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Kotsiliti E, Leone V, Schuehle S, Govaere O, Li H, Wolf MJ, Horvatic H, Bierwirth S, Hundertmark J, Inverso D, Zizmare L, Sarusi-Portuguez A, Gupta R, O'Connor T, Giannou AD, Shiri AM, Schlesinger Y, Beccaria MG, Rennert C, Pfister D, Öllinger R, Gadjalova I, Ramadori P, Rahbari M, Rahbari N, Healy ME, Fernández-Vaquero M, Yahoo N, Janzen J, Singh I, Fan C, Liu X, Rau M, Feuchtenberger M, Schwaneck E, Wallace SJ, Cockell S, Wilson-Kanamori J, Ramachandran P, Kho C, Kendall TJ, Leblond AL, Keppler SJ, Bielecki P, Steiger K, Hofmann M, Rippe K, Zitzelsberger H, Weber A, Malek N, Luedde T, Vucur M, Augustin HG, Flavell R, Parnas O, Rad R, Pabst O, Henderson NC, Huber S, Macpherson A, Knolle P, Claassen M, Geier A, Trautwein C, Unger K, Elinav E, Waisman A, Abdullah Z, Haller D, Tacke F, Anstee QM, Heikenwalder M. Intestinal B cells license metabolic T-cell activation in NASH microbiota/antigen-independently and contribute to fibrosis by IgA-FcR signalling. J Hepatol 2023; 79:296-313. [PMID: 37224925 PMCID: PMC10360918 DOI: 10.1016/j.jhep.2023.04.037] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [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: 02/02/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 05/26/2023]
Abstract
BACKGROUND & AIMS The progression of non-alcoholic steatohepatitis (NASH) to fibrosis and hepatocellular carcinoma (HCC) is aggravated by auto-aggressive T cells. The gut-liver axis contributes to NASH, but the mechanisms involved and the consequences for NASH-induced fibrosis and liver cancer remain unknown. We investigated the role of gastrointestinal B cells in the development of NASH, fibrosis and NASH-induced HCC. METHODS C57BL/6J wild-type (WT), B cell-deficient and different immunoglobulin-deficient or transgenic mice were fed distinct NASH-inducing diets or standard chow for 6 or 12 months, whereafter NASH, fibrosis, and NASH-induced HCC were assessed and analysed. Specific pathogen-free/germ-free WT and μMT mice (containing B cells only in the gastrointestinal tract) were fed a choline-deficient high-fat diet, and treated with an anti-CD20 antibody, whereafter NASH and fibrosis were assessed. Tissue biopsy samples from patients with simple steatosis, NASH and cirrhosis were analysed to correlate the secretion of immunoglobulins to clinicopathological features. Flow cytometry, immunohistochemistry and single-cell RNA-sequencing analysis were performed in liver and gastrointestinal tissue to characterise immune cells in mice and humans. RESULTS Activated intestinal B cells were increased in mouse and human NASH samples and licensed metabolic T-cell activation to induce NASH independently of antigen specificity and gut microbiota. Genetic or therapeutic depletion of systemic or gastrointestinal B cells prevented or reverted NASH and liver fibrosis. IgA secretion was necessary for fibrosis induction by activating CD11b+CCR2+F4/80+CD11c-FCGR1+ hepatic myeloid cells through an IgA-FcR signalling axis. Similarly, patients with NASH had increased numbers of activated intestinal B cells; additionally, we observed a positive correlation between IgA levels and activated FcRg+ hepatic myeloid cells, as well the extent of liver fibrosis. CONCLUSIONS Intestinal B cells and the IgA-FcR signalling axis represent potential therapeutic targets for the treatment of NASH. IMPACT AND IMPLICATIONS There is currently no effective treatment for non-alcoholic steatohepatitis (NASH), which is associated with a substantial healthcare burden and is a growing risk factor for hepatocellular carcinoma (HCC). We have previously shown that NASH is an auto-aggressive condition aggravated, amongst others, by T cells. Therefore, we hypothesized that B cells might have a role in disease induction and progression. Our present work highlights that B cells have a dual role in NASH pathogenesis, being implicated in the activation of auto-aggressive T cells and the development of fibrosis via activation of monocyte-derived macrophages by secreted immunoglobulins (e.g., IgA). Furthermore, we show that the absence of B cells prevented HCC development. B cell-intrinsic signalling pathways, secreted immunoglobulins, and interactions of B cells with other immune cells are potential targets for combinatorial NASH therapies against inflammation and fibrosis.
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Affiliation(s)
- Elena Kotsiliti
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Valentina Leone
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany; Research Unit of Radiation Cytogenetics (ZYTO), Helmholtz Zentrum München, Neuherberg, Germany; Institute of Molecular Oncology and Functional Genomics, Clinic and Polyclinic for Internal Medicine II, Klinikum rechts der Isar of the Technical University of Munich (TUM), Munich, Germany; Translational Pancreatic Cancer Research Center, Clinic and Polyclinic for Internal Medicine II, Klinikum rechts der Isar of the Technical University of Munich (TUM), Munich, Germany
| | - Svenja Schuehle
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Olivier Govaere
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Hai Li
- Maurice Müller Laboratories (DBMR), University Department of Visceral Surgery and Medicine Inselspital, University of Bern, Bern, Switzerland
| | - Monika J Wolf
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Helena Horvatic
- Institute of Molecular Medicine and Experimental Immunology, University Hospital, Bonn, Germany
| | - Sandra Bierwirth
- Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany; ZIEL - Institute for Food and Health, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Jana Hundertmark
- Department of Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, Berlin, Germany
| | - Donato Inverso
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany; European Center of Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Laimdota Zizmare
- Department of Preclinical Imaging and Radiopharmacy, Werner Siemens Imaging Center (WSIC), Tübingen University, Tübingen, Germany
| | - Avital Sarusi-Portuguez
- The Concern Foundation Laboratories at the Lautenberg Center for Immunology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Revant Gupta
- Internal Medicine I, University Hospital Tübingen, Faculty of Medicine, University of Tübingen, Tübingen, Germany; Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Tracy O'Connor
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany; North Park University, Chicago, IL, USA
| | - Anastasios D Giannou
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Department of Medicine II, University Hospital Freiburg - Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ahmad Mustafa Shiri
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yehuda Schlesinger
- The Concern Foundation Laboratories at the Lautenberg Center for Immunology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Maria Garcia Beccaria
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Charlotte Rennert
- Department of Medicine II, University Hospital Freiburg - Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dominik Pfister
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, Clinic and Polyclinic for Internal Medicine II, Klinikum rechts der Isar of the Technical University of Munich (TUM), Munich, Germany
| | - Iana Gadjalova
- Center for Translational Cancer Research (TranslaTUM), Technical University of Munich (TUM), Munich, Germany
| | - Pierluigi Ramadori
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Mohammad Rahbari
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Nuh Rahbari
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Marc E Healy
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Mirian Fernández-Vaquero
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Neda Yahoo
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Jakob Janzen
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Indrabahadur Singh
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany; Emmy Noether Research Group Epigenetic Machineries and Cancer, Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Chaofan Fan
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Xinyuan Liu
- Research Center for Immunotherapy (FZI), University Medical Center at the Johannes Gutenberg University, Mainz, Germany; Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Monika Rau
- Division of Hepatology, University-Hospital Würzburg, Würzburg, Germany
| | - Martin Feuchtenberger
- Rheumatology/Clinical Immunology, Kreiskliniken Altötting-Burghausen, Burghausen, Germany
| | - Eva Schwaneck
- Rheumatology, Medical Clinic II, Julius-Maximilians-University Würzburg, Germany
| | - Sebastian J Wallace
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Simon Cockell
- School of Biomedical, Nutrition and Sports Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - John Wilson-Kanamori
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Prakash Ramachandran
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Celia Kho
- Institute of Molecular Medicine and Experimental Immunology, University Hospital, Bonn, Germany
| | - Timothy J Kendall
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Anne-Laure Leblond
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Selina J Keppler
- Center for Translational Cancer Research (TranslaTUM), Technical University of Munich (TUM), Munich, Germany
| | - Piotr Bielecki
- Department of Immunobiology, Yale University School of Medicine, New Haven, USA
| | - Katja Steiger
- Institute of Pathology, Technical University of Munich (TUM), Munich, Germany; Comparative Experimental Pathology, Technical University of Munich (TUM), Munich, Germany
| | - Maike Hofmann
- Internal Medicine I, University Hospital Tübingen, Faculty of Medicine, University of Tübingen, Tübingen, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Horst Zitzelsberger
- Research Unit of Radiation Cytogenetics (ZYTO), Helmholtz Zentrum München, Neuherberg, Germany
| | - Achim Weber
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Nisar Malek
- Department Internal Medicine I, Eberhard-Karls University, Tübingen, Germany
| | - Tom Luedde
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Duesseldorf, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Mihael Vucur
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Duesseldorf, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Hellmut G Augustin
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany; European Center of Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Richard Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, USA
| | - Oren Parnas
- European Center of Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, Clinic and Polyclinic for Internal Medicine II, Klinikum rechts der Isar of the Technical University of Munich (TUM), Munich, Germany; Center for Translational Cancer Research (TranslaTUM), Technical University of Munich (TUM), Munich, Germany
| | - Olivier Pabst
- Institute of Molecular Medicine, RWTH Aachen University, Aachen, Germany
| | - Neil C Henderson
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Samuel Huber
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andrew Macpherson
- Maurice Müller Laboratories (DBMR), University Department of Visceral Surgery and Medicine Inselspital, University of Bern, Bern, Switzerland
| | - Percy Knolle
- Institute of Molecular Immunology and Experimental Oncology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Manfred Claassen
- Internal Medicine I, University Hospital Tübingen, Faculty of Medicine, University of Tübingen, Tübingen, Germany; Department of Computer Science, University of Tübingen, Tübingen, Germany; Department Internal Medicine I, Eberhard-Karls University, Tübingen, Germany
| | - Andreas Geier
- Division of Hepatology, University-Hospital Würzburg, Würzburg, Germany
| | - Christoph Trautwein
- Department of Preclinical Imaging and Radiopharmacy, Werner Siemens Imaging Center (WSIC), Tübingen University, Tübingen, Germany
| | - Kristian Unger
- Research Unit of Radiation Cytogenetics (ZYTO), Helmholtz Zentrum München, Neuherberg, Germany
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel; Cancer-Microbiome Research Division, DKFZ, Heidelberg, Germany
| | - Ari Waisman
- Research Center for Immunotherapy (FZI), University Medical Center at the Johannes Gutenberg University, Mainz, Germany; Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Zeinab Abdullah
- Institute of Molecular Medicine and Experimental Immunology, University Hospital, Bonn, Germany
| | - Dirk Haller
- Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany; ZIEL - Institute for Food and Health, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Frank Tacke
- Department of Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, Berlin, Germany
| | - Quentin M Anstee
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK; Newcastle NIHR Biomedical Research Center, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, United Kingdom
| | - Mathias Heikenwalder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany; M3 Research Institute, Eberhard Karls University Tübingen, Tübingen, Germany.
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Govaere O, Hasoon M, Alexander L, Cockell S, Tiniakos D, Ekstedt M, Schattenberg JM, Boursier J, Bugianesi E, Ratziu V, Daly AK, Anstee QM. A proteo-transcriptomic map of non-alcoholic fatty liver disease signatures. Nat Metab 2023; 5:572-578. [PMID: 37037945 PMCID: PMC10132975 DOI: 10.1038/s42255-023-00775-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [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: 12/15/2022] [Accepted: 03/06/2023] [Indexed: 04/12/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a common, progressive liver disease strongly associated with the metabolic syndrome. It is unclear how progression of NAFLD towards cirrhosis translates into systematic changes in circulating proteins. Here, we provide a detailed proteo-transcriptomic map of steatohepatitis and fibrosis during progressive NAFLD. In this multicentre proteomic study, we characterize 4,730 circulating proteins in 306 patients with histologically characterized NAFLD and integrate this with transcriptomic analysis in paired liver tissue. We identify circulating proteomic signatures for active steatohepatitis and advanced fibrosis, and correlate these with hepatic transcriptomics to develop a proteo-transcriptomic signature of 31 markers. Deconvolution of this signature by single-cell RNA sequencing reveals the hepatic cell types likely to contribute to proteomic changes with disease progression. As an exemplar of use as a non-invasive diagnostic, logistic regression establishes a composite model comprising four proteins (ADAMTSL2, AKR1B10, CFHR4 and TREM2), body mass index and type 2 diabetes mellitus status, to identify at-risk steatohepatitis.
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Affiliation(s)
- Olivier Govaere
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Department of Imaging and Pathology, KU Leuven and University Hospitals Leuven, Leuven, Belgium
| | - Megan Hasoon
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | | | - Simon Cockell
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Dina Tiniakos
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Department of Pathology, Aretaieio Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Mattias Ekstedt
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
| | | | - Jerome Boursier
- Hepatology Department, Angers University Hospital, Angers, France
| | - Elisabetta Bugianesi
- Department of Medical Sciences, Division of Gastro-Hepatology, City of Health and Science of Turin, University of Turin, Turin, Italy
| | - Vlad Ratziu
- Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpêtrière, Sorbonne University, ICAN (Institute of Cardiometabolism and Nutrition), Paris, France
| | - Ann K Daly
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Quentin M Anstee
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
- Newcastle NIHR Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, UK.
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3
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Anstee QM, Darlay R, Cockell S, Meroni M, Govaere O, Tiniakos D, Burt AD, Bedossa P, Palmer J, Liu YL, Aithal GP, Allison M, Yki-Järvinen H, Vacca M, Dufour JF, Invernizzi P, Prati D, Ekstedt M, Kechagias S, Francque S, Petta S, Bugianesi E, Clement K, Ratziu V, Schattenberg JM, Valenti L, Day CP, Cordell HJ, Daly AK. Corrigendum to: "Genome-wide association study of non-alcoholic fatty liver and steatohepatitis in a histologically characterised cohort ☆" [J Hepatol (2020) 505-515]. J Hepatol 2023; 78:1085-1086. [PMID: 36922251 DOI: 10.1016/j.jhep.2023.02.028] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Affiliation(s)
- Quentin M Anstee
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom; Newcastle NIHR Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom.
| | - Rebecca Darlay
- Population & Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Simon Cockell
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marica Meroni
- Department of Pathophysiology and Transplantation, University of Milan, Translational Medicine - Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Olivier Govaere
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Dina Tiniakos
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom; Dept of Pathology, Aretaieio Hospital, National & Kapodistrian University of Athens, Greece
| | - Alastair D Burt
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom; Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
| | - Pierre Bedossa
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jeremy Palmer
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yang-Lin Liu
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Guruprasad P Aithal
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Michael Allison
- Liver Unit, Department of Medicine, Cambridge Biomedical Research Centre, Cambridge University NHS Foundation Trust, United Kingdom
| | - Hannele Yki-Järvinen
- Department of Medicine, University of Helsinki, Helsinki, Finland; Helsinki University Hospital, Helsinki, Finland
| | - Michele Vacca
- Liver Unit, Department of Medicine, Cambridge Biomedical Research Centre, Cambridge University NHS Foundation Trust, United Kingdom; Department of Biochemistry and Wellcome Trust/MRC Institute of Metabolic Science, MRC Metabolic Diseases Unit, Metabolic Research Laboratories, University of Cambridge, UK
| | - Jean-Francois Dufour
- University Clinic for Visceral Surgery and Medicine, University of Berne, Freiburgstrasse, Berne 3010, Switzerland
| | - Pietro Invernizzi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Daniele Prati
- Department of Pathophysiology and Transplantation, University of Milan, Translational Medicine - Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Mattias Ekstedt
- Division of Gastroenterology and Hepatology, Department of Medicine and Health Sciences, Linköping University, Linkoping, Sweden
| | - Stergios Kechagias
- Division of Gastroenterology and Hepatology, Department of Medicine and Health Sciences, Linköping University, Linkoping, Sweden
| | - Sven Francque
- Department of Gastroenterology and Hepatology, Antwerp University Hospital, Antwerp, Belgium
| | - Salvatore Petta
- Sezione di Gastroenterologia, Dipartimento Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Elisabetta Bugianesi
- Department of Medical Sciences, Division of Gastro-Hepatology, A.O. Città della Salute e della Scienza di Torino, University of Turin, Turin, Italy
| | - Karine Clement
- Sorbonne University, Inserm, Nutrition and Obesity: Systemic Approaches, Nutrition department, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, 75013 Paris, France
| | - Vlad Ratziu
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Institute of Cardiometabolism and Nutrition (ICAN), Paris, France
| | - Jörn M Schattenberg
- NAFLD Research Center, Department of Medicine, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, University of Milan, Translational Medicine - Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Christopher P Day
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Heather J Cordell
- Population & Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ann K Daly
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.
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4
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Sen P, Govaere O, Sinioja T, McGlinchey A, Geng D, Ratziu V, Bugianesi E, Schattenberg JM, Vidal-Puig A, Allison M, Cockell S, Daly AK, Hyötyläinen T, Anstee QM, Orešič M. Quantitative modeling of human liver reveals dysregulation of glycosphingolipid pathways in nonalcoholic fatty liver disease. iScience 2022; 25:104949. [PMID: 36065182 PMCID: PMC9440293 DOI: 10.1016/j.isci.2022.104949] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/21/2022] [Accepted: 08/11/2022] [Indexed: 11/09/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is an increasingly prevalent disease that is associated with multiple metabolic disturbances, yet the metabolic pathways underlying its progression are poorly understood. Here, we studied metabolic pathways of the human liver across the full histological spectrum of NAFLD. We analyzed whole liver tissue transcriptomics and serum metabolomics data obtained from a large, prospectively enrolled cohort of 206 histologically characterized patients derived from the European NAFLD Registry and developed genome-scale metabolic models (GEMs) of human hepatocytes at different stages of NAFLD. We identified several metabolic signatures in the liver and blood of these patients, specifically highlighting the alteration of vitamins (A, E) and glycosphingolipids, and their link with complex glycosaminoglycans in advanced fibrosis. Furthermore, we derived GEMs and identified metabolic signatures of three common NAFLD-associated gene variants (PNPLA3, TM6SF2, and HSD17B13). The study demonstrates dysregulated liver metabolic pathways which may contribute to the progression of NAFLD.
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Affiliation(s)
- Partho Sen
- School of Medical Sciences, Örebro University, 70281 Örebro, Sweden
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Olivier Govaere
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Tim Sinioja
- Department of Chemistry, Örebro University, 70281 Örebro, Sweden
| | - Aidan McGlinchey
- School of Medical Sciences, Örebro University, 70281 Örebro, Sweden
| | - Dawei Geng
- Department of Chemistry, Örebro University, 70281 Örebro, Sweden
| | - Vlad Ratziu
- Assistance Publique-Hôpitaux de Paris, hôpital Beaujon, University Paris-Diderot, Paris, France
| | - Elisabetta Bugianesi
- Department of Medical Sciences, Division of Gastro-Hepatology, A.O. Città della Salute e della Scienza di Torino, University of Turin, Turin, Italy
| | - Jörn M. Schattenberg
- Metabolic Liver Research Programm, Department of Medicine, University Hospital Mainz, Mainz, Germany
| | - Antonio Vidal-Puig
- University of Cambridge Metabolic Research Laboratories, Wellcome-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
| | - Michael Allison
- Liver Unit, Department of Medicine, Cambridge Biomedical Research Centre, Cambridge University NHS Foundation Trust, UK
| | - Simon Cockell
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Ann K. Daly
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | | | - Quentin M. Anstee
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Newcastle NIHR Biomedical Research Center, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Matej Orešič
- School of Medical Sciences, Örebro University, 70281 Örebro, Sweden
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
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5
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Oud MS, Smits RM, Smith HE, Mastrorosa FK, Holt GS, Houston BJ, de Vries PF, Alobaidi BKS, Batty LE, Ismail H, Greenwood J, Sheth H, Mikulasova A, Astuti GDN, Gilissen C, McEleny K, Turner H, Coxhead J, Cockell S, Braat DDM, Fleischer K, D’Hauwers KWM, Schaafsma E, Nagirnaja L, Conrad DF, Friedrich C, Kliesch S, Aston KI, Riera-Escamilla A, Krausz C, Gonzaga-Jauregui C, Santibanez-Koref M, Elliott DJ, Vissers LELM, Tüttelmann F, O’Bryan MK, Ramos L, Xavier MJ, van der Heijden GW, Veltman JA. A de novo paradigm for male infertility. Nat Commun 2022; 13:154. [PMID: 35013161 PMCID: PMC8748898 DOI: 10.1038/s41467-021-27132-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 11/02/2021] [Indexed: 12/29/2022] Open
Abstract
De novo mutations are known to play a prominent role in sporadic disorders with reduced fitness. We hypothesize that de novo mutations play an important role in severe male infertility and explain a portion of the genetic causes of this understudied disorder. To test this hypothesis, we utilize trio-based exome sequencing in a cohort of 185 infertile males and their unaffected parents. Following a systematic analysis, 29 of 145 rare (MAF < 0.1%) protein-altering de novo mutations are classified as possibly causative of the male infertility phenotype. We observed a significant enrichment of loss-of-function de novo mutations in loss-of-function-intolerant genes (p-value = 1.00 × 10-5) in infertile men compared to controls. Additionally, we detected a significant increase in predicted pathogenic de novo missense mutations affecting missense-intolerant genes (p-value = 5.01 × 10-4) in contrast to predicted benign de novo mutations. One gene we identify, RBM5, is an essential regulator of male germ cell pre-mRNA splicing and has been previously implicated in male infertility in mice. In a follow-up study, 6 rare pathogenic missense mutations affecting this gene are observed in a cohort of 2,506 infertile patients, whilst we find no such mutations in a cohort of 5,784 fertile men (p-value = 0.03). Our results provide evidence for the role of de novo mutations in severe male infertility and point to new candidate genes affecting fertility.
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Affiliation(s)
- M. S. Oud
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - R. M. Smits
- grid.10417.330000 0004 0444 9382Department of Obstetrics and Gynaecology, Radboudumc, Nijmegen, The Netherlands
| | - H. E. Smith
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - F. K. Mastrorosa
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - G. S. Holt
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - B. J. Houston
- grid.1008.90000 0001 2179 088XSchool of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC Australia
| | - P. F. de Vries
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - B. K. S. Alobaidi
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - L. E. Batty
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - H. Ismail
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - J. Greenwood
- grid.420004.20000 0004 0444 2244Department of Genetic Medicine, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - H. Sheth
- Foundation for Research in Genetics and Endocrinology, Institute of Human Genetics, Ahmedabad, India
| | - A. Mikulasova
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - G. D. N. Astuti
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands ,grid.412032.60000 0001 0744 0787Division of Human Genetics, Center for Biomedical Research, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - C. Gilissen
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - K. McEleny
- grid.420004.20000 0004 0444 2244Newcastle Fertility Centre, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - H. Turner
- grid.420004.20000 0004 0444 2244Department of Cellular Pathology, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - J. Coxhead
- grid.1006.70000 0001 0462 7212Genomics Core Facility, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - S. Cockell
- Bioinformatics Support Unit, Faculty of Medical Sciences New, castle University, Newcastle upon Tyne, UK
| | - D. D. M. Braat
- grid.10417.330000 0004 0444 9382Department of Obstetrics and Gynaecology, Radboudumc, Nijmegen, The Netherlands
| | - K. Fleischer
- grid.10417.330000 0004 0444 9382Department of Obstetrics and Gynaecology, Radboudumc, Nijmegen, The Netherlands
| | - K. W. M. D’Hauwers
- grid.10417.330000 0004 0444 9382Department of Urology, Radboudumc, Nijmegen, The Netherlands
| | - E. Schaafsma
- grid.10417.330000 0004 0444 9382Department of Pathology, Radboudumc, Nijmegen, The Netherlands
| | | | - L. Nagirnaja
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - D. F. Conrad
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - C. Friedrich
- grid.5949.10000 0001 2172 9288Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - S. Kliesch
- grid.16149.3b0000 0004 0551 4246Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital Münster, Münster, Germany
| | - K. I. Aston
- grid.223827.e0000 0001 2193 0096Department of Surgery, Division of Urology, University of Utah School of Medicine, Salt Lake City, UT USA
| | - A. Riera-Escamilla
- grid.418813.70000 0004 1767 1951Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Catalonia Spain
| | - C. Krausz
- grid.8404.80000 0004 1757 2304Department of Biomedical, Experimental and Clinical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - C. Gonzaga-Jauregui
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - M. Santibanez-Koref
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - D. J. Elliott
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - L. E. L. M. Vissers
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - F. Tüttelmann
- grid.5949.10000 0001 2172 9288Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - M. K. O’Bryan
- grid.1008.90000 0001 2179 088XSchool of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC Australia
| | - L. Ramos
- grid.10417.330000 0004 0444 9382Department of Obstetrics and Gynaecology, Radboudumc, Nijmegen, The Netherlands
| | - M. J. Xavier
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - G. W. van der Heijden
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Obstetrics and Gynaecology, Radboudumc, Nijmegen, The Netherlands
| | - J. A. Veltman
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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6
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Kozumi K, Kodama T, Murai H, Sakane S, Govaere O, Cockell S, Motooka D, Kakita N, Yamada Y, Kondo Y, Tahata Y, Yamada R, Hikita H, Sakamori R, Kamada Y, Daly AK, Anstee QM, Tatsumi T, Morii E, Takehara T. Transcriptomics Identify Thrombospondin-2 as a Biomarker for NASH and Advanced Liver Fibrosis. Hepatology 2021; 74:2452-2466. [PMID: 34105780 PMCID: PMC8596693 DOI: 10.1002/hep.31995] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 05/07/2021] [Accepted: 05/09/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS NAFLD is the most common liver disease worldwide. NASH, the progressive form of NAFLD, and advanced fibrosis are associated with poor outcomes. We searched for their noninvasive biomarkers. APPROACH AND RESULTS Global RNA sequencing of liver tissue from 98 patients with biopsy-proven NAFLD was performed. Unsupervised hierarchical clustering well distinguished NASH from nonalcoholic fatty liver (NAFL), and patients with NASH exhibited molecular abnormalities reflecting their pathological features. Transcriptomic analysis identified proteins up-regulated in NASH and/or advanced fibrosis (stage F3-F4), including matricellular glycoprotein thrombospondin-2 (TSP-2), encoded by the thrombospondin 2 (THBS2) gene. The intrahepatic THBS2 expression level showed the highest areas under the receiver operating characteristic curves (AUROCs) of 0.915 and 0.957 for diagnosing NASH and advanced fibrosis, respectively. THBS2 positively correlated with inflammation and ballooning according to NAFLD activity score, serum aspartate aminotransferase and hyaluronic acid (HA) levels, and NAFLD Fibrosis Score (NFS). THBS2 was associated with extracellular matrix and collagen biosynthesis, platelet activation, caspase-mediated cleavage of cytoskeletal proteins, and immune cell infiltration. Serum TSP-2 expression was measured in 213 patients with biopsy-proven NAFLD, was significantly higher in NASH than in NAFL, and increased parallel to fibrosis stage. The AUROCs for predicting NASH and advanced fibrosis were 0.776 and 0.856, respectively, which were comparable to Fibrosis-4 index, serum HA level, and NFS in advanced fibrosis diagnosis. Serum TSP-2 level and platelet count were independent predictors of NASH and advanced fibrosis. Serum TSP-2 levels could stratify patients with NAFLD according to the risk of hepatic complications, including liver cancer and decompensated cirrhotic events. CONCLUSIONS TSP-2 may be a useful biomarker for NASH and advanced fibrosis diagnosis in patients with NAFLD.
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Affiliation(s)
- Kazuhiro Kozumi
- Department of Gastroenterology and HepatologyOsaka University Graduate School of MedicineSuitaJapan
| | - Takahiro Kodama
- Department of Gastroenterology and HepatologyOsaka University Graduate School of MedicineSuitaJapan
| | - Hiroki Murai
- Department of Gastroenterology and HepatologyOsaka University Graduate School of MedicineSuitaJapan
| | - Sadatsugu Sakane
- Department of Gastroenterology and HepatologyOsaka University Graduate School of MedicineSuitaJapan
| | - Olivier Govaere
- Translational and Clinical Research InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUnited Kingdom
| | - Simon Cockell
- Translational and Clinical Research InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUnited Kingdom
| | - Daisuke Motooka
- Genome Information Research CenterResearch Institute for Microbial DiseasesOsaka UniversitySuitaJapan
| | - Naruyasu Kakita
- Department of Gastroenterology and HepatologyKaizuka City HospitalOsakaJapan
| | - Yukinori Yamada
- Department of Gastroenterology and HepatologyKaizuka City HospitalOsakaJapan
| | - Yasuteru Kondo
- Department of HepatologySendai Kousei HospitalSendaiJapan
| | - Yuki Tahata
- Department of Gastroenterology and HepatologyOsaka University Graduate School of MedicineSuitaJapan
| | - Ryoko Yamada
- Department of Gastroenterology and HepatologyOsaka University Graduate School of MedicineSuitaJapan
| | - Hayato Hikita
- Department of Gastroenterology and HepatologyOsaka University Graduate School of MedicineSuitaJapan
| | - Ryotaro Sakamori
- Department of Gastroenterology and HepatologyOsaka University Graduate School of MedicineSuitaJapan
| | - Yoshihiro Kamada
- Department of Advanced Metabolic HepatologyOsaka University Graduate School of MedicineSuitaJapan
| | - Ann K. Daly
- Translational and Clinical Research InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUnited Kingdom
| | - Quentin M. Anstee
- Translational and Clinical Research InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUnited Kingdom,Newcastle National Institute for Health Research Biomedical Research CentreNewcastle Upon Tyne Hospitals National Health Service Foundation TrustNewcastle Upon TyneUnited Kingdom
| | - Tomohide Tatsumi
- Department of Gastroenterology and HepatologyOsaka University Graduate School of MedicineSuitaJapan
| | - Eiichi Morii
- Department of PathologyOsaka University Graduate School of MedicineOsakaJapan
| | - Tetsuo Takehara
- Department of Gastroenterology and HepatologyOsaka University Graduate School of MedicineSuitaJapan
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7
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Anstee QM, Darlay R, Cockell S, Meroni M, Govaere O, Tiniakos D, Burt AD, Bedossa P, Palmer J, Liu YL, Aithal GP, Allison M, Yki-Järvinen H, Vacca M, Dufour JF, Invernizzi P, Prati D, Ekstedt M, Kechagias S, Francque S, Petta S, Bugianesi E, Clement K, Ratziu V, Schattenberg JM, Valenti L, Day CP, Cordell HJ, Daly AK. Corrigendum to: "Genome-wide association study of non-alcoholic fatty liver and steatohepatitis in a histologically characterised cohort"☆ (J Hepatol [2020] 505-515). J Hepatol 2021; 74:1274-1275. [PMID: 33678471 DOI: 10.1016/j.jhep.2021.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Quentin M Anstee
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom; Newcastle NIHR Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom.
| | - Rebecca Darlay
- Population & Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Simon Cockell
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marica Meroni
- Department of Pathophysiology and Transplantation, University of Milan, Translational Medicine - Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Olivier Govaere
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Dina Tiniakos
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom; Department of Pathology, Aretaieio Hospital, National & Kapodistrian University of Athens, Greece
| | - Alastair D Burt
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom; Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
| | - Pierre Bedossa
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jeremy Palmer
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yang-Lin Liu
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Guruprasad P Aithal
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Michael Allison
- Liver Unit, Department of Medicine, Cambridge Biomedical Research Centre, Cambridge University NHS Foundation Trust, United Kingdom
| | - Hannele Yki-Järvinen
- Department of Medicine, University of Helsinki, Helsinki, Finland Helsinki & University Hospital, Helsinki, Finland
| | - Michele Vacca
- Liver Unit, Department of Medicine, Cambridge Biomedical Research Centre, Cambridge University NHS Foundation Trust, United Kingdom; Department of Biochemistry and Wellcome Trust/MRC Institute of Metabolic Science, MRC Metabolic Diseases Unit, Metabolic Research Laboratories, University of Cambridge, UK
| | - Jean-Francois Dufour
- University Clinic for Visceral Surgery and Medicine, University of Berne, Freiburgstrasse, Berne, 3010, Switzerland
| | - Pietro Invernizzi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Daniele Prati
- Department of Pathophysiology and Transplantation, University of Milan, Translational Medicine - Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Mattias Ekstedt
- Division of Gastroenterology and Hepatology, Department of Medicine and Health Sciences, Linköping University, Linkoping, Sweden
| | - Stergios Kechagias
- Division of Gastroenterology and Hepatology, Department of Medicine and Health Sciences, Linköping University, Linkoping, Sweden
| | - Sven Francque
- Department of Gastroenterology and Hepatology, Antwerp University Hospital, Antwerp, Belgium
| | - Salvatore Petta
- Sezione di Gastroenterologia, Dipartimento Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Elisabetta Bugianesi
- Department of Medical Sciences, Division of Gastro-Hepatology, A.O. Città della Salute e della Scienza di Torino, University of Turin, Turin, Italy
| | - Karine Clement
- Sorbonne University, Inserm, Nutrition and obesity: Systemic approaches, Nutrition department, Pitié-Salpêtrière hospital, Assistance Publique-Hôpitaux de Paris, 75013, Paris, France
| | - Vlad Ratziu
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Institute of Cardiometabolism and Nutrition (ICAN), Paris, France
| | - Jörn M Schattenberg
- NAFLD Research Center, Department of Medicine, University Medical Center of the Johannes Gutenberg, University, Mainz, Germany
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, University of Milan, Translational Medicine - Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Christopher P Day
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Heather J Cordell
- Population & Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ann K Daly
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.
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8
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Pfister D, Núñez NG, Pinyol R, Govaere O, Pinter M, Szydlowska M, Gupta R, Qiu M, Deczkowska A, Weiner A, Müller F, Sinha A, Friebel E, Engleitner T, Lenggenhager D, Moncsek A, Heide D, Stirm K, Kosla J, Kotsiliti E, Leone V, Dudek M, Yousuf S, Inverso D, Singh I, Teijeiro A, Castet F, Montironi C, Haber PK, Tiniakos D, Bedossa P, Cockell S, Younes R, Vacca M, Marra F, Schattenberg JM, Allison M, Bugianesi E, Ratziu V, Pressiani T, D'Alessio A, Personeni N, Rimassa L, Daly AK, Scheiner B, Pomej K, Kirstein MM, Vogel A, Peck-Radosavljevic M, Hucke F, Finkelmeier F, Waidmann O, Trojan J, Schulze K, Wege H, Koch S, Weinmann A, Bueter M, Rössler F, Siebenhüner A, De Dosso S, Mallm JP, Umansky V, Jugold M, Luedde T, Schietinger A, Schirmacher P, Emu B, Augustin HG, Billeter A, Müller-Stich B, Kikuchi H, Duda DG, Kütting F, Waldschmidt DT, Ebert MP, Rahbari N, Mei HE, Schulz AR, Ringelhan M, Malek N, Spahn S, Bitzer M, Ruiz de Galarreta M, Lujambio A, Dufour JF, Marron TU, Kaseb A, Kudo M, Huang YH, Djouder N, Wolter K, Zender L, Marche PN, Decaens T, Pinato DJ, Rad R, Mertens JC, Weber A, Unger K, Meissner F, Roth S, Jilkova ZM, Claassen M, Anstee QM, Amit I, Knolle P, Becher B, Llovet JM, Heikenwalder M. NASH limits anti-tumour surveillance in immunotherapy-treated HCC. Nature 2021. [PMID: 33762733 DOI: 10.1038/s41586-021-03362-0.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hepatocellular carcinoma (HCC) can have viral or non-viral causes1-5. Non-alcoholic steatohepatitis (NASH) is an important driver of HCC. Immunotherapy has been approved for treating HCC, but biomarker-based stratification of patients for optimal response to therapy is an unmet need6,7. Here we report the progressive accumulation of exhausted, unconventionally activated CD8+PD1+ T cells in NASH-affected livers. In preclinical models of NASH-induced HCC, therapeutic immunotherapy targeted at programmed death-1 (PD1) expanded activated CD8+PD1+ T cells within tumours but did not lead to tumour regression, which indicates that tumour immune surveillance was impaired. When given prophylactically, anti-PD1 treatment led to an increase in the incidence of NASH-HCC and in the number and size of tumour nodules, which correlated with increased hepatic CD8+PD1+CXCR6+, TOX+, and TNF+ T cells. The increase in HCC triggered by anti-PD1 treatment was prevented by depletion of CD8+ T cells or TNF neutralization, suggesting that CD8+ T cells help to induce NASH-HCC, rather than invigorating or executing immune surveillance. We found similar phenotypic and functional profiles in hepatic CD8+PD1+ T cells from humans with NAFLD or NASH. A meta-analysis of three randomized phase III clinical trials that tested inhibitors of PDL1 (programmed death-ligand 1) or PD1 in more than 1,600 patients with advanced HCC revealed that immune therapy did not improve survival in patients with non-viral HCC. In two additional cohorts, patients with NASH-driven HCC who received anti-PD1 or anti-PDL1 treatment showed reduced overall survival compared to patients with other aetiologies. Collectively, these data show that non-viral HCC, and particularly NASH-HCC, might be less responsive to immunotherapy, probably owing to NASH-related aberrant T cell activation causing tissue damage that leads to impaired immune surveillance. Our data provide a rationale for stratification of patients with HCC according to underlying aetiology in studies of immunotherapy as a primary or adjuvant treatment.
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Affiliation(s)
- Dominik Pfister
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Liver Disease Research, Global Drug Discovery, Novo Nordisk A/S, Malov, Denmark
| | | | - Roser Pinyol
- Liver Cancer Translational Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)-Hospital Clínic, Liver Unit, Universitat de Barcelona, Barcelona, Spain
| | - Olivier Govaere
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Matthias Pinter
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria.,Liver Cancer (HCC) Study Group Vienna, Medical University of Vienna, Vienna, Austria
| | - Marta Szydlowska
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Revant Gupta
- Internal Medicine I, University Hospital Tübingen, Faculty of Medicine, University of Tübingen, Tübingen, Germany.,Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Mengjie Qiu
- Department of General, Visceral and Transplantation Surgery, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | | | - Assaf Weiner
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Florian Müller
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ankit Sinha
- Experimental Systems Immunology Laboratory, Max-Planck Institute of Biochemistry, Munich, Germany.,Institute of Translational Cancer Research and Experimental Cancer Therapy, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Ekaterina Friebel
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Thomas Engleitner
- Center for Translational Cancer Research (TranslaTUM), Technical University Munich, Munich, Germany.,Department of Medicine II, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Munich, Germany
| | - Daniela Lenggenhager
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Anja Moncsek
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Danijela Heide
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristin Stirm
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan Kosla
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eleni Kotsiliti
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Valentina Leone
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Research Unit of Radiation Cytogenetics, Helmholtz Zentrum Munich, Munich, Germany
| | - Michael Dudek
- Institute of Molecular Immunology and Experimental Oncology, Technical University Munich, Munich, Germany
| | - Suhail Yousuf
- Department of General, Visceral and Transplantation Surgery, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Donato Inverso
- Division of Vascular Oncology and Metastasis, German Cancer Research Center (DKFZ-ZMBH Alliance), Heidelberg, Germany.,European Center of Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Indrabahadur Singh
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Emmy Noether Research Group Epigenetic Machineries and Cancer, Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ana Teijeiro
- Cancer Cell Biology Programme, Growth Factors, Nutrients and Cancer Group, Spanish National Cancer Research Centre, CNIO, Madrid, Spain
| | - Florian Castet
- Liver Cancer Translational Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)-Hospital Clínic, Liver Unit, Universitat de Barcelona, Barcelona, Spain
| | - Carla Montironi
- Liver Cancer Translational Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)-Hospital Clínic, Liver Unit, Universitat de Barcelona, Barcelona, Spain
| | - Philipp K Haber
- Mount Sinai Liver Cancer Program, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dina Tiniakos
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.,Department of Pathology, Aretaeion Hospita, National and Kapodistrian University of Athens, Athens, Greece
| | - Pierre Bedossa
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Simon Cockell
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Ramy Younes
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.,Department of Medical Sciences, Division of Gastro-Hepatology, A.O. Città della Salute e della Scienza di Torino, University of Turin, Turn, Italy
| | - Michele Vacca
- University of Cambridge Metabolic Research Laboratories, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Fabio Marra
- Dipartimento di Medicina Sperimentale e Clinica, University of Florence, Florence, Italy
| | - Jörn M Schattenberg
- Metabolic Liver Research Program, I. Department of Medicine, University Medical Center Mainz, Mainz, Germany
| | - Michael Allison
- Liver Unit, Department of Medicine, Cambridge Biomedical Research Centre, Cambridge University NHS Foundation Trust, Cambridge, UK
| | - Elisabetta Bugianesi
- Department of Medical Sciences, Division of Gastro-Hepatology, A.O. Città della Salute e della Scienza di Torino, University of Turin, Turn, Italy
| | - Vlad Ratziu
- Assistance Publique-Hôpitaux de Paris, Hôpital Beaujon, University Paris-Diderot, Paris, France
| | - Tiziana Pressiani
- Medical Oncology and Hematology Unit, Humanitas Cancer Center, Humanitas Clinical and Research Center-IRCCS, Milan, Italy
| | - Antonio D'Alessio
- Medical Oncology and Hematology Unit, Humanitas Cancer Center, Humanitas Clinical and Research Center-IRCCS, Milan, Italy
| | - Nicola Personeni
- Medical Oncology and Hematology Unit, Humanitas Cancer Center, Humanitas Clinical and Research Center-IRCCS, Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Lorenza Rimassa
- Medical Oncology and Hematology Unit, Humanitas Cancer Center, Humanitas Clinical and Research Center-IRCCS, Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Ann K Daly
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Bernhard Scheiner
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria.,Liver Cancer (HCC) Study Group Vienna, Medical University of Vienna, Vienna, Austria
| | - Katharina Pomej
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria.,Liver Cancer (HCC) Study Group Vienna, Medical University of Vienna, Vienna, Austria
| | - Martha M Kirstein
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany.,University Medical Center Schleswig-Holstein, Schleswig-Holstein, Germany
| | - Arndt Vogel
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Markus Peck-Radosavljevic
- Department of Internal Medicine and Gastroenterology (IMuG), Hepatology, Endocrinology, Rheumatology and Nephrology including Centralized Emergency Department (ZAE), Klinikum Klagenfurt am Wörthersee, Klagenfurt, Austria
| | - Florian Hucke
- Department of Internal Medicine and Gastroenterology (IMuG), Hepatology, Endocrinology, Rheumatology and Nephrology including Centralized Emergency Department (ZAE), Klinikum Klagenfurt am Wörthersee, Klagenfurt, Austria
| | - Fabian Finkelmeier
- Department of Gastroenterology, Hepatology and Endocrinology, University Hospital Frankfurt, Frankfurt, Germany
| | - Oliver Waidmann
- Department of Gastroenterology, Hepatology and Endocrinology, University Hospital Frankfurt, Frankfurt, Germany
| | - Jörg Trojan
- Department of Gastroenterology, Hepatology and Endocrinology, University Hospital Frankfurt, Frankfurt, Germany
| | - Kornelius Schulze
- Department of Internal Medicine, Gastroenterology & Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Henning Wege
- Department of Internal Medicine, Gastroenterology & Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sandra Koch
- Department of Internal Medicine, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Arndt Weinmann
- Department of Internal Medicine, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Marco Bueter
- Department of Surgery and Transplantation, University Hospital Zurich, Zurich, Switzerland
| | - Fabian Rössler
- Department of Surgery and Transplantation, University Hospital Zurich, Zurich, Switzerland
| | - Alexander Siebenhüner
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Sara De Dosso
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Jan-Philipp Mallm
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Viktor Umansky
- Clinical Cooperation Unit Dermato-Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Heidelberg, Germany
| | - Manfred Jugold
- Core Facility Small Animal Imaging, German Cancer Research Center Heidelberg, Heidelberg, Germany
| | - Tom Luedde
- Department of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Andrea Schietinger
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Brinda Emu
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hellmut G Augustin
- Division of Vascular Oncology and Metastasis, German Cancer Research Center (DKFZ-ZMBH Alliance), Heidelberg, Germany.,European Center of Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Adrian Billeter
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Beat Müller-Stich
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Hiroto Kikuchi
- Edwin L. Steele Laboratories for Tumor Biology, Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Dan G Duda
- Edwin L. Steele Laboratories for Tumor Biology, Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Fabian Kütting
- Department of Gastroenterology and Hepatology, University of Cologne, Cologne, Germany
| | | | - Matthias Philip Ebert
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Nuh Rahbari
- Department of Surgery at University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Henrik E Mei
- Mass Cytometry Lab, Deutsches Rheumaforschungszentrum Berlin, a Leibniz Institute, Berlin, Germany
| | - Axel Ronald Schulz
- Mass Cytometry Lab, Deutsches Rheumaforschungszentrum Berlin, a Leibniz Institute, Berlin, Germany
| | - Marc Ringelhan
- Institute of Virology, Technical University Munich/Helmholtz Zentrum Munich, Munich, Germany.,Department of Internal Medicine II, University Hospital rechts der Isar, Technical University Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Nisar Malek
- Medical University Hospital Department of Internal Medicine I, Tübingen, Germany
| | - Stephan Spahn
- Medical University Hospital Department of Internal Medicine I, Tübingen, Germany
| | - Michael Bitzer
- Medical University Hospital Department of Internal Medicine I, Tübingen, Germany
| | - Marina Ruiz de Galarreta
- Mount Sinai Liver Cancer Program, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amaia Lujambio
- Mount Sinai Liver Cancer Program, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Francois Dufour
- University Clinic for Visceral Surgery and Medicine, Inselspital, Bern, Switzerland.,Hepatology, Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Thomas U Marron
- Mount Sinai Liver Cancer Program, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Medicine, Division of Hematology/Oncology, Tisch Cancer Institute, Mount Sinai Hospital, New York, NY, USA
| | - Ahmed Kaseb
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Masatoshi Kudo
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osaka-, Sayama, Japan
| | - Yi-Hsiang Huang
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Division of Gastroenterology and Hepatology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Nabil Djouder
- Cancer Cell Biology Programme, Growth Factors, Nutrients and Cancer Group, Spanish National Cancer Research Centre, CNIO, Madrid, Spain
| | - Katharina Wolter
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence 'Image Guided and Functionally Instructed Tumor Therapies' (iFIT), Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Lars Zender
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence 'Image Guided and Functionally Instructed Tumor Therapies' (iFIT), Eberhard-Karls University of Tübingen, Tübingen, Germany.,German Consortium for Translational Cancer Research (DKTK), Partner Site Tübingen, German Cancer Research Center (DKFZ), Tübingen, Germany
| | - Parice N Marche
- Université Grenoble Alpes, Grenoble, France.,Institute for Advanced Biosciences, Research Center UGA/Inserm U 1209/CNRS 5309, Grenoble, France
| | - Thomas Decaens
- Université Grenoble Alpes, Grenoble, France.,Institute for Advanced Biosciences, Research Center UGA/Inserm U 1209/CNRS 5309, Grenoble, France.,Service d'hépato-gastroentérologie, Pôle Digidune, CHU Grenoble Alpes, Grenoble, France
| | - David J Pinato
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital, London, UK.,Division of Oncology, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Roland Rad
- Center for Translational Cancer Research (TranslaTUM), Technical University Munich, Munich, Germany.,Department of Medicine II, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Munich, Germany
| | - Joachim C Mertens
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Achim Weber
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland.,Institute of Molecular Cancer Research (IMCR), University of Zurich, Zurich, Switzerland
| | - Kristian Unger
- Research Unit of Radiation Cytogenetics, Helmholtz Zentrum Munich, Munich, Germany
| | - Felix Meissner
- Experimental Systems Immunology Laboratory, Max-Planck Institute of Biochemistry, Munich, Germany
| | - Susanne Roth
- Department of General, Visceral and Transplantation Surgery, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Zuzana Macek Jilkova
- Université Grenoble Alpes, Grenoble, France.,Institute for Advanced Biosciences, Research Center UGA/Inserm U 1209/CNRS 5309, Grenoble, France.,Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Manfred Claassen
- Internal Medicine I, University Hospital Tübingen, Faculty of Medicine, University of Tübingen, Tübingen, Germany.,Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Quentin M Anstee
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.,Newcastle NIHR Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Trust, Newcastle, UK
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Percy Knolle
- Institute of Molecular Immunology and Experimental Oncology, Technical University Munich, Munich, Germany
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Josep M Llovet
- Liver Cancer Translational Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)-Hospital Clínic, Liver Unit, Universitat de Barcelona, Barcelona, Spain. .,Mount Sinai Liver Cancer Program, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Mathias Heikenwalder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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9
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Govaere O, Cockell S, Tiniakos D, Queen R, Younes R, Vacca M, Alexander L, Ravaioli F, Palmer J, Petta S, Boursier J, Rosso C, Johnson K, Wonders K, Day CP, Ekstedt M, Orešič M, Darlay R, Cordell HJ, Marra F, Vidal-Puig A, Bedossa P, Schattenberg JM, Clément K, Allison M, Bugianesi E, Ratziu V, Daly AK, Anstee QM. Transcriptomic profiling across the nonalcoholic fatty liver disease spectrum reveals gene signatures for steatohepatitis and fibrosis. Sci Transl Med 2020; 12:eaba4448. [PMID: 33268509 DOI: 10.1126/scitranslmed.aba4448] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [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: 12/04/2019] [Revised: 07/01/2020] [Accepted: 11/09/2020] [Indexed: 12/13/2022]
Abstract
The mechanisms that drive nonalcoholic fatty liver disease (NAFLD) remain incompletely understood. This large multicenter study characterized the transcriptional changes that occur in liver tissue across the NAFLD spectrum as disease progresses to cirrhosis to identify potential circulating markers. We performed high-throughput RNA sequencing on a discovery cohort comprising histologically characterized NAFLD samples from 206 patients. Unsupervised clustering stratified NAFLD on the basis of disease activity and fibrosis stage with differences in age, aspartate aminotransferase (AST), type 2 diabetes mellitus, and carriage of PNPLA3 rs738409, a genetic variant associated with NAFLD. Relative to early disease, we consistently identified 25 differentially expressed genes as fibrosing steatohepatitis progressed through stages F2 to F4. This 25-gene signature was independently validated by logistic modeling in a separate replication cohort (n = 175), and an integrative analysis with publicly available single-cell RNA sequencing data elucidated the likely relative contribution of specific intrahepatic cell populations. Translating these findings to the protein level, SomaScan analysis in more than 300 NAFLD serum samples confirmed that circulating concentrations of proteins AKR1B10 and GDF15 were strongly associated with disease activity and fibrosis stage. Supporting the biological plausibility of these data, in vitro functional studies determined that endoplasmic reticulum stress up-regulated expression of AKR1B10, GDF15, and PDGFA, whereas GDF15 supplementation tempered the inflammatory response in macrophages upon lipid loading and lipopolysaccharide stimulation. This study provides insights into the pathophysiology of progressive fibrosing steatohepatitis, and proof of principle that transcriptomic changes represent potentially tractable and clinically relevant markers of disease progression.
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Affiliation(s)
- Olivier Govaere
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Simon Cockell
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Dina Tiniakos
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Pathology, Aretaieio Hospital, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Rachel Queen
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Ramy Younes
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Medical Sciences, Division of Gastro-Hepatology, A.O. Città della Salute e della Scienza di Torino, University of Turin, 10124 Turin, Italy
| | - Michele Vacca
- University of Cambridge Metabolic Research Laboratories, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | | | - Federico Ravaioli
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Medical and Surgical Sciences, University of Bologna, 40126 Bologna, Italy
| | - Jeremy Palmer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Salvatore Petta
- Sezione di Gastroenterologia, Dipartimento Biomedico di Medicina Interna e Specialistica, Università di Palermo, 90133 Palermo, Italy
| | - Jerome Boursier
- Hepatology Department, Angers University Hospital, 49933 Angers, France
| | - Chiara Rosso
- Department of Medical Sciences, Division of Gastro-Hepatology, A.O. Città della Salute e della Scienza di Torino, University of Turin, 10124 Turin, Italy
| | - Katherine Johnson
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Kristy Wonders
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Christopher P Day
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Mattias Ekstedt
- Department of Health, Medicine and Caring Sciences, Linköping University, 581 83 Linköping, Sweden
| | - Matej Orešič
- School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden
| | - Rebecca Darlay
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Heather J Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Fabio Marra
- Dipartimento di Medicina Sperimentale e Clinica, University of Florence, 50121 Florence, Italy
| | - Antonio Vidal-Puig
- University of Cambridge Metabolic Research Laboratories, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Pierre Bedossa
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpêtrière, Sorbonne University, ICAN (Institute of Cardiometabolism and Nutrition), 75013 Paris, France
| | | | - Karine Clément
- Nutrition and Obesities: Systemic Approaches, INSERM, Sorbonne University, 75006 Paris, France
| | - Michael Allison
- Liver Unit, Department of Medicine, NIHR Cambridge Biomedical Research Centre, Cambridge University NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Elisabetta Bugianesi
- Department of Medical Sciences, Division of Gastro-Hepatology, A.O. Città della Salute e della Scienza di Torino, University of Turin, 10124 Turin, Italy
| | - Vlad Ratziu
- Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpêtrière, Sorbonne University, ICAN (Institute of Cardiometabolism and Nutrition), 75013 Paris, France
| | - Ann K Daly
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Quentin M Anstee
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
- NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne NE7 7DN, UK
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10
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Cheung K, Burgers MJ, Young DA, Cockell S, Reynard LN. Correlation of Infinium HumanMethylation450K and MethylationEPIC BeadChip arrays in cartilage. Epigenetics 2019; 15:594-603. [PMID: 31833794 PMCID: PMC7574380 DOI: 10.1080/15592294.2019.1700003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
DNA methylation of CpG sites is commonly measured using Illumina Infinium BeadChip platforms. The Infinium MethylationEPIC array has replaced the Infinium Methylation450K array. The two arrays use the same technology, with the EPIC array assaying almost double the number of sites than the 450K array. In this study, we compare DNA methylation values of shared CpGs of the same human cartilage samples assayed using both platforms. DNA methylation was measured in 21 human cartilage samples using the both 450K and EPIC arrays. Additional matched 450K and EPIC data in whole tumour and whole blood were downloaded from GEO GSE92580 and GSE86833, respectively. Data were processed using the Bioconductor package Minfi. DNA methylation of six CpG sites was validated for the same 21 cartilage samples by pyrosequencing. In cartilage samples, overall sample correlations of methylation values between arrays were high (Pearson’s r > 0.96). However, 50.5% of CpG sites showed poor correlation (r < 0.2) between arrays. Sites with limited variance and with either very high or very low methylation levels in cartilage exhibited lower correlation values, corroborating prior studies in whole blood. Bisulphite pyrosequencing did not highlight one array as generating more accurate methylation values. For a specific CpG site, the array methylation correlation coefficient differed between cartilage, tumour, and whole blood, reflecting the difference in methylation variance between cell types. Researchers should be cautious when analysing methylation of CpG sites that show low methylation variance within the cell type of interest, regardless of the method used to assay methylation.
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Affiliation(s)
- Kathleen Cheung
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway , Newcastle upon Tyne, UK.,Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University , Newcastle upon Tyne, UK
| | - Marjolein J Burgers
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway , Newcastle upon Tyne, UK
| | - David A Young
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway , Newcastle upon Tyne, UK
| | - Simon Cockell
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University , Newcastle upon Tyne, UK
| | - Louise N Reynard
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway , Newcastle upon Tyne, UK
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11
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Davies HR, Hodgson K, Schwalbe E, Coxhead J, Sinclair N, Zou X, Cockell S, Husain A, Nik-Zainal S, Rajan N. Epigenetic modifiers DNMT3A and BCOR are recurrently mutated in CYLD cutaneous syndrome. Nat Commun 2019; 10:4717. [PMID: 31624251 PMCID: PMC6797807 DOI: 10.1038/s41467-019-12746-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/23/2019] [Indexed: 01/27/2023] Open
Abstract
Patients with CYLD cutaneous syndrome (CCS; syn. Brooke-Spiegler syndrome) carry germline mutations in the tumor suppressor CYLD and develop multiple skin tumors with diverse histophenotypes. Here, we comprehensively profile the genomic landscape of 42 benign and malignant tumors across 13 individuals from four multigenerational families and discover recurrent mutations in epigenetic modifiers DNMT3A and BCOR in 29% of benign tumors. Multi-level and microdissected sampling strikingly reveal that many clones with different DNMT3A mutations exist in these benign tumors, suggesting that intra-tumor heterogeneity is common. Integrated genomic, methylation and transcriptomic profiling in selected tumors suggest that isoform-specific DNMT3A2 mutations are associated with dysregulated methylation. Phylogenetic and mutational signature analyses confirm cylindroma pulmonary metastases from primary skin tumors. These findings contribute to existing paradigms of cutaneous tumorigenesis and metastasis.
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Affiliation(s)
- Helen R Davies
- Wellcome Trust Sanger Institute, Hinxton, UK
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
| | - Kirsty Hodgson
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Edward Schwalbe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Jonathan Coxhead
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Naomi Sinclair
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Xueqing Zou
- Wellcome Trust Sanger Institute, Hinxton, UK
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
| | - Simon Cockell
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Akhtar Husain
- Department of Pathology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Hinxton, UK.
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK.
- MRC Cancer Unit, University of Cambridge, Cambridge, UK.
| | - Neil Rajan
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK.
- Department of Dermatology, Royal Victoria Infirmary, Newcastle upon Tyne, UK.
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12
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Roberts R, Weatherhead S, Cockell S, Reynolds N. 532 Role of apoptosis and key canonical pathways in psoriasis plaque clearance in response to UVB phototherapy. J Invest Dermatol 2019. [DOI: 10.1016/j.jid.2019.07.447] [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: 10/26/2022]
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13
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Govaere O, Cockell S, Van Haele M, Wouters J, Van Delm W, Van den Eynde K, Bianchi A, van Eijsden R, Van Steenbergen W, Monbaliu D, Nevens F, Roskams T. High-throughput sequencing identifies aetiology-dependent differences in ductular reaction in human chronic liver disease. J Pathol 2019; 248:66-76. [PMID: 30584802 DOI: 10.1002/path.5228] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/27/2018] [Accepted: 12/23/2018] [Indexed: 12/15/2022]
Abstract
Ductular reaction (DR) represents the activation of hepatic progenitor cells (HPCs) and has been associated with features of advanced chronic liver disease; yet it is not clear whether these cells contribute to disease progression and how the composition of their micro-environment differs depending on the aetiology. This study aimed to identify HPC-associated signalling pathways relevant in different chronic liver diseases using a high-throughput sequencing approach. DR/HPCs were isolated using laser microdissection from patient samples diagnosed with HCV or primary sclerosing cholangitis (PSC), as models for hepatocellular or biliary regeneration. Key signals were validated at the protein level for a cohort of 56 patients (20 early and 36 advanced stage). In total, 330 genes were significantly differentially expressed between the HPCs in HCV and PSC. Recruitment and homing of inflammatory cells were distinctly different depending on the aetiology. HPCs in PSC were characterised by a response to oxidative stress (e.g. JUN, VNN1) and neutrophil-attractant chemokines (CXCL5, CXCL6, IL-8), whereas HPCs in HCV were identified by T- and B-lymphocyte infiltration. Moreover, we found that communication between HPCs and macrophages was aetiology driven. In PSC, a high frequency of CCL28-positive macrophages was observed in the portal infiltrate, already in early disease in the absence of advanced fibrosis, while in HCV, HPCs showed a strong expression of the macrophage scavenger receptor MARCO. Interestingly, DR/HPCs in PSC showed more deposition of ECM (e.g. FN1, LAMC2, collagens) compared to HCV, where an increase of pro-invasive genes (e.g. PDGFRA, IGF2) was observed. Additionally, endothelial cells in the vicinity of DR/HPCs showed differential immunopositivity (e.g. IGF2 and INHBA expression). In conclusion, our data shine light on the role of DR/HPCs in immune signalling, fibrogenesis and angiogenesis in chronic liver disease. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Olivier Govaere
- Department of Imaging and Pathology, KU Leuven and University Hospitals Leuven, Leuven, Belgium.,Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Simon Cockell
- Bioinformatics Support Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Matthias Van Haele
- Department of Imaging and Pathology, KU Leuven and University Hospitals Leuven, Leuven, Belgium
| | - Jasper Wouters
- VIB Center for Brain and Disease Research, KU Leuven, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Kathleen Van den Eynde
- Department of Imaging and Pathology, KU Leuven and University Hospitals Leuven, Leuven, Belgium
| | - Arianna Bianchi
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Diethard Monbaliu
- Department of Abdominal Transplant Surgery, KU Leuven and University Hospitals Leuven, Leuven, Belgium
| | - Frederik Nevens
- Department of Hepatology, KU Leuven and University Hospitals Leuven, Leuven, Belgium
| | - Tania Roskams
- Department of Imaging and Pathology, KU Leuven and University Hospitals Leuven, Leuven, Belgium
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14
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Ehrmann I, Crichton JH, Gazzara MR, James K, Liu Y, Grellscheid SN, Curk T, de Rooij D, Steyn JS, Cockell S, Adams IR, Barash Y, Elliott DJ. An ancient germ cell-specific RNA-binding protein protects the germline from cryptic splice site poisoning. eLife 2019; 8:39304. [PMID: 30674417 PMCID: PMC6345566 DOI: 10.7554/elife.39304] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 06/18/2018] [Accepted: 12/18/2018] [Indexed: 12/28/2022] Open
Abstract
Male germ cells of all placental mammals express an ancient nuclear RNA binding protein of unknown function called RBMXL2. Here we find that deletion of the retrogene encoding RBMXL2 blocks spermatogenesis. Transcriptome analyses of age-matched deletion mice show that RBMXL2 controls splicing patterns during meiosis. In particular, RBMXL2 represses the selection of aberrant splice sites and the insertion of cryptic and premature terminal exons. Our data suggest a Rbmxl2 retrogene has been conserved across mammals as part of a splicing control mechanism that is fundamentally important to germ cell biology. We propose that this mechanism is essential to meiosis because it buffers the high ambient concentrations of splicing activators, thereby preventing poisoning of key transcripts and disruption to gene expression by aberrant splice site selection. In humans and other mammals, a sperm from a male fuses with an egg cell from a female to produce an embryo that may ultimately grow into a new individual. Sperm and egg cells are made when certain cells in the body divide in a process called meiosis. Many proteins are required for meiosis to happen and these proteins are made using instructions provided by genes, which are made of a molecule called DNA. The DNA within a gene is transcribed to make molecules of ribonucleic acid (or RNA for short). The cell then modifies many of these RNAs in a process called splicing before using them as templates to make proteins. During splicing, segments of RNA known as introns are discarded and other segments termed exons are joined together. Some exons may also be removed from RNAs in different combinations to create different proteins from the same gene. A protein called RBMXL2 is able to bind to RNA molecules and is only made during and after meiosis in humans and most other mammals. RBMXL2 can also bind to other proteins that are known to be involved in controlling splicing of RNAs, but its role in splicing remains unclear. To address this question, Ehrmann et al. studied the gene that encodes the RBMXL2 protein in mice. Removing this gene prevented male mice from being able to make sperm. Further experiments using a technique called RNA sequencing showed that the RBMXL2 protein helps to ensure that splicing happens correctly by preventing bits of exons and introns in mouse genes from being rearranged. These findings suggest that the gene encoding RBMXL2 is part of a splicing control mechanism that is important for making sperm and egg cells. The work of Ehrmann et al. could eventually help some couples understand why they have problems conceiving children. Male infertility is poorly understood, and not knowing its causes can harm the mental health of affected men. Furthermore, these findings may help researchers to understand the role of a closely related protein called RBMY that has also been linked to infertility in men, but is much more difficult to study.
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Affiliation(s)
- Ingrid Ehrmann
- Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom
| | - James H Crichton
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Matthew R Gazzara
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Katherine James
- Life Sciences, Natural History Museum, London, United Kingdom
| | - Yilei Liu
- Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom.,Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Sushma Nagaraja Grellscheid
- Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom.,School of Biological and Biomedical Sciences, University of Durham, Durham, United Kingdom
| | - Tomaž Curk
- Laboratory of Bioinformatics, Faculty of Computer and Information Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - Dirk de Rooij
- Reproductive Biology Group, Division of Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands.,Center for Reproductive Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Jannetta S Steyn
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle, United Kingdom
| | - Simon Cockell
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle, United Kingdom
| | - Ian R Adams
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Computer and Information Science, University of Pennsylvania, Philadelphia, United States
| | - David J Elliott
- Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom
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15
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Collin J, Queen R, Zerti D, Dorgau B, Hussain R, Coxhead J, Cockell S, Lako M. Deconstructing Retinal Organoids: Single Cell RNA-Seq Reveals the Cellular Components of Human Pluripotent Stem Cell-Derived Retina. Stem Cells 2019; 37:593-598. [PMID: 30548510 PMCID: PMC6519347 DOI: 10.1002/stem.2963] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/07/2018] [Accepted: 12/03/2018] [Indexed: 11/11/2022]
Abstract
The rapid improvements in single cell sequencing technologies and analyses afford greater scope for dissecting organoid cultures composed of multiple cell types and create an opportunity to interrogate these models to understand tissue biology, cellular behavior and interactions. To this end, retinal organoids generated from human embryonic stem cells (hESCs) were analyzed by single cell RNA-sequencing (scRNA-Seq) at three time points of differentiation. Combinatorial data from all time points revealed the presence of nine clusters, five of which corresponded to key retinal cell types: retinal pigment epithelium (RPE), retinal ganglion cells (RGCs), cone and rod photoreceptors, and Müller glia. The remaining four clusters expressed genes typical of mitotic cells, extracellular matrix components and those involved in homeostasis. The cell clustering analysis revealed the decreasing presence of mitotic cells and RGCs, formation of a distinct RPE cluster, the emergence of cone and rod photoreceptors from photoreceptor precursors, and an increasing number of Müller glia cells over time. Pseudo-time analysis resembled the order of cell birth during retinal development, with the mitotic cluster commencing the trajectory and the large majority of Müller glia completing the time line. Together, these data demonstrate the feasibility and potential of scRNA-Seq to dissect the inherent complexity of retinal organoids and the orderly birth of key retinal cell types. Stem Cells 2019;37:593-598.
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Affiliation(s)
- Joseph Collin
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Rachel Queen
- Bioinformatics Support Unit, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Darin Zerti
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Birthe Dorgau
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Rafiqul Hussain
- Genomics Core Facility, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jonathan Coxhead
- Genomics Core Facility, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Simon Cockell
- Bioinformatics Support Unit, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Majlinda Lako
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
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16
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Munkley J, Li L, Krishnan SRG, Hysenaj G, Scott E, Dalgliesh C, Oo HZ, Maia TM, Cheung K, Ehrmann I, Livermore KE, Zielinska H, Thompson O, Knight B, McCullagh P, McGrath J, Crundwell M, Harries LW, Daugaard M, Cockell S, Barbosa-Morais NL, Oltean S, Elliott DJ. Androgen-regulated transcription of ESRP2 drives alternative splicing patterns in prostate cancer. eLife 2019; 8:47678. [PMID: 31478829 PMCID: PMC6788855 DOI: 10.7554/elife.47678] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/02/2019] [Indexed: 12/14/2022] Open
Abstract
Prostate is the most frequent cancer in men. Prostate cancer progression is driven by androgen steroid hormones, and delayed by androgen deprivation therapy (ADT). Androgens control transcription by stimulating androgen receptor (AR) activity, yet also control pre-mRNA splicing through less clear mechanisms. Here we find androgens regulate splicing through AR-mediated transcriptional control of the epithelial-specific splicing regulator ESRP2. Both ESRP2 and its close paralog ESRP1 are highly expressed in primary prostate cancer. Androgen stimulation induces splicing switches in many endogenous ESRP2-controlled mRNA isoforms, including splicing switches correlating with disease progression. ESRP2 expression in clinical prostate cancer is repressed by ADT, which may thus inadvertently dampen epithelial splice programmes. Supporting this, treatment with the AR antagonist bicalutamide (Casodex) induced mesenchymal splicing patterns of genes including FLNB and CTNND1. Our data reveals a new mechanism of splicing control in prostate cancer with important implications for disease progression.
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Affiliation(s)
- Jennifer Munkley
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Ling Li
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and HealthUniversity of ExeterExeterUnited Kingdom
| | - S R Gokul Krishnan
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Gerald Hysenaj
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Emma Scott
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Caroline Dalgliesh
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Htoo Zarni Oo
- Department of Urologic SciencesUniversity of British ColumbiaVancouverCanada,Vancouver Prostate CentreVancouverCanada
| | - Teresa Mendes Maia
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de MedicinaUniversidade de LisboaLisboaPortugal,VIB Center for Medical BiotechnologyVIBGhentBelgium,VIB Proteomics CoreVIBGhentBelgium,Department for Biomolecular MedicineGhent UniversityGhentBelgium
| | - Kathleen Cheung
- Bioinformatics Support Unit, Faculty of Medical SciencesNewcastle UniversityNewcastleUnited Kingdom
| | - Ingrid Ehrmann
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Karen E Livermore
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Hanna Zielinska
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and HealthUniversity of ExeterExeterUnited Kingdom
| | - Oliver Thompson
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and HealthUniversity of ExeterExeterUnited Kingdom
| | - Bridget Knight
- NIHR Exeter Clinical Research FacilityRoyal Devon and Exeter NHS Foundation TrustExeterUnited Kingdom
| | - Paul McCullagh
- Department of PathologyRoyal Devon and Exeter NHS Foundation TrustExeterUnited Kingdom
| | - John McGrath
- Exeter Surgical Health Services Research UnitRoyal Devon and Exeter NHS Foundation TrustExeterUnited Kingdom
| | - Malcolm Crundwell
- Department of UrologyRoyal Devon and Exeter NHS Foundation TrustExeterUnited Kingdom
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and HealthUniversity of ExeterExeterUnited Kingdom
| | - Mads Daugaard
- Department of Urologic SciencesUniversity of British ColumbiaVancouverCanada,Vancouver Prostate CentreVancouverCanada
| | - Simon Cockell
- Bioinformatics Support Unit, Faculty of Medical SciencesNewcastle UniversityNewcastleUnited Kingdom
| | - Nuno L Barbosa-Morais
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de MedicinaUniversidade de LisboaLisboaPortugal
| | - Sebastian Oltean
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and HealthUniversity of ExeterExeterUnited Kingdom
| | - David J Elliott
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
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17
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Szołtysek K, Janus P, Zając G, Stokowy T, Walaszczyk A, Widłak W, Wojtaś B, Gielniewski B, Cockell S, Perkins ND, Kimmel M, Widlak P. RRAD, IL4I1, CDKN1A, and SERPINE1 genes are potentially co-regulated by NF-κB and p53 transcription factors in cells exposed to high doses of ionizing radiation. BMC Genomics 2018; 19:813. [PMID: 30419821 PMCID: PMC6233266 DOI: 10.1186/s12864-018-5211-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 10/30/2018] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The cellular response to ionizing radiation involves activation of p53-dependent pathways and activation of the atypical NF-κB pathway. The crosstalk between these two transcriptional networks include (co)regulation of common gene targets. Here we looked for novel genes potentially (co)regulated by p53 and NF-κB using integrative genomics screening in human osteosarcoma U2-OS cells irradiated with a high dose (4 and 10 Gy). Radiation-induced expression in cells with silenced TP53 or RELA (coding the p65 NF-κB subunit) genes was analyzed by RNA-Seq while radiation-enhanced binding of p53 and RelA in putative regulatory regions was analyzed by ChIP-Seq, then selected candidates were validated by qPCR. RESULTS We identified a subset of radiation-modulated genes whose expression was affected by silencing of both TP53 and RELA, and a subset of radiation-upregulated genes where radiation stimulated binding of both p53 and RelA. For three genes, namely IL4I1, SERPINE1, and CDKN1A, an antagonistic effect of the TP53 and RELA silencing was consistent with radiation-enhanced binding of both p53 and RelA. This suggested the possibility of a direct antagonistic (co)regulation by both factors: activation by NF-κB and inhibition by p53 of IL4I1, and activation by p53 and inhibition by NF-κB of CDKN1A and SERPINE1. On the other hand, radiation-enhanced binding of both p53 and RelA was observed in a putative regulatory region of the RRAD gene whose expression was downregulated both by TP53 and RELA silencing, which suggested a possibility of direct (co)activation by both factors. CONCLUSIONS Four new candidates for genes directly co-regulated by NF-κB and p53 were revealed.
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Affiliation(s)
- Katarzyna Szołtysek
- Maria Skłodowska-Curie Institute – Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Patryk Janus
- Maria Skłodowska-Curie Institute – Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Gracjana Zając
- Maria Skłodowska-Curie Institute – Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Tomasz Stokowy
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Anna Walaszczyk
- Maria Skłodowska-Curie Institute – Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Wiesława Widłak
- Maria Skłodowska-Curie Institute – Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Bartosz Wojtaś
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | | | - Simon Cockell
- Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Neil D. Perkins
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, UK
| | | | - Piotr Widlak
- Maria Skłodowska-Curie Institute – Oncology Center, Gliwice Branch, Gliwice, Poland
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18
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Janus P, Szołtysek K, Zając G, Stokowy T, Walaszczyk A, Widłak W, Wojtaś B, Gielniewski B, Iwanaszko M, Braun R, Cockell S, Perkins ND, Kimmel M, Widlak P. Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes. Cell Signal 2018; 46:23-31. [PMID: 29476964 DOI: 10.1016/j.cellsig.2018.02.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 12/22/2022]
Abstract
The NF-κB transcription factors are activated via diverse molecular mechanisms in response to various types of stimuli. A plethora of functions associated with specific sets of target genes could be regulated differentially by this factor, affecting cellular response to stress including an anticancer treatment. Here we aimed to compare subsets of NF-κB-dependent genes induced in cells stimulated with a pro-inflammatory cytokine and in cells damaged by a high dose of ionizing radiation (4 and 10 Gy). The RelA-containing NF-κB species were activated by the canonical TNFα-induced and the atypical radiation-induced pathways in human osteosarcoma cells. NF-κB-dependent genes were identified using the gene expression profiling (by RNA-Seq) in cells with downregulated RELA combined with the global profiling of RelA binding sites (by ChIP-Seq), with subsequent validation of selected candidates by quantitative PCR. There were 37 NF-κB-dependent protein-coding genes identified: in all cases RelA bound in their regulatory regions upon activation while downregulation of RELA suppressed their stimulus-induced upregulation, which apparently indicated the positive regulation mode. This set of genes included a few "novel" NF-κB-dependent species. Moreover, the evidence for possible negative regulation of ATF3 gene by NF-κB was collected. The kinetics of the NF-κB activation was slower in cells exposed to radiation than in cytokine-stimulated ones. However, subsets of NF-κB-dependent genes upregulated by both types of stimuli were essentially the same. Hence, one should expect that similar cellular processes resulting from activation of the NF-κB pathway could be induced in cells responding to pro-inflammatory cytokines and in cells where so-called "sterile inflammation" response was initiated by radiation-induced damage.
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Affiliation(s)
- Patryk Janus
- Maria Skłodowska-Curie Institute, Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Katarzyna Szołtysek
- Maria Skłodowska-Curie Institute, Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Gracjana Zając
- Maria Skłodowska-Curie Institute, Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Tomasz Stokowy
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Anna Walaszczyk
- Maria Skłodowska-Curie Institute, Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Wiesława Widłak
- Maria Skłodowska-Curie Institute, Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Bartosz Wojtaś
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | | | - Marta Iwanaszko
- Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Rosemary Braun
- Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Simon Cockell
- Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Neil D Perkins
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, UK
| | | | - Piotr Widlak
- Maria Skłodowska-Curie Institute, Oncology Center, Gliwice Branch, Gliwice, Poland.
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19
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Elder A, Bomken S, Wilson I, Blair HJ, Cockell S, Ponthan F, Dormon K, Pal D, Heidenreich O, Vormoor J. Abundant and equipotent founder cells establish and maintain acute lymphoblastic leukaemia. Leukemia 2017; 31:2577-2586. [PMID: 28487542 PMCID: PMC5558874 DOI: 10.1038/leu.2017.140] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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: 11/18/2016] [Revised: 03/29/2017] [Accepted: 04/25/2017] [Indexed: 12/19/2022]
Abstract
High frequencies of blasts in primary acute lymphoblastic leukaemia (ALL) samples have the potential to induce leukaemia and to engraft mice. However, it is unclear how individual ALL cells each contribute to drive leukaemic development in a bulk transplant and the extent to which these blasts vary functionally. We used cellular barcoding as a fate mapping tool to track primograft ALL blasts in vivo. Our results show that high numbers of ALL founder cells contribute at similar frequencies to leukaemic propagation over serial transplants, without any clear evidence of clonal succession. These founder cells also exhibit equal capacity to home and engraft to different organs, although stochastic processes may alter the composition in restrictive niches. Our findings enhance the stochastic stem cell model of ALL by demonstrating equal functional abilities of singular ALL blasts and show that successful treatment strategies must eradicate the entire leukaemic cell population.
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Affiliation(s)
- A Elder
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - S Bomken
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
- Department of Paediatric and Adolescent Haematology and Oncology, Great North Children’s Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - I Wilson
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - H J Blair
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - S Cockell
- Bioinformatics Support Unit, Newcastle University, Newcastle upon Tyne, UK
| | - F Ponthan
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - K Dormon
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - D Pal
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - O Heidenreich
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - J Vormoor
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
- Department of Paediatric and Adolescent Haematology and Oncology, Great North Children’s Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
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20
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Méplan C, Johnson IT, Polley ACJ, Cockell S, Bradburn DM, Commane DM, Arasaradnam RP, Mulholland F, Zupanic A, Mathers JC, Hesketh J. Transcriptomics and proteomics show that selenium affects inflammation, cytoskeleton, and cancer pathways in human rectal biopsies. FASEB J 2016; 30:2812-25. [PMID: 27103578 DOI: 10.1096/fj.201600251r] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/12/2016] [Indexed: 01/11/2023]
Abstract
Epidemiologic studies highlight the potential role of dietary selenium (Se) in colorectal cancer prevention. Our goal was to elucidate whether expression of factors crucial for colorectal homoeostasis is affected by physiologic differences in Se status. Using transcriptomics and proteomics followed by pathway analysis, we identified pathways affected by Se status in rectal biopsies from 22 healthy adults, including 11 controls with optimal status (mean plasma Se = 1.43 μM) and 11 subjects with suboptimal status (mean plasma Se = 0.86 μM). We observed that 254 genes and 26 proteins implicated in cancer (80%), immune function and inflammatory response (40%), cell growth and proliferation (70%), cellular movement, and cell death (50%) were differentially expressed between the 2 groups. Expression of 69 genes, including selenoproteins W1 and K, which are genes involved in cytoskeleton remodelling and transcription factor NFκB signaling, correlated significantly with Se status. Integrating proteomics and transcriptomics datasets revealed reduced inflammatory and immune responses and cytoskeleton remodelling in the suboptimal Se status group. This is the first study combining omics technologies to describe the impact of differences in Se status on colorectal expression patterns, revealing that suboptimal Se status could alter inflammatory signaling and cytoskeleton in human rectal mucosa and so influence cancer risk.-Méplan, C., Johnson, I. T., Polley, A. C. J., Cockell, S., Bradburn, D. M., Commane, D. M., Arasaradnam, R. P., Mulholland, F., Zupanic, A., Mathers, J. C., Hesketh, J. Transcriptomics and proteomics show that selenium affects inflammation, cytoskeleton, and cancer pathways in human rectal biopsies.
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Affiliation(s)
- Catherine Méplan
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, United Kingdom; School of Biomedical Sciences, Newcastle University, Newcastle-upon-Tyne, United Kingdom; Human Nutrition Research Centre, Newcastle University, Newcastle-upon-Tyne, United Kingdom; The Medical School, Newcastle University, Newcastle-upon-Tyne, United Kingdom;
| | - Ian T Johnson
- Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - Abigael C J Polley
- Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - Simon Cockell
- Bioinformatics Support Unit, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | | | - Daniel M Commane
- Human Nutrition Research Centre, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Ramesh P Arasaradnam
- School of Biomedical Sciences, Newcastle University, Newcastle-upon-Tyne, United Kingdom; Wansbeck General Hospital, Ashingon, United Kingdom; and **Institute of Cellular Medicine, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Francis Mulholland
- Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - Anze Zupanic
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - John C Mathers
- Human Nutrition Research Centre, Newcastle University, Newcastle-upon-Tyne, United Kingdom; **Institute of Cellular Medicine, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - John Hesketh
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, United Kingdom; Human Nutrition Research Centre, Newcastle University, Newcastle-upon-Tyne, United Kingdom; The Medical School, Newcastle University, Newcastle-upon-Tyne, United Kingdom
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Manville CM, Smith K, Sondka Z, Rance H, Cockell S, Cowell IG, Lee KC, Morris NJ, Padget K, Jackson GH, Austin CA. Genome-wide ChIP-seq analysis of human TOP2B occupancy in MCF7 breast cancer epithelial cells. Biol Open 2015; 4:1436-47. [PMID: 26459242 PMCID: PMC4728365 DOI: 10.1242/bio.014308] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We report the whole genome ChIP seq for human TOP2B from MCF7 cells. Using three different peak calling methods, regions of binding were identified in the presence or absence of the nuclear hormone estradiol, as TOP2B has been reported to play a role in ligand-induced transcription. TOP2B peaks were found across the whole genome, 50% of the peaks fell either within a gene or within 5 kb of a transcription start site. TOP2B peaks coincident with gene promoters were less frequently associated with epigenetic features marking active promoters in estradiol treated than in untreated cells. Significantly enriched transcription factor motifs within the DNA sequences underlying the peaks were identified. These included SP1, KLF4, TFAP2A, MYF, REST, CTCF, ESR1 and ESR2. Gene ontology analysis of genes associated with TOP2B peaks found neuronal development terms including axonogenesis and axon guidance were significantly enriched. In the absence of functional TOP2B there are errors in axon guidance in the zebrafish eye. Specific heparin sulphate structures are involved in retinal axon targeting. The glycosaminoglycan biosynthesis–heparin sulphate/heparin pathway is significantly enriched in the TOP2B gene ontology analysis, suggesting changes in this pathway in the absence of TOP2B may cause the axon guidance faults. Summary: Gene ontology enrichment analysis of genes associated with human TOP2B peaks, identified by whole genome ChIP seq used to identify regions of binding, highlighted a number of processes in neuronal development including axonogenesis and axon guidance.
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Affiliation(s)
- Catriona M Manville
- Institute for Cellular and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Kayleigh Smith
- Institute for Cellular and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Zbyslaw Sondka
- Institute for Cellular and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Holly Rance
- Institute for Cellular and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Simon Cockell
- The Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Ian G Cowell
- Institute for Cellular and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Ka Cheong Lee
- Institute for Cellular and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Nicholas J Morris
- School of Biomedical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Kay Padget
- Department of Applied Biology, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Graham H Jackson
- Institute for Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Caroline A Austin
- Institute for Cellular and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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Tarn J, Cockell S, Gillespie C, Al-Ali S, James K, Locke J, Bowman S, Griffiths B, Young D, Ng WF. A7.5 A whole blood micro-RNA signature for primary SjÖgren’s syndrome-related lymphoma. Ann Rheum Dis 2015. [DOI: 10.1136/annrheumdis-2015-207259.175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Flanagan K, Cockell S, Harwood C, Hallinan J, Nakjang S, Lawry B, Wipat A. A distributed computational search strategy for the identification of diagnostics targets: Application to finding aptamer targets for methicillin-resistant staphylococci. J Integr Bioinform 2014. [DOI: 10.1515/jib-2014-242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Summary The rapid and cost-effective identification of bacterial species is crucial, especially for clinical diagnosis and treatment. Peptide aptamers have been shown to be valuable for use as a component of novel, direct detection methods. These small peptides have a number of advantages over antibodies, including greater specificity and longer shelf life. These properties facilitate their use as the detector components of biosensor devices. However, the identification of suitable aptamer targets for particular groups of organisms is challenging. We present a semi-automated processing pipeline for the identification of candidate aptamer targets from whole bacterial genome sequences. The pipeline can be configured to search for protein sequence fragments that uniquely identify a set of strains of interest. The system is also capable of identifying additional organisms that may be of interest due to their possession of protein fragments in common with the initial set. Through the use of Cloud computing technology and distributed databases, our system is capable of scaling with the rapidly growing genome repositories, and consequently of keeping the resulting data sets up-to-date. The system described is also more generically applicable to the discovery of specific targets for other diagnostic approaches such as DNA probes, PCR primers and antibodies.
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Affiliation(s)
- Keith Flanagan
- 1School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom of Great Britain and Northern Ireland
| | - Simon Cockell
- 2Bioinformatics Support Unit, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom of Great Britain and Northern Ireland
| | - Colin Harwood
- 3Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom of Great Britain and Northern Ireland
| | - Jennifer Hallinan
- 1School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom of Great Britain and Northern Ireland
| | - Sirintra Nakjang
- 3Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom of Great Britain and Northern Ireland
| | - Beth Lawry
- 1School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom of Great Britain and Northern Ireland
| | - Anil Wipat
- 1School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom of Great Britain and Northern Ireland
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Werner A, Cockell S, Falconer J, Carlile M, Alnumeir S, Robinson J. Contribution of natural antisense transcription to an endogenous siRNA signature in human cells. BMC Genomics 2014; 15:19. [PMID: 24410956 PMCID: PMC3898206 DOI: 10.1186/1471-2164-15-19] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 12/15/2013] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Eukaryotic cells express a complex layer of noncoding RNAs. An intriguing family of regulatory RNAs includes transcripts from the opposite strand of protein coding genes, so called natural antisense transcripts (NATs). Here, we test the hypothesis that antisense transcription triggers RNA interference and gives rise to endogenous short RNAs (endo-siRNAs). RESULTS We used cloned human embryonic kidney cells (HEK293) followed by short RNAseq to investigate the small genic RNA transcriptome. 378 genes gave rise to short RNA reads that mapped to exons of RefSeq genes. The length profile of short RNAs showed a broad peak of 20-24 nucleotides, indicative of endo-siRNAs. Collapsed reads mapped predominantly to the first and the last exon of genes (74%). RNAs reads were intersected with sequences occupied by RNAPII or bound to Argonaute (AGO1 by crosslinking, ligation, and sequencing of hybrids, CLASH). In the first exon, 94% of the reads correlated with RNAPII occupancy with an average density of 130 (relative units); this decreased to 65%/20 in middle exons and 54%/12 in the last exon. CLASH reads mapping to multi-exon genes showed little distribution bias with an average of about 5 CLASH reads overlapping with 60% of the endo-siRNA reads. However, endo-siRNAs (21-25 nt) intersecting with CLASH reads were enriched at the 5'end and decreased towards the 3'end.We then investigated the 378 genes with particular focus on features indicative for short RNA production; however, found that endo-siRNA numbers did not correlate with gene structures that favor convergent transcription. In contrast, our gene set was found notably over-represented in the NATsDB sense/antisense group as compared to non-overlapping and non-bidirectional groups. Moreover, read counts showed no correlation with the steady-state levels of the related mRNAs and the pattern of endo-siRNAs proved reproducible after an induced mutagenic insult. CONCLUSIONS Our results suggest that antisense transcripts contribute to low levels of endo-siRNAs in fully differentiated human cells. A characteristic endo-siRNA footprint is being produced at sites of RNAPII transcription which is also related to AGO1. This endo-siRNA signature represents an intriguing finding and its reproducibility suggests that the production of endo-siRNAs is a regulated process with potential homoeostatic impact.
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Affiliation(s)
- Andreas Werner
- RNA Biology Group, Institute of Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle NE2 4HH, UK.
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Nesbitt V, Pitceathly R, Cockell S, Poulton J, Rahman S, Hanna M, Taylor R, Chinnery P, Turnbull D, McFarland R. THE MEDICAL RESEARCH COUNCIL NEUROMUSCULAR CENTRE FOR TRANSLATIONAL RESEARCH MITOCHONDRIAL DISEASE PATIENT COHORT STUDY UK: FROM CONCEPTUALISATION TO UTILISATION. J Neurol Neurosurg Psychiatry 2013. [DOI: 10.1136/jnnp-2013-306573.69] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Young Q, Cockell S, Cannon C. N004 A Practical Tool for Addressing Psychological Distress. Can J Cardiol 2012. [DOI: 10.1016/j.cjca.2012.07.750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Nesbitt V, Pitceathly R, Cockell S, Poulton J, Rahman S, Hanna M, Turnbull D, McFarland R. P63 The medical research council neuromuscular centre for translational research mitochondrial disease patient cohort study UK: from conceptualisation to utilisation. Neuromuscul Disord 2012. [DOI: 10.1016/s0960-8966(12)70071-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Kaan A, Young QR, Cockell S, Mackay M. 440: Emotional Experiences of Caregivers of Patients Discharged on Ventricular Assist Device (EECVAD). J Heart Lung Transplant 2009. [DOI: 10.1016/j.healun.2008.11.447] [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: 10/21/2022] Open
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