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Busch F, De Paepe KN, Gibbs P, Allison M, Hoare M, See TC. The clinical value of the hepatic venous pressure gradient in patients undergoing hepatic resection for hepatocellular carcinoma with or without liver cirrhosis. Open Med (Wars) 2024; 19:20230851. [PMID: 38584825 PMCID: PMC10996929 DOI: 10.1515/med-2023-0851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/03/2023] [Accepted: 10/27/2023] [Indexed: 04/09/2024] Open
Abstract
The role of hepatic venous pressure gradient (HVPG) measurement in risk stratification before liver resection is an ongoing area of debate. This study examines the impact of preoperative HVPG levels on overall survival (OS)/time to recurrence (TTR) and postoperative complications after hepatic resection of hepatocellular carcinoma (HCC). Thirty-eight HCC patients undergoing HVPG measurement before liver resection at Cambridge University Hospitals NHS Foundation Trust between January 2014 and April 2022 were retrospectively analysed. Statistical analysis comprised univariable/multivariable Cox/logistic regression to identify risk factors of reduced OS/TTR or 90-day post-resection complications and Kaplan-Meier estimator, log-rank, chi-squared, Fisher's exact, and Mann-Whitney U test, or Student's t-test for survival/subgroup analysis. The median HPVG was 6 (range: 0-14) mmHg. The HVPG was an independent risk factor for poorer TTR in the overall cohort (cut-off: ≥7.5 mmHg (17.18/43.81 months; P = 0.009)). In the subgroup analysis of cirrhotic patients (N = 29 (76%)), HVPG was additionally an independent risk factor for lower OS (cut-off: ≥8.5 mmHg [44.39/76.84 months; P = 0.012]). The HVPG had no impact on OS/TTR in non-cirrhotic patients (N = 9 (24%)), nor was it associated with postoperative complications in any cohort. In conclusion, preoperative HVPG levels are useful predictors for TTR and OS in cirrhotic HCC patients undergoing hepatic resection.
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Affiliation(s)
- Felix Busch
- Department of Radiology, Charité – Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin, 12203, Germany
- Department of Radiology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, CB2 0QQ, United Kingdom
| | - Katja N. De Paepe
- Department of Radiology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, CB2 0QQ, United Kingdom
| | - Paul Gibbs
- Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, CB2 0QQ, United Kingdom
| | - Michael Allison
- Department of Hepatology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, CB2 0QQ, United Kingdom
| | - Matthew Hoare
- Department of Hepatology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, CB2 0QQ, United Kingdom
- Early Cancer Institute, University of Cambridge, Hutchison Research Institute, Cambridge, CB2 0XZ, United Kingdom
| | - Teik Choon See
- Department of Radiology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, CB2 0QQ, United Kingdom
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Wilkinson AL, Hulme S, Kennedy JI, Mann ER, Horn P, Shepherd EL, Yin K, Zaki MY, Hardisty G, Lu WY, Rantakari P, Adams DH, Salmi M, Hoare M, Patten DA, Shetty S. The senescent secretome drives PLVAP expression in cultured human hepatic endothelial cells to promote monocyte transmigration. iScience 2023; 26:107966. [PMID: 37810232 PMCID: PMC10558774 DOI: 10.1016/j.isci.2023.107966] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/31/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023] Open
Abstract
Liver sinusoidal endothelial cells (LSEC) undergo significant phenotypic change in chronic liver disease (CLD), and yet the factors that drive this process and the impact on their function as a vascular barrier and gatekeeper for immune cell recruitment are poorly understood. Plasmalemma-vesicle-associated protein (PLVAP) has been characterized as a marker of LSEC in CLD; notably we found that PLVAP upregulation strongly correlated with markers of tissue senescence. Furthermore, exposure of human LSEC to the senescence-associated secretory phenotype (SASP) led to a significant upregulation of PLVAP. Flow-based assays demonstrated that SASP-driven leukocyte recruitment was characterized by paracellular transmigration of monocytes while the majority of lymphocytes migrated transcellularly. Knockdown studies confirmed that PLVAP selectively supported monocyte transmigration mediated through PLVAP's impact on LSEC permeability by regulating phospho-VE-cadherin expression and endothelial gap formation. PLVAP may therefore represent an endothelial target that selectively shapes the senescence-mediated immune microenvironment in liver disease.
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Affiliation(s)
- Alex L. Wilkinson
- Centre for Liver and Gastrointestinal Research, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Samuel Hulme
- Centre for Liver and Gastrointestinal Research, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - James I. Kennedy
- Centre for Liver and Gastrointestinal Research, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Emily R. Mann
- Centre for Liver and Gastrointestinal Research, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Paul Horn
- Centre for Liver and Gastrointestinal Research, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Emma L. Shepherd
- College of Health and Life Sciences, Aston University, Birmingham B4 7ET, UK
| | - Kelvin Yin
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge CB2 0RE, UK
| | - Marco Y.W. Zaki
- Department of Biochemistry, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Gareth Hardisty
- Centre for Inflammation Research, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Wei-Yu Lu
- Centre for Inflammation Research, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Pia Rantakari
- Institute of Biomedicine, University of Turku, Turku, Finland
- MediCity Research Laboratory, University of Turku, Turku, Finland
| | - David H. Adams
- Centre for Liver and Gastrointestinal Research, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Marko Salmi
- Institute of Biomedicine, University of Turku, Turku, Finland
- MediCity Research Laboratory, University of Turku, Turku, Finland
| | - Matthew Hoare
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge CB2 0RE, UK
- University of Cambridge, Department of Medicine, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
| | - Daniel A. Patten
- Centre for Liver and Gastrointestinal Research, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
- National Institute for Health Research, Birmingham Biomedical Research Centre at University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Shishir Shetty
- Centre for Liver and Gastrointestinal Research, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
- National Institute for Health Research, Birmingham Biomedical Research Centre at University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
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3
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Passman AM, Haughey MJ, Carlotti E, Williams MJ, Cereser B, Lin ML, Devkumar S, Gabriel JP, Gringeri E, Cillo U, Russo FP, Hoare M, ChinAleong J, Jansen M, Wright NA, Kocher HM, Huang W, Alison MR, McDonald SAC. Hepatocytes undergo punctuated expansion dynamics from a periportal stem cell niche in normal human liver. J Hepatol 2023; 79:417-432. [PMID: 37088309 DOI: 10.1016/j.jhep.2023.03.044] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/25/2023]
Abstract
BACKGROUND & AIMS While normal human liver is thought to be generally quiescent, clonal hepatocyte expansions have been observed, though neither their cellular source nor their expansion dynamics have been determined. Knowing the hepatocyte cell of origin, and their subsequent dynamics and trajectory within the human liver will provide an important basis to understand disease-associated dysregulation. METHODS Herein, we use in vivo lineage tracing and methylation sequence analysis to demonstrate normal human hepatocyte ancestry. We exploit next-generation mitochondrial sequencing to determine hepatocyte clonal expansion dynamics across spatially distinct areas of laser-captured, microdissected, clones, in tandem with computational modelling in morphologically normal human liver. RESULTS Hepatocyte clones and rare SOX9+ hepatocyte progenitors commonly associate with portal tracts and we present evidence that clones can lineage-trace with cholangiocytes, indicating the presence of a bipotential common ancestor at this niche. Within clones, we demonstrate methylation CpG sequence diversity patterns indicative of periportal not pericentral ancestral origins, indicating a portal to central vein expansion trajectory. Using spatial analysis of mitochondrial DNA variants by next-generation sequencing coupled with mathematical modelling and Bayesian inference across the portal-central axis, we demonstrate that patterns of mitochondrial DNA variants reveal large numbers of spatially restricted mutations in conjunction with limited numbers of clonal mutations. CONCLUSIONS These datasets support the existence of a periportal progenitor niche and indicate that clonal patches exhibit punctuated but slow growth, then quiesce, likely due to acute environmental stimuli. These findings crucially contribute to our understanding of hepatocyte dynamics in the normal human liver. IMPACT AND IMPLICATIONS The liver is mainly composed of hepatocytes, but we know little regarding the source of these cells or how they multiply over time within the disease-free human liver. In this study, we determine a source of new hepatocytes by combining many different lab-based methods and computational predictions to show that hepatocytes share a common cell of origin with bile ducts. Both our experimental and computational data also demonstrate hepatocyte clones are likely to expand in slow waves across the liver in a specific trajectory, but often lie dormant for many years. These data show for the first time the expansion dynamics of hepatocytes in normal liver and their cell of origin enabling the accurate measurment of changes to their dynamics that may lead to liver disease. These findings are important for researchers determining cancer risk in human liver.
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Affiliation(s)
- Adam M Passman
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Magnus J Haughey
- School of Mathematical Sciences, Queen Mary University of London, London, UK
| | - Emanuela Carlotti
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Marc J Williams
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Bianca Cereser
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Meng-Lay Lin
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Shruthi Devkumar
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Jonathan P Gabriel
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Enrico Gringeri
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Umberto Cillo
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Francesco Paolo Russo
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Matthew Hoare
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Marnix Jansen
- Department of Cellular Pathology, University College London, London, UK; UCL Cancer Centre, University College London, London, UK
| | - Nicholas A Wright
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Hermant M Kocher
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK; Cancer Tissue Bank, Barts Cancer Institute, Queen Mary University of London, London, UK; Barts and the London HPB Centre, The Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Weini Huang
- School of Mathematical Sciences, Queen Mary University of London, London, UK; Group of Theoretical Biology, The State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, China
| | - Malcolm R Alison
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Stuart A C McDonald
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
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4
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Ferrandino G, De Palo G, Murgia A, Birch O, Tawfike A, Smith R, Debiram-Beecham I, Gandelman O, Kibble G, Lydon AM, Groves A, Smolinska A, Allsworth M, Boyle B, van der Schee MP, Allison M, Fitzgerald RC, Hoare M, Snowdon VK. Breath Biopsy ® to Identify Exhaled Volatile Organic Compounds Biomarkers for Liver Cirrhosis Detection. J Clin Transl Hepatol 2023; 11:638-648. [PMID: 36969895 PMCID: PMC10037526 DOI: 10.14218/jcth.2022.00309] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/30/2022] [Accepted: 11/01/2022] [Indexed: 03/29/2023] Open
Abstract
Background and Aims The prevalence of chronic liver disease in adults exceeds 30% in some countries and there is significant interest in developing tests and treatments to help control disease progression and reduce healthcare burden. Breath is a rich sampling matrix that offers non-invasive solutions suitable for early-stage detection and disease monitoring. Having previously investigated targeted analysis of a single biomarker, here we investigated a multiparametric approach to breath testing that would provide more robust and reliable results for clinical use. Methods To identify candidate biomarkers we compared 46 breath samples from cirrhosis patients and 42 from controls. Collection and analysis used Breath Biopsy OMNI™, maximizing signal and contrast to background to provide high confidence biomarker detection based upon gas chromatography mass spectrometry (GC-MS). Blank samples were also analyzed to provide detailed information on background volatile organic compounds (VOCs) levels. Results A set of 29 breath VOCs differed significantly between cirrhosis and controls. A classification model based on these VOCs had an area under the curve (AUC) of 0.95±0.04 in cross-validated test sets. The seven best performing VOCs were sufficient to maximize classification performance. A subset of 11 VOCs was correlated with blood metrics of liver function (bilirubin, albumin, prothrombin time) and separated patients by cirrhosis severity using principal component analysis. Conclusions A set of seven VOCs consisting of previously reported and novel candidates show promise as a panel for liver disease detection and monitoring, showing correlation to disease severity and serum biomarkers at late stage.
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Affiliation(s)
| | | | | | | | | | | | - Irene Debiram-Beecham
- Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, UK
| | | | - Graham Kibble
- Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, UK
| | - Anne Marie Lydon
- Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, UK
| | - Alice Groves
- Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, UK
| | - Agnieszka Smolinska
- Owlstone Medical, Cambridge, UK
- Department of Pharmacology and Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center, the Netherlands
| | | | | | | | - Michael Allison
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
- Addenbrookes Hepatology and Liver Transplantation Unit, Addenbrookes Hospital, Cambridge, UK
| | - Rebecca C. Fitzgerald
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Matthew Hoare
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
- Addenbrookes Hepatology and Liver Transplantation Unit, Addenbrookes Hospital, Cambridge, UK
- CRUK Cambridge Institute, Cambridge, UK
| | - Victoria K. Snowdon
- Addenbrookes Hepatology and Liver Transplantation Unit, Addenbrookes Hospital, Cambridge, UK
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5
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Assante G, Chandrasekaran S, Ng S, Tourna A, Chung CH, Isse KA, Banks JL, Soffientini U, Filippi C, Dhawan A, Liu M, Rozen SG, Hoare M, Campbell P, Ballard JWO, Turner N, Morris MJ, Chokshi S, Youngson NA. Correction: Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease. Genome Med 2023; 15:38. [PMID: 37202796 DOI: 10.1186/s13073-023-01190-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Affiliation(s)
- Gabriella Assante
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Sriram Chandrasekaran
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- Center for Bioinformatics and Computational Medicine, Ann Arbor, MI, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Stanley Ng
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Aikaterini Tourna
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Carolina H Chung
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kowsar A Isse
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Jasmine L Banks
- UNSW Sydney, Sydney, Australia
- Cellular Bioenergetics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Ugo Soffientini
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Celine Filippi
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Anil Dhawan
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Mo Liu
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Steven G Rozen
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Matthew Hoare
- CRUK Cambridge Institute, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | | | - J William O Ballard
- Department of Ecology, Environment and Evolution, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia
| | - Nigel Turner
- UNSW Sydney, Sydney, Australia
- Cellular Bioenergetics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | | | - Shilpa Chokshi
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Neil A Youngson
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK.
- Faculty of Life Sciences and Medicine, King's College London, London, UK.
- UNSW Sydney, Sydney, Australia.
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6
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Hoare M. Mouse models of hepatocyte biology - Known unknowns. J Hepatol 2023; 78:898-900. [PMID: 36781086 DOI: 10.1016/j.jhep.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/01/2023] [Accepted: 02/01/2023] [Indexed: 02/15/2023]
Affiliation(s)
- Matthew Hoare
- Early Cancer Institute, University of Cambridge, Cambridge, CB2 0XZ, UK; Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK.
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7
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Evans RA, Leavy OC, Richardson M, Elneima O, McAuley HJC, Shikotra A, Singapuri A, Sereno M, Saunders RM, Harris VC, Houchen-Wolloff L, Aul R, Beirne P, Bolton CE, Brown JS, Choudhury G, Diar-Bakerly N, Easom N, Echevarria C, Fuld J, Hart N, Hurst J, Jones MG, Parekh D, Pfeffer P, Rahman NM, Rowland-Jones SL, Shah AM, Wootton DG, Chalder T, Davies MJ, De Soyza A, Geddes JR, Greenhalf W, Greening NJ, Heaney LG, Heller S, Howard LS, Jacob J, Jenkins RG, Lord JM, Man WDC, McCann GP, Neubauer S, Openshaw PJM, Porter JC, Rowland MJ, Scott JT, Semple MG, Singh SJ, Thomas DC, Toshner M, Lewis KE, Thwaites RS, Briggs A, Docherty AB, Kerr S, Lone NI, Quint J, Sheikh A, Thorpe M, Zheng B, Chalmers JD, Ho LP, Horsley A, Marks M, Poinasamy K, Raman B, Harrison EM, Wain LV, Brightling CE, Abel K, Adamali H, Adeloye D, Adeyemi O, Adrego R, Aguilar Jimenez LA, Ahmad S, Ahmad Haider N, Ahmed R, Ahwireng N, Ainsworth M, Al-Sheklly B, Alamoudi A, Ali M, Aljaroof M, All AM, Allan L, Allen RJ, Allerton L, Allsop L, Almeida P, Altmann D, Alvarez Corral M, Amoils S, Anderson D, Antoniades C, Arbane G, Arias A, Armour C, Armstrong L, Armstrong N, Arnold D, Arnold H, Ashish A, Ashworth A, Ashworth M, Aslani S, Assefa-Kebede H, Atkin C, Atkin P, Aung H, Austin L, Avram C, Ayoub A, Babores M, Baggott R, Bagshaw J, Baguley D, Bailey L, Baillie JK, Bain S, Bakali M, Bakau M, Baldry E, Baldwin D, Ballard C, Banerjee A, Bang B, Barker RE, Barman L, Barratt S, Barrett F, Basire D, Basu N, Bates M, Bates A, Batterham R, Baxendale H, Bayes H, Beadsworth M, Beckett P, Beggs M, Begum M, Bell D, Bell R, Bennett K, Beranova E, Bermperi A, Berridge A, Berry C, Betts S, Bevan E, Bhui K, Bingham M, Birchall K, Bishop L, Bisnauthsing K, Blaikely J, Bloss A, Bolger A, Bonnington J, Botkai A, Bourne C, Bourne M, Bramham K, Brear L, Breen G, Breeze J, Bright E, Brill S, Brindle K, Broad L, Broadley A, Brookes C, Broome M, Brown A, Brown A, Brown J, Brown J, Brown M, Brown M, Brown V, Brugha T, Brunskill N, Buch M, Buckley P, Bularga A, Bullmore E, Burden L, Burdett T, Burn D, Burns G, Burns A, Busby J, Butcher R, Butt A, Byrne S, Cairns P, Calder PC, Calvelo E, Carborn H, Card B, Carr C, Carr L, Carson G, Carter P, Casey A, Cassar M, Cavanagh J, Chablani M, Chambers RC, Chan F, Channon KM, Chapman K, Charalambou A, Chaudhuri N, Checkley A, Chen J, Cheng Y, Chetham L, Childs C, Chilvers ER, Chinoy H, Chiribiri A, Chong-James K, Choudhury N, Chowienczyk P, Christie C, Chrystal M, Clark D, Clark C, Clarke J, Clohisey S, Coakley G, Coburn Z, Coetzee S, Cole J, Coleman C, Conneh F, Connell D, Connolly B, Connor L, Cook A, Cooper B, Cooper J, Cooper S, Copeland D, Cosier T, Coulding M, Coupland C, Cox E, Craig T, Crisp P, Cristiano D, Crooks MG, Cross A, Cruz I, Cullinan P, Cuthbertson D, Daines L, Dalton M, Daly P, Daniels A, Dark P, Dasgin J, David A, David C, Davies E, Davies F, Davies G, Davies GA, Davies K, Dawson J, Daynes E, Deakin B, Deans A, Deas C, Deery J, Defres S, Dell A, Dempsey K, Denneny E, Dennis J, Dewar A, Dharmagunawardena R, Dickens C, Dipper A, Diver S, Diwanji SN, Dixon M, Djukanovic R, Dobson H, Dobson SL, Donaldson A, Dong T, Dormand N, Dougherty A, Dowling R, Drain S, Draxlbauer K, Drury K, Dulawan P, Dunleavy A, Dunn S, Earley J, Edwards S, Edwardson C, El-Taweel H, Elliott A, Elliott K, Ellis Y, Elmer A, Evans D, Evans H, Evans J, Evans R, Evans RI, Evans T, Evenden C, Evison L, Fabbri L, Fairbairn S, Fairman A, Fallon K, Faluyi D, Favager C, Fayzan T, Featherstone J, Felton T, Finch J, Finney S, Finnigan J, Finnigan L, Fisher H, Fletcher S, Flockton R, Flynn M, Foot H, Foote D, Ford A, Forton D, Fraile E, Francis C, Francis R, Francis S, Frankel A, Fraser E, Free R, French N, Fu X, Furniss J, Garner L, Gautam N, George J, George P, Gibbons M, Gill M, Gilmour L, Gleeson F, Glossop J, Glover S, Goodman N, Goodwin C, Gooptu B, Gordon H, Gorsuch T, Greatorex M, Greenhaff PL, Greenhalgh A, Greenwood J, Gregory H, Gregory R, Grieve D, Griffin D, Griffiths L, Guerdette AM, Guillen Guio B, Gummadi M, Gupta A, Gurram S, Guthrie E, Guy Z, H Henson H, Hadley K, Haggar A, Hainey K, Hairsine B, Haldar P, Hall I, Hall L, Halling-Brown M, Hamil R, Hancock A, Hancock K, Hanley NA, Haq S, Hardwick HE, Hardy E, Hardy T, Hargadon B, Harrington K, Harris E, Harrison P, Harvey A, Harvey M, Harvie M, Haslam L, Havinden-Williams M, Hawkes J, Hawkings N, Haworth J, Hayday A, Haynes M, Hazeldine J, Hazelton T, Heeley C, Heeney JL, Heightman M, Henderson M, Hesselden L, Hewitt M, Highett V, Hillman T, Hiwot T, Hoare A, Hoare M, Hockridge J, Hogarth P, Holbourn A, Holden S, Holdsworth L, Holgate D, Holland M, Holloway L, Holmes K, Holmes M, Holroyd-Hind B, Holt L, Hormis A, Hosseini A, Hotopf M, Howard K, Howell A, Hufton E, Hughes AD, Hughes J, Hughes R, Humphries A, Huneke N, Hurditch E, Husain M, Hussell T, Hutchinson J, Ibrahim W, Ilyas F, Ingham J, Ingram L, Ionita D, Isaacs K, Ismail K, Jackson T, James WY, Jarman C, Jarrold I, Jarvis H, Jastrub R, Jayaraman B, Jezzard P, Jiwa K, Johnson C, Johnson S, Johnston D, Jolley CJ, Jones D, Jones G, Jones H, Jones H, Jones I, Jones L, Jones S, Jose S, Kabir T, Kaltsakas G, Kamwa V, Kanellakis N, Kaprowska S, Kausar Z, Keenan N, Kelly S, Kemp G, Kerslake H, Key AL, Khan F, Khunti K, Kilroy S, King B, King C, Kingham L, Kirk J, Kitterick P, Klenerman P, Knibbs L, Knight S, Knighton A, Kon O, Kon S, Kon SS, Koprowska S, Korszun A, Koychev I, Kurasz C, Kurupati P, Laing C, Lamlum H, Landers G, Langenberg C, Lasserson D, Lavelle-Langham L, Lawrie A, Lawson C, Lawson C, Layton A, Lea A, Lee D, Lee JH, Lee E, Leitch K, Lenagh R, Lewis D, Lewis J, Lewis V, Lewis-Burke N, Li X, Light T, Lightstone L, Lilaonitkul W, Lim L, Linford S, Lingford-Hughes A, Lipman M, Liyanage K, Lloyd A, Logan S, Lomas D, Loosley R, Lota H, Lovegrove W, Lucey A, Lukaschuk E, Lye A, Lynch C, MacDonald S, MacGowan G, Macharia I, Mackie J, Macliver L, Madathil S, Madzamba G, Magee N, Magtoto MM, Mairs N, Majeed N, Major E, Malein F, Malim M, Mallison G, Mandal S, Mangion K, Manisty C, Manley R, March K, Marciniak S, Marino P, Mariveles M, Marouzet E, Marsh S, Marshall B, Marshall M, Martin J, Martineau A, Martinez LM, Maskell N, Matila D, Matimba-Mupaya W, Matthews L, Mbuyisa A, McAdoo S, Weir McCall J, McAllister-Williams H, McArdle A, McArdle P, McAulay D, McCormick J, McCormick W, McCourt P, McGarvey L, McGee C, Mcgee K, McGinness J, McGlynn K, McGovern A, McGuinness H, McInnes IB, McIntosh J, McIvor E, McIvor K, McLeavey L, McMahon A, McMahon MJ, McMorrow L, Mcnally T, McNarry M, McNeill J, McQueen A, McShane H, Mears C, Megson C, Megson S, Mehta P, Meiring J, Melling L, Mencias M, Menzies D, Merida Morillas M, Michael A, Milligan L, Miller C, Mills C, Mills NL, Milner L, Misra S, Mitchell J, Mohamed A, Mohamed N, Mohammed S, Molyneaux PL, Monteiro W, Moriera S, Morley A, Morrison L, Morriss R, Morrow A, Moss AJ, Moss P, Motohashi K, Msimanga N, Mukaetova-Ladinska E, Munawar U, Murira J, Nanda U, Nassa H, Nasseri M, Neal A, Needham R, Neill P, Newell H, Newman T, Newton-Cox A, Nicholson T, Nicoll D, Nolan CM, Noonan MJ, Norman C, Novotny P, Nunag J, Nwafor L, Nwanguma U, Nyaboko J, O'Donnell K, O'Brien C, O'Brien L, O'Regan D, Odell N, Ogg G, Olaosebikan O, Oliver C, Omar Z, Orriss-Dib L, Osborne L, Osbourne R, Ostermann M, Overton C, Owen J, Oxton J, Pack J, Pacpaco E, Paddick S, Painter S, Pakzad A, Palmer S, Papineni P, Paques K, Paradowski K, Pareek M, Parfrey H, Pariante C, Parker S, Parkes M, Parmar J, Patale S, Patel B, Patel M, Patel S, Pattenadk D, Pavlides M, Payne S, Pearce L, Pearl JE, Peckham D, Pendlebury J, Peng Y, Pennington C, Peralta I, Perkins E, Peterkin Z, Peto T, Petousi N, Petrie J, Phipps J, Pimm J, Piper Hanley K, Pius R, Plant H, Plein S, Plekhanova T, Plowright M, Polgar O, Poll L, Porter J, Portukhay S, Powell N, Prabhu A, Pratt J, Price A, Price C, Price C, Price D, Price L, Price L, Prickett A, Propescu J, Pugmire S, Quaid S, Quigley J, Qureshi H, Qureshi IN, Radhakrishnan K, Ralser M, Ramos A, Ramos H, Rangeley J, Rangelov B, Ratcliffe L, Ravencroft P, Reddington A, Reddy R, Redfearn H, Redwood D, Reed A, Rees M, Rees T, Regan K, Reynolds W, Ribeiro C, Richards A, Richardson E, Rivera-Ortega P, Roberts K, Robertson E, Robinson E, Robinson L, Roche L, Roddis C, Rodger J, Ross A, Ross G, Rossdale J, Rostron A, Rowe A, Rowland A, Rowland J, Roy K, Roy M, Rudan I, Russell R, Russell E, Saalmink G, Sabit R, Sage EK, Samakomva T, Samani N, Sampson C, Samuel K, Samuel R, Sanderson A, Sapey E, Saralaya D, Sargant J, Sarginson C, Sass T, Sattar N, Saunders K, Saunders P, Saunders LC, Savill H, Saxon W, Sayer A, Schronce J, Schwaeble W, Scott K, Selby N, Sewell TA, Shah K, Shah P, Shankar-Hari M, Sharma M, Sharpe C, Sharpe M, Shashaa S, Shaw A, Shaw K, Shaw V, Shelton S, Shenton L, Shevket K, Short J, Siddique S, Siddiqui S, Sidebottom J, Sigfrid L, Simons G, Simpson J, Simpson N, Singh C, Singh S, Sissons D, Skeemer J, Slack K, Smith A, Smith D, Smith S, Smith J, Smith L, Soares M, Solano TS, Solly R, Solstice AR, Soulsby T, Southern D, Sowter D, Spears M, Spencer LG, Speranza F, Stadon L, Stanel S, Steele N, Steiner M, Stensel D, Stephens G, Stephenson L, Stern M, Stewart I, Stimpson R, Stockdale S, Stockley J, Stoker W, Stone R, Storrar W, Storrie A, Storton K, Stringer E, Strong-Sheldrake S, Stroud N, Subbe C, Sudlow CL, Suleiman Z, Summers C, Summersgill C, Sutherland D, Sykes DL, Sykes R, Talbot N, Tan AL, Tarusan L, Tavoukjian V, Taylor A, Taylor C, Taylor J, Te A, Tedd H, Tee CJ, Teixeira J, Tench H, Terry S, Thackray-Nocera S, Thaivalappil F, Thamu B, Thickett D, Thomas C, Thomas S, Thomas AK, Thomas-Woods T, Thompson T, Thompson AAR, Thornton T, Tilley J, Tinker N, Tiongson GF, Tobin M, Tomlinson J, Tong C, Touyz R, Tripp KA, Tunnicliffe E, Turnbull A, Turner E, Turner S, Turner V, Turner K, Turney S, Turtle L, Turton H, Ugoji J, Ugwuoke R, Upthegrove R, Valabhji J, Ventura M, Vere J, Vickers C, Vinson B, Wade E, Wade P, Wainwright T, Wajero LO, Walder S, Walker S, Walker S, Wall E, Wallis T, Walmsley S, Walsh JA, Walsh S, Warburton L, Ward TJC, Warwick K, Wassall H, Waterson S, Watson E, Watson L, Watson J, Welch C, Welch H, Welsh B, Wessely S, West S, Weston H, Wheeler H, White S, Whitehead V, Whitney J, Whittaker S, Whittam B, Whitworth V, Wight A, Wild J, Wilkins M, Wilkinson D, Williams N, Williams N, Williams J, Williams-Howard SA, Willicombe M, Willis G, Willoughby J, Wilson A, Wilson D, Wilson I, Window N, Witham M, Wolf-Roberts R, Wood C, Woodhead F, Woods J, Wormleighton J, Worsley J, Wraith D, Wrey Brown C, Wright C, Wright L, Wright S, Wyles J, Wynter I, Xu M, Yasmin N, Yasmin S, Yates T, Yip KP, Young B, Young S, Young A, Yousuf AJ, Zawia A, Zeidan L, Zhao B, Zongo O. Clinical characteristics with inflammation profiling of long COVID and association with 1-year recovery following hospitalisation in the UK: a prospective observational study. Lancet Respir Med 2022; 10:761-775. [PMID: 35472304 PMCID: PMC9034855 DOI: 10.1016/s2213-2600(22)00127-8] [Citation(s) in RCA: 144] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/23/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND No effective pharmacological or non-pharmacological interventions exist for patients with long COVID. We aimed to describe recovery 1 year after hospital discharge for COVID-19, identify factors associated with patient-perceived recovery, and identify potential therapeutic targets by describing the underlying inflammatory profiles of the previously described recovery clusters at 5 months after hospital discharge. METHODS The Post-hospitalisation COVID-19 study (PHOSP-COVID) is a prospective, longitudinal cohort study recruiting adults (aged ≥18 years) discharged from hospital with COVID-19 across the UK. Recovery was assessed using patient-reported outcome measures, physical performance, and organ function at 5 months and 1 year after hospital discharge, and stratified by both patient-perceived recovery and recovery cluster. Hierarchical logistic regression modelling was performed for patient-perceived recovery at 1 year. Cluster analysis was done using the clustering large applications k-medoids approach using clinical outcomes at 5 months. Inflammatory protein profiling was analysed from plasma at the 5-month visit. This study is registered on the ISRCTN Registry, ISRCTN10980107, and recruitment is ongoing. FINDINGS 2320 participants discharged from hospital between March 7, 2020, and April 18, 2021, were assessed at 5 months after discharge and 807 (32·7%) participants completed both the 5-month and 1-year visits. 279 (35·6%) of these 807 patients were women and 505 (64·4%) were men, with a mean age of 58·7 (SD 12·5) years, and 224 (27·8%) had received invasive mechanical ventilation (WHO class 7-9). The proportion of patients reporting full recovery was unchanged between 5 months (501 [25·5%] of 1965) and 1 year (232 [28·9%] of 804). Factors associated with being less likely to report full recovery at 1 year were female sex (odds ratio 0·68 [95% CI 0·46-0·99]), obesity (0·50 [0·34-0·74]) and invasive mechanical ventilation (0·42 [0·23-0·76]). Cluster analysis (n=1636) corroborated the previously reported four clusters: very severe, severe, moderate with cognitive impairment, and mild, relating to the severity of physical health, mental health, and cognitive impairment at 5 months. We found increased inflammatory mediators of tissue damage and repair in both the very severe and the moderate with cognitive impairment clusters compared with the mild cluster, including IL-6 concentration, which was increased in both comparisons (n=626 participants). We found a substantial deficit in median EQ-5D-5L utility index from before COVID-19 (retrospective assessment; 0·88 [IQR 0·74-1·00]), at 5 months (0·74 [0·64-0·88]) to 1 year (0·75 [0·62-0·88]), with minimal improvements across all outcome measures at 1 year after discharge in the whole cohort and within each of the four clusters. INTERPRETATION The sequelae of a hospital admission with COVID-19 were substantial 1 year after discharge across a range of health domains, with the minority in our cohort feeling fully recovered. Patient-perceived health-related quality of life was reduced at 1 year compared with before hospital admission. Systematic inflammation and obesity are potential treatable traits that warrant further investigation in clinical trials. FUNDING UK Research and Innovation and National Institute for Health Research.
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Mann JP, Hoare M. A minority of somatically mutated genes in pre-existing fatty liver disease have prognostic importance in the development of NAFLD. Liver Int 2022; 42:1823-1835. [PMID: 35474605 PMCID: PMC9544140 DOI: 10.1111/liv.15283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Understanding the genetics of liver disease has the potential to facilitate clinical risk stratification. We recently identified acquired somatic mutations in six genes and one lncRNA in pre-existing fatty liver disease. We hypothesised that germline variation in these genes might be associated with the risk of developing steatosis and contribute to the prediction of disease severity. METHODS Genome-wide association study (GWAS) summary statistics were extracted from seven studies (>1.7 million participants) for variants near ACVR2A, ALB, CIDEB, FOXO1, GPAM, NEAT1 and TNRC6B for: aminotransferases, liver fat, HbA1c, diagnosis of NAFLD, ARLD and cirrhosis. Findings were replicated using GWAS data from multiple independent cohorts. A phenome-wide association study was performed to examine for related metabolic traits, using both common and rare variants, including gene-burden testing. RESULTS There was no evidence of association between rare germline variants or SNPs near five genes (ACVR2A, ALB, CIDEB, FOXO1 and TNRC6B) and risk or severity of liver disease. Variants in GPAM (proxies for p.Ile43Val) were associated with liver fat (p = 3.6 × 10-13 ), ALT (p = 2.8 × 10-39 ) and serum lipid concentrations. Variants in NEAT1 demonstrated borderline significant associations with ALT (p = 1.9 × 10-11 ) and HbA1c, but not with liver fat, as well as influencing waist-to-hip ratio, adjusted for BMI. CONCLUSIONS Despite the acquisition of somatic mutations at these loci during progressive fatty liver disease, we did not find associations between germline variation and markers of liver disease, except in GPAM. In the future, larger sample sizes may identify associations. Currently, germline polygenic risk scores will not capture data from genes affected by somatic mutations.
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Affiliation(s)
- Jake P. Mann
- Institute of Metabolic ScienceUniversity of CambridgeCambridgeUK
- School of Clinical MedicineUniversity of CambridgeCambridgeUK
| | - Matthew Hoare
- School of Clinical MedicineUniversity of CambridgeCambridgeUK
- CRUK Cambridge InstituteUniversity of CambridgeCambridgeUK
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Assante G, Chandrasekaran S, Ng S, Tourna A, Chung CH, Isse KA, Banks JL, Soffientini U, Filippi C, Dhawan A, Liu M, Rozen SG, Hoare M, Campbell P, Ballard JWO, Turner N, Morris MJ, Chokshi S, Youngson NA. Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease. Genome Med 2022; 14:67. [PMID: 35739588 PMCID: PMC9219160 DOI: 10.1186/s13073-022-01071-5] [Citation(s) in RCA: 10] [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] [Received: 08/10/2021] [Accepted: 06/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The incidence of non-alcoholic fatty liver disease (NAFLD)-associated hepatocellular carcinoma (HCC) is increasing worldwide, but the steps in precancerous hepatocytes which lead to HCC driver mutations are not well understood. Here we provide evidence that metabolically driven histone hyperacetylation in steatotic hepatocytes can increase DNA damage to initiate carcinogenesis. METHODS Global epigenetic state was assessed in liver samples from high-fat diet or high-fructose diet rodent models, as well as in cultured immortalized human hepatocytes (IHH cells). The mechanisms linking steatosis, histone acetylation and DNA damage were investigated by computational metabolic modelling as well as through manipulation of IHH cells with metabolic and epigenetic inhibitors. Chromatin immunoprecipitation and next-generation sequencing (ChIP-seq) and transcriptome (RNA-seq) analyses were performed on IHH cells. Mutation locations and patterns were compared between the IHH cell model and genome sequence data from preneoplastic fatty liver samples from patients with alcohol-related liver disease and NAFLD. RESULTS Genome-wide histone acetylation was increased in steatotic livers of rodents fed high-fructose or high-fat diet. In vitro, steatosis relaxed chromatin and increased DNA damage marker γH2AX, which was reversed by inhibiting acetyl-CoA production. Steatosis-associated acetylation and γH2AX were enriched at gene clusters in telomere-proximal regions which contained HCC tumour suppressors in hepatocytes and human fatty livers. Regions of metabolically driven epigenetic change also had increased levels of DNA mutation in non-cancerous tissue from NAFLD and alcohol-related liver disease patients. Finally, genome-scale network modelling indicated that redox balance could be a key contributor to this mechanism. CONCLUSIONS Abnormal histone hyperacetylation facilitates DNA damage in steatotic hepatocytes and is a potential initiating event in hepatocellular carcinogenesis.
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Affiliation(s)
- Gabriella Assante
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Sriram Chandrasekaran
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- Center for Bioinformatics and Computational Medicine, Ann Arbor, MI, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Stanley Ng
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Aikaterini Tourna
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Carolina H Chung
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kowsar A Isse
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Jasmine L Banks
- UNSW Sydney, Sydney, Australia
- Cellular Bioenergetics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Ugo Soffientini
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Celine Filippi
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Anil Dhawan
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Mo Liu
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Steven G Rozen
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Matthew Hoare
- CRUK Cambridge Institute, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | | | - J William O Ballard
- Department of Ecology, Environment and Evolution, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia
| | - Nigel Turner
- UNSW Sydney, Sydney, Australia
- Cellular Bioenergetics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | | | - Shilpa Chokshi
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Neil A Youngson
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK.
- King's College London, Faculty of Life Sciences and Medicine, London, UK.
- UNSW Sydney, Sydney, Australia.
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Yin K, Patten D, Gough S, de Barros Gonçalves S, Chan A, Olan I, Cassidy L, Poblocka M, Zhu H, Lun A, Schuijs M, Young A, Martinez-Jimenez C, Halim TYF, Shetty S, Narita M, Hoare M. Senescence-induced endothelial phenotypes underpin immune-mediated senescence surveillance. Genes Dev 2022; 36:533-549. [PMID: 35618311 PMCID: PMC9186388 DOI: 10.1101/gad.349585.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/16/2022] [Indexed: 12/13/2022]
Abstract
Senescence is a stress-responsive tumor suppressor mechanism associated with expression of the senescence-associated secretory phenotype (SASP). Through the SASP, senescent cells trigger their own immune-mediated elimination, which if evaded leads to tumorigenesis. Senescent parenchymal cells are separated from circulating immunocytes by the endothelium, which is targeted by microenvironmental signaling. Here we show that SASP induces endothelial cell NF-κB activity and that SASP-induced endothelial expression of the canonical NF-κB component Rela underpins senescence surveillance. Using human liver sinusoidal endothelial cells (LSECs), we show that SASP-induced endothelial NF-κB activity regulates a conserved transcriptional program supporting immunocyte recruitment. Furthermore, oncogenic hepatocyte senescence drives murine LSEC NF-κB activity in vivo. Critically, we show two distinct endothelial pathways in senescence surveillance. First, endothelial-specific loss of Rela prevents development of Stat1-expressing CD4+ T lymphocytes. Second, the SASP up-regulates ICOSLG on LSECs, with the ICOS-ICOSLG axis contributing to senescence cell clearance. Our results show that the endothelium is a nonautonomous SASP target and an organizing center for immune-mediated senescence surveillance.
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Affiliation(s)
- Kelvin Yin
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764 München, Germany
| | - Daniel Patten
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Sarah Gough
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | | | - Adelyne Chan
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Ioana Olan
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Liam Cassidy
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Marta Poblocka
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Haoran Zhu
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Aaron Lun
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Martijn Schuijs
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Andrew Young
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | | | - Timotheus Y F Halim
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Shishir Shetty
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-0026, Japan
| | - Matthew Hoare
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
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Ng SWK, Rouhani FJ, Brunner SF, Brzozowska N, Aitken SJ, Yang M, Abascal F, Moore L, Nikitopoulou E, Chappell L, Leongamornlert D, Ivovic A, Robinson P, Butler T, Sanders MA, Williams N, Coorens THH, Teague J, Raine K, Butler AP, Hooks Y, Wilson B, Birtchnell N, Naylor H, Davies SE, Stratton MR, Martincorena I, Rahbari R, Frezza C, Hoare M, Campbell PJ. Convergent somatic mutations in metabolism genes in chronic liver disease. Nature 2021; 598:473-478. [PMID: 34646017 DOI: 10.1038/s41586-021-03974-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [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: 06/17/2020] [Accepted: 08/31/2021] [Indexed: 02/08/2023]
Abstract
The progression of chronic liver disease to hepatocellular carcinoma is caused by the acquisition of somatic mutations that affect 20-30 cancer genes1-8. Burdens of somatic mutations are higher and clonal expansions larger in chronic liver disease9-13 than in normal liver13-16, which enables positive selection to shape the genomic landscape9-13. Here we analysed somatic mutations from 1,590 genomes across 34 liver samples, including healthy controls, alcohol-related liver disease and non-alcoholic fatty liver disease. Seven of the 29 patients with liver disease had mutations in FOXO1, the major transcription factor in insulin signalling. These mutations affected a single hotspot within the gene, impairing the insulin-mediated nuclear export of FOXO1. Notably, six of the seven patients with FOXO1S22W hotspot mutations showed convergent evolution, with variants acquired independently by up to nine distinct hepatocyte clones per patient. CIDEB, which regulates lipid droplet metabolism in hepatocytes17-19, and GPAM, which produces storage triacylglycerol from free fatty acids20,21, also had a significant excess of mutations. We again observed frequent convergent evolution: up to fourteen independent clones per patient with CIDEB mutations and up to seven clones per patient with GPAM mutations. Mutations in metabolism genes were distributed across multiple anatomical segments of the liver, increased clone size and were seen in both alcohol-related liver disease and non-alcoholic fatty liver disease, but rarely in hepatocellular carcinoma. Master regulators of metabolic pathways are a frequent target of convergent somatic mutation in alcohol-related and non-alcoholic fatty liver disease.
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Affiliation(s)
- Stanley W K Ng
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | - Foad J Rouhani
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
- Department of Surgery, Addenbrooke's Hospital, Cambridge, UK
| | - Simon F Brunner
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | | | - Sarah J Aitken
- CRUK Cambridge Institute, Cambridge, UK
- Department of Pathology, Addenbrooke's Hospital, Cambridge, UK
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Ming Yang
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
| | | | - Luiza Moore
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | | | - Lia Chappell
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | | | | | - Philip Robinson
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | - Timothy Butler
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | - Mathijs A Sanders
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Tim H H Coorens
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | - Jon Teague
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | - Keiran Raine
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | - Adam P Butler
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | - Yvette Hooks
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | - Beverley Wilson
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | | | - Huw Naylor
- Department of Surgery, Addenbrooke's Hospital, Cambridge, UK
| | - Susan E Davies
- Department of Pathology, Addenbrooke's Hospital, Cambridge, UK
| | | | | | - Raheleh Rahbari
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | | | - Matthew Hoare
- CRUK Cambridge Institute, Cambridge, UK.
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK.
- Stem Cell Institute, University of Cambridge, Cambridge, UK.
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12
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Kolamunnage-Dona R, Berhane S, Potts H, Williams EH, Tanner J, Janowitz T, Hoare M, Johnson P. Sorafenib is associated with a reduced rate of tumour growth and liver function deterioration in HCV-induced hepatocellular carcinoma. J Hepatol 2021; 75:879-887. [PMID: 34052255 PMCID: PMC9158473 DOI: 10.1016/j.jhep.2021.05.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Sorafenib has been the standard of care for patients with advanced hepatocellular carcinoma and although immunotherapeutic approaches are now challenging this position, it retains an advantage in HCV-seropositive patients. We aimed to quantify the rate of tumour progression in patients receiving sorafenib and relate this figure to survival, both overall, and according to viral status. METHODS Using serial data from an international clinical trial we applied a joint model to combine survival and progression over time in order to estimate the rate of tumour growth as assessed by tumour burden and serum alpha-fetoprotein, and the impact of treatment on liver function. RESULTS High tumour burden at baseline was associated with an increased risk of death. In patients still alive at the end of the study, the progression in relation to tumour burden was very low compared to those who died within the study. Overall, the change in mean tumour burden was 0.12 mm per day or an absolute growth rate of 3.6 mm/month. Median doubling time was 665 days. For those who progressed above 0.12 mm per day or the 12% rate, median survival was 234 days compared to 384 days if the rate was below 12%. Tumour growth rate and serum alpha-fetoprotein rise were significantly lower in those who were HCV seropositive as was the rate of decline in liver function. These results were replicated in 2 independent patient groups. CONCLUSION Our analysis suggests that sorafenib treatment is associated with improved survival in patients with advanced hepatocellular carcinoma mainly by decreasing the rate of tumour growth and liver function deterioration among patients with HCV infection. LAY SUMMARY Among patients receiving sorafenib for advanced hepatocellular carcinoma the rate of tumour growth (as assessed by changes in tumour size and the biomarker alpha-fetoprotein) and the deterioration of liver function is less in those who have the hepatitis C virus, than in those who do not.
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Affiliation(s)
| | - Sarah Berhane
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, UK; Institute of Applied Health Research, University of Birmingham, UK
| | - Harry Potts
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | - James Tanner
- Department of Radiology, University of Cambridge, Cambridge, UK
| | - Tobias Janowitz
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK; Cold Spring Harbor Laboratory, NY, USA; Northwell Health Cancer Institute, NY, USA
| | - Matthew Hoare
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Philip Johnson
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, UK.
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13
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Escudero Sanchez L, Rundo L, Gill AB, Hoare M, Mendes Serrao E, Sala E. Robustness of radiomic features in CT images with different slice thickness, comparing liver tumour and muscle. Sci Rep 2021; 11:8262. [PMID: 33859265 PMCID: PMC8050292 DOI: 10.1038/s41598-021-87598-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 12/06/2020] [Accepted: 03/30/2021] [Indexed: 12/11/2022] Open
Abstract
Radiomic image features are becoming a promising non-invasive method to obtain quantitative measurements for tumour classification and therapy response assessment in oncological research. However, despite its increasingly established application, there is a need for standardisation criteria and further validation of feature robustness with respect to imaging acquisition parameters. In this paper, the robustness of radiomic features extracted from computed tomography (CT) images is evaluated for liver tumour and muscle, comparing the values of the features in images reconstructed with two different slice thicknesses of 2.0 mm and 5.0 mm. Novel approaches are presented to address the intrinsic dependencies of texture radiomic features, choosing the optimal number of grey levels and correcting for the dependency on volume. With the optimal values and corrections, feature values are compared across thicknesses to identify reproducible features. Normalisation using muscle regions is also described as an alternative approach. With either method, a large fraction of features (75-90%) was found to be highly robust (< 25% difference). The analyses were performed on a homogeneous CT dataset of 43 patients with hepatocellular carcinoma, and consistent results were obtained for both tumour and muscle tissue. Finally, recommended guidelines are included for radiomic studies using variable slice thickness.
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Affiliation(s)
- Lorena Escudero Sanchez
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK.
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK.
| | - Leonardo Rundo
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK.
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK.
| | - Andrew B Gill
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, UK
| | - Matthew Hoare
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Eva Mendes Serrao
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
| | - Evis Sala
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
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14
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Gonçalves S, Yin K, Ito Y, Chan A, Olan I, Gough S, Cassidy L, Serrao E, Smith S, Young A, Narita M, Hoare M. COX2 regulates senescence secretome composition and senescence surveillance through PGE 2. Cell Rep 2021; 34:108860. [PMID: 33730589 PMCID: PMC7972992 DOI: 10.1016/j.celrep.2021.108860] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [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: 07/02/2020] [Revised: 01/06/2021] [Accepted: 02/19/2021] [Indexed: 12/11/2022] Open
Abstract
Senescent cells trigger their own immune-mediated destruction, termed senescence surveillance. This is dependent on the inflammatory senescence-associated secretory phenotype (SASP), which includes COX2, an enzyme with complex roles in cancer. The role COX2 plays during senescence surveillance is unknown. Here, we show that during RAS-induced senescence (RIS), COX2 is a critical regulator of SASP composition and senescence surveillance in vivo. COX2 regulates the expression of multiple inflammatory SASP components through an autocrine feedback loop involving its downstream product, prostaglandin E2 (PGE2), binding to EP4. During in vivo hepatocyte RIS, Cox2 is critical to tumor suppression, Cxcl1 expression, and immune-mediated senescence surveillance, partially through PGE2. Loss of Cox2 in RIS dysregulates the intrahepatic immune microenvironment, with enrichment of immunosuppressive immature myeloid cells and CD4+ regulatory T lymphocytes. Therefore, COX2 and PGE2 play a critical role in senescence, shaping SASP composition, promoting senescence surveillance and tumor suppression in the earliest stages of tumorigenesis.
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Affiliation(s)
- Susana Gonçalves
- CRUK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Kelvin Yin
- CRUK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Yoko Ito
- CRUK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Adelyne Chan
- CRUK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Ioana Olan
- CRUK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Sarah Gough
- CRUK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Liam Cassidy
- CRUK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Eva Serrao
- CRUK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Stephen Smith
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Andrew Young
- CRUK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Masashi Narita
- CRUK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-0026, Japan
| | - Matthew Hoare
- CRUK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.
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15
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Hall Z, Chiarugi D, Charidemou E, Leslie J, Scott E, Pellegrinet L, Allison M, Mocciaro G, Anstee QM, Evan GI, Hoare M, Vidal-Puig A, Oakley F, Vacca M, Griffin JL. Lipid Remodeling in Hepatocyte Proliferation and Hepatocellular Carcinoma. Hepatology 2021; 73:1028-1044. [PMID: 32460431 DOI: 10.1002/hep.31391] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/08/2020] [Accepted: 04/27/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND AND AIMS Hepatocytes undergo profound metabolic rewiring when primed to proliferate during compensatory regeneration and in hepatocellular carcinoma (HCC). However, the metabolic control of these processes is not fully understood. In order to capture the metabolic signature of proliferating hepatocytes, we applied state-of-the-art systems biology approaches to models of liver regeneration, pharmacologically and genetically activated cell proliferation, and HCC. APPROACH AND RESULTS Integrating metabolomics, lipidomics, and transcriptomics, we link changes in the lipidome of proliferating hepatocytes to altered metabolic pathways including lipogenesis, fatty acid desaturation, and generation of phosphatidylcholine (PC). We confirm this altered lipid signature in human HCC and show a positive correlation of monounsaturated PC with hallmarks of cell proliferation and hepatic carcinogenesis. CONCLUSIONS Overall, we demonstrate that specific lipid metabolic pathways are coherently altered when hepatocytes switch to proliferation. These represent a source of targets for the development of therapeutic strategies and prognostic biomarkers of HCC.
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Affiliation(s)
- Zoe Hall
- Department of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridgeUnited Kingdom
- Biomolecular MedicineDivision of Systems MedicineDepartment of Metabolism, Digestion and ReproductionImperial College LondonLondonUnited Kingdom
| | - Davide Chiarugi
- Metabolic Research LaboratoriesWellcome Trust-MRC Institute of Metabolic ScienceCambridgeUnited Kingdom
| | - Evelina Charidemou
- Department of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridgeUnited Kingdom
| | - Jack Leslie
- Institute of Cellular MedicineFaculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Emma Scott
- Institute of Cellular MedicineFaculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Luca Pellegrinet
- Department of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridgeUnited Kingdom
| | - Michael Allison
- Department of MedicineAddenbrooke's HospitalCambridge Biomedical Research CentreCambridgeUnited Kingdom
| | - Gabriele Mocciaro
- Department of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridgeUnited Kingdom
| | - Quentin M Anstee
- Institute of Cellular MedicineFaculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUnited Kingdom
- Newcastle NIHR Biomedical Research CentreNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUnited Kingdom
| | - Gerard I Evan
- Department of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridgeUnited Kingdom
| | - Matthew Hoare
- Department of MedicineAddenbrooke's HospitalCambridge Biomedical Research CentreCambridgeUnited Kingdom
- CRUK Cambridge InstituteRobinson WayCambridgeUnited Kingdom
| | - Antonio Vidal-Puig
- Metabolic Research LaboratoriesWellcome Trust-MRC Institute of Metabolic ScienceCambridgeUnited Kingdom
| | - Fiona Oakley
- Institute of Cellular MedicineFaculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Michele Vacca
- Department of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridgeUnited Kingdom
- Metabolic Research LaboratoriesWellcome Trust-MRC Institute of Metabolic ScienceCambridgeUnited Kingdom
| | - Julian L Griffin
- Department of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridgeUnited Kingdom
- Biomolecular MedicineDivision of Systems MedicineDepartment of Metabolism, Digestion and ReproductionImperial College LondonLondonUnited Kingdom
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16
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Ferrandino G, Orf I, Smith R, Calcagno M, Thind AK, Debiram-Beecham I, Williams M, Gandelman O, de Saedeleer A, Kibble G, Lydon AM, Mayhew CA, Allsworth M, Boyle B, van der Schee MP, Allison M, Hoare M, Snowdon VK. Breath Biopsy Assessment of Liver Disease Using an Exogenous Volatile Organic Compound-Toward Improved Detection of Liver Impairment. Clin Transl Gastroenterol 2020; 11:e00239. [PMID: 33094960 PMCID: PMC7498135 DOI: 10.14309/ctg.0000000000000239] [Citation(s) in RCA: 19] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/21/2020] [Indexed: 12/29/2022] Open
Abstract
INTRODUCTION Liver cirrhosis and its complication - hepatocellular carcinoma (HCC) - have been associated with increased exhaled limonene. It is currently unclear whether this increase is more strongly associated with the presence of HCC or with the severity of liver dysfunction. METHODS We compared the exhaled breath of 40 controls, 32 cirrhotic patients, and 12 cirrhotic patients with HCC using the Breath Biopsy platform. Breath samples were analyzed by thermal desorption-gas chromatography-mass spectrometry. Limonene levels were compared between the groups and correlated to bilirubin, albumin, prothrombin time international normalized ratio, and alanine aminotransferase. RESULTS Breath limonene concentration was significantly elevated in subjects with cirrhosis-induced HCC (M: 82.1 ng/L, interquartile range [IQR]: 16.33-199.32 ng/L) and cirrhosis (M: 32.6 ng/L, IQR: 6.55-123.07 ng/L) compared with controls (M: 6.2 ng/L, IQR: 2.62-9.57 ng/L) (P value = 0.0005 and 0.0001, respectively) with no significant difference between 2 diseased groups (P value = 0.37). Levels of exhaled limonene correlated with serum bilirubin (R = 0.25, P value = 0.0016, r = 0.51), albumin (R = 0.58, P value = 5.3e-8, r = -0.76), and international normalized ratio (R = 0.29, P value = 0.0003, r = 0.51), but not with alanine aminotransferase (R = 0.01, P value = 0.36, r = 0.19). DISCUSSION Exhaled limonene levels are primarily affected by the presence of cirrhosis through reduced liver functional capacity, as indicated by limonene correlation with blood metrics of impaired hepatic clearance and protein synthesis capacity, without further alterations observed in subjects with HCC. This suggests that exhaled limonene is a potential non-invasive marker of liver metabolic capacity (see Visual abstract, Supplementary Digital Content 1, http://links.lww.com/CTG/A388).
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Affiliation(s)
| | - Isabel Orf
- Owlstone Medical, Cambridge, UK
- Current affiliation: Human Metabolome Technologies, Leiden, the Netherlands
| | | | | | | | - Irene Debiram-Beecham
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, UK
| | | | | | | | - Graham Kibble
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Anne Marie Lydon
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Chris A. Mayhew
- Institute for Breath Research, Leopold-Franzens-Universität Innsbruck, Dornbirn, Austria
- Molecular Physics Group, School of Physics and Astronomy, University of Birmingham, Birmingham, UK
| | | | | | | | - Michael Allison
- Department of Medicine, Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Addenbrooke's Hepatology and Liver Transplantation Unit, Addenbrooke's Hospital, Cambridge, UK
| | - Matthew Hoare
- Addenbrooke's Hepatology and Liver Transplantation Unit, Addenbrooke's Hospital, Cambridge, UK
- CRUK Cambridge Institute, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Victoria K. Snowdon
- Addenbrooke's Hepatology and Liver Transplantation Unit, Addenbrooke's Hospital, Cambridge, UK
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17
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Brunner SF, Roberts ND, Wylie LA, Moore L, Aitken SJ, Davies SE, Sanders MA, Ellis P, Alder C, Hooks Y, Abascal F, Stratton MR, Martincorena I, Hoare M, Campbell PJ. Somatic mutations and clonal dynamics in healthy and cirrhotic human liver. Nature 2019; 574:538-542. [PMID: 31645727 PMCID: PMC6837891 DOI: 10.1038/s41586-019-1670-9] [Citation(s) in RCA: 202] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 09/12/2019] [Indexed: 12/22/2022]
Abstract
The most common causes of chronic liver disease are excess alcohol intake, viral hepatitis and non-alcoholic fatty liver disease, with the clinical spectrum ranging in severity from hepatic inflammation to cirrhosis, liver failure or hepatocellular carcinoma (HCC). The genome of HCC exhibits diverse mutational signatures, resulting in recurrent mutations across more than 30 cancer genes1-7. Stem cells from normal livers have a low mutational burden and limited diversity of signatures8, which suggests that the complexity of HCC arises during the progression to chronic liver disease and subsequent malignant transformation. Here, by sequencing whole genomes of 482 microdissections of 100-500 hepatocytes from 5 normal and 9 cirrhotic livers, we show that cirrhotic liver has a higher mutational burden than normal liver. Although rare in normal hepatocytes, structural variants, including chromothripsis, were prominent in cirrhosis. Driver mutations, such as point mutations and structural variants, affected 1-5% of clones. Clonal expansions of millimetres in diameter occurred in cirrhosis, with clones sequestered by the bands of fibrosis that surround regenerative nodules. Some mutational signatures were universal and equally active in both non-malignant hepatocytes and HCCs; some were substantially more active in HCCs than chronic liver disease; and others-arising from exogenous exposures-were present in a subset of patients. The activity of exogenous signatures between adjacent cirrhotic nodules varied by up to tenfold within each patient, as a result of clone-specific and microenvironmental forces. Synchronous HCCs exhibited the same mutational signatures as background cirrhotic liver, but with higher burden. Somatic mutations chronicle the exposures, toxicity, regeneration and clonal structure of liver tissue as it progresses from health to disease.
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Affiliation(s)
- Simon F Brunner
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Nicola D Roberts
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Luke A Wylie
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Luiza Moore
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Sarah J Aitken
- CRUK Cambridge Institute, Cambridge, UK
- Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Susan E Davies
- Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Mathijs A Sanders
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Pete Ellis
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Chris Alder
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Yvette Hooks
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Federico Abascal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | | | - Matthew Hoare
- CRUK Cambridge Institute, Cambridge, UK.
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK.
- Department of Haematology and Stem Cell Institute, University of Cambridge, Cambridge, UK.
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18
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Parry AJ, Hoare M, Bihary D, Hänsel-Hertsch R, Smith S, Tomimatsu K, Mannion E, Smith A, D'Santos P, Russell IA, Balasubramanian S, Kimura H, Samarajiwa SA, Narita M. NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence. Nat Commun 2018; 9:1840. [PMID: 29743479 PMCID: PMC5943456 DOI: 10.1038/s41467-018-04283-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [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: 10/15/2017] [Accepted: 04/16/2018] [Indexed: 12/16/2022] Open
Abstract
Senescent cells interact with the surrounding microenvironment achieving diverse functional outcomes. We have recently identified that NOTCH1 can drive 'lateral induction' of a unique senescence phenotype in adjacent cells by specifically upregulating the NOTCH ligand JAG1. Here we show that NOTCH signalling can modulate chromatin structure autonomously and non-autonomously. In addition to senescence-associated heterochromatic foci (SAHF), oncogenic RAS-induced senescent (RIS) cells exhibit a massive increase in chromatin accessibility. NOTCH signalling suppresses SAHF and increased chromatin accessibility in this context. Strikingly, NOTCH-induced senescent cells, or cancer cells with high JAG1 expression, drive similar chromatin architectural changes in adjacent cells through cell-cell contact. Mechanistically, we show that NOTCH signalling represses the chromatin architectural protein HMGA1, an association found in multiple human cancers. Thus, HMGA1 is involved not only in SAHFs but also in RIS-driven chromatin accessibility. In conclusion, this study identifies that the JAG1-NOTCH-HMGA1 axis mediates the juxtacrine regulation of chromatin architecture.
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Affiliation(s)
- Aled J Parry
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Matthew Hoare
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Dóra Bihary
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Robert Hänsel-Hertsch
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Stephen Smith
- Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Kosuke Tomimatsu
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Elizabeth Mannion
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Amy Smith
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Paula D'Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - I Alasdair Russell
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Hiroshi Kimura
- Cell Biology Centre, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Shamith A Samarajiwa
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK.
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.
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19
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Abstract
Cellular senescence is a state of stable proliferative arrest triggered by various stimuli, including oncogenic and other cellular stress. Senescent cells are highly metabolically active and have diverse and profound nonautonomous effects through the senescence-associated secretory phenotype (SASP). It has become increasingly evident that senescent cells can have tumour suppressive or pro-oncogenic effects on adjacent cancer cells and other players in the tumor microenvironment such as the stroma, vasculature, and immune system. Thus, the last decade or so has witnessed a huge leap forward in our understanding of the biology of senescence, promoting it from an autonomous tumor suppressor to a complex, dynamic, and interactive phenotype. It is perhaps not a coincidence that the concept of the “hallmarks of cancer” has also evolved during this period, with the latest iteration ( Hanahan & Weinberg 2011 ) focusing more on the microenvironment. Here, we suggest that cellular senescence could underpin the biology of many of the hallmarks of cancer, making it the true power behind the throne.
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Affiliation(s)
- Matthew Hoare
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom;,
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom;,
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20
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Abstract
Cellular senescence, previously thought of as an autonomous tumour suppressor mechanism, is emerging as a phenotype and effector present throughout the life of an organism from embryogenesis to senile decline. Senescent cells have powerful non-autonomous effects upon multiple players within their microenvironment mainly through their secretory phenotype. How senescent cells co-ordinate numerous, sometimes functionally contrasting outputs through their secretome had previously been unclear. The Notch pathway, originally identified for its involvement in Drosophila wing development, has more recently been found to underpin diverse effects in human cancer. Here we discuss recent findings that suggest that Notch is intimately involved in the development of senescence and how it acts to co-ordinate the composition and functional effects of the senescence secretome. We also highlight the complex physical and functional interplay between Notch and p53, critical to both senescence and cancer. Understanding the interplay between Notch, p53 and senescence could allow us develop the therapeutics of the future for cancer and ageing.
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Affiliation(s)
- Matthew Hoare
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK.
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
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21
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Abstract
Cellular senescence is an autonomous tumor suppressor mechanism leading to stable cell cycle arrest. Senescent cells are highly secretory, driving a range of different functions through the senescence-associated secretory phenotype (SASP). Recent findings have suggested that the composition of the SASP is dynamically and spatially regulated and that the changing composition of the SASP can determine the beneficial and detrimental aspects of the senescence program, tipping the balance to either an immunosuppressive/profibrotic environment or proinflammatory/fibrolytic state. Here, we discuss the current understanding of the temporal and spatial regulation of the SASP and the novel finding of NOTCH signaling as a regulator of SASP composition.
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Affiliation(s)
- Yoko Ito
- Cancer Research UK Cambridge Centre, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Matthew Hoare
- Cancer Research UK Cambridge Centre, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Masashi Narita
- Cancer Research UK Cambridge Centre, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, UK.
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22
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Affiliation(s)
- Matthew Hoare
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
- University of Cambridge, Department of Medicine, Addenbrooke’s Hospital, Cambridge, UK
| | - Masashi Narita
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
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23
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Hoare M, Ito Y, Kang TW, Weekes MP, Matheson NJ, Patten DA, Shetty S, Parry AJ, Menon S, Salama R, Antrobus R, Tomimatsu K, Howat W, Lehner PJ, Zender L, Narita M. NOTCH1 mediates a switch between two distinct secretomes during senescence. Nat Cell Biol 2016; 18:979-92. [PMID: 27525720 PMCID: PMC5008465 DOI: 10.1038/ncb3397] [Citation(s) in RCA: 303] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 07/12/2016] [Indexed: 12/15/2022]
Abstract
Senescence, a persistent form of cell-cycle arrest, is often associated with a diverse secretome, which provides complex functionality for senescent cells within the tissue microenvironment. We show that oncogene-induced senescence is accompanied by a dynamic fluctuation of NOTCH1 activity, which drives a TGF-β-rich secretome, while suppressing the senescence-associated pro-inflammatory secretome through inhibition of C/EBPβ. NOTCH1 and NOTCH1-driven TGF-β contribute to 'lateral induction of senescence' through a juxtacrine NOTCH-JAG1 pathway. In addition, NOTCH1 inhibition during senescence facilitates upregulation of pro-inflammatory cytokines, promoting lymphocyte recruitment and senescence surveillance in vivo. As enforced activation of NOTCH1 signalling confers a near mutually exclusive secretory profile compared with typical senescence, our data collectively indicate that the dynamic alteration of NOTCH1 activity during senescence dictates a functional balance between these two distinct secretomes: one representing TGF-β and the other pro-inflammatory cytokines, highlighting that NOTCH1 is a temporospatial controller of secretome composition.
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Affiliation(s)
- Matthew Hoare
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
- University of Cambridge, Department of Medicine, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK
| | - Yoko Ito
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Tae-Won Kang
- Division of Translational Gastrointestinal Oncology, Dept. of Internal Medicine I, University Hospital Tuebingen, Otfried-Mueller-Strasse 12, 72076 Tuebingen, Germany & Translational Gastrointestinal Oncology Group within the German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael P. Weekes
- University of Cambridge, Department of Medicine, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK
- University of Cambridge, Cambridge Institute for Medical Research, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK
| | - Nicholas J. Matheson
- University of Cambridge, Department of Medicine, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK
- University of Cambridge, Cambridge Institute for Medical Research, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK
| | - Daniel A. Patten
- National Institute of Health Research (NIHR) Birmingham Liver Biomedical Research Unit (BRU), Centre for Liver Research, University of Birmingham, Birmingham, B15 2TT, UK
| | - Shishir Shetty
- National Institute of Health Research (NIHR) Birmingham Liver Biomedical Research Unit (BRU), Centre for Liver Research, University of Birmingham, Birmingham, B15 2TT, UK
| | - Aled J. Parry
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Suraj Menon
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Rafik Salama
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Robin Antrobus
- University of Cambridge, Cambridge Institute for Medical Research, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK
| | - Kosuke Tomimatsu
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - William Howat
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Paul J. Lehner
- University of Cambridge, Department of Medicine, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK
- University of Cambridge, Cambridge Institute for Medical Research, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK
| | - Lars Zender
- Division of Translational Gastrointestinal Oncology, Dept. of Internal Medicine I, University Hospital Tuebingen, Otfried-Mueller-Strasse 12, 72076 Tuebingen, Germany & Translational Gastrointestinal Oncology Group within the German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Masashi Narita
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
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Chen AY, Hoare M, Shankar AN, Allison M, Alexander GJM, Michalak TI. Persistence of Hepatitis C Virus Traces after Spontaneous Resolution of Hepatitis C. PLoS One 2015; 10:e0140312. [PMID: 26473969 PMCID: PMC4608821 DOI: 10.1371/journal.pone.0140312] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 09/24/2015] [Indexed: 12/22/2022] Open
Abstract
Hepatitis C virus (HCV) frequently causes chronic hepatitis, while spontaneous recovery from infection is infrequent. Persistence of HCV after self-limited (spontaneous) resolution of hepatitis C was rarely investigated. The current study aimed to assess incidence and robustness of HCV persistence after self-resolved hepatitis C in individuals with normal liver enzymes and undetectable virus by conventional tests. Applying high sensitivity HCV RNA detection approaches, we analyzed plasma and peripheral blood mononuclear cells (PBMC) from individuals with previous hepatitis C infection. Parallel plasma and PBMC from 24 such non-viraemic individuals followed for 0.3–14.4 (mean 6.4) years were examined. Additional samples from 9 of them were obtained 4.5–7.2 (mean 5.9) years later. RNA was extracted from 250 μl plasma and, if HCV negative, from ~5 ml after ultracentrifugation, and from ex vivo stimulated PBMC. PBMC with evidence of HCV replication from 4 individuals were treated with HCV protease inhibitor, telaprevir. HCV RNA was detected in 14/24 (58.3%) plasma and 11/23 (47.8%) PBMC obtained during the first collection. HCV RNA replicative strand was evident in 7/11 (63.6%) PBMC. Overall, 17/24 (70.8%) individuals carried HCV RNA at mean follow-up of 5.9 years. Samples collected 4.5–7.2 years later revealed HCV in 4/9 (44.4%) plasma and 5/9 (55.5%) PBMC, while 4 (80%) of these 5 PBMC demonstrated virus replicative strand. Overall, 6/9 (66.7%) individuals remained viraemic for up to 20.7 (mean 12.7) years. Telaprevir entirely eliminated HCV replication in the PBMC examined. In conclusion, our results indicate that HCV can persist long after spontaneous resolution of hepatitis C at levels undetectable by current testing. An apparently effective host immune response curtailing hepatitis appears insufficient to completely eliminate the virus. The long-term morbidity of asymptomatic HCV carriage should be examined even in individuals who achieve undetectable HCV by standard testing and their need for treatment should be assessed.
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Affiliation(s)
- Annie Y. Chen
- Molecular Virology and Hepatology Research Group, Faculty of Medicine, Memorial University, St. John’s, Newfoundland and Labrador, Canada
| | - Matthew Hoare
- Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Arun N. Shankar
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Michael Allison
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Tomasz I. Michalak
- Molecular Virology and Hepatology Research Group, Faculty of Medicine, Memorial University, St. John’s, Newfoundland and Labrador, Canada
- * E-mail:
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25
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Delahaye M, Lawrence K, Ward SJ, Hoare M. An ultra scale-down analysis of the recovery by dead-end centrifugation of human cells for therapy. Biotechnol Bioeng 2015; 112:997-1011. [PMID: 25545057 PMCID: PMC4402021 DOI: 10.1002/bit.25519] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 11/28/2014] [Accepted: 12/09/2014] [Indexed: 01/07/2023]
Abstract
An ultra scale-down method is described to determine the response of cells to recovery by dead-end (batch) centrifugation under commercially defined manufacturing conditions. The key variables studied are the cell suspension hold time prior to centrifugation, the relative centrifugal force (RCF), time of centrifugation, cell pellet resuspension velocities, and number of resuspension passes. The cell critical quality attributes studied are the cell membrane integrity and the presence of selected surface markers. Greater hold times and higher RCF values for longer spin times all led to the increased loss of cell membrane integrity. However, this loss was found to occur during intense cell resuspension rather than the preceding centrifugation stage. Controlled resuspension at low stress conditions below a possible critical stress point led to essentially complete cell recovery even at conditions of extreme centrifugation (e.g., RCF of 10000 g for 30 mins) and long (∼2 h) holding times before centrifugation. The susceptibility to cell loss during resuspension under conditions of high stress depended on cell type and the age of cells before centrifugation and the level of matrix crosslinking within the cell pellet as determined by the presence of detachment enzymes or possibly the nature of the resuspension medium. Changes in cell surface markers were significant in some cases but to a lower extent than loss of cell membrane integrity. Biotechnol. Bioeng. 2015;112: 997–1011. © 2014 Wiley Periodicals, Inc.
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Affiliation(s)
- M Delahaye
- Department of Biochemical Engineering, Advanced Centre for Biochemical Engineering, University College London, Torrington Place, London, WC1E 7JE, UK
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26
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Shah M, Shankar A, Gee I, Nash K, Hoare M, Gibbs P, Davies S, Alexander GJM. A retrospective 15-year review: survival advantage after switching to sirolimus in hepatitis C virus infected liver graft recipients. Aliment Pharmacol Ther 2015; 41:379-92. [PMID: 25496225 DOI: 10.1111/apt.13049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 11/05/2014] [Accepted: 11/21/2014] [Indexed: 12/18/2022]
Abstract
BACKGROUND The use of sirolimus-based immune suppression in liver transplantation, particularly in hepatitis C virus (HCV)-infected recipients, remains contentious. There is some evidence that sirolimus retards hepatic fibrosis, is renal sparing and may be of benefit in preventing hepatocellular carcinoma (HCC) recurrence. Sirolimus has not been adopted by many transplant centres because of persistent concerns regarding an increased risk of hepatic artery thrombosis, graft loss and death with de novo sirolimus. AIM To review the impact of switching to sirolimus monotherapy in HCV-infected liver recipients with respect to survival, graft loss and hepatic fibrosis. METHODS A retrospective review of 190 patients from a single centre undergoing first liver transplantation for HCV over 15 years. 113 patients were switched from calcineurin inhibitor (CNI)-based therapy to low-dose sirolimus monotherapy at a median of 15 months after transplantation for HCV-related fibrosis (72%), renal impairment (14%) or high-risk HCC (5%). RESULTS Patients switched to sirolimus had improved survival (P < 0.001) and slower progression to cirrhosis (P = 0.001). In patients with HCC (n = 91), sirolimus duration rather than strategy was an independent predictor of survival (P = 0.001) and extended time to HCC recurrence (33 vs. 16 months). Patients switched for renal dysfunction showed improvement in serum creatinine (140-108 μmol/L, P = 0.001). Those remaining on CNI-therapy were more likely to develop post-transplant diabetes (P = 0.03). CONCLUSION These data suggest selective switching to low-dose sirolimus monotherapy in HCV-positive liver recipients improves clinical outcome.
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Affiliation(s)
- M Shah
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge University Hospitals, Cambridge, UK
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27
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Aravinthan A, Challis B, Shannon N, Hoare M, Heaney J, Alexander GJM. Selective insulin resistance in hepatocyte senescence. Exp Cell Res 2014; 331:38-45. [PMID: 25263463 DOI: 10.1016/j.yexcr.2014.09.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 09/14/2014] [Accepted: 09/18/2014] [Indexed: 12/22/2022]
Abstract
Insulin resistance has been described in association with chronic liver disease for decades. Hepatocyte senescence has been demonstrated in chronic liver disease and as many as 80% of hepatocytes show a senescent phenotype in advanced liver disease. The aim of this study was to understand the role of hepatocyte senescence in the development of insulin resistance. Senescence was induced in HepG2 cells via oxidative stress. The insulin metabolic pathway was studied in control and senescent cells following insulin stimulation. GLUT2 and GLUT4 expressions were studied in HepG2 cells and human liver tissue. Further, GLUT2 and GLUT4 expressions were studied in three independent chronic liver disease cohorts. Signalling impairment distal to Akt in phosphorylation of AS160 and FoxO1 was evident in senescent HepG2 cells. Persistent nuclear localisation of FoxO1 was demonstrated in senescent cells despite insulin stimulation. Increased GLUT4 and decreased GLUT2 expressions were evident in senescent cells, human cirrhotic liver tissue and publically available liver disease datasets. Changes in GLUT expressions were associated with a poor clinical prognosis. In conclusion, selective insulin resistance is evident in senescent HepG2 cells and changes in GLUT expressions can be used as surrogate markers of hepatocyte senescence.
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Affiliation(s)
- Aloysious Aravinthan
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Benjamin Challis
- Institute of Metabolic Sciences, University of Cambridge, Cambridge, UK
| | | | - Matthew Hoare
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, UK; Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Judith Heaney
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, UK; Foundation for Liver Research, Institute of Hepatology, London, UK
| | - Graeme J M Alexander
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, UK.
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28
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Abstract
Cellular senescence is a stress response that accompanies stable exit from the cell cycle. Classically, senescence, particularly in human cells, involves the p53 and p16/Rb pathways, and often both of these tumor suppressor pathways need to be abrogated to bypass senescence. In parallel, a number of effector mechanisms of senescence have been identified and characterized. These studies suggest that senescence is a collective phenotype of these multiple effectors, and their intensity and combination can be different depending on triggers and cell types, conferring a complex and diverse nature to senescence. Series of studies on senescence-associated secretory phenotype (SASP) in particular have revealed various layers of functionality of senescent cells in vivo. Here we discuss some key features of senescence effectors and attempt to functionally link them when it is possible.
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Affiliation(s)
- Rafik Salama
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Mahito Sadaie
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Matthew Hoare
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
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29
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Aravinthan A, Pietrosi G, Hoare M, Jupp J, Marshall A, Verrill C, Davies S, Bateman A, Sheron N, Allison M, Alexander GJM. Hepatocyte expression of the senescence marker p21 is linked to fibrosis and an adverse liver-related outcome in alcohol-related liver disease. PLoS One 2013; 8:e72904. [PMID: 24086266 PMCID: PMC3781134 DOI: 10.1371/journal.pone.0072904] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 07/13/2013] [Indexed: 12/19/2022] Open
Abstract
Background and Aim Alcohol-related liver disease (ALD) remains a leading cause of liver-related morbidity and mortality. Age, fibrosis stage, MELD score and continued alcohol consumption predict outcome in everyday clinical practice. In previous studies increased hepatocyte nuclear area and hepatocyte expression of p21, both markers of senescence, were associated with increased fibrosis stage and a poor outcome in non-alcohol-related fatty liver disease, while increased hepatocyte nuclear area was related to liver dysfunction in ALD cirrhosis. This study, therefore, investigated the pattern of hepatocyte cell cycle phase distribution and hepatocyte p21 expression in relation to outcome in ALD. Methods Liver sections from two cohorts were studied. The first comprised 42 patients across the full spectrum of ALD. The second cohort comprised 77 patients with ALD cirrhosis. Immunohistochemistry assessed hepatocyte expression of cell cycle phase markers and p21. Regenerating liver (n=12) and “normal” liver sections (n=5) served as positive and negative controls, respectively. Results In the first cohort there was little cell cycle progression beyond G1/S phase and increased hepatocyte p21 expression (p<0.0001), which correlated independently with fibrosis stage (p=0.005) and an adverse liver-related outcome (p=0.03). In the second cohort, both hepatocyte p21 expression (p<0.001) and MELD score (p=0.006) were associated independently with an adverse liver-related outcome; this association was stronger with hepatocyte p21 expression (AUROC 0.74; p=0.0002) than with MELD score (AUROC 0.59; p=0.13). Further, hepatocyte p21 expression co-localised with increased hepatic stellate cell activation. Conclusions The findings are consistent with impaired cell cycle progression beyond the G1/S phase in ALD. The striking independent associations between increased hepatocyte p21 expression and both fibrosis stage and an adverse liver-related outcome in both cohorts suggests hepatocyte senescence plays an important role in ALD. Measuring hepatocyte p21 expression is simple and cheap and in this series was a useful measure of long-term prognosis in ALD.
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Affiliation(s)
| | - Giada Pietrosi
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Matthew Hoare
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - James Jupp
- Department of Hepatology, University Hospital Southampton, Southampton, United Kingdom
| | - Aileen Marshall
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Clare Verrill
- Department of Hepatology, University Hospital Southampton, Southampton, United Kingdom
| | - Susan Davies
- Department of Histopathology, Cambridge University Hospital, Cambridge, United Kingdom
| | - Adrian Bateman
- Department of Histopathology, University Hospital Southampton, Southampton, United Kingdom
| | - Nick Sheron
- Department of Hepatology, University Hospital Southampton, Southampton, United Kingdom
| | - Michael Allison
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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Abstract
Senescence, a cell-autonomous tumour suppressor mechanism, also has pro-tumorigenic effects on neighbouring pre-malignant cells through the senescence-associated secretory phenotype (SASP). The SASP is now shown to be regulated by inflammasomes and to induce paracrine senescence in healthy cells, indicating that senescence may also represent a non-cell-autonomous tumour suppressor mechanism linked to innate immunity.
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Affiliation(s)
- Matthew Hoare
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
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Hoare M, Shankar A, Shah M, Rushbrook S, Gelson W, Davies S, Akbar A, Alexander GJ. γ-H2AX+CD8+ T lymphocytes cannot respond to IFN-α, IL-2 or IL-6 in chronic hepatitis C virus infection. J Hepatol 2013; 58:868-74. [PMID: 23257612 PMCID: PMC3625113 DOI: 10.1016/j.jhep.2012.12.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 11/30/2012] [Accepted: 12/05/2012] [Indexed: 12/26/2022]
Abstract
BACKGROUND & AIMS Age is the dominant prognostic factor influencing the natural history of hepatitis C virus (HCV) infection and treatment response. Accelerated lymphocyte telomere shortening in HCV infection correlates with adverse clinical outcomes. Critical telomere shortening generates double-stranded DNA breaks (DSB) inducing the DNA damage response, leading to replicative senescence. The phenotype and function of CD8+ T lymphocytes and the in vitro response to IFN-α in relation to the DNA damage response were investigated in patients with chronic HCV infection. METHODS CD8+ T lymphocytes with DSB were identified by expression of γ-H2AX (Ser-139) in 134 HCV-exposed subjects and 27 controls. Telomere length was determined by flow-FISH; cytokine expression by intracellular cytokine staining; in vitro responses to IFN-α, IL-2 or IL-6 by phospho-STAT1 (Y701) or phospho-STAT5 (Y694) expression. RESULTS The proportion of circulating CD8+γ-H2AX+ T lymphocytes rose with increasing fibrosis stage (p=0.0023). CD8+γ-H2AX+ T lymphocytes were enriched in liver compared to blood (p=0.03). CD8+γ-H2AX+ T lymphocytes demonstrated increased IFN-γ (p=0.02) and reduced IL-2 expression (p=0.02). CD8+γ-H2AX+ T lymphocytes failed to phosphorylate STAT1 in response to IFN-α compared to unfractionated CD8+ T lymphocytes (p <0.0001). More widespread failure of Jak/Stat signalling in CD8+γ-H2AX+ T lymphocytes was suggested by impaired phosphorylation of STAT1 with IL-6 (p=0.002) and STAT5 with IL-2 (p=0.0039) compared to unfractionated CD8+ T-lymphocytes. CONCLUSIONS In chronic HCV infection, CD8+γ-H2AX+ T lymphocytes are highly differentiated with shortened telomeres, are more frequent within the liver, are associated with severe fibrosis and fail to activate Jak/Stat pathways in response to IFN-α, IL-2 or IL-6, perhaps explaining treatment failure in those with severe fibrosis.
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Affiliation(s)
- Matthew Hoare
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Arun Shankar
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Meera Shah
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Simon Rushbrook
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - William Gelson
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Susan Davies
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Arne Akbar
- Department of Immunology, University College London, London, UK
| | - Graeme J.M. Alexander
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, UK,Corresponding author. Address: Department of Medicine, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 2QQ, UK. Tel.: +44 1223 336008; fax: +44 1223 216111.
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Eames I, Chau G, Landeryou M, Town M, Levy M, Lye G, Hoare M, Mason C. Study of a novel tube forming method for preparing engineered blood vessels. Chem Eng Sci 2012. [DOI: 10.1016/j.ces.2012.09.001] [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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Pope BD, Chandra T, Buckley Q, Hoare M, Ryba T, Wiseman FK, Kuta A, Wilson MD, Odom DT, Gilbert DM. Replication-timing boundaries facilitate cell-type and species-specific regulation of a rearranged human chromosome in mouse. Hum Mol Genet 2012; 21:4162-70. [PMID: 22736031 PMCID: PMC3441118 DOI: 10.1093/hmg/dds232] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 06/07/2012] [Accepted: 06/11/2012] [Indexed: 01/04/2023] Open
Abstract
In multicellular organisms, developmental changes to replication timing occur in 400-800 kb domains across half the genome. While examples of epigenetic control of replication timing have been described, a role for DNA sequence in mammalian replication-timing regulation has not been substantiated. To assess the role of DNA sequences in directing developmental changes to replication timing, we profiled replication timing in mice carrying a genetically rearranged Human Chromosome 21 (Hsa21). In two distinct mouse cell types, Hsa21 sequences maintained human-specific replication timing, except at points of Hsa21 rearrangement. Changes in replication timing at rearrangements extended up to 900 kb and consistently reconciled with the wild-type replication pattern at developmental boundaries of replication-timing domains. Our results are consistent with DNA sequence-driven regulation of Hsa21 replication timing during development and provide evidence that mammalian chromosomes consist of multiple independent units of replication-timing regulation.
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Affiliation(s)
- Benjamin D. Pope
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Tamir Chandra
- Cancer Research UK, Cambridge Research Institute, Cambridge CB2 0RE, UK
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK and
| | - Quinton Buckley
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Matthew Hoare
- Cancer Research UK, Cambridge Research Institute, Cambridge CB2 0RE, UK
| | - Tyrone Ryba
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Frances K. Wiseman
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Anna Kuta
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Michael D. Wilson
- Cancer Research UK, Cambridge Research Institute, Cambridge CB2 0RE, UK
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK and
| | - Duncan T. Odom
- Cancer Research UK, Cambridge Research Institute, Cambridge CB2 0RE, UK
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK and
| | - David M. Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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Abstract
Autophagy, one of two major intracellular degradation pathways, plays a critical role in energy homeostasis and the quality control of macromolecules and intracellular organelles. Previous work has demonstrated the importance of autophagy in maintaining cellular fitness, both in healthy and stressful conditions, revealing the complex interplay between autophagy and other stress-responsive phenotypes. The complex outcomes of stress-responsive autophagy confer on it both pro- and anti-tumourigenic roles, depending on the cellular and environmental context. Furthermore, recent findings that functionally link autophagy to the tumour suppressor mechanism, cellular senescence, have revealed a new role of autophagy in cancer biology. In this review we summarise the current evidence on the relationship between autophagy and cancer, with a focus on its role in senescence.
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Affiliation(s)
- Matthew Hoare
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
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35
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Reid CQ, Tait A, Baldascini H, Mohindra A, Racher A, Bilsborough S, Smales CM, Hoare M. Rapid whole monoclonal antibody analysis by mass spectrometry: An ultra scale-down study of the effect of harvesting by centrifugation on the post-translational modification profile. Biotechnol Bioeng 2010; 107:85-95. [PMID: 20506289 DOI: 10.1002/bit.22790] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
With the trend towards the generation and production of increasing numbers of complex biopharmaceutical (protein based) products, there is an increased need and requirement to characterize both the product and production process in terms of robustness and reproducibility. This is of particular importance for products from mammalian cell culture which have large molecular structures and more often than not complex post-translational modifications (PTMs) that can impact the efficacy, stability and ultimately the safety of the final product. It is therefore vital to understand how the operating conditions of a bioprocess affect the distribution and make up of these PTMs to ensure a consistent quality and activity in the final product. Here we have characterized a typical bioprocess and determined (a) how the time of harvest from a mammalian cell culture and, (b) through the use of an ultra scale-down mimic how the nature of the primary recovery stages, affect the distribution and make up of the PTMs observed on a recombinant IgG(4) monoclonal antibody. In particular we describe the use of rapid whole antibody analysis by mass spectrometry to analyze simultaneously the changes that occur to the cleavage of heavy chain C-terminal lysine residues and the glycosylation pattern, as well as the presence of HL dimers. The time of harvest was found to have a large impact upon the range of glycosylation patterns observed, but not upon C-terminal lysine cleavage. The culture age had a profound impact on the ratio of different glycan moieties found on antibody molecules. The proportion of short glycans increased (e.g., (G0F)(2) 20-35%), with an associated decrease in the proportion of long glycans with culture age (e.g., (G2F)(2) 7-4%, and G1F/G2F from 15.2% to 7.8%). Ultra scale-down mimics showed that subsequent processing of these cultures did not change the post-translational modifications investigated, but did increase the proportion of half antibodies present in the process stream. The combination of ultra scale-down methodology and whole antibody analysis by mass spectrometry has demonstrated that the effects of processing on the detailed molecular structure of a monoclonal antibody can be rapidly determined early in the development process. In this study we have demonstrated this analysis to be applicable to critical process design decisions (e.g., time of harvest) in terms of achieving a desired molecular structure, but this approach could also be applied as a selection criterion as to the suitability of a platform process for the preparation of a new drug candidate. Also the methodology provides means for bioprocess engineers to predict at the discovery phase how a bioprocess will impact upon the quality of the final product.
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Affiliation(s)
- C Q Reid
- Department of Biochemical Engineering, University College London, UK
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Hoare M, Gelson WT, Das A, Fletcher JM, Davies SE, Curran MD, Vowler SL, Maini MK, Akbar AN, Alexander GJ. CD4+ T-lymphocyte telomere length is related to fibrosis stage, clinical outcome and treatment response in chronic hepatitis C virus infection. J Hepatol 2010; 53:252-60. [PMID: 20462651 PMCID: PMC2913243 DOI: 10.1016/j.jhep.2010.03.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Revised: 02/04/2010] [Accepted: 03/03/2010] [Indexed: 12/26/2022]
Abstract
BACKGROUND & AIMS Increasing age is associated with impaired immune function and in chronic HCV infection specifically, with progressive fibrosis, liver failure, HCC and impaired responses to antiviral therapy. T-lymphocyte telomere length declines with age. We hypothesised that shorter T-lymphocyte telomere length would be associated with poor clinical outcome in HCV infection. METHODS Circulating T-lymphocyte telomere length, an objective measure of immune senescence, was measured by flow-FISH in 135 HCV-RNA-positive, treatment-naïve patients and 41 healthy controls in relation to clinical outcome. RESULTS Shorter CD4+CD45RO+ T-lymphocyte telomeres were associated with severe fibrosis (p=0.003), independent of male sex (p=0.04), CMV positivity (p=0.003), previous HBV infection (p=0.007), and age (p=ns) in viraemic patients compared to controls. There were inverse correlations between CD4+CD45RO+ telomere length and fibrosis stage (p<0.001), portal tract inflammatory grade (p=0.035), prothrombin time (p<0.001) and bilirubin (p=0.001). One hundred and twenty-four viraemic individuals were followed prospectively to a composite endpoint of death, hepatic decompensation or HCC. Independent of age, those with shorter CD4+CD45RO+ telomeres were less likely to be complication free after 2-years than those with longer telomeres (86% versus 96%, p=0.009) with an age-adjusted hazard ratio of 0.93 (0.90-0.96). In addition, CD4+CD45RO+ telomere length predicted successful antiviral therapy (p=0.001) independent of other factors. CONCLUSIONS CD4+ T-lymphocyte telomere length, independent of age, was related to inflammatory grade, fibrosis stage, laboratory indices of severity, subsequent hepatic decompensation and treatment outcome in patients with chronic HCV infection.
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Key Words
- hcv, hepatitis c virus
- hcc, hepatocellular carcinoma
- cmv, cytomegalovirus
- hbv, hepatitis b virus
- ebv, epstein–barr virus
- hiv, human immunodeficiency virus
- ifn-α, interferon-α
- pbmcs, peripheral blood mononuclear cells
- apcs, antigen presenting cells
- hr, hazard ratio
- hepatitis c
- telomere
- t-lymphocyte
- immune senescence
- human
- ageing
- hepatocellular carcinoma
- outcome study
- interferon-α
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Affiliation(s)
- Matthew Hoare
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - William T.H. Gelson
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Abhi Das
- Department of Immunology, University College London, London, UK
| | | | - Susan E. Davies
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Martin D. Curran
- Clinical Microbiology and Public Health Laboratory, Health Protection Agency, Addenbrooke’s Hospital, Cambridge, UK
| | - Sarah L. Vowler
- Centre for Applied Medical Statistics, Department of Public Health and Primary Care, University of Cambridge, Institute of Public Health, Forvie Site, Robinson Way, Cambridge, UK
| | - Mala K. Maini
- Department of Immunology, University College London, London, UK
| | - Arne N. Akbar
- Department of Immunology, University College London, London, UK
| | - Graeme J.M. Alexander
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, UK,Corresponding author. Address: Department of Medicine, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 2QQ, UK. Tel.: +44 1223 336008; fax: +44 1223 216111.
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Acosta-Martinez J, Papantoniou I, Lawrence K, Ward S, Hoare M. Ultra scale-down stress analysis of the bioprocessing of whole human cells as a basis for cancer vaccines. Biotechnol Bioeng 2010; 107:953-63. [DOI: 10.1002/bit.22888] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Gelson W, Hoare M, Vowler S, Shankar A, Gibbs P, Akbar AN, Alexander GJM. Features of immune senescence in liver transplant recipients with established grafts. Liver Transpl 2010; 16:577-87. [PMID: 20440767 DOI: 10.1002/lt.22033] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Immune senescence is the normal process whereby the human immune system ages, but becomes less effective. We investigated whether liver transplant recipients have features of immune senescence. Lymphocytes from 97 liver transplant recipients with established grafts and 41 age-matched and sex-matched controls were subjected to an 8-color flow cytometry assay that measured expression of killer cell lectin-like receptor subfamily G member 1, cluster of differentiation 127 (CD127), CD45RO, CD27, CD28, CD4, CD8, and CD57. Lymphocyte telomere length was assessed by flow-fluorescence in situ hybridization. Cases were compared with controls for each marker of immune senescence using a Mann-Whitney U test. For liver transplant recipients, linear regression analyses identified associations between markers of immune senescence and clinical or demographic characteristics. Lymphocytes from liver transplant recipients expressed more phenotypic markers of maturity than did lymphocytes from controls. Lymphocyte telomeres were shorter in liver transplant recipients than in controls. Age, hepatocellular carcinoma at transplantation, and skin malignancy developing after transplantation were associated independently with shortened lymphocyte telomeres. Increasing age and previous cytomegalovirus infection were associated independently with phenotypic markers of lymphocyte maturity. Thus, lymphocytes from liver transplant recipients are older "biologically" than lymphocytes from age-matched and sex-matched controls. Hepatocellular carcinoma at transplantation, subsequent skin malignancy, and previous cytomegalovirus infection are associated with lymphocyte senescence in liver transplant recipients.
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Affiliation(s)
- William Gelson
- Department of Medicine, University of Cambridge, Cambridge, UK
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Gelson W, Hoare M, Unitt E, Palmer C, Gibbs P, Coleman N, Davies S, Alexander GJM. Heterogeneous inflammatory changes in liver graft recipients with normal biochemistry. Transplantation 2010; 89:739-48. [PMID: 20134396 DOI: 10.1097/tp.0b013e3181c96b32] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Patients with established liver grafts may receive excessive immune suppression. Liver biopsies were analyzed in those with normal liver biochemistry to identify parameters that might identify such cases. METHODS Patients with established grafts (>3 years from engraftment) and normal liver biochemistry (normal alanine transaminase, alkaline phosphatase, and bilirubin) were invited to undergo liver biopsy. Liver tissue was assessed by routine histopathology, a modified Ishak score, and immunohistochemistry for lymphocyte and cell-cycle markers. Circulating and intrahepatic lymphocytes were subjected to flow cytometry. Data were subjected to principal component analysis. RESULTS Two hundred twenty-five (40%) patients under regular review had an established graft with normal liver biochemistry; liver tissue was obtained in 55. Liver histology was normal in eight cases (14.5%). The most common abnormalities were mild nonspecific hepatitis in 25 (45.4%) and disease recurrence in 14 (25.4%). Principal component analysis identified a cluster of variables that accounted for a significant degree of variation within the dataset. These were lobular inflammation, portal inflammation, interface hepatitis, and fibrosis. CONCLUSIONS Inflammation persisted in established grafted livers in most patients with normal liver biochemistry. Systematic histological and lymphocyte phenotype analysis generated an index that distinguished patient groups. Those with least inflammation and the lowest alanine transaminase may have a reduced requirement for immune suppression.
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Affiliation(s)
- William Gelson
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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Tait A, Aucamp J, Bugeon A, Hoare M. Ultra scale-down prediction using microwell technology of the industrial scale clarification characteristics by centrifugation of mammalian cell broths. Biotechnol Bioeng 2009; 104:321-31. [DOI: 10.1002/bit.22393] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Zoro B, Owen S, Drake R, Mason C, Hoare M. Regenerative medicine bioprocessing: Concentration and behavior of adherent cell suspensions and pastes. Biotechnol Bioeng 2009; 103:1236-47. [DOI: 10.1002/bit.22356] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Hutchinson N, Chhatre S, Baldascini H, Davies JL, Bracewell DG, Hoare M. Ultra scale-down approach to correct dispersive and retentive effects in small-scale columns when predicting larger scale elution profiles. Biotechnol Prog 2009; 25:1103-10. [DOI: 10.1002/btpr.172] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Hoare M, Gelson WTH, Rushbrook SM, Curran MD, Woodall T, Coleman N, Davies SE, Alexander GJM. Histological changes in HCV antibody-positive, HCV RNA-negative subjects suggest persistent virus infection. Hepatology 2008; 48:1737-45. [PMID: 18925639 PMCID: PMC2680218 DOI: 10.1002/hep.22484] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
UNLABELLED It is unclear whether hepatitis C virus (HCV) has been eradicated or persists at a low level in HCV antibody-positive HCV RNA-negative individuals. The natural history and liver histology are not well characterized. One hundred seventy-two HCV antibody-positive, serum HCV RNA-negative patients underwent diagnostic liver biopsy between 1992 and 2000 and were followed a median 7 years (range, 5-12). Patients with any possible cause of liver injury other than HCV were excluded. A single histopathologist scored sections using Ishak criteria. Characterization of the inflammatory infiltrate in selected cases used a novel semiquantitative technique and compared with HCV RNA-positive patients and healthy controls. One hundred two patients were excluded because of a risk factor for liver injury other than HCV. Seventy patients met the study criteria; four (5.7%) became HCV RNA-positive during follow-up. Sixty-six cases remained HCV RNA-negative; five (7.5%) had a normal liver biopsy; 54 (82%) had fibrosis (stage 2 or 3 in 16 (24%)). Nonviremic cases revealed expanded portal tracts (P < 0.05), with fewer CD4+ (P < 0.05) and more CD8+ cells (P < 0.05) than healthy controls, but were indistinguishable from HCV RNA-positive cases for these parameters. Lobular CD4 staining, absent in healthy controls, was noted in both HCV RNA-negative and -positive cases and was more marked in the latter (P < 0.05) with a sinusoidal lining cell distribution. CONCLUSION Nonviremic HCV antibody-positive patients have a liver biopsy that is usually abnormal. Fibrosis was present in most with similar inflammatory infiltrate to viremic cases. The presence of a CD8+ rich inflammatory infiltrate suggests an ongoing immune response in the liver, supporting the view that HCV may persist in the liver in the majority of HCV RNA-negative cases.
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Affiliation(s)
- Matthew Hoare
- Department of Medicine, School of Clinical Medicine, University of CambridgeCambridge, UK
| | - William T H Gelson
- Department of Medicine, School of Clinical Medicine, University of CambridgeCambridge, UK
| | - Simon M Rushbrook
- Department of Medicine, School of Clinical Medicine, University of CambridgeCambridge, UK
| | - Martin D Curran
- Clinical Microbiology and Public Health Laboratory, Health Protection Agency, Addenbrooke's HospitalCambridge, UK
| | - Tracy Woodall
- Department of Medicine, School of Clinical Medicine, University of CambridgeCambridge, UK
| | - Nicholas Coleman
- Medical Research Council (MRC) Cancer Cell Unit, Hutchison/MRC Research CentreCambridge, UK
| | - Susan E Davies
- Department of Pathology, University of CambridgeCambridge, UK
| | - Graeme J M Alexander
- Department of Medicine, School of Clinical Medicine, University of CambridgeCambridge, UK
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Das A, Hoare M, Davies N, Lopes AR, Dunn C, Kennedy PTF, Alexander G, Finney H, Lawson A, Plunkett FJ, Bertoletti A, Akbar AN, Maini MK. Functional skewing of the global CD8 T cell population in chronic hepatitis B virus infection. ACTA ACUST UNITED AC 2008; 205:2111-24. [PMID: 18695005 PMCID: PMC2526205 DOI: 10.1084/jem.20072076] [Citation(s) in RCA: 190] [Impact Index Per Article: 11.9] [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: 12/21/2022]
Abstract
The inflamed liver in chronic hepatitis B virus (HBV) infection (CHB) is characterized by a large influx of non–virus-specific CD8 T cells. Little is known about the functional capacity of these lymphocytes, which could provide insights into mechanisms of failure of viral control and liver damage in this setting. We compared the effector function of total circulating and intrahepatic CD8 T cells in CHB patients and healthy donors. We demonstrated that CD8 T cells from CHB patients, regardless of their antigen specificity, were impaired in their ability to produce interleukin-2 and proliferate upon TCR-dependent stimulation. In contrast, these CD8 T cells had preserved production of the proinflammatory cytokines interferon-γ and tumor necrosis factor-α. This aberrant functional profile was partially attributable to down-regulation of the proximal T cell receptor signaling molecule CD3ζ, and could be corrected in vitro by transfection of CD3ζ or replenishment of the amino acid arginine required for its expression. We provide evidence for depletion of arginine in the inflamed hepatic microenvironment as a potential mechanism for these defects in global CD8 T cell signaling and function. These data imply that polarized CD8 T cells within the HBV-infected liver may impede proliferative antiviral effector function, while contributing to the proinflammatory cytokine environment.
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Affiliation(s)
- Abhishek Das
- Division of Infection and Immunity, University College London, London W1T 4JF, England, UK
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Zoro BJH, Owen S, Drake RAL, Hoare M. The impact of process stress on suspended anchorage-dependent mammalian cells as an indicator of likely challenges for regenerative medicines. Biotechnol Bioeng 2008; 99:468-74. [PMID: 17626302 DOI: 10.1002/bit.21544] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
To quantify the engineering shear constraint on processing, the effect of capillary shear stress (pipe flow) on suspended anchorage-dependent mammalian cells has been investigated. Exposure of cultured rat aortic smooth muscle cells to repeated capillary shear stress (2-120 N m(-2)) causes a decrease in total number of cells, number of intact cells and number of cells able to grow. The optimum wall shear stress for cell survival was found to be 10-50 N m(-2) (flowrate 4-20 mL/min, I.D. 0.45 mm). Cell populations which are able to grow after exposure to shear stress do not exhibit reduced growth rate or altered metabolism.
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Affiliation(s)
- B J H Zoro
- Department of Biochemical Engineering, Advanced Centre for Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
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Titchener-Hooker NJ, Dunnill P, Hoare M. Micro biochemical engineering to accelerate the design of industrial-scale downstream processes for biopharmaceutical proteins. Biotechnol Bioeng 2008; 100:473-87. [PMID: 18438873 DOI: 10.1002/bit.21788] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- N J Titchener-Hooker
- Department of Biochemical Engineering, Advanced Centre for Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
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Bracewell D, Boychyn M, Baldascini H, Storey S, Bulmer M, More J, Hoare M. Impact of clarification strategy on chromatographic separations: Pre-processing of cell homogenates. Biotechnol Bioeng 2008; 100:941-9. [DOI: 10.1002/bit.21823] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Tustian A, Salte H, Willoughby N, Hassan I, Rose M, Baganz F, Hoare M, Titchener-Hooker N. Adapted Ultra Scale-Down Approach for Predicting the Centrifugal Separation Behavior of High Cell Density Cultures. Biotechnol Prog 2007; 23:1404-10. [DOI: 10.1021/bp070175d] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Both hepatitis B virus (HBV) and hepatitis C virus (HCV) can cause persistent viral infection in humans. Chronic infection is associated with a risk of cirrhosis and hepatocellular carcinoma. The cause of chronic infection is unknown. A large body of evidence suggests that a failure of the adaptive immune response is critical in the establishment of chronic infection. Recently a new group of T cells (T-regulatory cells), that express CD4(+)CD25(+) and Foxp3, which can inhibit the cellular (CD4(+)/CD8(+)) immune response have been described. In this review the authors explore the thoughts regarding immune responses to HBV and HCV infections and the role of these T-regulatory cells in relation to the pathogenesis of chronic HBV and HCV infection and the potential for therapeutic intervention.
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Affiliation(s)
- Simon M Rushbrook
- University of Cambridge School of Clinical Medicine, Department of Medicine, Box 157, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 2QQ, UK
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Meacle FJ, Zhang H, Papantoniou I, Ward JM, Titchener-Hooker NJ, Hoare M. Degradation of supercoiled plasmid DNA within a capillary device. Biotechnol Bioeng 2007; 97:1148-57. [PMID: 17115451 DOI: 10.1002/bit.21275] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Supercoiled plasmid DNA is susceptible to fluid stress in large-scale manufacturing processes. A capillary device was used to generate controlled shear conditions and the effects of different stresses on plasmid DNA structure were investigated. Computational fluid dynamics (CFD) analysis was employed to characterize the flow environment in the capillary device and different analytical techniques were used to quantify the DNA breakage. It was found that the degradation of plasmid DNA occurred at the entrance of the capillary and that the shear stress within the capillary did not affect the DNA structure. The degradation rate of plasmids was well correlated with the average elongational strain rate or the pressure drop at the entrance region. The conclusion may also be drawn that laminar shear stress does not play a significant role in plasmid DNA degradation.
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Affiliation(s)
- F J Meacle
- The Advanced Centre for Biochemical Engineering, University College London, Torrington Place, London, United Kingdom
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