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Lucena MI, Villanueva-Paz M, Alvarez-Alvarez I, Aithal GP, Björnsson ES, Cakan-Akdogan G, Cubero FJ, Esteves F, Falcon-Perez JM, Fromenty B, Garcia-Ruiz C, Grove JI, Konu O, Kranendonk M, Kullak-Ublick GA, Miranda JP, Remesal-Doblado A, Sancho-Bru P, Nelson L, Andrade RJ, Daly AK, Fernandez-Checa JC. Roadmap to DILI research in Europe. A proposal from COST action ProEuroDILINet. Pharmacol Res 2024; 200:107046. [PMID: 38159783 DOI: 10.1016/j.phrs.2023.107046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
In the current article the aims for a constructive way forward in Drug-Induced Liver Injury (DILI) are to highlight the most important priorities in research and clinical science, therefore supporting a more informed, focused, and better funded future for European DILI research. This Roadmap aims to identify key challenges, define a shared vision across all stakeholders for the opportunities to overcome these challenges and propose a high-quality research program to achieve progress on the prediction, prevention, diagnosis and management of this condition and impact on healthcare practice in the field of DILI. This will involve 1. Creation of a database encompassing optimised case report form for prospectively identified DILI cases with well-characterised controls with competing diagnoses, biological samples, and imaging data; 2. Establishing of preclinical models to improve the assessment and prediction of hepatotoxicity in humans to guide future drug safety testing; 3. Emphasis on implementation science and 4. Enhanced collaboration between drug-developers, clinicians and regulatory scientists. This proposed operational framework will advance DILI research and may bring together basic, applied, translational and clinical research in DILI.
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Affiliation(s)
- M I Lucena
- Servicios de Aparato Digestivo y Farmacología Clínica, Hospital Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Universidad de Málaga, Málaga, Spain; Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Plataforma de Investigación Clínica y Ensayos Clínicos UICEC-IBIMA, Plataforma ISCIII de Investigación Clínica, Madrid, Spain.
| | - M Villanueva-Paz
- Servicios de Aparato Digestivo y Farmacología Clínica, Hospital Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Universidad de Málaga, Málaga, Spain; Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - I Alvarez-Alvarez
- Servicios de Aparato Digestivo y Farmacología Clínica, Hospital Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Universidad de Málaga, Málaga, Spain; Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - G P Aithal
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, United Kingdom; NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, United Kingdom
| | - E S Björnsson
- Faculty of Medicine, University of Iceland, Department of Gastroenterology and Hepatology, Landspitali University Hospital, Reykjavik, Iceland
| | - G Cakan-Akdogan
- Izmir Biomedicine and Genome Center, Izmir, Turkey. Department of Medical Biology, Faculty of Medicine, Dokuz Eylül University, Izmir, Turkey
| | - F J Cubero
- Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Department of Immunology, Ophthalmology and ORL, Complutense University School of Medicine, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - F Esteves
- Center for Toxicogenomics and Human Health (ToxOmics), NMS | FCM, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - J M Falcon-Perez
- Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, 48160, Spain. IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia 48009, Spain
| | - B Fromenty
- INSERM, Univ Rennes, INRAE, Institut NUMECAN (Nutrition Metabolisms and Cancer) UMR_A 1341, UMR_S 1317, F-35000 Rennes, France
| | - C Garcia-Ruiz
- Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. University of Barcelona, Barcelona, Spain; Department of Cell Death and Proliferation, Institute of Biomedical Research of Barcelona (IIBB), CSIC, Barcelona, Spain
| | - J I Grove
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, United Kingdom; NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, United Kingdom
| | - O Konu
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara, Turkey; Interdisciplinary Neuroscience Program, Bilkent University, Ankara, Turkey; UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, Ankara, Turkey
| | - M Kranendonk
- Center for Toxicogenomics and Human Health (ToxOmics), NMS | FCM, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - G A Kullak-Ublick
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zurich, Zurich, Switzerland; CMO & Patient Safety, Global Drug Development, Novartis Pharma, Basel, Switzerland
| | - J P Miranda
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - A Remesal-Doblado
- Servicios de Aparato Digestivo y Farmacología Clínica, Hospital Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Universidad de Málaga, Málaga, Spain
| | - P Sancho-Bru
- Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. University of Barcelona, Barcelona, Spain
| | - L Nelson
- Institute for Bioengineering, School of Engineering, Faraday Building, The University of Edinburgh, Scotland, UK
| | - R J Andrade
- Servicios de Aparato Digestivo y Farmacología Clínica, Hospital Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Universidad de Málaga, Málaga, Spain; Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - A K Daly
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - J C Fernandez-Checa
- Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. University of Barcelona, Barcelona, Spain; Department of Cell Death and Proliferation, Institute of Biomedical Research of Barcelona (IIBB), CSIC, Barcelona, Spain; Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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Astbury S, Baskar A, Grove JI, Kaye P, Aravinthan AD, James MW, Clarke C, Aithal GP, Venkatachalapathy SV. Next-generation sequencing of pancreatic cyst wall specimens obtained using micro-forceps for improving diagnostic accuracy. Endosc Int Open 2023; 11:E983-E991. [PMID: 37941539 PMCID: PMC10629470 DOI: 10.1055/a-2163-8805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/15/2023] [Indexed: 11/10/2023] Open
Abstract
Background and study aims Pancreatic cysts are common incidental findings, with an estimated prevalence of 13% to 15% in imaging done for other reasons. Diagnosis often relies on collection of cyst fluid, but tissue sampling using micro-forceps may allow for a more reliable diagnosis and higher yield of DNA for next-generation sequencing (NGS). The primary aim was to assess the performance of NGS in identifying mucinous cyst. The secondary aims were to assess DNA yield between the cyst fluid and cyst wall tissue, complication rate and performance of conventional investigations. Patients and methods Twenty-four patients referred for endoscopic ultrasound were recruited. Biopsies were taken using micro-forceps and the AmpliSeq Cancer Hotspot panel was used for NGS, a polymerase chain reaction assay targeting several hotspots within 50 genes, including GNAS , KRAS and VHL . Results The concentration of DNA extracted from 24 cyst wall samples was significantly higher than in the nine of 24 available matched cyst fluid samples. The sensitivity, specificity, and diagnostic accuracy of NGS for diagnosing mucinous cyst were 93%, 50% and 84%; for standard of care, they were -66.6%, 50% and 63.1%; and for standard of care with NGS, they were 100%, 50%, and 89.4% respectively. Cyst wall biopsy was able to diagnose 19 of 24 cysts (4 high risk, 7 intraductal papillary mucinous neoplasms, 4 cysts of mucinous origin, and 4 benign). Conclusions NGS data correlate well with histology and may aid in diagnosis and risk stratification of pancreatic cysts. Cyst wall biopsy performs well in diagnosing cysts but was inadequate in five of 24 patients.
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Affiliation(s)
- Stuart Astbury
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Aishwarya Baskar
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
| | - Jane I. Grove
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Philip Kaye
- Department of Pathology, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Aloysious D. Aravinthan
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Martin W. James
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Christopher Clarke
- Department of Radiology, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Guruprasad P. Aithal
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Suresh Vasan Venkatachalapathy
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
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Grove JI, Stephens C, Lucena MI, Andrade RJ, Weber S, Gerbes A, Bjornsson ES, Stirnimann G, Daly AK, Hackl M, Khamina-Kotisch K, Marin JJG, Monte MJ, Paciga SA, Lingaya M, Forootan SS, Goldring CEP, Poetz O, Lombaard R, Stege A, Bjorrnsson HK, Robles-Diaz M, Li D, Tran TDB, Ramaiah SK, Samodelov SL, Kullak-Ublick GA, Aithal GP. Study design for development of novel safety biomarkers of drug-induced liver injury by the translational safety biomarker pipeline (TransBioLine) consortium: a study protocol for a nested case-control study. Diagn Progn Res 2023; 7:18. [PMID: 37697410 PMCID: PMC10496294 DOI: 10.1186/s41512-023-00155-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/08/2023] [Indexed: 09/13/2023] Open
Abstract
A lack of biomarkers that detect drug-induced liver injury (DILI) accurately continues to hinder early- and late-stage drug development and remains a challenge in clinical practice. The Innovative Medicines Initiative's TransBioLine consortium comprising academic and industry partners is developing a prospective repository of deeply phenotyped cases and controls with biological samples during liver injury progression to facilitate biomarker discovery, evaluation, validation and qualification.In a nested case-control design, patients who meet one of these criteria, alanine transaminase (ALT) ≥ 5 × the upper limit of normal (ULN), alkaline phosphatase ≥ 2 × ULN or ALT ≥ 3 ULN with total bilirubin > 2 × ULN, are enrolled. After completed clinical investigations, Roussel Uclaf Causality Assessment and expert panel review are used to adjudicate episodes as DILI or alternative liver diseases (acute non-DILI controls). Two blood samples are taken: at recruitment and follow-up. Sample size is as follows: 300 cases of DILI and 130 acute non-DILI controls. Additional cross-sectional cohorts (1 visit) are as follows: Healthy volunteers (n = 120), controls with chronic alcohol-related or non-alcoholic fatty liver disease (n = 100 each) and patients with psoriasis or rheumatoid arthritis (n = 100, 50 treated with methotrexate) are enrolled. Candidate biomarkers prioritised for evaluation include osteopontin, glutamate dehydrogenase, cytokeratin-18 (full length and caspase cleaved), macrophage-colony-stimulating factor 1 receptor and high mobility group protein B1 as well as bile acids, sphingolipids and microRNAs. The TransBioLine project is enabling biomarker discovery and validation that could improve detection, diagnostic accuracy and prognostication of DILI in premarketing clinical trials and for clinical healthcare application.
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Affiliation(s)
- Jane I Grove
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Camilla Stephens
- Servicios de Aparato Digestivo Y Farmacologia Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA Plataforma Bionand, Hospital Universitario Virgen de La Victoria, Universidad de Málaga, Malaga, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas Y Digestivas (CIBERehd), Madrid, Spain
| | - M Isabel Lucena
- Servicios de Aparato Digestivo Y Farmacologia Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA Plataforma Bionand, Hospital Universitario Virgen de La Victoria, Universidad de Málaga, Malaga, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas Y Digestivas (CIBERehd), Madrid, Spain
| | - Raúl J Andrade
- Servicios de Aparato Digestivo Y Farmacologia Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA Plataforma Bionand, Hospital Universitario Virgen de La Victoria, Universidad de Málaga, Malaga, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas Y Digestivas (CIBERehd), Madrid, Spain
| | - Sabine Weber
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Alexander Gerbes
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Einar S Bjornsson
- Department of Gastroenterology, Landspitali University Hospital Reykjavik, University of Iceland, Reykjavík, Iceland
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Guido Stirnimann
- University Clinic for Visceral Surgery and Medicine, University Hospital Inselspital and University of Bern, Bern, Switzerland
| | - Ann K Daly
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, NE2 4HH, UK
| | | | | | - Jose J G Marin
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas Y Digestivas (CIBERehd), Madrid, Spain
- Experimental Hepatology and Drug Targeting (HEVEPHARM), Institute of Biomedical Research of Salamanca (IBSAL), University of Salamanca, Salamanca, Spain
| | - Maria J Monte
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas Y Digestivas (CIBERehd), Madrid, Spain
- Experimental Hepatology and Drug Targeting (HEVEPHARM), Institute of Biomedical Research of Salamanca (IBSAL), University of Salamanca, Salamanca, Spain
| | - Sara A Paciga
- Worldwide Research Development and Medical, Pfizer, NY, USA
| | - Melanie Lingaya
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Shiva S Forootan
- Centre for Drug Safety Science, University of Liverpool, Liverpool, UK
| | | | | | - Rudolf Lombaard
- ABX-CRO Advanced Pharmaceutical Services, Forschungsgesellschaft mbH, Cape Town, 7441, South Africa
| | - Alexandra Stege
- Charité-Universitätsmedizin Berlin, Central Biobank Charité (ZeBanC), Berlin, Germany
| | - Helgi K Bjorrnsson
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Mercedes Robles-Diaz
- Servicios de Aparato Digestivo Y Farmacologia Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA Plataforma Bionand, Hospital Universitario Virgen de La Victoria, Universidad de Málaga, Malaga, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas Y Digestivas (CIBERehd), Madrid, Spain
| | - Dingzhou Li
- Worldwide Research Development and Medical, Pfizer, NY, USA
| | | | | | - Sophia L Samodelov
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zurich, 8006, Zurich, Switzerland
| | - Gerd A Kullak-Ublick
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zurich, 8006, Zurich, Switzerland
- Mechanistic Safety, CMO & Patient Safety, Global Drug Development, Novartis Pharma, 4056, Basel, Switzerland
| | - Guruprasad P Aithal
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK.
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK.
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Lønsmann I, Grove JI, Haider A, Kaye P, Karsdal MA, Leeming DJ, Aithal GP. Biomarkers of Type IV Collagen Turnover Reflect Disease Activity in Patients with Early-Stage Non-Alcoholic Fatty Liver (NAFL). Biology (Basel) 2023; 12:1087. [PMID: 37626973 PMCID: PMC10451710 DOI: 10.3390/biology12081087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023]
Abstract
BACKGROUND Identification of progressive liver disease necessitates the finding of novel non-invasive methods to identify and monitor patients in need of early intervention. Investigating patients with early-liver injury may help identify unique biomarkers. Early-liver injury is characterized by remodeling of the hepatocyte basement membrane (BM) of the extracellular matrix. Thus, we quantified biomarkers targeting two distinct neo-epitopes of the major BM collagen, type IV collagen (PRO-C4 and C4M), in patients spanning the non-alcoholic fatty liver disease (NAFLD) spectrum. METHODS We evaluated PRO-C4 and C4M in a cross-sectional study with 97 patients with NAFLD confirmed on histology. Serological levels of PRO-C4 and C4M were quantified using validated competitive enzyme-linked immunosorbent assays (ELISA). Using the fatty liver inhibition of progression (FLIP) algorithm, we stratified patients into two groups: non-alcoholic fatty liver (NAFL) and non-alcoholic steatohepatitis (NASH). Biomarker levels were investigated in the two groups in patients stratified by the NAFLD activity score (NAS). In both groups, biomarker measurements were analyzed in relation to histological scorings of steatosis, inflammation, ballooning, and fibrosis. RESULTS Patients had a body mass index (BMI) of 30.9 ± 5.6 kg/m2, age of 53 ± 13 years and a NAS range of 1-8. Upon stratification by FLIP, the NASH patients had higher platelets, ALT, and AST levels than the NAFL group. Both PRO-C4 (p = 0.0125) and C4M (p = 0.003) increased with increasing NAS solely within the NAFL group; however, a large variability was present in the NASH group. Furthermore, both markers were significantly associated with lobular inflammation (p = 0.020 and p = 0.048) and steatosis (p = 0.004 and p = 0.015) in patients with NAFL. CONCLUSIONS This study found that type IV collagen turnover increased with the increase in NAS in patients with NAFL; however, this was not the case in patients with NASH. These findings support the assessments of the BM turnover using biomarkers in patients with early-disease development. These biomarkers may be used to track specific processes involved in the early pathobiology of NAFL.
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Affiliation(s)
- Ida Lønsmann
- Nordic Bioscience Biomarkers and Research A/S, 2730 Herlev, Denmark
- Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, 5000 Odense, Denmark
| | - Jane I. Grove
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, University of Nottingham, Nottingham NG7 2UH, UK
- MRC/EPSRC Nottingham Molecular Pathology Node, University of Nottingham, Nottingham NG7 2UH, UK
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
| | - Asma Haider
- Department of Pathology, Nottingham University Hospitals NHS Trust, Nottingham NG7 2UH, UK
| | - Philip Kaye
- Department of Pathology, Nottingham University Hospitals NHS Trust, Nottingham NG7 2UH, UK
| | | | - Diana J. Leeming
- Nordic Bioscience Biomarkers and Research A/S, 2730 Herlev, Denmark
| | - Guruprasad P. Aithal
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, University of Nottingham, Nottingham NG7 2UH, UK
- MRC/EPSRC Nottingham Molecular Pathology Node, University of Nottingham, Nottingham NG7 2UH, UK
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
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Grove JI, Lo PC, Shrine N, Barwell J, Wain LV, Tobin MD, Salter AM, Borkar AN, Cuevas-Ocaña S, Bennett N, John C, Ntalla I, Jones GE, Neal CP, Thomas MG, Kuht H, Gupta P, Vemala VM, Grant A, Adewoye AB, Shenoy KT, Balakumaran LK, Hollox EJ, Hannan NR, Aithal GP. Identification and characterisation of a rare MTTP variant underlying hereditary non-alcoholic fatty liver disease. JHEP Rep 2023; 5:100764. [PMID: 37484212 PMCID: PMC10362796 DOI: 10.1016/j.jhepr.2023.100764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/28/2023] [Accepted: 04/11/2023] [Indexed: 07/25/2023] Open
Abstract
Background & Aims Non-alcoholic fatty liver disease (NAFLD) is a complex trait with an estimated prevalence of 25% globally. We aimed to identify the genetic variant underlying a four-generation family with progressive NAFLD leading to cirrhosis, decompensation, and development of hepatocellular carcinoma in the absence of common risk factors such as obesity and type 2 diabetes. Methods Exome sequencing and genome comparisons were used to identify the likely causal variant. We extensively characterised the clinical phenotype and post-prandial metabolic responses of family members with the identified novel variant in comparison with healthy non-carriers and wild-type patients with NAFLD. Variant-expressing hepatocyte-like cells (HLCs) were derived from human-induced pluripotent stem cells generated from homozygous donor skin fibroblasts and restored to wild-type using CRISPR-Cas9. The phenotype was assessed using imaging, targeted RNA analysis, and molecular expression arrays. Results We identified a rare causal variant c.1691T>C p.I564T (rs745447480) in MTTP, encoding microsomal triglyceride transfer protein (MTP), associated with progressive NAFLD, unrelated to metabolic syndrome and without characteristic features of abetalipoproteinaemia. HLCs derived from a homozygote donor had significantly lower MTP activity and lower lipoprotein ApoB secretion than wild-type cells, while having similar levels of MTP mRNA and protein. Cytoplasmic triglyceride accumulation in HLCs triggered endoplasmic reticulum stress, secretion of pro-inflammatory mediators, and production of reactive oxygen species. Conclusions We have identified and characterised a rare causal variant in MTTP, and homozygosity for MTTP p.I564T is associated with progressive NAFLD without any other manifestations of abetalipoproteinaemia. Our findings provide insights into mechanisms driving progressive NAFLD. Impact and Implications A rare genetic variant in the gene MTTP has been identified as responsible for the development of severe non-alcoholic fatty liver disease in a four-generation family with no typical disease risk factors. A cell line culture created harbouring this variant gene was characterised to understand how this genetic variation leads to a defect in liver cells, which results in accumulation of fat and processes that promote disease. This is now a useful model for studying the disease pathways and to discover new ways to treat common types of fatty liver disease.
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Affiliation(s)
- Jane I. Grove
- National Institute of Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust & University of Nottingham, Nottingham, UK
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
| | - Peggy C.K. Lo
- Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
- University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Nick Shrine
- Genetic Epidemiology Group, Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Julian Barwell
- Clinical Genetics Department, University Hospitals Leicester NHS Trust, Leicester, UK
| | - Louise V. Wain
- Genetic Epidemiology Group, Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Martin D. Tobin
- Genetic Epidemiology Group, Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | | | - Aditi N. Borkar
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Sara Cuevas-Ocaña
- Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
- University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Neil Bennett
- Genetic Epidemiology Group, Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Catherine John
- Genetic Epidemiology Group, Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Ioanna Ntalla
- Clinical Genetics Department, University Hospitals Leicester NHS Trust, Leicester, UK
| | - Gabriela E. Jones
- Clinical Genetics Department, University Hospitals Leicester NHS Trust, Leicester, UK
| | | | - Mervyn G. Thomas
- Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK
| | - Helen Kuht
- Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK
| | - Pankaj Gupta
- Department of Chemical Pathology and Metabolic Diseases, University Hospitals of Leicester NHS Trust, Leicester, UK
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Vishwaraj M. Vemala
- Department of Gastroenterology, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Allister Grant
- Department of Gastroenterology, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Adeolu B. Adewoye
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | | | - Edward J. Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Nicholas R.F. Hannan
- Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
- University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Guruprasad P. Aithal
- National Institute of Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust & University of Nottingham, Nottingham, UK
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
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Nielsen MJ, Dolman GE, Harris R, Frederiksen P, Chalmers J, Grove JI, Irving WL, Karsdal MA, Patel K, Leeming DJ, Guha IN. PRO-C3 is a predictor of clinical outcomes in distinct cohorts of patients with advanced liver disease. JHEP Rep 2023; 5:100743. [PMID: 37284140 PMCID: PMC10240276 DOI: 10.1016/j.jhepr.2023.100743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/24/2023] [Accepted: 03/15/2023] [Indexed: 06/08/2023] Open
Abstract
Background & Aims Fibroblast activity is a key feature of fibrosis progression and organ function loss, leading to liver-related complications and mortality. The fibrogenesis marker, PRO-C3, has been shown to have prognostic significance in relation to fibrosis progression and as a treatment efficacy marker. We investigated whether PRO-C3 was prognostic for clinical outcome and mortality in two distinct cohorts of compensated cirrhosis. Methods Cohort 1 was a rapid fibrosis progression cohort including 104 patients with HCV and biopsy-proven Ishak fibrosis stage ≥3 without prior clinical events. Cohort 2 was a prospective cohort including 172 patients with compensated cirrhosis of mixed aetiology. Patients were assessed for clinical outcomes. PRO-C3 was assessed in serum at baseline in cohorts 1 and 2, and compared with model for end-stage liver disease and albumin-bilirubin (ALBI) scores. Results In cohort 1, a 2-fold increase in PRO-C3 was associated with 2.7-fold increased hazard of liver-related events (95% CI 1.6-4.6), whereas a one unit increase in ALBI score was associated with a 6.5-fold increased hazard (95% CI 2.9-14.6). In cohort 2, a 2-fold increase in PRO-C3 was associated with a 2.7-fold increased hazard (95% CI 1.8-3.9), whereas a one unit increase in ALBI score was associated with a 6.3-fold increased hazard (95% CI 3.0-13.2). A multivariable Cox regression analysis identified PRO-C3 and ALBI as being independently associated with the hazard of liver-related outcomes. Conclusions PRO-C3 and ALBI were independent prognostic factors for predicting liver-related clinical outcomes. Understanding the dynamic range of PRO-C3 might enhance its use for both drug development and clinical practice. Impact and Implications We tested novel proteins of liver scarring (PRO-C3) in two groups of liver patients with advanced disease to see if they could predict clinical events. We found that this marker and an established test called ALBI were both independently associated with future liver-related clinical outcomes.
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Affiliation(s)
| | - Grace E. Dolman
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Rebecca Harris
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | | | - Jane Chalmers
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Jane I. Grove
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - William L. Irving
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | - Keyur Patel
- Division of Gastroenterology and Hepatology, University of Toronto Health Network, Toronto, ON, Canada
| | | | - Indra Neil Guha
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
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7
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Nicoletti P, Dellinger A, Li YJ, Barnhart HX, Chalasani N, Fontana RJ, Odin JA, Serrano J, Stolz A, Etheridge AS, Innocenti F, Govaere O, Grove JI, Stephens C, Aithal GP, Andrade RJ, Bjornsson ES, Daly AK, Lucena MI, Watkins PB. Identification of Reduced ERAP2 Expression and a Novel HLA Allele as Components of a Risk Score for Susceptibility to Liver Injury Due to Amoxicillin-Clavulanate. Gastroenterology 2023; 164:454-466. [PMID: 36496055 PMCID: PMC9974860 DOI: 10.1053/j.gastro.2022.11.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 11/21/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023]
Abstract
BACKGROUND & AIMS Drug-induced liver injury (DILI) due to amoxicillin-clavulanate (AC) has been associated with HLA-A∗02:01, HLA-DRB1∗15:01, and rs2476601, a missense variant in PTPN22. The aim of this study was to identify novel risk factors for AC-DILI and to construct a genetic risk score (GRS). METHODS Transcriptome-wide association study and genome-wide association study analyses were performed on 444 AC-DILI cases and 10,397 population-based controls of European descent. Associations were confirmed in a validation cohort (n = 133 cases and 17,836 population-based controls). Discovery and validation AC-DILI cases were also compared with 1358 and 403 non-AC-DILI cases. RESULTS Transcriptome-wide association study revealed a significant association of AC-DILI risk with reduced liver expression of ERAP2 (P = 3.7 × 10-7), coding for an aminopeptidase involved in antigen presentation. The lead eQTL single nucleotide polymorphism, rs1363907 (G), was associated with AC-DILI risk in the discovery (odds ratio [OR], 1.68; 95% CI, 1.23-1.66; P = 1.7 × 10-7) and validation cohorts (OR, 1.2; 95% CI, 1.04-2.05; P = .03), following a recessive model. We also identified HLA-B∗15:18 as a novel AC-DILI risk factor in both discovery (OR, 4.19; 95% CI, 2.09-8.36; P = 4.9 × 10-5) and validation (OR, 7.78; 95% CI, 2.75-21.99; P = .0001) cohorts. GRS, incorporating rs1363907, rs2476601, HLA-B∗15:18, HLA-A∗02:01, and HLA-DRB1∗15:01, was highly predictive of AC-DILI risk when cases were analyzed against both general population and non-AC-DILI control cohorts. GRS was the most significant predictor in a regression model containing known AC-DILI clinical risk characteristics and significantly improved the predictive model. CONCLUSIONS We identified novel associations of AC-DILI risk with ERAP2 low expression and with HLA-B∗15:18. GRS based on the 5 risk variants may assist AC-DILI causality assessment and risk management.
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Affiliation(s)
- Paola Nicoletti
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Andrew Dellinger
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina
| | - Yi Ju Li
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina; Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina
| | - Huiman X Barnhart
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina; Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina
| | - Naga Chalasani
- Division of Gastroenterology and Hepatology, Indiana University School of Medicine, Indianapolis, Indiana
| | | | - Joseph A Odin
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jose Serrano
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland
| | - Andrew Stolz
- University of Southern California, Los Angeles, California
| | - Amy S Etheridge
- University of North Carolina Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Federico Innocenti
- University of North Carolina Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Olivier Govaere
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jane I Grove
- Nottingham Digestive Diseases Centre and National Institute for Health Research Nottingham Biomedical Research Centre at the Nottingham University Hospital National Health Service Trust, Nottingham, United Kingdom; University of Nottingham, Nottingham, United Kingdom
| | - Camilla Stephens
- Servicios de Digestivo y Farmacologia Clínica, Instituto de Investigación Biomédica de Málaga (IBIMA_Plataforma Bionand), Hospital Universitario Virgen de la Victoria, Universidad de Málaga, Málaga, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Guruprasad P Aithal
- Nottingham Digestive Diseases Centre and National Institute for Health Research Nottingham Biomedical Research Centre at the Nottingham University Hospital National Health Service Trust, Nottingham, United Kingdom; University of Nottingham, Nottingham, United Kingdom
| | - Raul J Andrade
- Servicios de Digestivo y Farmacologia Clínica, Instituto de Investigación Biomédica de Málaga (IBIMA_Plataforma Bionand), Hospital Universitario Virgen de la Victoria, Universidad de Málaga, Málaga, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Einar S Bjornsson
- Department of Internal Medicine, Landspitali University Hospital, Reykjavik, Iceland; Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Ann K Daly
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - M Isabel Lucena
- Servicios de Digestivo y Farmacologia Clínica, Instituto de Investigación Biomédica de Málaga (IBIMA_Plataforma Bionand), Hospital Universitario Virgen de la Victoria, Universidad de Málaga, Málaga, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Paul B Watkins
- University of North Carolina Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; University of North Carolina Institute for Drug Safety Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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8
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Björnsson ES, Stephens C, Atallah E, Robles‐Diaz M, Alvarez‐Alvarez I, Gerbes A, Weber S, Stirnimann G, Kullak‐Ublick G, Cortez‐Pinto H, Grove JI, Lucena MI, Andrade RJ, Aithal GP. A new framework for advancing in drug-induced liver injury research. The Prospective European DILI Registry. Liver Int 2023; 43:115-126. [PMID: 35899490 PMCID: PMC7614006 DOI: 10.1111/liv.15378] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/10/2022] [Accepted: 07/27/2022] [Indexed: 01/04/2023]
Abstract
BACKGROUND & AIMS No multi-national prospective study of drug-induced liver injury (DILI) has originated in Europe. The design of a prospective European DILI registry, clinical features and short-term outcomes of the cases and controls is reported. METHODS Patients with suspected DILI were prospectively enrolled in the United Kingdom, Spain, Germany, Switzerland, Portugal and Iceland, 2016-2021. DILI cases or non-DILI acute liver injury controls following causality assessment were enrolled. RESULTS Of 446 adjudicated patients, 246 DILI patients and 100 had acute liver injury due to other aetiologies, mostly autoimmune hepatitis (n = 42) and viral hepatitis (n = 34). DILI patients (mean age 56 years), 57% women, 60% with jaundice and 3.6% had pre-existing liver disease. DILI cases and non-DILI acute liver injury controls had similar demographics, clinical features and outcomes. A single agent was implicated in 199 (81%) DILI cases. Amoxicillin-clavulanate, flucloxacillin, atorvastatin, nivolumab/ipilimumab, infliximab and nitrofurantoin were the most commonly implicated drugs. Multiple conventional medications were implicated in 37 (15%) and 18 cases were caused by herbal and dietary supplements. The most common single causative drug classes were antibacterials (40%) and antineoplastic/immunomodulating agents (27%). Overall, 13 (5.3%) had drug-induced autoimmune-like hepatitis due to nitrofurantoin, methyldopa, infliximab, methylprednisolone and minocycline. Only six (2.4%) DILI patients died (50% had liver-related death), and another six received liver transplantation. CONCLUSIONS In this first multi-national European prospective DILI Registry study, antibacterials were the most commonly implicated medications, whereas antineoplastic and immunomodulating agents accounted for higher proportion of DILI than previously described. This European initiative provides an important opportunity to advance the study on DILI.
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Affiliation(s)
- Einar S. Björnsson
- Faculty of MedicineUniversity of IcelandReykjavíkIceland
- Department of GastroenterologyLandspitali University Hospital ReykjavikReykjavíkIceland
| | - Camilla Stephens
- Servicios de Aparato Digestivo y Farmacología ClínicaHospital Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina‐IBIMA Plataforma BIONAND, Universidad de MálagaMálagaSpain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)MadridSpain
| | - Edmond Atallah
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of MedicineUniversity of NottinghamNottinghamUK
- NIHR Nottingham Biomedical Research CentreNottingham University Hospitals NHS Trust and the University of NottinghamNottinghamUK
| | - Mercedes Robles‐Diaz
- Servicios de Aparato Digestivo y Farmacología ClínicaHospital Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina‐IBIMA Plataforma BIONAND, Universidad de MálagaMálagaSpain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)MadridSpain
| | - Ismael Alvarez‐Alvarez
- Servicios de Aparato Digestivo y Farmacología ClínicaHospital Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina‐IBIMA Plataforma BIONAND, Universidad de MálagaMálagaSpain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)MadridSpain
| | | | - Sabine Weber
- Department of Medicine IILMU Klinikum MunichMunichGermany
| | - Guido Stirnimann
- Department of Visceral Surgery and MedicineInselspital University Hospital and University of BernBernSwitzerland
| | - Gerd Kullak‐Ublick
- Department of Clinical Pharmacology and ToxicologyUniversity Hospital Zurich, University of ZurichZurichSwitzerland
| | - Helena Cortez‐Pinto
- Clínica Universitária de Gastrenterologia, Faculdade de Medicina de LisboaUniversidade de Lisboa, Centro Hospitalar Lisboa Norte, HSMLisbonPortugal
| | - Jane I. Grove
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of MedicineUniversity of NottinghamNottinghamUK
- NIHR Nottingham Biomedical Research CentreNottingham University Hospitals NHS Trust and the University of NottinghamNottinghamUK
| | - M. Isabel Lucena
- Servicios de Aparato Digestivo y Farmacología ClínicaHospital Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina‐IBIMA Plataforma BIONAND, Universidad de MálagaMálagaSpain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)MadridSpain
| | - Raul J. Andrade
- Servicios de Aparato Digestivo y Farmacología ClínicaHospital Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina‐IBIMA Plataforma BIONAND, Universidad de MálagaMálagaSpain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)MadridSpain
| | - Guruprasad P. Aithal
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of MedicineUniversity of NottinghamNottinghamUK
- NIHR Nottingham Biomedical Research CentreNottingham University Hospitals NHS Trust and the University of NottinghamNottinghamUK
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9
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Vijay A, Al-Awadi A, Chalmers J, Balakumaran L, Grove JI, Valdes AM, Taylor MA, Shenoy KT, Aithal GP. Development of Food Group Tree-Based Analysis and Its Association with Non-Alcoholic Fatty Liver Disease (NAFLD) and Co-Morbidities in a South Indian Population: A Large Case-Control Study. Nutrients 2022; 14:nu14142808. [PMID: 35889764 PMCID: PMC9322963 DOI: 10.3390/nu14142808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD) is a global problem growing in parallel to the epidemics of obesity and diabetes, with South Asians being particularly susceptible. Nutrition and behaviour are important modifiers of the disease; however, studies to date have only described dietary patterns and nutrients associated with susceptibility to NAFLD. METHODS This cross-sectional case-control study included 993 NAFLD patients and 973 healthy controls from Trivandrum (India). Dietary data was collected using a locally validated food frequency questionnaire. A tree-based classification categorised 2165 ingredients into three levels (food groups, sub-types, and cooking methods) and intakes were associated with clinical outcomes. RESULTS NAFLD patients had significantly higher consumption of refined rice, animal fat, red meat, refined sugar, and fried foods, and had lower consumption of vegetables, pulses, nuts, seeds, and milk compared to controls. The consumption of red meat, animal fat, nuts, and refined rice was positively associated with NAFLD diagnosis and the presence of fibrosis, whereas consumption of leafy vegetables, fruits, and dried pulses was negatively associated. Fried food consumption was positively associated with NAFLD, whilst boiled food consumption had a negative association. Increased consumption of animal fats was associated with diabetes, hypertension, and cardiovascular outcomes among those with NAFLD, whereas consumption of wholegrain rice was negatively associated with these clinical-related outcomes. CONCLUSIONS The tree-based approach provides the first comprehensive method of classifying food intakes to enable the identification of specific dietary factors associated with NAFLD and related clinical outcomes. This could inform culturally sensitive dietary guidelines to reduce risk of NAFLD development and/or its progression.
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Affiliation(s)
- Amrita Vijay
- Inflammation, Injury and Recovery Sciences, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK; (A.V.); (A.M.V.)
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham NG7 2UH, UK; (A.A.-A.); (J.C.); (J.I.G.)
| | - Amina Al-Awadi
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham NG7 2UH, UK; (A.A.-A.); (J.C.); (J.I.G.)
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
| | - Jane Chalmers
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham NG7 2UH, UK; (A.A.-A.); (J.C.); (J.I.G.)
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
| | - Leena Balakumaran
- Population Health Research Institute (PHRI), Trivandrum, Kerala 695011, India; (L.B.); (K.T.S.)
| | - Jane I. Grove
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham NG7 2UH, UK; (A.A.-A.); (J.C.); (J.I.G.)
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
| | - Ana M. Valdes
- Inflammation, Injury and Recovery Sciences, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK; (A.V.); (A.M.V.)
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham NG7 2UH, UK; (A.A.-A.); (J.C.); (J.I.G.)
| | - Moira A. Taylor
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2UH, UK;
| | - Kotacherry T. Shenoy
- Population Health Research Institute (PHRI), Trivandrum, Kerala 695011, India; (L.B.); (K.T.S.)
| | - Guruprasad P. Aithal
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham NG7 2UH, UK; (A.A.-A.); (J.C.); (J.I.G.)
- Nottingham Digestive Diseases Centre, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
- Correspondence: ; Tel.: +44-01158231149
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10
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Hashim A, Bremner S, Grove JI, Astbury S, Mengozzi M, O'Sullivan M, Macken L, Worthley T, Katarey D, Aithal GP, Verma S. Chronic liver disease in homeless individuals and performance of non-invasive liver fibrosis and injury markers: VALID study. Liver Int 2022; 42:628-639. [PMID: 34846794 DOI: 10.1111/liv.15122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND/AIMS Community-based assessment and management of chronic liver disease (CLD) in people who are homeless (PWAH) remain poorly described. We aimed to determine prevalence/predictors of CLD in PWAH and assess the performance of non-invasive liver fibrosis and injury markers. METHODS The Vulnerable Adult LIver Disease (VALID) study provided a "one-stop" liver service based at homeless hostels. Our primary outcome was the prevalence of clinically significant hepatic fibrosis (CSHF; liver stiffness measurement (LSM) ≥8 kPa). RESULTS Total individuals recruited were 127, mean ± SD age 47 ± 9.4 years, 50% (95% CI 41%-59%) and 39% (95% CI 31%-48%) having alcohol dependence and a positive HCV RNA respectively. CSHF was detected in 26% (95% CI 17%-35%), independent predictors being total alcohol unit/week (OR 1.01, 95% CI 1.00-1.02, P = .002) and HCV RNA positivity (OR 2.93, 95% CI 1.12-7.66, P = .029). There was moderate agreement between LSM and Enhanced Liver Fibrosis (ELF) score (kappa 0.536, P < .001) for CSHF as assessed by LSM ≥8 kPa. Those with CSHF had significantly higher levels of IFN-γ (P = .002), IL-6 (P = .001), MMP-2 (P = .006), ccCK-18 (P < .001) and ELF biomarkers (P < .001), compared to those without CSHF. Service uptake was ≥95%. Direct acting antiviral (DAA) treatment completion was 93% (95% CI 77%-99%), sustained virological response (SVR) being 83% (95% CI 64%-94%). CONCLUSION There is a significant liver disease burden from HCV and alcohol in PWAH. Non-invasive liver fibrosis and injury markers can help in identifying such individuals in the community. Despite a challenging cohort, excellent service uptake and high DAA-based SVRs can be achieved.
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Affiliation(s)
- Ahmed Hashim
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, UK.,Department of Gastroenterology and Hepatology, University Hospitals Sussex NHS Foundation Trust, Brighton, UK
| | - Stephen Bremner
- Department of Primary Care and Public Health, Brighton and Sussex Medical School, Brighton, UK
| | - Jane I Grove
- NIHR Nottingham Biomedical Research Centre, University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham, UK.,Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Stuart Astbury
- NIHR Nottingham Biomedical Research Centre, University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham, UK.,Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Manuela Mengozzi
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, UK
| | - Margaret O'Sullivan
- Department of Gastroenterology and Hepatology, University Hospitals Sussex NHS Foundation Trust, Brighton, UK
| | - Lucia Macken
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, UK.,Department of Gastroenterology and Hepatology, University Hospitals Sussex NHS Foundation Trust, Brighton, UK
| | | | - Dev Katarey
- Department of Hepatology, Royal Free Hospital, London, UK
| | - Guruprasad P Aithal
- NIHR Nottingham Biomedical Research Centre, University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham, UK.,Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Sumita Verma
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, UK.,Department of Gastroenterology and Hepatology, University Hospitals Sussex NHS Foundation Trust, Brighton, UK
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11
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Abstract
As the worldwide prevalence of chronic liver diseases is high and continuing to increase, there is an urgent need for treatment to prevent cirrhosis-related morbidity and mortality. Integrins are heterodimeric cell-surface proteins that are promising targets for therapeutic intervention. αv integrins are central in the development of fibrosis as they activate latent TGFβ, a known profibrogenic cytokine. The αv subunit can form heterodimers with β1, β3, β5, β6 or β8 subunits and one or more of these integrins are central to the development of liver fibrosis, however, their relative importance is not understood. This review summarises the current knowledge of αv integrins and their respective β subunits in different organs, with a focus on liver fibrosis and the emerging preclinical and clinical data with regards to αv integrin inhibitors.
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Affiliation(s)
- Syedia R Rahman
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK.,FRAME Alternatives Laboratory, Life Sciences, University of Nottingham Medical School, Queen's Medical Centre, Nottingham, UK.,Nottingham Digestive Diseases Centre, Translational Medical Sciences, Medicine, University of Nottingham, Nottingham, UK
| | - James A Roper
- Novel Human Genetics Research Unit, GlaxoSmithKline, Stevenage, UK
| | - Jane I Grove
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK.,Nottingham Digestive Diseases Centre, Translational Medical Sciences, Medicine, University of Nottingham, Nottingham, UK
| | - Guruprasad P Aithal
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK.,Nottingham Digestive Diseases Centre, Translational Medical Sciences, Medicine, University of Nottingham, Nottingham, UK
| | - K Tao Pun
- Novel Human Genetics Research Unit, GlaxoSmithKline, Stevenage, UK
| | - Andrew J Bennett
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK.,FRAME Alternatives Laboratory, Life Sciences, University of Nottingham Medical School, Queen's Medical Centre, Nottingham, UK.,Nottingham Digestive Diseases Centre, Translational Medical Sciences, Medicine, University of Nottingham, Nottingham, UK
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12
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Innes H, Walker AJ, Benselin J, Grove JI, Pedergnana V, Azim Ansari M, Lin SK, McLauchlan J, Hutchinson SJ, Barnes E, Irving WL, Guha IN. Comprehensive Comparative Analysis of Standard Validated, Genetic, and Novel Biomarkers to Enhance Prognostic Risk-Stratification in Patients With Hepatitis C Virus Cirrhosis. Clin Transl Gastroenterol 2022; 13:e00462. [PMID: 35142723 PMCID: PMC8963831 DOI: 10.14309/ctg.0000000000000462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/06/2021] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION Risk-stratifying patients with hepatitis C virus (HCV) cirrhosis according to medium-term prognosis will inform clinical decision-making. It is unclear which biomarkers/models are optimal for this purpose. We quantified the discriminative ability of 14 diverse biomarkers for prognosis prediction over a 4-year time. METHODS We recruited 1196 patients with HCV cirrhosis from the United Kingdom for a prospective study. Genetic risk score, collagen (e.g., PROC3), comorbidity (e.g., CirCom), and validated biomarkers from routine data were measured at enrollment. Participants were linked to UK hospital admission, cancer, and mortality registries. Primary endpoints were (i) liver-related outcomes for patients with compensated cirrhosis and (ii) all-cause mortality for decompensated cirrhosis. The discriminative ability of all biomarkers was quantified individually and also by the fraction of new prognostic information provided. RESULTS At enrollment, 289 (24%) and 907 (76%) had decompensated and compensated cirrhosis, respectively. Participants were followed for 3-4 years on average, with >70% of the follow-up time occurring post-HCV cure. Seventy-five deaths in the decompensated subgroup and 98 liver-related outcomes in the compensated subgroup were reported. The discriminative ability of the albumin-bilirubin-fibrosis-4 index (C-index: 0.71-0.72) was superior to collagen biomarkers (C-index = 0.58-0.67), genetic risk scores (C-index = 0.50-0.57), and comorbidity markers (0.53-0.60). Validated biomarkers showed the greatest prognostic improvement when combined with a comorbidity or a collagen biomarker (generally >30% of new prognostic information added). DISCUSSION Inexpensive biomarkers such as the albumin-bilirubin-fibrosis-4 index predict medium-term cirrhosis prognosis moderately well and outperform collagen, genetic, and comorbidity biomarkers. Improvement of performance was greatest when a validated test was combined with comorbidity or collagen biomarker.
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Affiliation(s)
- Hamish Innes
- School of Health and Life Sciences, Glasgow Caledonian University, Glasgow, UK
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK
- Public Health Scotland, Glasgow, UK
| | - Alex J. Walker
- The DataLab, Centre for Evidence-Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK
| | - Jennifer Benselin
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Jane I. Grove
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Vincent Pedergnana
- Laboratoire MIVEGEC (UMR CNRS 5290, UR IRD 224, UM), Montpellier, France
| | - M. Azim Ansari
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the Oxford NIHR Biomedical Research Centre, Oxford University, UK
| | - Shang-Kuan Lin
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the Oxford NIHR Biomedical Research Centre, Oxford University, UK
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Sharon J. Hutchinson
- School of Health and Life Sciences, Glasgow Caledonian University, Glasgow, UK
- Public Health Scotland, Glasgow, UK
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the Oxford NIHR Biomedical Research Centre, Oxford University, UK
| | - William L. Irving
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Indra Neil Guha
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
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13
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Astbury S, Grove JI, Dorward DA, Guha IN, Fallowfield JA, Kendall TJ. Reliable computational quantification of liver fibrosis is compromised by inherent staining variation. J Pathol Clin Res 2021; 7:471-481. [PMID: 34076968 PMCID: PMC8363922 DOI: 10.1002/cjp2.227] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/31/2021] [Accepted: 05/06/2021] [Indexed: 12/22/2022]
Abstract
Biopsy remains the gold-standard measure for staging liver disease, both to inform prognosis and to assess the response to a given treatment. Semiquantitative scores such as the Ishak fibrosis score are used for evaluation. These scores are utilised in clinical trials, with the US Food and Drug Administration mandating particular scores as inclusion criteria for participants and using the change in score as evidence of treatment efficacy. There is an urgent need for improved, quantitative assessment of liver biopsies to detect small incremental changes in liver architecture over the course of a clinical trial. Artificial intelligence (AI) methods have been proposed as a way to increase the amount of information extracted from a biopsy and to potentially remove bias introduced by manual scoring. We have trained and evaluated an AI tool for measuring the amount of scarring in sections of picrosirius red-stained liver. The AI methodology was compared with both manual scoring and widely available colour space thresholding. Four sequential sections from each case were stained on two separate occasions by two independent clinical laboratories using routine protocols to study the effect of inter- and intra-laboratory staining variation on these tools. Finally, we compared these methods to second harmonic generation (SHG) imaging, a stain-free quantitative measure of collagen. Although AI methods provided a modest improvement over simpler computer-assisted measures, staining variation both within and between laboratories had a dramatic effect on quantitation, with manual assignment of scar proportion being the most consistent. Manual assessment also most strongly correlated with collagen measured by SHG. In conclusion, results suggest that computational measures of liver scarring from stained sections are compromised by inter- and intra-laboratory staining. Stain-free quantitative measurement using SHG avoids staining-related variation and may prove more accurate in detecting small changes in scarring that may occur in therapeutic trials.
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Affiliation(s)
- Stuart Astbury
- NIHR Nottingham Biomedical Research CentreNottingham University Hospitals NHS Trust and the University of NottinghamNottinghamUK
- Nottingham Digestive Diseases Centre, School of MedicineUniversity of NottinghamNottinghamUK
| | - Jane I Grove
- NIHR Nottingham Biomedical Research CentreNottingham University Hospitals NHS Trust and the University of NottinghamNottinghamUK
- Nottingham Digestive Diseases Centre, School of MedicineUniversity of NottinghamNottinghamUK
| | - David A Dorward
- University of Edinburgh Centre for Inflammation ResearchUniversity of EdinburghEdinburghUK
- Edinburgh PathologyUniversity of EdinburghEdinburghUK
| | - Indra N Guha
- NIHR Nottingham Biomedical Research CentreNottingham University Hospitals NHS Trust and the University of NottinghamNottinghamUK
- Nottingham Digestive Diseases Centre, School of MedicineUniversity of NottinghamNottinghamUK
| | - Jonathan A Fallowfield
- University of Edinburgh Centre for Inflammation ResearchUniversity of EdinburghEdinburghUK
| | - Timothy J Kendall
- University of Edinburgh Centre for Inflammation ResearchUniversity of EdinburghEdinburghUK
- Edinburgh PathologyUniversity of EdinburghEdinburghUK
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14
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Mehta O, Inbaraj LR, Astbury S, Grove JI, Norman G, Aithal GP, Valdes AM, Vijay A. Gut Microbial Profile Is Associated With Residential Settings and Not Nutritional Status in Adults in Karnataka, India. Front Nutr 2021; 8:595756. [PMID: 33708787 PMCID: PMC7940358 DOI: 10.3389/fnut.2021.595756] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Undernutrition is a leading contributor to disease and disability in people of all ages. Several studies have reported significant association between nutritional status and gut microbiome composition but other factors such as demographic settings may also influence the adult microbiome. The relationship between undernourishment and gut microbiome in adults has not been described to date. In this study, we compared the gut microbiome in fecal samples of 48 individuals, from two demographic settings (rural and urban slum) in Karnataka, India using 16S rRNA sequencing. Nutritional status was assessed based on BMI, with a BMI of < 18.5 kg/m2 classified as undernourished, and a BMI in the range 18.5–25 kg/m2 as nourished. We analyzed 25 individuals from rural settings (12 undernourished and 13 nourished) and 23 individuals from urban slum settings (11 undernourished and 12 nourished). We found no significant difference in overall gut microbial diversity (Shannon and Unweighted UniFrac) between undernourished and nourished individuals in either geographical settings, however, microbial taxa at the phylum level (i.e., Firmicutes and Proteobacteria) and beta diversity (unweighted UniFrac) differed significantly between the rural and urban slum settings. By predicting microbial function from 16S data profiling we found significant differences in metabolic pathways present in the gut microbiota from people residing in different settings; specifically, those related to carbohydrate and lipid metabolism. The weighted sum of the KEGG Orthologs associated with carbohydrate metabolism (Spearman's correlation coefficient, ρ = −0.707, p < 0.001), lipid metabolism (Spearman's correlation coefficient, ρ = −0.330, p < 0.022) and biosynthesis of secondary metabolites (Spearman's correlation coefficient, ρ = −0.507, p < 0.001) were decreased in the urban slum group compared to the rural group. In conclusion, we report that the geographical location of residence is associated with differences in gut microbiome composition in adults. We found no significant differences in microbiome composition between nourished and undernourished adults from urban slum or rural settings in India.
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Affiliation(s)
- Ojasvi Mehta
- Nottingham Digestive Diseases Center, School of Medicine, University of Nottingham, Nottingham, United Kingdom.,National Institute of Health Research (NIHR) Nottingham Biomedical Research Center, Nottingham University Hospitals National Health Service (NHS) Trust and University of Nottingham, Nottingham, United Kingdom
| | | | - Stuart Astbury
- Nottingham Digestive Diseases Center, School of Medicine, University of Nottingham, Nottingham, United Kingdom.,National Institute of Health Research (NIHR) Nottingham Biomedical Research Center, Nottingham University Hospitals National Health Service (NHS) Trust and University of Nottingham, Nottingham, United Kingdom
| | - Jane I Grove
- Nottingham Digestive Diseases Center, School of Medicine, University of Nottingham, Nottingham, United Kingdom.,National Institute of Health Research (NIHR) Nottingham Biomedical Research Center, Nottingham University Hospitals National Health Service (NHS) Trust and University of Nottingham, Nottingham, United Kingdom
| | - Gift Norman
- Department of Community Health, Bangalore Baptist Hospital, Bangalore, India
| | - Guruprasad P Aithal
- Nottingham Digestive Diseases Center, School of Medicine, University of Nottingham, Nottingham, United Kingdom.,National Institute of Health Research (NIHR) Nottingham Biomedical Research Center, Nottingham University Hospitals National Health Service (NHS) Trust and University of Nottingham, Nottingham, United Kingdom
| | - Ana M Valdes
- National Institute of Health Research (NIHR) Nottingham Biomedical Research Center, Nottingham University Hospitals National Health Service (NHS) Trust and University of Nottingham, Nottingham, United Kingdom.,Division of Rheumatology, Orthopedics and Dermatology, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Amrita Vijay
- Nottingham Digestive Diseases Center, School of Medicine, University of Nottingham, Nottingham, United Kingdom.,National Institute of Health Research (NIHR) Nottingham Biomedical Research Center, Nottingham University Hospitals National Health Service (NHS) Trust and University of Nottingham, Nottingham, United Kingdom.,Division of Rheumatology, Orthopedics and Dermatology, School of Medicine, University of Nottingham, Nottingham, United Kingdom
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15
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Scott RA, Williams HG, Hoad CL, Alyami A, Ortori CA, Grove JI, Marciani L, Moran GW, Spiller RC, Menys A, Aithal GP, Gowland PA. MR Measures of Small Bowel Wall
T2
Are Associated With Increased Permeability. J Magn Reson Imaging 2020; 53:1422-1431. [DOI: 10.1002/jmri.27463] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Affiliation(s)
- Robert A. Scott
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre at the Nottingham University Hospitals NHS Trust and University of Nottingham Nottingham UK
- Nottingham Digestive Diseases Centre University of Nottingham Nottingham UK
| | - Hannah G. Williams
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre at the Nottingham University Hospitals NHS Trust and University of Nottingham Nottingham UK
- Sir Peter Mansfield Imaging Centre, School of Physics and Astronomy University of Nottingham Nottingham UK
| | - Caroline L. Hoad
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre at the Nottingham University Hospitals NHS Trust and University of Nottingham Nottingham UK
- Sir Peter Mansfield Imaging Centre, School of Physics and Astronomy University of Nottingham Nottingham UK
| | - Ali Alyami
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre at the Nottingham University Hospitals NHS Trust and University of Nottingham Nottingham UK
| | - Catherine A. Ortori
- Centre for Analytical Bioscience, School of Pharmacy University of Nottingham Nottingham UK
| | - Jane I. Grove
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre at the Nottingham University Hospitals NHS Trust and University of Nottingham Nottingham UK
- Nottingham Digestive Diseases Centre University of Nottingham Nottingham UK
| | - Luca Marciani
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre at the Nottingham University Hospitals NHS Trust and University of Nottingham Nottingham UK
- Nottingham Digestive Diseases Centre University of Nottingham Nottingham UK
| | - Gordon W. Moran
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre at the Nottingham University Hospitals NHS Trust and University of Nottingham Nottingham UK
- Nottingham Digestive Diseases Centre University of Nottingham Nottingham UK
| | - Robin C. Spiller
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre at the Nottingham University Hospitals NHS Trust and University of Nottingham Nottingham UK
- Nottingham Digestive Diseases Centre University of Nottingham Nottingham UK
| | | | - Guruprasad P. Aithal
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre at the Nottingham University Hospitals NHS Trust and University of Nottingham Nottingham UK
- Nottingham Digestive Diseases Centre University of Nottingham Nottingham UK
| | - Penny A. Gowland
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre at the Nottingham University Hospitals NHS Trust and University of Nottingham Nottingham UK
- Sir Peter Mansfield Imaging Centre, School of Physics and Astronomy University of Nottingham Nottingham UK
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16
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Nicoletti P, Devarbhavi H, Goel A, Venkatesan R, Eapen CE, Grove JI, Zafer S, Bjornsson E, Lucena MI, Andrade RJ, Pirmohamed M, Wadelius M, Larrey D, Maitland-van der Zee AH, Ibanez L, Watkins PB, Daly AK, Aithal GP. Genetic Risk Factors in Drug-Induced Liver Injury Due to Isoniazid-Containing Antituberculosis Drug Regimens. Clin Pharmacol Ther 2020; 109:1125-1135. [PMID: 33135175 DOI: 10.1002/cpt.2100] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022]
Abstract
Drug-induced liver injury (DILI) is a complication of treatment with antituberculosis (TB) drugs, especially in isoniazid (INH)-containing regimens. To investigate genetic risk factors, we performed a genomewide association study (GWAS) involving anti-TB DILI cases (55 Indian and 70 European) and controls (1,199 Indian and 10,397 European). Most cases were treated with a standard anti-TB drug regimen; all received INH. We imputed single nucleotide polymorphism and HLA genotypes and performed trans-ethnic meta-analysis on GWAS and candidate gene genotypes. GWAS found one significant association (rs117491755) in Europeans only. For HLA, HLA-B*52:01 was significant (meta-analysis odds ratio (OR) 2.67, 95% confidence interval (CI) 1.63-4.37, P = 9.4 × 10-5 ). For N-acetyltransferase 2 (NAT2), NAT2*5 frequency was lower in cases (OR 0.69, 95% CI 0.57-0.83, P = 0.01). NAT2*6 and NAT2*7 were more common, with homozygotes for NAT2*6 and/or NAT2*7 enriched among cases (OR 1.89, 95% CI 0.84-4.22, P = 0.004). We conclude HLA genotype makes a small contribution to TB drug-related DILI and that the NAT2 contribution is complex, but consistent with previous reports when differences in the metabolic effect of NAT2*5 compared with those of NAT2*6 and NAT2*7 are considered.
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Affiliation(s)
- Paola Nicoletti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Harshad Devarbhavi
- Department of Gastroenterology, St John's Medical College Hospital, Bangalore, India
| | | | - Radha Venkatesan
- Department of Molecular Genetics, Madras Diabetes Research Foundation, Chennai, India
| | | | - Jane I Grove
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, University of Nottingham, UK.,Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Samreen Zafer
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Einar Bjornsson
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, The National University Hospital of Iceland, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - M Isabel Lucena
- UGC Digestivo y Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Universitario Virgen de la Victoria, Universidad de Málaga, Málaga, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Raul J Andrade
- UGC Digestivo y Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Universitario Virgen de la Victoria, Universidad de Málaga, Málaga, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Munir Pirmohamed
- Department of Pharmacology and Therapeutics, Liverpool University Hospitals and Liverpool Health Partners, University of Liverpool, Liverpool, UK
| | - Mia Wadelius
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Anke-Hilse Maitland-van der Zee
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, Netherlands.,Division of Pharmacoepidemiology and Clinical Pharmacology, Department of Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Luisa Ibanez
- Fundació Institut Català de Farmacologia, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Paul B Watkins
- Eshelman School of Pharmacy, University of North Carolina Institute for Drug Safety Sciences, Chapel Hill, North Carolina, USA
| | - Ann K Daly
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Guruprasad P Aithal
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, University of Nottingham, UK.,Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
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17
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Atkinson SR, Grove JI, Liebig S, Astbury S, Vergis N, Goldin R, Quaglia A, Bantel H, Guha IN, Thursz MR, Newcombe P, Strnad P, Aithal GP. In Severe Alcoholic Hepatitis, Serum Keratin-18 Fragments Are Diagnostic, Prognostic, and Theragnostic Biomarkers. Am J Gastroenterol 2020; 115:1857-1868. [PMID: 33156105 DOI: 10.14309/ajg.0000000000000912] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Up to 40% of patients with severe alcoholic hepatitis (AH) die within 6 months of presentation, making prompt diagnosis and appropriate treatment essential. We determined the associations between serum keratin-18 (K18) and histological features, prognosis, and differential response to prednisolone in patients with severe AH. METHODS Total (K18-M65) and caspase-cleaved K18 (K18-M30) were quantified in pretreatment sera from 824 patients enrolled in the Steroids or Pentoxifylline for Alcoholic Hepatitis trial (87 with suitable histological samples) and disease controls. RESULTS K18 fragments were markedly elevated in severe AH and strongly predicted steatohepatitis (alcoholic steatohepatitis) on biopsy (area under receiver operating characteristics: 0.787 and 0.807). Application of published thresholds to predict alcoholic steatohepatitis would have rendered biopsy unnecessary in 84% of all AH cases. K18-M30 and M65 were associated with 90-day mortality, independent of age and Model for End-stage Liver Disease score in untreated patients. The association for K18-M65 was independent of both age and Model for End-stage Liver Disease in prednisolone-treated patients. Modelling of the effect of prednisolone on 90-day mortality as a function of pretreatment serum K18 levels indicated benefit in those with high serum levels of K18-M30. At low pretreatment serum K18 levels, prednisolone was potentially harmful. A threshold of K18-M30 5 kIU/L predicted therapeutic benefit from prednisolone above this level (odds ratio: 0.433, 95% confidence interval: 0.19-0.95, P = 0.0398), but not below (odds ratio: 1.271, 95% confidence interval: 0.88-1.84, P = 0.199). Restricting prednisolone usage to the former group would have reduced exposure by 87%. DISCUSSION In a large cohort of patients with severe AH, serum K18 strongly correlated with histological severity, independently associated with 90-day mortality, and predicted response to prednisolone therapy. Quantification of serum K18 levels could assist in clinical decision-making.
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Affiliation(s)
| | - Jane I Grove
- NIHR Nottingham Biomedical Research Centre (BRC), Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Stephanie Liebig
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Stuart Astbury
- NIHR Nottingham Biomedical Research Centre (BRC), Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Nikhil Vergis
- Department of Hepatology, Imperial College London, London, UK
| | - Robert Goldin
- Department of Hepatology, Imperial College London, London, UK
| | - Alberto Quaglia
- Department of Cellular Pathology, Royal Free London and UCL Cancer Institute, London, UK
| | - Heike Bantel
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Indra Neil Guha
- NIHR Nottingham Biomedical Research Centre (BRC), Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Mark R Thursz
- Department of Hepatology, Imperial College London, London, UK
| | - Paul Newcombe
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Pavel Strnad
- Medical Clinic III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH Aachen, Aachen, German
| | - Guruprasad P Aithal
- NIHR Nottingham Biomedical Research Centre (BRC), Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
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18
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Stickel F, Lutz P, Buch S, Nischalke HD, Silva I, Rausch V, Fischer J, Weiss KH, Gotthardt D, Rosendahl J, Marot A, Elamly M, Krawczyk M, Casper M, Lammert F, Buckley TWM, McQuillin A, Spengler U, Eyer F, Vogel A, Marhenke S, von Felden J, Wege H, Sharma R, Atkinson S, Franke A, Nehring S, Moser V, Schafmayer C, Spahr L, Lackner C, Stauber RE, Canbay A, Link A, Valenti L, Grove JI, Aithal GP, Marquardt JU, Fateen W, Zopf S, Dufour JF, Trebicka J, Datz C, Deltenre P, Mueller S, Berg T, Hampe J, Morgan MY. Genetic Variation in HSD17B13 Reduces the Risk of Developing Cirrhosis and Hepatocellular Carcinoma in Alcohol Misusers. Hepatology 2020; 72:88-102. [PMID: 31630428 DOI: 10.1002/hep.30996] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/18/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Carriage of rs738409:G in patatin-like phospholipase domain containing 3 (PNPLA3) is associated with an increased risk for developing alcohol-related cirrhosis and hepatocellular carcinoma (HCC). Recently, rs72613567:TA in hydroxysteroid 17-beta dehydrogenase 13 (HSD17B13) was shown to be associated with a reduced risk for developing alcohol-related liver disease and to attenuate the risk associated with carriage of PNPLA3 rs738409:G. This study explores the risk associations between these two genetic variants and the development of alcohol-related cirrhosis and HCC. APPROACH AND RESULTS Variants in HSD17B13 and PNPLA3 were genotyped in 6,171 participants, including 1,031 with alcohol-related cirrhosis and HCC, 1,653 with alcohol-related cirrhosis without HCC, 2,588 alcohol misusers with no liver disease, and 899 healthy controls. Genetic associations with the risks for developing alcohol-related cirrhosis and HCC were determined using logistic regression analysis. Carriage of HSD17B13 rs72613567:TA was associated with a lower risk for developing both cirrhosis (odds ratio [OR], 0.79; 95% confidence interval [CI], 0.72-0.88; P = 8.13 × 10-6 ) and HCC (OR, 0.77; 95% CI, 0.68-0.89; P = 2.27 × 10-4 ), whereas carriage of PNPLA3 rs738409:G was associated with an increased risk for developing cirrhosis (OR, 1.70; 95% CI, 1.54-1.88; P = 1.52 × 10-26 ) and HCC (OR, 1.77; 95% CI, 1.58-1.98; P = 2.31 × 10-23 ). These associations remained significant after adjusting for age, sex, body mass index, type 2 diabetes, and country. Carriage of HSD17B13 rs72613567:TA attenuated the risk for developing cirrhosis associated with PNPLA3 rs738409:G in both men and women, but the protective effect against the subsequent development of HCC was only observed in men (ORallelic , 0.75; 95% CI, 0.64-0.87; P = 1.72 × 10-4 ). CONCLUSIONS Carriage of variants in PNPLA3 and HSD17B13 differentially affect the risk for developing advanced alcohol-related liver disease. A genotypic/phenotypic risk score might facilitate earlier diagnosis of HCC in this population.
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Affiliation(s)
- Felix Stickel
- Department of Gastroenterology and Hepatology, University Hospital of Zürich, Switzerland
| | - Philipp Lutz
- Department of Internal Medicine I, University of Bonn, Bonn, Germany
| | - Stephan Buch
- Medical Department 1, University Hospital Dresden, TU Dresden, Germany
| | | | - Ines Silva
- Department of Internal Medicine and Center for Alcohol Research, Salem Medical Center University Hospital Heidelberg, Heidelberg, Germany
| | - Vanessa Rausch
- Department of Internal Medicine and Center for Alcohol Research, Salem Medical Center University Hospital Heidelberg, Heidelberg, Germany
| | - Janett Fischer
- Division of Hepatology, Clinic and Polyclinic for Gastroenterology, Hepatology, Infectiology and Pneumology, University Clinic Leipzig, Leipzig, Germany
| | - Karl Heinz Weiss
- Department of Internal Medicine IV, Medical University of Heidelberg, Germany
| | - Daniel Gotthardt
- Department of Internal Medicine IV, Medical University of Heidelberg, Germany
| | - Jonas Rosendahl
- Department of Gastroenterology, University Hospital Halle/Saale, Germany
| | - Astrid Marot
- Division of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Switzerland
| | - Mona Elamly
- Division of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Switzerland
| | - Marcin Krawczyk
- Department of Medicine II, Saarland University Medical Center, Homburg, Germany.,Laboratory of Metabolic Liver Diseases, Department of General, Transplant and Liver Surgery, Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Markus Casper
- Department of Medicine II, Saarland University Medical Center, Homburg, Germany
| | - Frank Lammert
- Department of Medicine II, Saarland University Medical Center, Homburg, Germany
| | - Thomas W M Buckley
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, UK
| | - Andrew McQuillin
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, UK
| | - Ulrich Spengler
- Department of Internal Medicine I, University of Bonn, Bonn, Germany
| | - Florian Eyer
- Department of Clinical Toxicology, Klinikum Rechts der Isar, Technical University of Munich, Germany
| | - Arndt Vogel
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Germany
| | - Silke Marhenke
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Germany
| | - Johann von Felden
- First Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Henning Wege
- First Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Rohini Sharma
- Department of Metabolism, Digestion & Reproduction, Division of Surgery and Cancer, Imperial College London, London, UK
| | - Stephen Atkinson
- Department of Metabolism, Digestion & Reproduction, Division of Surgery and Cancer, Imperial College London, London, UK
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Sophie Nehring
- Medical Department 1, University Hospital Dresden, TU Dresden, Germany
| | - Vincent Moser
- Medical Department 1, University Hospital Dresden, TU Dresden, Germany
| | - Clemens Schafmayer
- Department of Visceral and Thoracic Surgery, Kiel University, Kiel, Germany
| | - Laurent Spahr
- Departments of Gastroenterology and Hepatology, University Hospitals of Geneva and Faculty of Medicine, Geneva, Switzerland
| | | | - Rudolf E Stauber
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Austria
| | - Ali Canbay
- Ruhr-Universität Bochum, Universitätsklinikum Knappschaftskrankenhaus Bochum GmbH, Bochum, Germany
| | - Alexander Link
- Ruhr-Universität Bochum, Universitätsklinikum Knappschaftskrankenhaus Bochum GmbH, Bochum, Germany
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,Translational Medicine - Department of Transfusion Medicine and Hematology, Fondazione IRCCS Ca'Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Jane I Grove
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK.,Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, UK
| | - Guruprasad P Aithal
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK.,Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, UK
| | - Jens U Marquardt
- Department of Medicine I, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Waleed Fateen
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK.,Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, UK
| | - Steffen Zopf
- Medical Department 1, University of Erlangen-Nuremberg, Germany
| | - Jean-Francois Dufour
- University Clinic for Visceral Surgery and Medicine, Inselspital, University of Berne, Berne, Switzerland
| | - Jonel Trebicka
- Department of Internal Medicine I, Goethe University Frankfurt, Frankfurt, Germany
| | - Christian Datz
- Department of Internal Medicine, Hospital Oberndorf, Teaching Hospital of the Paracelsus Private Medical University of Salzburg, Oberndorf, Austria
| | - Pierre Deltenre
- Division of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Switzerland
| | - Sebastian Mueller
- Department of Internal Medicine and Center for Alcohol Research, Salem Medical Center University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas Berg
- Division of Hepatology, Clinic and Polyclinic for Gastroenterology, Hepatology, Infectiology and Pneumology, University Clinic Leipzig, Leipzig, Germany
| | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, TU Dresden, Germany
| | - Marsha Y Morgan
- UCL Institute for Liver & Digestive Health, Division of Medicine, Royal Free Campus, University College London, UK
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19
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Astbury S, Atallah E, Vijay A, Aithal GP, Grove JI, Valdes AM. Lower gut microbiome diversity and higher abundance of proinflammatory genus Collinsella are associated with biopsy-proven nonalcoholic steatohepatitis. Gut Microbes 2020; 11:569-580. [PMID: 31696774 PMCID: PMC7524262 DOI: 10.1080/19490976.2019.1681861] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
There is increasing evidence for the role of gut microbial composition in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). Nonalcoholic steatohepatitis (NASH) is the most serious form of NAFLD where inflammation causes liver damage that can progress to cirrhosis. We have characterized the gut microbiome composition in UK patients with biopsy-proven NASH (n = 65) and compared it to that in healthy controls (n = 76). We report a 7% lower Shannon alpha diversity in NASH patients without cirrhosis (n = 40) compared to controls (p = 2.7x 10-4) and a 14% drop in NASH patients with cirrhosis (n = 25, p = 5.0x 10-4). Beta diversity (Unweighted UniFrac distance) was also significantly reduced in both NASH (p = 5.6x 10-25) and NASH-cirrhosis (p = 8.1x 10-7) groups. The genus most strongly associated with NASH in this study was Collinsella (0.29% abundance in controls, 3.45% in NASH without cirrhosis (False Discovery Rate (FDR) p = .008), and 4.38% in NASH with cirrhosis (FDR p = .02)). This genus, which has been linked previously to obesity and atherosclerosis, was also positively correlated with fasting levels of triglycerides (p = .01) and total cholesterol (p = 1.2x 10-4) and negatively correlated with high-density lipoprotein cholesterol (p = 2.8x 10-6) suggesting that some of the pathways present in this microbial genus may influence lipid metabolism in the host. In patients, we also found decreased abundance of some of the Ruminococcaceae which are known to produce high levels of short-chain fatty acids which can lower inflammation. This may thus contribute to pathology associated with NASH.
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Affiliation(s)
- Stuart Astbury
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK,National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Edmond Atallah
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK,National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Amrita Vijay
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK,Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Guruprasad P Aithal
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK,National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Jane I Grove
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK,National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK,CONTACT Jane I Grove Nottingham Digestive Diseases Centre, E Floor, West Block, Queen’s Medical Centre, NottinghamNG7 2UH, UK
| | - Ana M Valdes
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK,Division of Rheumatology, Orthopaedics and Dermatology, School of Medicine, University of Nottingham, Nottingham, UK
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20
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Vijay A, Mohan L, Taylor MA, Grove JI, Valdes AM, Aithal GP, Shenoy K. The Evaluation and Use of a Food Frequency Questionnaire Among the Population in Trivandrum, South Kerala, India. Nutrients 2020; 12:nu12020383. [PMID: 32024020 PMCID: PMC7071154 DOI: 10.3390/nu12020383] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/27/2020] [Accepted: 01/27/2020] [Indexed: 11/25/2022] Open
Abstract
Dietary record tools such as food frequency questionnaire (FFQ) and food diaries (FD) are the most commonly used choices for assessing dietary intakes in most large-scale epidemiological studies. The authors developed a self-administered 360-item food frequency questionnaire (FFQ) to assess dietary intakes amongst a population-based cohort in South Kerala. In the validation study (n = 460), the data were collected using FFQs that were administered on three different occasions which were then compared to 7-day food records. The intake of foods and nutrients was higher as determined by the FFQ than that assessed using food records. Spearman correlations for macro-nutrients ranged from 0.72 for protein to 0.61 for carbohydrates and for micronutrients, from 0.71 for vitamin B6 to 0.34 for magnesium. The correlation was improved with energy-adjusted nutrient intakes. On average, the exact agreement for the macronutrients ranged from 48.2% to 57.1%, and that for micronutrients ranged from 66.7% to 41.9%, with the median percentage of 49.58%. The authors conclude that the FFQ has an acceptable reproducibility, however, there was a systematic trend towards higher estimates with the FFQ for most nutrients compared to the FD records.
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Affiliation(s)
- Amrita Vijay
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK; (M.A.T.); (J.I.G.); (G.P.A.)
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
- Correspondence:
| | - Leena Mohan
- Population Health Research Institute, Trivandrum, Kerala, 695011, India; (L.M.)
| | - Moira A. Taylor
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK; (M.A.T.); (J.I.G.); (G.P.A.)
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, NG7 2TQ, UK
| | - Jane I. Grove
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK; (M.A.T.); (J.I.G.); (G.P.A.)
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham NG7 2UH, UK;
| | - Ana M. Valdes
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham NG7 2UH, UK;
- Division of Rheumatology, Orthopedics and Dermatology, School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Guruprasad P. Aithal
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK; (M.A.T.); (J.I.G.); (G.P.A.)
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham NG7 2UH, UK;
| | - K.T. Shenoy
- Population Health Research Institute, Trivandrum, Kerala, 695011, India; (L.M.)
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21
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Nicoletti P, Aithal GP, Chamberlain TC, Coulthard S, Alshabeeb M, Grove JI, Andrade RJ, Bjornsson E, Dillon JF, Hallberg P, Lucena MI, Maitland‐van der Zee AH, Martin JH, Molokhia M, Pirmohamed M, Wadelius M, Shen Y, Nelson MR, Daly AK. Drug‐Induced Liver Injury due to Flucloxacillin: Relevance of Multiple Human Leukocyte Antigen Alleles. Clin Pharmacol Ther 2019; 106:245-253. [DOI: 10.1002/cpt.1375] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 12/13/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Paola Nicoletti
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount Sinai New York New York USA
- Sema4, a Mount Sinai Venture Stamford Connecticut USA
| | - Guruprasad P. Aithal
- National Institute for Health Research (NIHR) Nottingham Biomedical Research CentreNottingham University Hospital NHS Trust and University of Nottingham Nottingham UK
| | - Thomas C. Chamberlain
- Institute of Cellular MedicineNewcastle University Newcastle upon Tyne UK
- University of British ColumbiaVancouver British Columbia Canada
| | - Sally Coulthard
- Institute of Cellular MedicineNewcastle University Newcastle upon Tyne UK
| | - Mohammad Alshabeeb
- Institute of Cellular MedicineNewcastle University Newcastle upon Tyne UK
- Developmental Medicine DepartmentKing Abdullah International Medical Research Center Riyadh Kingdom of Saudi Arabia
| | - Jane I. Grove
- National Institute for Health Research (NIHR) Nottingham Biomedical Research CentreNottingham University Hospital NHS Trust and University of Nottingham Nottingham UK
- Nottingham Digestive Diseases CentreSchool of MedicineUniversity of Nottingham Nottingham UK
| | - Raul J. Andrade
- UGC Digestivo y Servicio de Farmacología ClínicaInstituto de Investigación Biomédica de Málaga (IBIMA)Hospital Universitario Virgen de la VictoriaUniversidad de MálagaMálagaSpain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)MadridSpain
| | - Einar Bjornsson
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineThe National University Hospital of Iceland Reykjavik Iceland
| | - John F. Dillon
- Medical Research InstituteUniversity of DundeeNinewells Hospital Dundee UK
| | - Par Hallberg
- Department of Medical Sciences and Science for Life LaboratoryUppsala University Uppsala Sweden
| | - M. Isabel Lucena
- UGC Digestivo y Servicio de Farmacología ClínicaInstituto de Investigación Biomédica de Málaga (IBIMA)Hospital Universitario Virgen de la VictoriaUniversidad de MálagaMálagaSpain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)MadridSpain
| | - Anke H. Maitland‐van der Zee
- Department of Respiratory MedicineAcademic Medical Center (AMC)University of Amsterdam Amsterdam The Netherlands
| | - Jennifer H. Martin
- School of Medicine and Public HealthUniversity of Newcastle Callaghan New South Wales Australia
| | - Mariam Molokhia
- School of Population Health and Environmental SciencesFaculty of Life Sciences and MedicineKing's College London UK
| | - Munir Pirmohamed
- Department of Molecular and Clinical PharmacologyUniversity of Liverpool Liverpool UK
| | - Mia Wadelius
- Department of Medical Sciences and Science for Life LaboratoryUppsala University Uppsala Sweden
| | - Yufeng Shen
- The Herbert Irving Comprehensive Cancer CenterColumbia University New York New York USA
- Department of Biomedical InformaticsColumbia University New York New York USA
| | | | - Ann K. Daly
- Institute of Cellular MedicineNewcastle University Newcastle upon Tyne UK
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22
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Daniels SJ, Leeming DJ, Eslam M, Hashem AM, Nielsen MJ, Krag A, Karsdal MA, Grove JI, Neil Guha I, Kawaguchi T, Torimura T, McLeod D, Akiba J, Kaye P, de Boer B, Aithal GP, Adams LA, George J. ADAPT: An Algorithm Incorporating PRO-C3 Accurately Identifies Patients With NAFLD and Advanced Fibrosis. Hepatology 2019; 69:1075-1086. [PMID: 30014517 DOI: 10.1002/hep.30163] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 07/03/2018] [Indexed: 12/14/2022]
Abstract
Given the high global prevalence of nonalcoholic fatty liver disease (NAFLD), the need for relevant noninvasive biomarkers and algorithms to accurately stage disease severity is a critical unmet medical need. Identifying those with advanced fibrosis (≥ F3) is the most crucial, as these individuals have the greatest risk of adverse, long-term, liver-related outcomes. We aimed to investigate the role of PRO-C3 (a marker of type III collagen formation) as a biomarker for advanced fibrosis in NAFLD. We measured PRO-C3 by enzyme-linked immunosorbent assay in two large independent cohorts with extensive clinical phenotyping and liver biopsy: 150 in the derivation and 281 in the validation cohort. A PRO-C3-based fibrosis algorithm that included age, presence of diabetes, PRO-C3, and platelet count (ADAPT) was developed. PRO-C3 increased with fibrosis stage (Rho 0.50; P < 0.0001) and was independently associated with advanced fibrosis (odds ratio = 1.05; 95% confidence interval [CI] 1.02-1.08; P = 0.003). ADAPT showed areas under the receiver operating characteristics curve of 0.86 (95% CI 0.79-0.91) in the derivation and 0.87 in the validation cohort (95% CI 0.83-0.91) for advanced fibrosis. This was superior to the existing fibrosis scores, aspartate aminotransferase to platelet ratio index (APRI), FIB-4, and NAFLD fibrosis score (NFS) in most comparisons. Conclusion: PRO-C3 is an independent predictor of fibrosis stage in NAFLD. A PRO-C3-based score (ADAPT) accurately identifies patients with NAFLD and advanced fibrosis and is superior to APRI, FIB-4, and NFS.
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Affiliation(s)
- Samuel J Daniels
- Nordic Bioscience Biomarkers and Research A/S, Herlev, Denmark.,Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Diana J Leeming
- Nordic Bioscience Biomarkers and Research A/S, Herlev, Denmark
| | - Mohammed Eslam
- Storr Liver Centre, Westmead Institute for Medical Research, University of Sydney and Westmead Hospital, Westmead, Australia
| | - Ahmed M Hashem
- Department of Systems and Biomedical Engineering, Faculty of Engineering, Minia University, Minia, Egypt
| | - Mette J Nielsen
- Nordic Bioscience Biomarkers and Research A/S, Herlev, Denmark
| | - Aleksander Krag
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Gastroenterology and Hepatology, Odense University Hospital, Odense, Denmark
| | | | - Jane I Grove
- Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, United Kingdom.,NIHR Nottingham Biomedical Research Centre at the Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, United Kingdom.,Medical Research Council (MRC) Nottingham Molecular Pathology Node, University of Nottingham, Nottingham, United Kingdom
| | - Indra Neil Guha
- Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, United Kingdom.,NIHR Nottingham Biomedical Research Centre at the Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, United Kingdom.,Medical Research Council (MRC) Nottingham Molecular Pathology Node, University of Nottingham, Nottingham, United Kingdom
| | - Takumi Kawaguchi
- Department of Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Takuji Torimura
- Department of Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Duncan McLeod
- Department of Anatomical Pathology, Institute of Clinical Pathology and Medical Research (ICPMR), Westmead Hospital, Sydney, Australia
| | - Jun Akiba
- Department of Diagnostic Pathology, Kurume University Hospital, Kurume, Japan
| | - Philip Kaye
- Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, United Kingdom.,Medical Research Council (MRC) Nottingham Molecular Pathology Node, University of Nottingham, Nottingham, United Kingdom
| | - Bastiaan de Boer
- Department of Anatomical Pathology, PathWest, Fiona Stanley Hospital, Murdoch, Australia
| | - Guruprasad P Aithal
- Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, United Kingdom.,NIHR Nottingham Biomedical Research Centre at the Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, United Kingdom.,Medical Research Council (MRC) Nottingham Molecular Pathology Node, University of Nottingham, Nottingham, United Kingdom
| | - Leon A Adams
- Medical School, University of Western Australia, Nedlands, Australia
| | - Jacob George
- Storr Liver Centre, Westmead Institute for Medical Research, University of Sydney and Westmead Hospital, Westmead, Australia
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23
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Kaliyaperumal K, Grove JI, Delahay RM, Griffiths WJH, Duckworth A, Aithal GP. Pharmacogenomics of drug-induced liver injury (DILI): Molecular biology to clinical applications. J Hepatol 2018; 69:948-957. [PMID: 29792895 DOI: 10.1016/j.jhep.2018.05.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/02/2018] [Accepted: 05/11/2018] [Indexed: 12/14/2022]
Abstract
A 21-year old woman was admitted to hospital with a two-week history of painless jaundice, fatigue and anorexia having previously been fit and well. One month prior to presentation, the patient had taken a five-day course of amoxicillin-clavulanic acid for an infected skin cyst. Otherwise, she was only on the oral contraceptive pill and reported minimal alcohol intake. On examination, she was deeply jaundiced, but alert and oriented with no asterixis. She had no stigmata of chronic liver disease, but hepatomegaly extending 3 cm from below the right subcostal margin was evident. Investigations showed: white cell count 13.4 × 109/L (normal 3.6-9.3), haemoglobin 11.8 g/dl (normal 11-15), platelet count 356 × 109/L (normal 170-420), sodium 138 mmol/L (normal 134-144), potassium 3.5 mmol/L (normal 3.5-5.0), creatinine 32 µmol/L (normal 40-75), albumin 30 g/L (normal 35-48), alanine aminotransferase 707 IU/L (normal 15-54), alkaline phosphatase 151 IU/L (normal 30-130), bilirubin 384 µmol/L (normal 7-31) and prothrombin time 27.2 s (normal 11.7-14). Screening for hepatitis A, B, C, E, Epstein-Barr virus, cytomegalovirus and autoimmune hepatitis was negative. Tests for anti-smooth muscle, antinuclear, and anti-liver-kidney microsomal-1 antibodies were negative; immunoglobulin levels and ceruloplasmin levels were normal. Liver ultrasonography demonstrated a liver of normal contour with no biliary dilatation, a normal spleen size and patent vessels. Liver biopsy revealed severe portal interface hepatitis with lobular inflammation and scant plasma cells. Her clinical condition deteriorated in the following days with prothrombin time and bilirubin rising to 56.6 s and 470 µmol/L, respectively. At follow-up after 11 days, her alanine aminotransferase level was 1,931 IU/L. She developed grade 2 hepatic encephalopathy 14 days after presentation, and was listed for a super-urgent liver transplant. Human leucocyte antigen (HLA) typing was performed as a part of preparatory investigations and showed the patient carried the HLA haplotype HLA-DRB1∗15:02-DQB1∗06:01. Following orthotopic transplantation of a deceased donor graft her explant histology revealed severe ongoing hepatitis with multi-acinar necrosis (Fig. 1A and B). This case raised a number of important questions about the diagnosis of drug-induced liver injury and tools available for clinicians to make the best decisions for patient care: In this Grand Rounds article, we will explore these questions, describing the pathophysiology, diagnostic and prognostic biomarkers, and clinical management of drug-induced liver injury. We will also discuss ongoing areas of uncertainty.
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Affiliation(s)
- Kalaiyarasi Kaliyaperumal
- Department of Gastroenterology and Hepatology, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore 308433, Singapore
| | - Jane I Grove
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK; Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, UK
| | - Robin M Delahay
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK; Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, UK
| | | | - Adam Duckworth
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Guruprasad P Aithal
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK; Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, UK.
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24
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Grove JI, Thiagarajan P, Astbury S, Harris R, Delahooke T, Guha IN, Aithal GP. Analysis of genotyping for predicting liver injury marker, procollagen III in persons at risk of non-alcoholic fatty liver disease. Liver Int 2018; 38:1832-1838. [PMID: 29493856 DOI: 10.1111/liv.13733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/21/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Chronic liver disease presents a major global public health challenge. Stratification of asymptomatic, at-risk patients in primary care using non-invasive methods has the potential to address this by identifying those likely to progress. We, therefore, evaluated variant alleles at loci associated with non-alcoholic fatty liver disease as genetic determinants of substantial liver injury in patients with disease risk factors. METHODS Levels of serum procollagen III (PIIINP), an established fibrosis and steatohepatitis marker, were determined in 467 people who had type 2 diabetes and/or BMI > 27.3 (identified from registration with general practitioners) in this observational cross-sectional study. Patients were genotyped for characterised risk alleles in PNPLA3 (rs738409), GCKR (rs1260326) and TM6SF2 (rs58542926) and associations with PIIINP assessed. RESULTS The risk alleles in PNPLA3, GCKR or TM6SF2 were not found to be individually associated with the presence of a disease risk factor and were not significantly more common in patients with raised serum PIIINP. The prevalence of possession of both PNPLA3 and GCKR variant alleles combined was significantly higher in at-risk patients with clinically significant liver disease indicated by serum PIIINP above 11 ng/mL (P = .014). CONCLUSIONS Genotyping, therefore, has limited value for predicting severe liver disease in at-risk individuals identified in a community setting.
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Affiliation(s)
- Jane I Grove
- Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, UK.,NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Prarthana Thiagarajan
- Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, UK.,NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Stuart Astbury
- Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, UK.,NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Rebecca Harris
- Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, UK.,NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Toby Delahooke
- Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - I Neil Guha
- Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, UK.,NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Guruprasad P Aithal
- Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, UK.,NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
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25
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Alandiyjany MN, Croxall NJ, Grove JI, Delahay RM. A role for the tfs3 ICE-encoded type IV secretion system in pro-inflammatory signalling by the Helicobacter pylori Ser/Thr kinase, CtkA. PLoS One 2017; 12:e0182144. [PMID: 28759055 PMCID: PMC5536186 DOI: 10.1371/journal.pone.0182144] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/12/2017] [Indexed: 12/12/2022] Open
Abstract
Two distinct type IV secretion systems (T4SSs) can be identified in certain Helicobacter pylori strains, encoded on mobile genetic elements termed tfs3 and tfs4. Although their function remains unknown, both have been implicated in clinical outcomes of H. pylori infection. Here we provide evidence that the Tfs3 T4SS is required for activity of the pro-inflammatory Ser/Thr kinase protein, CtkA, in a gastric epithelial cell infection model. Previously, purified recombinant CtkA protein has been shown to upregulate NF-kappaB signalling and induce TNF-alpha and IL-8 cytokine secretion from cultured macrophages suggesting that it may potentiate the H. pylori-mediated inflammatory response. In this study, we show that CtkA expressed from its native host, H. pylori has a similar capacity for stimulation of a pro-inflammatory response from gastric epithelial cells. CtkA interaction was found to be dependent upon a complement of tfs3 T4SS genes, but independent of the T4SSs encoded by either tfs4 or the cag pathogenicity island. Moreover, the availability of CtkA for host cell interaction was shown to be conditional upon the carboxyl-terminus of CtkA, encoding a putative conserved secretion signal common to other variably encoded Tfs3 proteins. Collectively, our observations indicate a role for the Tfs3 T4SS in CtkA-mediated pro-inflammatory signalling by H. pylori and identify CtkA as a likely Tfs3 T4SS secretion substrate.
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Affiliation(s)
- Maher N. Alandiyjany
- NIHR Nottingham Digestive Diseases Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, United Kingdom
| | - Nicola J. Croxall
- NIHR Nottingham Digestive Diseases Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, United Kingdom
| | - Jane I. Grove
- NIHR Nottingham Digestive Diseases Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, United Kingdom
| | - Robin M. Delahay
- NIHR Nottingham Digestive Diseases Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, United Kingdom
- * E-mail:
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Nicoletti P, Aithal GP, Bjornsson ES, Andrade RJ, Sawle A, Arrese M, Barnhart HX, Bondon-Guitton E, Hayashi PH, Bessone F, Carvajal A, Cascorbi I, Cirulli ET, Chalasani N, Conforti A, Coulthard SA, Daly MJ, Day CP, Dillon JF, Fontana RJ, Grove JI, Hallberg P, Hernández N, Ibáñez L, Kullak-Ublick GA, Laitinen T, Larrey D, Lucena MI, Maitland-van der Zee AH, Martin JH, Molokhia M, Pirmohamed M, Powell EE, Qin S, Serrano J, Stephens C, Stolz A, Wadelius M, Watkins PB, Floratos A, Shen Y, Nelson MR, Urban TJ, Daly AK. Association of Liver Injury From Specific Drugs, or Groups of Drugs, With Polymorphisms in HLA and Other Genes in a Genome-Wide Association Study. Gastroenterology 2017; 152:1078-1089. [PMID: 28043905 PMCID: PMC5367948 DOI: 10.1053/j.gastro.2016.12.016] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 11/30/2016] [Accepted: 12/21/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS We performed a genome-wide association study (GWAS) to identify genetic risk factors for drug-induced liver injury (DILI) from licensed drugs without previously reported genetic risk factors. METHODS We performed a GWAS of 862 persons with DILI and 10,588 population-matched controls. The first set of cases was recruited before May 2009 in Europe (n = 137) and the United States (n = 274). The second set of cases were identified from May 2009 through May 2013 from international collaborative studies performed in Europe, the United States, and South America. For the GWAS, we included only cases with patients of European ancestry associated with a particular drug (but not flucloxacillin or amoxicillin-clavulanate). We used DNA samples from all subjects to analyze HLA genes and single nucleotide polymorphisms. After the discovery analysis was concluded, we validated our findings using data from 283 European patients with diagnosis of DILI associated with various drugs. RESULTS We associated DILI with rs114577328 (a proxy for A*33:01 a HLA class I allele; odds ratio [OR], 2.7; 95% confidence interval [CI], 1.9-3.8; P = 2.4 × 10-8) and with rs72631567 on chromosome 2 (OR, 2.0; 95% CI, 1.6-2.5; P = 9.7 × 10-9). The association with A*33:01 was mediated by large effects for terbinafine-, fenofibrate-, and ticlopidine-related DILI. The variant on chromosome 2 was associated with DILI from a variety of drugs. Further phenotypic analysis indicated that the association between DILI and A*33:01 was significant genome wide for cholestatic and mixed DILI, but not for hepatocellular DILI; the polymorphism on chromosome 2 was associated with cholestatic and mixed DILI as well as hepatocellular DILI. We identified an association between rs28521457 (within the lipopolysaccharide-responsive vesicle trafficking, beach and anchor containing gene) and only hepatocellular DILI (OR, 2.1; 95% CI, 1.6-2.7; P = 4.8 × 10-9). We did not associate any specific drug classes with genetic polymorphisms, except for statin-associated DILI, which was associated with rs116561224 on chromosome 18 (OR, 5.4; 95% CI, 3.0-9.5; P = 7.1 × 10-9). We validated the association between A*33:01 terbinafine- and sertraline-induced DILI. We could not validate the association between DILI and rs72631567, rs28521457, or rs116561224. CONCLUSIONS In a GWAS of persons of European descent with DILI, we associated HLA-A*33:01 with DILI due to terbinafine and possibly fenofibrate and ticlopidine. We identified polymorphisms that appear to be associated with DILI from statins, as well as 2 non-drug-specific risk factors.
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Affiliation(s)
- Paola Nicoletti
- Department of Systems Biology, Columbia University, New York, New York
| | - Guruprasad P Aithal
- National Institute for Health Research, Nottingham Digestive Diseases Biomedical Research Unit, Nottingham University Hospital, National Health Service Trust, and University of Nottingham, Nottingham, United Kingdom
| | - Einar S Bjornsson
- Department of Internal Medicine, Landspitali University Hospital, Reykjavik, Iceland
| | - Raul J Andrade
- Unidad de Gestión Clínica Digestivo, Instituto de Investigación Biomédica de Málaga, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Málaga, Spain
| | - Ashley Sawle
- Department of Systems Biology, Columbia University, New York, New York
| | - Marco Arrese
- Departmento de Gastroenterología, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | | | - Paul H Hayashi
- Department of Internal Medicine, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina
| | - Fernando Bessone
- Servicio de Gastroenterología y Hepatología, Universidad Nacional de Rosario, Rosario, Argentina
| | | | - Ingolf Cascorbi
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Naga Chalasani
- Division of Gastroenterology and Hepatology, Indiana University School of Medicine, Indianapolis, Indiana
| | | | - Sally A Coulthard
- Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Mark J Daly
- Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, Massachusetts
| | - Christopher P Day
- Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - John F Dillon
- Medical Research Institute, University of Dundee, Ninewells Hospital, Dundee, United Kingdom
| | | | - Jane I Grove
- National Institute for Health Research, Nottingham Digestive Diseases Biomedical Research Unit, Nottingham University Hospital, National Health Service Trust, and University of Nottingham, Nottingham, United Kingdom
| | - Pär Hallberg
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Nelia Hernández
- Facultad de Medicina, Universidad de la Republica, Montevideo, Uruguay
| | - Luisa Ibáñez
- Fundació Institut Català de Farmacologia, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Gerd A Kullak-Ublick
- Department of Clinical Pharmacology and Toxicology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Tarja Laitinen
- Clinical Research Unit for Pulmonary Diseases, Helsinki University Central Hospital, Helsinki, Finland
| | - Dominique Larrey
- Liver Unit, Centre Hospitalier Universitaire, St Eloi Hospital, Montpellier, France
| | - M Isabel Lucena
- Unidad de Gestión Clínica Digestivo, Instituto de Investigación Biomédica de Málaga, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Málaga, Spain
| | | | - Jennifer H Martin
- School of Medicine and Public Health, University of Newcastle, New South Wales, Australia
| | - Mariam Molokhia
- Department of Primary Care and Public Health Sciences, King's College, London, United Kingdom
| | - Munir Pirmohamed
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
| | - Elizabeth E Powell
- Centre for Liver Disease Research, School of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, Shanghai, China
| | - Jose Serrano
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland
| | - Camilla Stephens
- Unidad de Gestión Clínica Digestivo, Instituto de Investigación Biomédica de Málaga, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Málaga, Spain
| | - Andrew Stolz
- University of Southern California, Los Angeles, California
| | - Mia Wadelius
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Paul B Watkins
- University of North Carolina Institute for Drug Safety Sciences, Eshelman School of Pharmacy, Chapel Hill, North Carolina
| | - Aris Floratos
- Department of Systems Biology, Columbia University, New York, New York
| | - Yufeng Shen
- Department of Systems Biology, Columbia University, New York, New York
| | | | - Thomas J Urban
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina
| | - Ann K Daly
- Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, United Kingdom.
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Grove JI, Austin M, Tibble J, Aithal GP, Verma S. Monozygotic twins with NASH cirrhosis: cumulative effect of multiple single nucleotide polymorphisms? Ann Hepatol 2017; 15:277-82. [PMID: 26845607 DOI: 10.5604/16652681.1193726] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Multiple genetic and environmental factors interact to determine an individual's predisposition to non-alcoholic fatty liver disease and its phenotypic characteristics. Association studies have found a number of alleles associated with the development of non-alcoholic steatohepatitis. Our aim was to investigate whether multiple risk-associated alleles may be present in affected monozygotic twins, indicating underlying genetic predisposition to non-alcoholic steatohepatitis. We determined the genotype of 14 candidate gene polymorphisms (at 11 unlinked loci) in a set of monozygotic twins who presented with cirrhosis within 18 months of each other. Genotyping revealed multiple single nucleotide polymorphisms at 9 independent loci in genes PNPLA3, APOC3, GCKR, TRIB1, LYPLAL1, PPP1R3B, COL13A1, and EFCAB4B, previously implicated in contributing to non-alcoholic steatohepatitis pathogenesis. In conclusion, this case series illustrates the potential cumulative effect of multiple polymorphisms in the development and potential progression of a complex trait such as NASH cirrhosis.
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Affiliation(s)
- Jane I Grove
- NIHR Nottingham Digestive Diseases Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham NG7 2UH, UK
| | - Mark Austin
- Department of Gastroenterology and Hepatology, Brighton and Sussex University Hospital, Brighton, BN2 5BE, UK
| | - Jeremy Tibble
- Department of Gastroenterology and Hepatology, Brighton and Sussex University Hospital, Brighton, BN2 5BE, UK
| | - Guruprasad P Aithal
- NIHR Nottingham Digestive Diseases Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham NG7 2UH, UK
| | - Sumita Verma
- Department of Gastroenterology and Hepatology, Brighton and Sussex University Hospital, Brighton, BN2 5BE, UK; Department of Medicine, Brighton and Sussex Medical School, Brighton, BN1 9PX, UK
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Abstract
Hepatotoxicity constrains drug development and accounts for a substantial burden on health services. Genome-wide association studies (GWASs) have investigated potential genetic factors that explain interindividual variations in response to medications leading to drug-induced liver injury (DILI). Although the proportion of GWASs investigating DILI is very small, those that have focused on this area have identified risk alleles with substantially higher risk ratios for susceptibility to DILI when compared with GWASs involving the majority of other complex diseases. Moreover, a relatively small number of human leukocyte antigen alleles are associated with DILI secondary to a range of medications. Because the encoded major histocompatibility complex proteins mediate antigen presentation to T cells, this provides evidence for a crucial central role for the adaptive immune system in DILI. Findings of GWASs should be considered during preclinical development of certain drugs. Genotyping may also have clinical applications, although it is currently limited to particular scenarios in relation to specific drugs.
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Affiliation(s)
- Guruprasad P Aithal
- National Institute for Health Research (NIHR), Nottingham Digestive Diseases Biomedical Research Unit, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, United Kingdom
| | - Jane I Grove
- National Institute for Health Research (NIHR), Nottingham Digestive Diseases Biomedical Research Unit, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, United Kingdom
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Abstract
INTRODUCTION Drug-induced liver injury (DILI) is a rare adverse drug reaction, which impacts significantly on patients. Human leukocyte antigen (HLA) risk alleles have been found to be associated with DILI supporting an immunological basis to DILI pathogenesis. AREAS COVERED HLA alleles associated with risk of liver injury induced by specific therapeutic drugs are described. The evidence for a role of the adaptive immune system in DILI is presented; case-control studies showing an association between DILI and HLA alleles are reviewed. Clinical applications of pharmacogenomics are considered. EXPERT OPINION Increasing evidence points to a crucial role for the adaptive immune system in the pathogenesis of DILI. Identification of specific HLA alleles as risk factors through large genome-wide association studies has been instrumental in this and in vitro analyses have facilitated improved understanding of the molecular mechanisms. This provides the basis for developing clinical pharmacogenomic applications. Already, genotyping for hypersensitivity HLA risk alleles has been implemented and opportunities for pre-prescription testing in DILI identified. However, although associations are strong, the rarity of DILI means routine testing has not been formally evaluated. Nevertheless, enhanced understanding of how HLA alleles contribute to injury risk is valuable for drug development. Translation of this research into effective pre-emption and primary prevention remains the goal.
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Affiliation(s)
- Jane I Grove
- Nottingham University Hospitals NHS Trust and University of Nottingham, NIHR Nottingham Digestive Diseases Biomedical Research Unit , Nottingham, NG7 2UH , UK +01159249924 Ext: 63822 ; +01159709012 ;
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Upton AL, Grove JI, Mahdi AA, Briggs GS, Milner DS, Rudolph CJ, Lloyd RG. Cellular location and activity of Escherichia coli RecG proteins shed light on the function of its structurally unresolved C-terminus. Nucleic Acids Res 2014; 42:5702-14. [PMID: 24692661 PMCID: PMC4027168 DOI: 10.1093/nar/gku228] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
RecG is a DNA translocase encoded by most species of bacteria. The Escherichia coli protein targets branched DNA substrates and drives the unwinding and rewinding of DNA strands. Its ability to remodel replication forks and to genetically interact with PriA protein have led to the idea that it plays an important role in securing faithful genome duplication. Here we report that RecG co-localises with sites of DNA replication and identify conserved arginine and tryptophan residues near its C-terminus that are needed for this localisation. We establish that the extreme C-terminus, which is not resolved in the crystal structure, is vital for DNA unwinding but not for DNA binding. Substituting an alanine for a highly conserved tyrosine near the very end results in a substantial reduction in the ability to unwind replication fork and Holliday junction structures but has no effect on substrate affinity. Deleting or substituting the terminal alanine causes an even greater reduction in unwinding activity, which is somewhat surprising as this residue is not uniformly present in closely related RecG proteins. More significantly, the extreme C-terminal mutations have little effect on localisation. Mutations that do prevent localisation result in only a slight reduction in the capacity for DNA repair.
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Affiliation(s)
- Amy L Upton
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jane I Grove
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Akeel A Mahdi
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Geoffrey S Briggs
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - David S Milner
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Christian J Rudolph
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK School of Health Sciences and Social Care, Division of Biosciences, Brunel University, Uxbridge, London UB8 3PH, UK
| | - Robert G Lloyd
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
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Grove JI, Alandiyjany MN, Delahay RM. Site-specific relaxase activity of a VirD2-like protein encoded within the tfs4 genomic island of Helicobacter pylori. J Biol Chem 2013; 288:26385-96. [PMID: 23900838 PMCID: PMC3772185 DOI: 10.1074/jbc.m113.496430] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Four different type IV secretion systems are variously represented in the genomes of different Helicobacter pylori strains. Two of these, encoded by tfs3 and tfs4 gene clusters are contained within self-transmissible genomic islands. Although chromosomal excision of tfs4 circular intermediates is reported to be dependent upon the function of a tfs4-encoded XerD tyrosine-like recombinase, other factors required for transfer to a recipient cell have not been demonstrated. Here, we characterize the functional activity of a putative tfs4-encoded VirD2-like relaxase protein. Tfs4 VirD2 was purified as a fusion to maltose-binding protein and demonstrated to bind and nick both supercoiled duplex DNA and oligonucleotides in vitro in a manner dependent upon the presence of Mg(2+) but independently of any auxiliary proteins. Unusually, concentration-dependent nicking of duplex DNA appeared to require only transient protein-DNA interaction. Although phylogenetically distinct from established relaxase families, site-specific cleavage of oligonucleotides by Tfs4 VirD2 required the nick region sequence 5'-ATCCTG-3' common to transfer origins (oriT) recognized by MOBP conjugative relaxases. Cleavage resulted in covalent attachment of MBP-VirD2 to the 5'-cleaved end, consistent with conventional relaxase activity. Identification of an oriT-like sequence upstream of tfs4 virD2 and demonstration of VirD2 protein-protein interaction with a putative VirC1 relaxosome component indicate that transfer initiation of the tfs4 genomic island is analogous to mechanisms underlying mobilization of other integrated mobile elements, such as integrating conjugative elements, requiring site-specific targeting of relaxase activity to a cognate oriT sequence.
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Affiliation(s)
- Jane I Grove
- From the Centre for Biomolecular Sciences and Nottingham Digestive Diseases Centre, National Institute for Health Research Biomedical Research Unit, University of Nottingham, Nottingham NG7 2RD, United Kingdom
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Grove JI, Wood SR, Briggs GS, Oldham NJ, Lloyd RG. A soluble RecN homologue provides means for biochemical and genetic analysis of DNA double-strand break repair in Escherichia coli. DNA Repair (Amst) 2009; 8:1434-43. [PMID: 19846353 DOI: 10.1016/j.dnarep.2009.09.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Revised: 07/30/2009] [Accepted: 09/29/2009] [Indexed: 10/20/2022]
Abstract
RecN is a highly conserved, SMC-like protein in bacteria. It plays an important role in the repair of DNA double-strand breaks and is therefore a key factor in maintaining genome integrity. The insolubility of Escherichia coli RecN has limited efforts to unravel its function. We overcame this limitation by replacing the resident coding sequence with that of Haemophilus influenzae RecN. The heterologous construct expresses Haemophilus RecN from the SOS-inducible E. coli promoter. The hybrid gene is fully functional, promoting survival after I-SceI induced DNA breakage, gamma irradiation or exposure to mitomycin C as effectively as the native gene, indicating that the repair activity is conserved between these two species. H. influenzae RecN is quite soluble, even when expressed at high levels, and is readily purified. Its analysis by ionisation-mass spectrometry, gel filtration and glutaraldehyde crosslinking indicates that it is probably a dimer under physiological conditions, although a higher multimer cannot be excluded. The purified protein displays a weak ATPase activity that is essential for its DNA repair function in vivo. However, no DNA-binding activity was detected, which contrasts with RecN from Bacillus subtilis. RecN proteins from Aquifex aeolicus and Bacteriodes fragilis also proved soluble. Neither binds DNA, but the Aquifex RecN has weak ATPase activity. Our findings support studies indicating that RecN, and the SOS response in general, behave differently in E. coli and B. subtilis. The hybrid recN reported provides new opportunities to study the genetics and biochemistry of how RecN operates in E. coli.
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Affiliation(s)
- Jane I Grove
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
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Jaberipour M, Vass SO, Guise CP, Grove JI, Knox RJ, Hu L, Hyde EI, Searle PF. Testing double mutants of the enzyme nitroreductase for enhanced cell sensitisation to prodrugs: effects of combining beneficial single mutations. Biochem Pharmacol 2009; 79:102-11. [PMID: 19665450 DOI: 10.1016/j.bcp.2009.07.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 07/29/2009] [Accepted: 07/31/2009] [Indexed: 10/20/2022]
Abstract
Prodrug activation gene therapy for cancer involves expressing prodrug-activating enzymes in tumour cells, so they can be selectively killed by systemically administered prodrug. For example, Escherichia colinfsB nitroreductase (E.C. 1.6.99.7)(NTR), sensitises cells to the prodrug CB1954 (5-[aziridin-1-yl]-2,4-dinitrobenzamide), which it converts to a potent DNA-crosslinking agent. However, low catalytic efficiency with this non-natural substrate appears to limit the efficacy of this enzyme prodrug combination for eliminating the target cancer cells. To improve this, we aim to engineer NTR for improved prodrug activation. Previously, a number of single amino acid substitutions at six positions around the active site of the enzyme were found to increase activity, resulting in up to approximately 5-fold enhanced cell sensitisation to CB1954. In this study we have made pairwise combinations among some of the best mutants at each of these 6 sites. A total of 53 double mutants were initially screened in E. coli, then the 7 most promising were inserted into an adenovirus vector and compared in SKOV3 human ovarian carcinoma cells for sensitisation to CB1954 and two alternative prodrugs. The most effective mutants, T41L/N71S and T41L/F70A, were 14-17-fold more potent than WT NTR at sensitising the cancer cells to CB1954. The best mutant for activation of the dinitrobenzamide mustard prodrug SN23862 was T41L/F70A (4.8-fold improvement); and S40A/F124M showed 1.7-fold improvement over WT with the nitrobenzylphosphoramide mustard prodrug LH7. In two tumour xenograft models using SKOV3 or human prostate carcinoma PC3, T41L/N71S NTR demonstrated greater CB1954-dependent anti-tumour activity than WT NTR.
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Affiliation(s)
- Mansooreh Jaberipour
- Cancer Research UK Institute for Cancer Studies, University of Birmingham, Birmingham B15 2TT, UK
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Guise CP, Grove JI, Hyde EI, Searle PF. Direct positive selection for improved nitroreductase variants using SOS triggering of bacteriophage lambda lytic cycle. Gene Ther 2007; 14:690-8. [PMID: 17301844 DOI: 10.1038/sj.gt.3302919] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Expression of prodrug-activating enzymes that convert non-toxic substrates to cytotoxic derivatives is a promising strategy for cancer gene therapy. However, their catalytic activity with unnatural, prodrug substrates is often suboptimal. Efforts to improve these enzymes have been limited by the inability to select directly for increased prodrug activation. We have focussed on developing variants of Escherichia coli (E. coli) nitroreductase (NTR) with improved ability to activate the prodrug 5-(aziridin-1-yl)-2,4-dinitrobenzamide (CB1954), and describe here a novel, direct, positive selection for improved enzymes that exploits the alternative life cycles of bacteriophage lambda. In lambda lysogens of E. coli, the activation of the prodrug CB1954 by NTR triggers the SOS response to DNA damage, switching integrated lambda prophages into lytic cycle. This provides a direct, positive selection for phages encoding improved NTR variants, as, upon limiting exposure of lysogenized E. coli to CB1954, only those encoding the most active enzyme variants are triggered into lytic cycle, allowing their selective recovery. We exemplify the selection by isolating highly improved 'turbo-NTR' variants from a library of 6.8 x 10(5) clones, conferring up to 50-fold greater sensitivity to CB1954 than the wild type. Carcinoma cells infected with adenovirus expressing T41Q/N71S/F124T-NTR were sensitized to CB1954 concentrations 40- to 80-fold lower than required with WT-NTR.
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Affiliation(s)
- C P Guise
- Cancer Research UK Institute for Cancer Studies, University of Birmingham, Birmingham, UK
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Race PR, Lovering AL, White SA, Grove JI, Searle PF, Wrighton CW, Hyde EI. Kinetic and structural characterisation of Escherichia coli nitroreductase mutants showing improved efficacy for the prodrug substrate CB1954. J Mol Biol 2007; 368:481-92. [PMID: 17350040 DOI: 10.1016/j.jmb.2007.02.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2006] [Revised: 01/29/2007] [Accepted: 02/06/2007] [Indexed: 11/17/2022]
Abstract
Escherichia coli nitroreductase (NTR) is a flavoprotein that reduces a variety of quinone and nitroaromatic substrates. Among these substrates is the prodrug 5-[aziridin-1-yl]-2,4-dinitrobenzamide (CB1954) that is activated by NTR to form two products, one of which is highly cytotoxic. NTR in combination with CB1954 has entered clinical trials for virus-directed enzyme-prodrug therapy of cancer. Enhancing the catalytic efficiency of NTR for CB1954 is likely to improve the therapeutic potential of this system. We previously identified a number of mutants at six positions around the active site of NTR that showed enhanced sensitisation to CB1954 in an E. coli cell-killing assay. In this study we have purified improved mutants at each of these positions and determined their steady-state kinetic parameters for CB1954 and for the antibiotic nitrofurazone. We have also made a double mutant, combining two of the most beneficial single mutations. All the mutants show enhanced specificity constants for CB1954, and, apart from N71S, the enhancement is selective for CB1954 over nitrofurazone. One mutant, T41L, also shows an increase in selectivity for reducing the 4-nitro group of CB1954 rather than the 2-nitro group. We have determined the three-dimensional structures of selected mutants bound to the substrate analogue nicotinic acid, using X-ray crystallography. The N71S mutation affects interactions of the FMN cofactor, while mutations at T41 and F124 affect the interactions with nicotinic acid. The structure of double mutant N71S/F124K combines the effects of the two individual single mutations, but it gives a greater selective enhancement of activity with CB1954 over nitrofurazone than either of these, and the highest specificity constant for CB1954 of all the mutations studied.
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Affiliation(s)
- Paul R Race
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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Meddows TR, Savory AP, Grove JI, Moore T, Lloyd RG. RecN protein and transcription factor DksA combine to promote faithful recombinational repair of DNA double-strand breaks. Mol Microbiol 2005; 57:97-110. [PMID: 15948952 DOI: 10.1111/j.1365-2958.2005.04677.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In rapidly dividing bacterial cells, the machinery for repair of DNA double-strand breaks has to contend not only with the forces driving replication and transmission of the DNA but also its transcription. By exploiting I-SceI homing endonuclease to break the Escherichia coli chromosome at one or more defined locations, we have been able to investigate how these processes are co-ordinated and repair is accomplished. When breaks are induced at a single site, the SOS-inducible RecN protein and the transcription factor DksA combine to promote efficient repair. When induced at two or more, distantly located sites, RecN becomes almost indispensable. Many cells that do survive have extensive deletions of sequences flanking the break, with end points often coinciding with imperfect repeat elements. These findings herald a much greater complexity for chromosome repair than suggested by current mechanistic models and reveal a role for RecN in protecting the chromosome from break-induced chromosome rearrangements.
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Affiliation(s)
- Tom R Meddows
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
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Searle PF, Chen MJ, Hu L, Race PR, Lovering AL, Grove JI, Guise C, Jaberipour M, James ND, Mautner V, Young LS, Kerr DJ, Mountain A, White SA, Hyde EI. Nitroreductase: a prodrug-activating enzyme for cancer gene therapy. Clin Exp Pharmacol Physiol 2005; 31:811-6. [PMID: 15566399 DOI: 10.1111/j.1440-1681.2004.04085.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
1. The prodrug CB1954 (5-(aziridin-1-yl)-2,4-dinitrobenzamide) is activated by Escherichia coli nitroreductase (NTR) to a potent DNA-crosslinking agent. 2. Virus-mediated expression of NTR in tumour cells sensitizes them to CB1954 in vitro and in vivo, providing the basis for a strategy of cancer gene therapy. 3. A phase I trial of CB1954 in cancer patients has been completed, documenting the pharmacokinetics and establishing an acceptable dose. Subsequent trials of the replication-defective adenovirus CTL102 in patients with resectable tumours have documented expression of NTR in injected colorectal liver metastases, hepatocellular carcinoma, head and neck cancer and prostate cancer. Trials combining CTL102 and CB1954 are underway. 4. An oncolytic (replication-competent) adenovirus vector allowed increased expression of NTR in vitro and in a mouse tumour model, resulting in a greater reduction in tumour growth when combined with CB1954 treatment. 5. Alternative prodrugs may eventually prove superior to CB1954; a nitroaryl phosphoramide mustard prodrug activated by NTR shows a greater therapeutic index than CB1954 in a human ovarian carcinoma. 6. The crystal structure of NTR provided the basis for site-directed mutagenesis, which has identified a number of mutants with improved kinetics of CB1954 activation. These can provide improved cell sensitization to CB1954. Combinations of these are being tested. 7. The basis for a positive selection for improved NTR variants has been demonstrated.
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Affiliation(s)
- Peter F Searle
- Cancer Research UK Institute for Cancer Studies, University of Birmingham, Edgbaston, Birmingham.
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Grove JI, Lovering AL, Guise C, Race PR, Wrighton CJ, White SA, Hyde EI, Searle PF. Generation of Escherichia coli nitroreductase mutants conferring improved cell sensitization to the prodrug CB1954. Cancer Res 2003; 63:5532-7. [PMID: 14500391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Escherichia coli nitroreductase (NTR) activates the prodrug CB1954 to a cytotoxic derivative, allowing selective sensitization of NTR-expressing cells or tumors to the prodrug. This is one of several enzyme-prodrug combinations that are under development for cancer gene therapy, and the system has now entered clinical trials. Enhancing the catalytic efficiency of NTR for CB1954 could improve its therapeutic potential. From the crystal structure of an enzyme-ligand complex, we identified nine amino acid residues within the active site that could directly influence prodrug binding and catalysis. Mutant libraries were generated for each of these residues and clones screened for their ability to sensitize E. coli to CB1954. Amino acid substitutions at six positions conferred markedly greater sensitivity to CB1954 than did the WT enzyme; the best mutants, at residue F124, resulted in approximately 5-fold improvement. Using an adenovirus vector, we introduced the F124K NTR mutant into human SK-OV-3 ovarian carcinoma cells and showed it to be approximately 5-fold more potent in sensitizing the cells to CB1954 at the clinically relevant prodrug concentration of 1 micro M than was the WT enzyme. Enhanced mutant NTRs such as F124K should improve the efficacy of the NTR/CB1954 combination in cancer gene therapy.
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Affiliation(s)
- Jane I Grove
- The University of Birmingham Cancer Research United Kingdom Institute for Cancer Studies, Edgbaston, Birmingham B15 2TT
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Grove JI, Searle PF, Weedon SJ, Green NK, McNeish IA, Kerr DJ. Virus-directed enzyme prodrug therapy using CB1954. Anticancer Drug Des 1999; 14:461-72. [PMID: 10834268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The virus-directed enzyme prodrug therapy (VDEPT) anti-cancer 'gene therapy' strategy relies on the use of viral vectors for the efficient delivery to tumour cells of a 'suicide gene' encoding an enzyme which converts a non-toxic prodrug to a cytotoxic agent. The prodrug 5-(aziridin-1-yl)-2,4 dinitrobenzamide, CB1954, has been proposed for use in enzyme-prodrug gene therapy systems with the Escherichia coli enzyme nitroreductase (Ntr). Ntr converts CB1954 to 2- and 4-hydroxylamino derivatives, whereupon the non-enzymatic reaction of the 4-hydroxylamino derivative with cellular thio- esters generates a potent cytotoxic bifunctional alkylating agent capable of cross-linking DNA. Ntr delivery has been achieved in vitro using retroviral and adenoviral vectors and confirmed by immunocytochemical demonstration of Ntr expression. The Ntr-expressing cells have been shown to be sensitized to CB1954 by up to 2000-fold. The Ntr-CB1954 system shows effective bystander killing in mixed populations of Ntr-expressing and non-expressing cells treated with CB1954. The efficacy of this enzyme-prodrug approach in model systems compared with other VDEPT approaches demonstrates the feasibility and future promise of this gene therapy strategy.
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Affiliation(s)
- J I Grove
- Cobra Therapeutics Ltd, The Science Park, Keele, Staffordshire, UK.
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