucklow LJ, Luxton HJ, Johnston T, Massie CE, Pugh M, Warren AY, Barker P, Burling K, Lynch AG, George A, Burge J, Corcoran M, Stearn S, Lamb AD, Sharma NL, Shaw GL, Neal DE, Whitaker HC. Whole blood mRNA in prostate cancer reveals a four-gene androgen regulated panel. Endocr Relat Cancer 2016; 23:797-812. [PMID: 27578825 DOI: 10.1530/erc-16-0287] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 08/10/2016] [Indexed: 01/05/2023]
Abstract
Due to increased sensitivity, the expression of circulating nucleotides is rapidly gaining popularity in cancer diagnosis. Whole blood mRNA has been used in studies on a number of cancers, most notably two separate studies that used whole blood mRNA to define non-overlapping signatures of prostate cancer that has become castration independent. Prostate cancer is known to rely on androgens for initial growth, and there is increasing evidence on the importance of the androgen axis in advanced disease. Using whole blood mRNA samples from patients with prostate cancer, we have identified the four-gene panel of FAM129A, MME, KRT7 and SOD2 in circulating mRNA that are differentially expressed in a discovery cohort of metastatic samples. Validation of these genes at the mRNA and protein level was undertaken in additional cohorts defined by risk of relapse following surgery and hormone status. All the four genes were downregulated at the mRNA level in the circulation and in primary tissue, but this was not always reflected in tissue protein expression. MME demonstrated significant differences in the hormone cohorts, whereas FAM129A is downregulated at the mRNA level but is raised at the protein level in tumours. Using published ChIP-seq data, we have demonstrated that this may be due to AR binding at the FAM129A and MME loci in multiple cell lines. These data suggest that whole blood mRNA of androgen-regulated genes has the potential to be used for diagnosis and monitoring of prostate cancer.
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Affiliation(s)
- Benjamin C Thomas
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Biomarker InitiativeCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Jonathan D Kay
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Biomarker InitiativeCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Molecular Diagnostics and Therapeutics GroupUniversity College London, London, UK
| | - Suraj Menon
- Bioinformatics and Statistics Core FacilityCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Astra Zeneca2 Riverside, Granta Park, Cambridge, UK
| | - Sarah L Vowler
- Bioinformatics and Statistics Core FacilityCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Astra Zeneca2 Riverside, Granta Park, Cambridge, UK
| | - Sarah N Dawson
- Bioinformatics and Statistics Core FacilityCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Laura J Bucklow
- Biomarker InitiativeCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Hayley J Luxton
- Biomarker InitiativeCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Molecular Diagnostics and Therapeutics GroupUniversity College London, London, UK
| | - Thomas Johnston
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Biomarker InitiativeCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Charlie E Massie
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Molecular and Computational Diagnostics GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Michelle Pugh
- Genomics Core FacilityCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Anne Y Warren
- Department of HistopathologyCambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Peter Barker
- National Institute for Health Research Cambridge Biomedical Research Centre Core Biochemistry Assay LaboratoryCambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Keith Burling
- National Institute for Health Research Cambridge Biomedical Research Centre Core Biochemistry Assay LaboratoryCambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Andy G Lynch
- Computational Biology GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Anne George
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Johanna Burge
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Marie Corcoran
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Sara Stearn
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Alastair D Lamb
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Naomi L Sharma
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Greg L Shaw
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK University College Hospital at Westmoreland StreetLondon, UK
| | - David E Neal
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Nuffield Department of Surgical SciencesJohn Radcliffe Hospital, Headington, Oxford, UK
| | - Hayley C Whitaker
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Biomarker InitiativeCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Molecular Diagnostics and Therapeutics GroupUniversity College London, London, UK
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Sebastian S, Geisler WS, Burge J. Defocus blur discrimination in natural viewing. J Vis 2014. [DOI: 10.1167/14.15.82] [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: 11/24/2022] Open
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10
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Burge J. Optimal speed estimation in natural image movies predicts human performance. J Vis 2014. [DOI: 10.1167/14.15.75] [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: 11/24/2022] Open
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11
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Mitchell K, Yates J, Huk A, Burge J. Quantifying contributions of natural image variability to neural representations of speed in Area MT. J Vis 2014. [DOI: 10.1167/14.15.48] [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: 11/24/2022] Open
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12
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Burge J, C. McCann B, S. Geisler W. 3D surface tilt estimation in natural scenes from image cue gradients. J Vis 2014. [DOI: 10.1167/14.10.1110] [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: 11/24/2022] Open
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13
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Geisler W, Burge J, Sebastian S. Estimating and discriminating defocus in natural images. J Vis 2013. [DOI: 10.1167/13.15.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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14
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Sebastian SP, Burge J, Geisler WS. Humans correct contrast for defocus blur: a new kind of contrast constancy. J Vis 2013. [DOI: 10.1167/13.9.1145] [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: 11/24/2022] Open
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15
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Burge J, Geisler W. Optimal retinal speed estimation in natural image movies. J Vis 2013. [DOI: 10.1167/13.9.453] [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: 11/24/2022] Open
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16
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Raheem O, Penttilä S, Suominen T, Kaakinen M, Burge J, Haworth A, Sud R, Schorge S, Haapasalo H, Sandell S, Metsikkö K, Hanna M, Udd B. G.P.101 New immunohistochemical method for improved myotonia and chloride channel mutation diagnostics. Neuromuscul Disord 2012. [DOI: 10.1016/j.nmd.2012.06.314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Raja Rayan DL, Haworth A, Sud R, Matthews E, Fialho D, Burge J, Portaro S, Schorge S, Tuin K, Lunt P, McEntagart M, Toscano A, Davis MB, Hanna MG. A new explanation for recessive myotonia congenita: exon deletions and duplications in CLCN1. Neurology 2012; 78:1953-8. [PMID: 22649220 DOI: 10.1212/wnl.0b013e318259e19c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVE To assess whether exon deletions or duplications in CLCN1 are associated with recessive myotonia congenita (MC). METHODS We performed detailed clinical and electrophysiologic characterization in 60 patients with phenotypes consistent with MC. DNA sequencing of CLCN1 followed by multiplex ligation-dependent probe amplification to screen for exon copy number variation was undertaken in all patients. RESULTS Exon deletions or duplications in CLCN1 were identified in 6% of patients with MC. Half had heterozygous exonic rearrangements. The other 2 patients (50%), with severe disabling infantile onset myotonia, were identified with both a homozygous mutation, Pro744Thr, which functional electrophysiology studies suggested was nonpathogenic, and a triplication/homozygous duplication involving exons 8-14, suggesting an explanation for the severe phenotype. CONCLUSIONS These data indicate that copy number variation in CLCN1 may be an important cause of recessive MC. Our observations suggest that it is important to check for exon deletions and duplications as part of the genetic analysis of patients with recessive MC, especially in patients in whom sequencing identifies no mutations or only a single recessive mutation. These results also indicate that additional, as yet unidentified, genetic mechanisms account for cases not currently explained by either CLCN1 point mutations or exonic deletions or duplications.
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Affiliation(s)
- D L Raja Rayan
- Medical Research Council Centre for Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Institute of Neurology, University College London, London, UK
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Burge J, Schorge S, Hanna M. P36 Progesterone reduces and shifts the voltage dependence of the skeletal muscle chloride conductance. Neuromuscul Disord 2012. [DOI: 10.1016/s0960-8966(12)70044-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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20
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Horga A, Raja Rayan DL, Matthews E, Fialho D, Sud R, Haworth A, Portaro S, Burge J, Davis MB, Hanna MG. 014 Prevalence study of skeletal muscle channelopathies in England. J Neurol Psychiatry 2012. [DOI: 10.1136/jnnp-2011-301993.56] [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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21
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Burge J, Geisler W. Optimal disparity estimation in stereo-images of natural scenes. J Vis 2011. [DOI: 10.1167/11.11.295] [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: 11/24/2022] Open
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22
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Rayan DR, Matthews E, Rajakulendran S, Barreto G, Tan S, Dewar L, Burge J, Griggs R, Barohn R, Hanna M. P27 Genotype-phenotype correlation and longitudinal three year natural history study in the non-dystrophic myotonias in the UK. Neuromuscul Disord 2011. [DOI: 10.1016/s0960-8966(11)70046-3] [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: 11/15/2022]
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Burge J, Horga A, Griggs R, Hanna M. P25 Double-blind, placebo-controlled, parallel group, phase III study comparing dichlorphenamide vs. placebo for the treatment of periodic paralysis (HYP HOP trial). Neuromuscul Disord 2011. [DOI: 10.1016/s0960-8966(11)70044-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Whitaker HC, Kote-Jarai Z, Ross-Adams H, Warren AY, Burge J, George A, Bancroft E, Jhavar S, Leongamornlert D, Tymrakiewicz M, Saunders E, Page E, Mitra A, Mitchell G, Lindeman GJ, Evans DG, Blanco I, Mercer C, Rubinstein WS, Clowes V, Douglas F, Hodgson S, Walker L, Donaldson A, Izatt L, Dorkins H, Male A, Tucker K, Stapleton A, Lam J, Kirk J, Lilja H, Easton D, Cooper C, Eeles R, Neal DE. The rs10993994 risk allele for prostate cancer results in clinically relevant changes in microseminoprotein-beta expression in tissue and urine. PLoS One 2010; 5:e13363. [PMID: 20967219 PMCID: PMC2954177 DOI: 10.1371/journal.pone.0013363] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 09/01/2010] [Indexed: 11/19/2022] Open
Abstract
Background Microseminoprotein-beta (MSMB) regulates apoptosis and using genome-wide association studies the rs10993994 single nucleotide polymorphism in the MSMB promoter has been linked to an increased risk of developing prostate cancer. The promoter location of the risk allele, and its ability to reduce promoter activity, suggested that the rs10993994 risk allele could result in lowered MSMB in benign tissue leading to increased prostate cancer risk. Methodology/Principal Findings MSMB expression in benign and malignant prostate tissue was examined using immunohistochemistry and compared with the rs10993994 genotype. Urinary MSMB concentrations were determined by ELISA and correlated with urinary PSA, the presence or absence of cancer, rs10993994 genotype and age of onset. MSMB levels in prostate tissue and urine were greatly reduced with tumourigenesis. Urinary MSMB was better than urinary PSA at differentiating men with prostate cancer at all Gleason grades. The high risk allele was associated with heterogeneity of MSMB staining and loss of MSMB in both tissue and urine in benign prostate. Conclusions These data show that some high risk alleles discovered using genome-wide association studies produce phenotypic effects with potential clinical utility. We provide the first link between a low penetrance polymorphism for prostate cancer and a potential test in human tissue and bodily fluids. There is potential to develop tissue and urinary MSMB for a biomarker of prostate cancer risk, diagnosis and disease monitoring.
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Affiliation(s)
- Hayley C Whitaker
- Uro-Oncology Research Group, CRUK Cambridge Research Institute, Cambridge, United Kingdom.
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Gori M, Burge J, Banks MS. Adapting the figure-ground cue of convexity: Haptic feedback changes the visual perception of depth. J Vis 2010. [DOI: 10.1167/9.8.709] [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: 11/24/2022] Open
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26
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Burge J, Geisler W. Optimal detection and estimation of defocus in natural images. J Vis 2010. [DOI: 10.1167/10.7.1382] [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: 11/24/2022] Open
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27
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Cooper EA, Burge J, Banks MS. Do People of Different Heights have Different Horopters? J Vis 2010. [DOI: 10.1167/10.7.372] [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: 11/24/2022] Open
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Al-Lamki RS, Sadler TJ, Wang J, Reid MJ, Warren AY, Movassagh M, Lu W, Mills IG, Neal DE, Burge J, Vandenebeele P, Pober JS, Bradley JR. Tumor necrosis factor receptor expression and signaling in renal cell carcinoma. Am J Pathol 2010; 177:943-54. [PMID: 20566746 DOI: 10.2353/ajpath.2010.091218] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC), a tubular epithelial cell (TEC) malignancy, frequently secretes tumor necrosis factor (TNF). TNF signals via two distinct receptors (TNFRs). TNFR1, expressed in normal kidney primarily on endothelial cells, activates apoptotic signaling kinase 1 and nuclear factor-kappaB (NF-kappaB) and induces cell death, whereas TNFR2, inducibly expressed on endothelial cells and on TECs by injury, activates endothelial/epithelial tyrosine kinase (Etk), which trans-activates vascular endothelial growth factor receptor 2 (VEGFR2) to promote cell proliferation. We investigated TNFR expression in clinical samples and function in short-term organ cultures of ccRCC tissue treated with wild-type TNF or specific muteins selective for TNFR1 (R1-TNF) or TNFR2 (R2-TNF). There is a significant increase in TNFR2 but not TNFR1 expression on malignant TECs that correlates with increasing malignant grade. In ccRCC organ cultures, R1-TNF increases TNFR1, activates apoptotic signaling kinase and NF-kappaB, and promotes apoptosis in malignant TECs. R2-TNF increases TNFR2, activates NF-kappaB, Etk, and VEGFR2 and increases entry into the cell cycle. Wild-type TNF induces both sets of responses. R2-TNF actions are blocked by pretreatment with a VEGFR2 kinase inhibitor. We conclude that TNF, acting through TNFR2, is an autocrine growth factor for ccRCC acting via Etk-VEGFR2 cross-talk, insights that may provide a more effective therapeutic approach to this disease.
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Affiliation(s)
- Rafia S Al-Lamki
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.
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Burge J, Held R, Banks MS. Blur and accommodation are metric depth cues. J Vis 2010. [DOI: 10.1167/8.6.80] [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: 11/24/2022] Open
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Girshick A, Burge J, Erlikhman G, Banks M. Prior expectations in slant perception: Has the visual system internalized natural scene geometry? J Vis 2010. [DOI: 10.1167/8.6.77] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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31
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Burge J, Ernst MO, Banks MS. The Kalman Filter as a model of visuo-motor adaptation behavior. J Vis 2010. [DOI: 10.1167/6.6.930] [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: 11/24/2022] Open
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Girshick AR, Burge J, Banks MS. Bayesian cue combination: coupling of disparity-texture information compared to coupling of visual-haptic information. J Vis 2010. [DOI: 10.1167/7.9.68] [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: 11/24/2022] Open
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Kim D, Burge J, Lane T, Pearlson GD, Kiehl KA, Calhoun VD. Hybrid ICA-Bayesian network approach reveals distinct effective connectivity differences in schizophrenia. Neuroimage 2008; 42:1560-8. [PMID: 18602482 DOI: 10.1016/j.neuroimage.2008.05.065] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2008] [Revised: 05/13/2008] [Accepted: 05/31/2008] [Indexed: 10/21/2022] Open
Abstract
We utilized a discrete dynamic Bayesian network (dDBN) approach (Burge, J., Lane, T., Link, H., Qiu, S., Clark, V.P., 2007. Discrete dynamic Bayesian network analysis of fMRI data. Hum Brain Mapp.) to determine differences in brain regions between patients with schizophrenia and healthy controls on a measure of effective connectivity, termed the approximate conditional likelihood score (ACL) (Burge, J., Lane, T., 2005. Learning Class-Discriminative Dynamic Bayesian Networks. Proceedings of the International Conference on Machine Learning, Bonn, Germany, pp. 97-104.). The ACL score represents a class-discriminative measure of effective connectivity by measuring the relative likelihood of the correlation between brain regions in one group versus another. The algorithm is capable of finding non-linear relationships between brain regions because it uses discrete rather than continuous values and attempts to model temporal relationships with a first-order Markov and stationary assumption constraint (Papoulis, A., 1991. Probability, random variables, and stochastic processes. McGraw-Hill, New York.). Since Bayesian networks are overly sensitive to noisy data, we introduced an independent component analysis (ICA) filtering approach that attempted to reduce the noise found in fMRI data by unmixing the raw datasets into a set of independent spatial component maps. Components that represented noise were removed and the remaining components reconstructed into the dimensions of the original fMRI datasets. We applied the dDBN algorithm to a group of 35 patients with schizophrenia and 35 matched healthy controls using an ICA filtered and unfiltered approach. We determined that filtering the data significantly improved the magnitude of the ACL score. Patients showed the greatest ACL scores in several regions, most markedly the cerebellar vermis and hemispheres. Our findings suggest that schizophrenia patients exhibit weaker connectivity than healthy controls in multiple regions, including bilateral temporal, frontal, and cerebellar regions during an auditory paradigm.
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Affiliation(s)
- D Kim
- The Mind Research Network, Albuquerque, NM 87131, USA.
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El-Osery AI, Burge J, Jamshidi M, Saba A, Fathi M, Akbarzadeh-T MR. V-Lab-a virtual laboratory for autonomous agents-SLA-based learning controllers. IEEE Trans Syst Man Cybern B Cybern 2008; 32:791-803. [PMID: 18244885 DOI: 10.1109/tsmcb.2002.1049613] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In this paper, we present the use of stochastic learning automata (SLA) in multiagent robotics. In order to fully utilize and implement learning control algorithms in the control of multiagent robotics, an environment for simulation has to be first created. A virtual laboratory for simulation of autonomous agents, called V-Lab is described. The V-Lab architecture can incorporate various models of the environment as well as the agent being trained. A case study to demonstrate the use of SLA is presented.
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Affiliation(s)
- A I El-Osery
- Dept. of Electr. & Comput. Eng., New Mexico Univ., Albuquerque, NM, USA
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Banks MS, Burge J, Schlerf JE. Disparity and texture gradients are combined in a slant estimate and a homogeneity estimate. J Vis 2005. [DOI: 10.1167/5.8.774] [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: 11/24/2022] Open
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Burge J, Ernst MO, Banks MS. Localization, not perturbation, affects visuomotor recalibration. J Vis 2005. [DOI: 10.1167/5.8.871] [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: 11/24/2022] Open
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Burge J, Peterson MA, Palmer SE. Perceived depth is influenced both by binocular disparity and configural cues. J Vis 2004. [DOI: 10.1167/4.8.193] [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: 11/24/2022] Open
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Gepshtein S, Burge J, Banks MS, Ernst MO. What is an inter-sensory object? Optimal combination of vision and touch depends on their spatial coincidence. J Vis 2004. [DOI: 10.1167/4.8.140] [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: 11/24/2022] Open
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Hall LD, Burge J, Evans S, Poole R. Quantitative measurements of articular cartilage by magnetic resonance imaging. Arthritis Res Ther 2004. [PMCID: PMC2833520 DOI: 10.1186/ar1390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- LD Hall
- Herchel Smith Laboratory for Medicinal Chemistry, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - J Burge
- Herchel Smith Laboratory for Medicinal Chemistry, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - S Evans
- Herchel Smith Laboratory for Medicinal Chemistry, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - R Poole
- Herchel Smith Laboratory for Medicinal Chemistry, University of Cambridge School of Clinical Medicine, Cambridge, UK
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Kemp L, Burge J, Choban P, Harden J, Mirtallo J, Flancbaum L. The effect of catheter type and site on infection rates in total parenteral nutrition patients. JPEN J Parenter Enteral Nutr 1994; 18:71-4. [PMID: 8164308 DOI: 10.1177/014860719401800171] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Infections pose a major problem in patients receiving total parenteral nutrition. Controversy continues concerning the effect of catheter type (triple-, double-, single-lumen, or pulmonary artery), insertion site (subclavian, internal jugular, or femoral vein), and the incidence of catheter-related infections. We retrospectively studied multi-lumen catheter use for total parenteral nutrition over a 6-month period in 192 patients, a total of 3334 catheter days. Nonintensive care unit catheters were inserted by the Nutrition Support Service, and intensive care unit catheters were inserted by the intensive care unit staff. All catheters were cared for using Nutrition Support Service protocols, with multi-lumen catheters changed every 7 to 10 days and pulmonary artery catheters changed every 4 days. Infections were determined by semiquantitative cultures (> 15 colonies/plate). The incidence of infections for triple-lumen catheters was 5 (subclavian), 17 (internal jugular), and 36% (femoral) respectively; total infection rate for triple-lumen catheters was 10%. Infection rates for pulmonary artery catheters were 4 (subclavian), and 6% internal (jugular site), respectively, the overall infection rate was 5%. There were no differences in infection rates at any site based on catheter type; however, when triple-lumen catheter sites were compared, the differences were significant (p < .001 vs subclavian, chi 2). Catheter duration was 7.8 days (subclavian),, 7.3 days (internal jugular), and 4.6 (femoral) days. These data suggest that the use of multi-lumen catheters for total parenteral nutrition is safe, that there is a benefit associated with the subclavian route, and that the femoral site should be avoided.
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Affiliation(s)
- L Kemp
- Nutrition Support Service, Ohio State University Hospitals
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Steinberg JS, Katz RJ, Somberg JC, Keefe D, Laddu AR, Burge J. Safety and efficacy of flestolol, a new ultrashort-acting beta-adrenergic blocking agent, for supraventricular tachyarrhythmias. Am J Cardiol 1986; 58:1005-8. [PMID: 2877563 DOI: 10.1016/s0002-9149(86)80028-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Flestolol, a new ultrashort-acting (half-life 6.9 minutes) beta-blocking drug, was administered by intravenous infusion to 18 patients with new-onset atrial fibrillation or flutter and rapid ventricular response (120 beats/min or more for at least 30 minutes). Drug dose of flestolol was progressively increased until at least 1 of 3 endpoints was achieved: at least a 20% reduction in heart rate from baseline, heart rate 100 beats/min or less, or conversion to normal sinus rhythm. Flestolol was then administered as a maintenance infusion up to 24 hours. When flestolol was discontinued, patients were monitored for 1 additional hour. The mean ventricular response at baseline of 133 +/- 12 beats/min decreased to 103 +/- 20 beats/min at the end of flestolol titration (p less than 0.0001). Fourteen patients (78%) achieved defined endpoints. All 14 patients who continued to receive maintenance infusion had a sustained response. When flestolol was discontinued, ventricular response increased 33 +/- 23% within 60 minutes. The only adverse effect seen was hypotension in 2 patients. Flestolol is effective in slowing ventricular response in new-onset atrial fibrillation and flutter, maintains a therapeutic effect during continuous infusion and rapidly loses therapeutic effect when discontinued.
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Turlapaty P, Burge J, Hulse J, Achari R, Bell V, Mosberg H, Laddu A. Tolerance and beta-adrenergic blocking activity of flestolol, a short-acting beta blocker. Clin Pharmacol Ther 1986; 39:543-9. [PMID: 3698462 DOI: 10.1038/clpt.1986.93] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The tolerance and beta-adrenergic blocking activity of flestolol, a short-acting beta-blocker, was investigated in 30 subjects. Flestolol infused intravenously at doses up to 100 micrograms/kg/min was found to be well tolerated. A dose-dependent attenuation of isoproterenol-induced tachycardia and increase in systolic blood pressure occurred with flestolol at doses ranging from 0.5 to 15.0 micrograms/kg/min. The average percent reduction in isoproterenol-induced tachycardia (beta-blockade) at each dose of flestolol, 0.5, 2.5, 5.0, 15.0, and 50.0 micrograms/kg/min, was 15.1%, 45.9%, 67.0%, 85.9%, and 90.3%, respectively. The onset of beta-blockade occurred within 30 minutes. After the end of flestolol infusion there was a marked reduction in beta-blockade within 6 minutes, with complete recovery from beta-blockade within 30 to 45 minutes. There was a statistically significant (P less than 0.01) positive correlation between flestolol dosage and its blood levels (r = 0.91) as well as between the flestolol-induced beta-blockade and its dosage (r = 0.62).
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Abstract
Flestolol (ACC-9089) is a nonselective, competitive, ultra-short-acting beta-adrenergic blocking agent, without any intrinsic sympathomimetic activity. Flestolol is metabolized by plasma esterases and has an elimination half-life of approximately 6.5 minutes. This agent was well tolerated in healthy volunteers at doses up to 100 micrograms/kg/min. In long-term infusion studies, flestolol was well tolerated at the effective beta-blocking dose (5 micrograms/kg/min) for up to seven days. Flestolol blood concentrations increased linearly with increasing dose and good correlation exists between blood concentrations of flestolol and beta-adrenergic blockade. Flestolol produced a dose-dependent attenuation of isoproterenol-induced tachycardia. Electrophysiologic and hemodynamic effects of flestolol are similar to those of other beta blockers. In contrast with other beta blockers, flestolol-induced effects reverse rapidly (within 30 minutes) following discontinuation because of its short half-life. Flestolol effectively reduced heart rate in patients with supraventricular tachyarrhythmia. In patients with unstable angina, flestolol infusion was found to be safe and effective in controlling chest pain. It is concluded that flestolol is a potent, well-tolerated, ultra-short-acting beta-adrenergic blocking agent. Use of flestolol in the critical care setting is currently undergoing investigation.
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Taylor RP, Horgan C, Hooper M, Burge J. Dynamics of interaction between complement-fixing antibody/dsDNA immune complexes and erythrocytes. In vitro studies and potential general applications to clinical immune complex testing. J Clin Invest 1985; 75:102-11. [PMID: 3917462 PMCID: PMC423414 DOI: 10.1172/jci111660] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Soluble antibody/3H-double-stranded PM2 DNA (dsDNA) immune complexes were briefly opsonized with complement and then allowed to bind to human erythrocytes (via complement receptors). The cells were washed and subsequently a volume of autologous blood in a variety of media was added, and the release of the bound immune complexes from the erythrocytes was studied as a function of temperature and time. After 1-2 h, the majority of the bound immune complexes were not released into the serum during blood clotting at either 37 degrees C or room temperature, but there was a considerably greater release of the immune complexes into the plasma of blood that was anticoagulated with EDTA. Similar results were obtained using various conditions of opsonization and also using complexes that contained lower molecular weight dsDNA. Thus, the kinetics of release of these antibody/dsDNA immune complexes differed substantially from the kinetics of release of antibody/bovine serum albumin complexes that was reported by others. Studies using the solution phase C1q immune complex binding assay confirmed that in approximately half of the SLE samples that were positive for immune complexes, there was a significantly higher level of detectable immune complexes in plasma vs. serum. Freshly drawn erythrocytes from some SLE patients exhibiting this plasma/serum discrepancy had IgG antigen on their surface that was released by incubation in EDTA plasma. Thus, the higher levels of immune complexes observed in EDTA plasma vs. serum using the C1q assay may often reflect the existence of immune complexes circulating in vivo bound to erythrocytes.
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Taylor RP, Horgan C, Harbin A, Burge J. Suramin inhibits the binding of complement-fixing antibody/double-stranded DNA immune complexes to CR1. Clin Immunol Immunopathol 1984; 33:220-31. [PMID: 6488590 DOI: 10.1016/0090-1229(84)90077-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The effects of varying concentrations of heparin and suramin on the complement-mediated binding of antibody/double-stranded DNA immune complexes to red blood cells (RBCs) and Raji cells have been investigated. If the immune complexes are briefly opsonized with complement, suramin can block binding to both cell types, and heparin can block binding to RBCs. In addition, if these complexes are first allowed to bind to RBCs or Raji cells, relatively brief incubations in suramin are sufficient to cause release of the complexes from the cells' C3b receptors. The potential clinical and diagnostic implications of these findings are discussed.
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Horgan C, Burge J, Crawford L, Taylor RP. The kinetics of [3H]-dsDNA/anti-DNA immune complex formation, binding by red blood cells, and release into serum: effect of DNA molecular weight and conditions of antibody excess. The Journal of Immunology 1984. [DOI: 10.4049/jimmunol.133.4.2079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
[3H]dsDNA/anti-DNA immune complexes (IC) formed, fixed complement, and bound rapidly to red blood cells (RBC) in whole blood (less than 5 min), but were released from the cells more slowly. The rate of release was dependent on both the antibody:DNA ratio and the m.w. of the DNA in the complex. For example, complexes formed with high m.w. DNA (6 X 10(6) daltons) were released more slowly (t1/2 = 60 min) than complexes formed with lower m.w. DNA (2 to 6 X 10(5) daltons, t1/2 = 15 to 20 min). The [3H]dsDNA/anti-DNA complexes, which were released from the cells as intact antigen/antibody/complement complexes, did not rebind to RBC, but did bind to Raji cells and could be precipitated by monoclonal antibody to C3d. When these released IC (RIC) containing high m.w. DNA were incubated with additional anti-DNA antibody and fresh complement, they rebound to RBC. However, RIC containing lower m.w. DNA (5 X 10(5) daltons) did not rebind to RBC under the same conditions. These data suggest that IC containing high m.w. DNA bind to and remain bound to RBC more effectively than IC containing lower m.w. DNA, and thus may be more easily cleared from the circulation by the RBC IC clearance mechanism. Thus, the size of the DNA in the IC may be a significant factor in the pathogenicity of DNA/anti-DNA complexes in SLE.
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Horgan C, Burge J, Crawford L, Taylor RP. The kinetics of [3H]-dsDNA/anti-DNA immune complex formation, binding by red blood cells, and release into serum: effect of DNA molecular weight and conditions of antibody excess. J Immunol 1984; 133:2079-84. [PMID: 6332147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
[3H]dsDNA/anti-DNA immune complexes (IC) formed, fixed complement, and bound rapidly to red blood cells (RBC) in whole blood (less than 5 min), but were released from the cells more slowly. The rate of release was dependent on both the antibody:DNA ratio and the m.w. of the DNA in the complex. For example, complexes formed with high m.w. DNA (6 X 10(6) daltons) were released more slowly (t1/2 = 60 min) than complexes formed with lower m.w. DNA (2 to 6 X 10(5) daltons, t1/2 = 15 to 20 min). The [3H]dsDNA/anti-DNA complexes, which were released from the cells as intact antigen/antibody/complement complexes, did not rebind to RBC, but did bind to Raji cells and could be precipitated by monoclonal antibody to C3d. When these released IC (RIC) containing high m.w. DNA were incubated with additional anti-DNA antibody and fresh complement, they rebound to RBC. However, RIC containing lower m.w. DNA (5 X 10(5) daltons) did not rebind to RBC under the same conditions. These data suggest that IC containing high m.w. DNA bind to and remain bound to RBC more effectively than IC containing lower m.w. DNA, and thus may be more easily cleared from the circulation by the RBC IC clearance mechanism. Thus, the size of the DNA in the IC may be a significant factor in the pathogenicity of DNA/anti-DNA complexes in SLE.
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Taylor RP, Burge J, Horgan C, Shasby DM. The complement-mediated binding of soluble antibody/dsDNA immune complexes to human neutrophils. J Immunol 1983; 130:2656-62. [PMID: 6854016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The complement-mediated binding of soluble antibody/3H-dsDNA immune complexes (prepared in vitro) to human polymorphonuclear leukocytes (PMN) has been investigated quantitatively. Studies with isolated complement components in conjunction with experiments on the binding of these complexes to human red blood cells suggest that the binding to both cell types is mediated predominantly by CR1 (C4b-C3b) receptors but that CR3 (iC3b or C3d-g) receptors may play a role in binding to PMN but probably not to RBC. Our results also indicate that under the standard conditions of these assays (37 degrees C, 20 to 40 min incubations) there is no significant internalization of the soluble antibody/dsDNA immune complexes after they are bound by the PMN.
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Taylor RP, Burge J, Horgan C, Shasby DM. The complement-mediated binding of soluble antibody/dsDNA immune complexes to human neutrophils. The Journal of Immunology 1983. [DOI: 10.4049/jimmunol.130.6.2656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
The complement-mediated binding of soluble antibody/3H-dsDNA immune complexes (prepared in vitro) to human polymorphonuclear leukocytes (PMN) has been investigated quantitatively. Studies with isolated complement components in conjunction with experiments on the binding of these complexes to human red blood cells suggest that the binding to both cell types is mediated predominantly by CR1 (C4b-C3b) receptors but that CR3 (iC3b or C3d-g) receptors may play a role in binding to PMN but probably not to RBC. Our results also indicate that under the standard conditions of these assays (37 degrees C, 20 to 40 min incubations) there is no significant internalization of the soluble antibody/dsDNA immune complexes after they are bound by the PMN.
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