1
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Javaid H, Barberis A, Chervova O, Nassiri I, Voloshin V, Sato Y, Ogawa S, Fairfax B, Buffa F, Humphrey TC. A role for SETD2 loss in tumorigenesis through DNA methylation dysregulation. BMC Cancer 2023; 23:721. [PMID: 37528416 PMCID: PMC10394884 DOI: 10.1186/s12885-023-11162-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/07/2023] [Indexed: 08/03/2023] Open
Abstract
SETD2-dependent H3 Lysine-36 trimethylation (H3K36me3) has been recently linked to the deposition of de-novo DNA methylation. SETD2 is frequently mutated in cancer, however, the functional impact of SETD2 loss and depletion on DNA methylation across cancer types and tumorigenesis is currently unknown. Here, we perform a pan-cancer analysis and show that both SETD2 mutation and reduced expression are associated with DNA methylation dysregulation across 21 out of the 24 cancer types tested. In renal cancer, these DNA methylation changes are associated with altered gene expression of oncogenes, tumour suppressors, and genes involved in neoplasm invasiveness, including TP53, FOXO1, and CDK4. This suggests a new role for SETD2 loss in tumorigenesis and cancer aggressiveness through DNA methylation dysregulation. Moreover, using a robust machine learning methodology, we develop and validate a 3-CpG methylation signature which is sufficient to predict SETD2 mutation status with high accuracy and correlates with patient prognosis.
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Affiliation(s)
- Hira Javaid
- Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Alessandro Barberis
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Olga Chervova
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Isar Nassiri
- Oxford Genomics Centre, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Vitaly Voloshin
- Royal Botanic Gardens Kew, Kew Green, Richmond, TW9 3AE, Surrey, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Yusuke Sato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Benjamin Fairfax
- The MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital/Headley Way, OX3 9DS, Oxford, UK
| | - Francesca Buffa
- Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Timothy C Humphrey
- Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK.
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, BN1 9RQ, Brighton, UK.
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2
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Nassiri I, Fairfax B, Lee A, Wu Y, Buck D, Piazza P. scQCEA: a framework for annotation and quality control report of single-cell RNA-sequencing data. BMC Genomics 2023; 24:381. [PMID: 37415108 DOI: 10.1186/s12864-023-09447-6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 06/13/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Systematic description of library quality and sequencing performance of single-cell RNA sequencing (scRNA-seq) data is imperative for subsequent downstream modules, including re-pooling libraries. While several packages have been developed to visualise quality control (QC) metrics for scRNA-seq data, they do not include expression-based QC to discriminate between true variation and background noise. RESULTS We present scQCEA (acronym of the single-cell RNA sequencing Quality Control and Enrichment Analysis), an R package to generate reports of process optimisation metrics for comparing sets of samples and visual evaluation of quality scores. scQCEA can import data from 10X or other single-cell platforms and includes functions for generating an interactive report of QC metrics for multi-omics data. In addition, scQCEA provides automated cell type annotation on scRNA-seq data using differential gene expression patterns for expression-based quality control. We provide a repository of reference gene sets, including 2348 marker genes, which are exclusively expressed in 95 human and mouse cell types. Using scRNA-seq data from 56 gene expressions and V(D)J T cell replicates, we show how scQCEA can be applied for the visual evaluation of quality scores for sets of samples. In addition, we use the summary of QC measures from 342 human and mouse shallow-sequenced gene expression profiles to specify optimal sequencing requirements to run a cell-type enrichment analysis function. CONCLUSIONS The open-source R tool will allow examining biases and outliers over biological and technical measures, and objective selection of optimal cluster numbers before downstream analysis. scQCEA is available at https://isarnassiri.github.io/scQCEA/ as an R package. Full documentation, including an example, is provided on the package website.
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Affiliation(s)
- Isar Nassiri
- Oxford Genomics Centre, Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Benjamin Fairfax
- MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford & Oxford Cancer Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Angela Lee
- Oxford Genomics Centre, Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yanxia Wu
- Oxford Genomics Centre, Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Buck
- Oxford Genomics Centre, Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Paolo Piazza
- Oxford Genomics Centre, Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
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3
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Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, Luchessi AD, Parra EJ, Cruz R, Carracedo A, Fawkes A, Murphy L, Rowan K, Pereira AC, Law A, Fairfax B, Hendry SC, Baillie JK. Author Correction: GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19. Nature 2023; 619:E61. [PMID: 37433877 PMCID: PMC10371859 DOI: 10.1038/s41586-023-06383-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)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Affiliation(s)
- Erola Pairo-Castineira
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Konrad Rawlik
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Andrew D Bretherick
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Pain Service, NHS Tayside, Ninewells Hospital and Medical School, Dundee, UK
| | - Ting Qi
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Isar Nassiri
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Marie Zechner
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Fiona Griffiths
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Wilna Oosthuyzen
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jonathan Millar
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Clark D Russell
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Tomas Malinauskas
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ryan Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Kirstie Morrice
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Alder Hey Children's Hospital, Liverpool, UK
| | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Manu Shankar-Hari
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | | | - Charles Hinds
- William Harvey Research Institute Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | | | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Colin Begg
- Royal Hospital for Children, Glasgow, UK
| | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- Centre for Biomedical Network Research on Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Department of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - José A Riancho
- IDIVAL, Santander, Spain
- Universidad de Cantabria, Santander, Spain
- Hospital U M Valdecilla, Santander, Spain
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud and Hospital San Jose TecSalud, Monterrey, Mexico
| | - Pablo Lapunzina
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IDIPAZ, Madrid, Spain
- ERN-ITHACA-European Reference Network, Paris, France
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Malak Abedalthagafi
- Genomic Research Department, King Fahad Medical City, Riyadh, Saudi Arabia
- Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
| | - Andre D Luchessi
- Department of Clinical Analysis and Toxicology, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Raquel Cruz
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Angel Carracedo
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
- Fundación Pública Galega de Medicina Xenómica, Sistema Galego de Saúde (SERGAS) Santiago de Compostela, Santiago de Compostela, Spain
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Kathy Rowan
- Intensive Care National Audit & Research Centre, London, UK
| | | | - Andy Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Benjamin Fairfax
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sara Clohisey Hendry
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - J Kenneth Baillie
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
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4
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Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, Luchessi AD, Parra EJ, Cruz R, Carracedo A, Fawkes A, Murphy L, Rowan K, Pereira AC, Law A, Fairfax B, Hendry SC, Baillie JK. GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19. Nature 2023; 617:764-768. [PMID: 37198478 PMCID: PMC10208981 DOI: 10.1038/s41586-023-06034-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/27/2023] [Indexed: 05/19/2023]
Abstract
Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown1 to be highly efficient for discovery of genetic associations2. Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group3. Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling (JAK1), monocyte-macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).
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Affiliation(s)
- Erola Pairo-Castineira
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Konrad Rawlik
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Andrew D Bretherick
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Pain Service, NHS Tayside, Ninewells Hospital and Medical School, Dundee, UK
| | - Ting Qi
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Isar Nassiri
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Marie Zechner
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Fiona Griffiths
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Wilna Oosthuyzen
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jonathan Millar
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Clark D Russell
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Tomas Malinauskas
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ryan Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Kirstie Morrice
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Alder Hey Children's Hospital, Liverpool, UK
| | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Manu Shankar-Hari
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | | | - Charles Hinds
- William Harvey Research Institute Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | | | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Colin Begg
- Royal Hospital for Children, Glasgow, UK
| | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- Centre for Biomedical Network Research on Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Department of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - José A Riancho
- IDIVAL, Santander, Spain
- Universidad de Cantabria, Santander, Spain
- Hospital U M Valdecilla, Santander, Spain
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud and Hospital San Jose TecSalud, Monterrey, Mexico
| | - Pablo Lapunzina
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IDIPAZ, Madrid, Spain
- ERN-ITHACA-European Reference Network, Paris, France
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Malak Abedalthagafi
- Genomic Research Department, King Fahad Medical City, Riyadh, Saudi Arabia
- Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
| | - Andre D Luchessi
- Department of Clinical Analysis and Toxicology, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Raquel Cruz
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Angel Carracedo
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
- Fundación Pública Galega de Medicina Xenómica, Sistema Galego de Saúde (SERGAS) Santiago de Compostela, Santiago de Compostela, Spain
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Kathy Rowan
- Intensive Care National Audit & Research Centre, London, UK
| | | | - Andy Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Benjamin Fairfax
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sara Clohisey Hendry
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - J Kenneth Baillie
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
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5
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Taylor CA, Watson RA, Tong O, Ye W, Nassiri I, Gilchrist JJ, de Los Aires AV, Sharma PK, Koturan S, Cooper RA, Woodcock VK, Jungkurth E, Shine B, Coupe N, Payne MJ, Church DN, Naranbhai V, Groha S, Emery P, Mankia K, Freedman ML, Choueiri TK, Middleton MR, Gusev A, Fairfax BP. IL7 genetic variation and toxicity to immune checkpoint blockade in patients with melanoma. Nat Med 2022; 28:2592-2600. [PMID: 36526722 PMCID: PMC9800275 DOI: 10.1038/s41591-022-02095-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 10/18/2022] [Indexed: 12/23/2022]
Abstract
Treatment with immune checkpoint blockade (ICB) frequently triggers immune-related adverse events (irAEs), causing considerable morbidity. In 214 patients receiving ICB for melanoma, we observed increased severe irAE risk in minor allele carriers of rs16906115, intronic to IL7. We found that rs16906115 forms a B cell-specific expression quantitative trait locus (eQTL) to IL7 in patients. Patients carrying the risk allele demonstrate increased pre-treatment B cell IL7 expression, which independently associates with irAE risk, divergent immunoglobulin expression and more B cell receptor mutations. Consistent with the role of IL-7 in T cell development, risk allele carriers have distinct ICB-induced CD8+ T cell subset responses, skewing of T cell clonality and greater proportional repertoire occupancy by large clones. Finally, analysis of TCGA data suggests that risk allele carriers independently have improved melanoma survival. These observations highlight key roles for B cells and IL-7 in both ICB response and toxicity and clinical outcomes in melanoma.
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Affiliation(s)
- Chelsea A Taylor
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Robert A Watson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - Orion Tong
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Weiyu Ye
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Isar Nassiri
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - James J Gilchrist
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alba Verge de Los Aires
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Piyush Kumar Sharma
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Surya Koturan
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Rosalin A Cooper
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Victoria K Woodcock
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - Elsita Jungkurth
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Brian Shine
- Department of Clinical Biochemistry, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Nicholas Coupe
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - Miranda J Payne
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - David N Church
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Vivek Naranbhai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Center for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Stefan Groha
- Department of Medical Oncology, Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Paul Emery
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
- National Institute for Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Kulveer Mankia
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
- National Institute for Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Mark R Middleton
- Department of Oncology, University of Oxford, Oxford, UK
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Alexander Gusev
- Department of Medical Oncology, Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Benjamin P Fairfax
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Department of Oncology, University of Oxford, Oxford, UK.
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
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Watson R, Taylor C, Tong O, Cooper R, Nassiri I, Jungkurth E, Sharma P, Verge de los Aires A, Ieremia E, Middleton M, Fairfax B. 734MO Deep sequencing of the T-cell receptor reveals common and reproducible CD8 T-cell receptor signatures of response to checkpoint immunotherapy. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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7
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Ahern DJ, Ai Z, Ainsworth M, Allan C, Allcock A, Angus B, Ansari MA, Arancibia-Cárcamo CV, Aschenbrenner D, Attar M, Baillie JK, Barnes E, Bashford-Rogers R, Bashyal A, Beer S, Berridge G, Beveridge A, Bibi S, Bicanic T, Blackwell L, Bowness P, Brent A, Brown A, Broxholme J, Buck D, Burnham KL, Byrne H, Camara S, Candido Ferreira I, Charles P, Chen W, Chen YL, Chong A, Clutterbuck EA, Coles M, Conlon CP, Cornall R, Cribbs AP, Curion F, Davenport EE, Davidson N, Davis S, Dendrou CA, Dequaire J, Dib L, Docker J, Dold C, Dong T, Downes D, Drakesmith H, Dunachie SJ, Duncan DA, Eijsbouts C, Esnouf R, Espinosa A, Etherington R, Fairfax B, Fairhead R, Fang H, Fassih S, Felle S, Fernandez Mendoza M, Ferreira R, Fischer R, Foord T, Forrow A, Frater J, Fries A, Gallardo Sanchez V, Garner LC, Geeves C, Georgiou D, Godfrey L, Golubchik T, Gomez Vazquez M, Green A, Harper H, Harrington HA, Heilig R, Hester S, Hill J, Hinds C, Hird C, Ho LP, Hoekzema R, Hollis B, Hughes J, Hutton P, Jackson-Wood MA, Jainarayanan A, James-Bott A, Jansen K, Jeffery K, Jones E, Jostins L, Kerr G, Kim D, Klenerman P, Knight JC, Kumar V, Kumar Sharma P, Kurupati P, Kwok A, Lee A, Linder A, Lockett T, Lonie L, Lopopolo M, Lukoseviciute M, Luo J, Marinou S, Marsden B, Martinez J, Matthews PC, Mazurczyk M, McGowan S, McKechnie S, Mead A, Mentzer AJ, Mi Y, Monaco C, Montadon R, Napolitani G, Nassiri I, Novak A, O'Brien DP, O'Connor D, O'Donnell D, Ogg G, Overend L, Park I, Pavord I, Peng Y, Penkava F, Pereira Pinho M, Perez E, Pollard AJ, Powrie F, Psaila B, Quan TP, Repapi E, Revale S, Silva-Reyes L, Richard JB, Rich-Griffin C, Ritter T, Rollier CS, Rowland M, Ruehle F, Salio M, Sansom SN, Sanches Peres R, Santos Delgado A, Sauka-Spengler T, Schwessinger R, Scozzafava G, Screaton G, Seigal A, Semple MG, Sergeant M, Simoglou Karali C, Sims D, Skelly D, Slawinski H, Sobrinodiaz A, Sousos N, Stafford L, Stockdale L, Strickland M, Sumray O, Sun B, Taylor C, Taylor S, Taylor A, Thongjuea S, Thraves H, Todd JA, Tomic A, Tong O, Trebes A, Trzupek D, Tucci FA, Turtle L, Udalova I, Uhlig H, van Grinsven E, Vendrell I, Verheul M, Voda A, Wang G, Wang L, Wang D, Watkinson P, Watson R, Weinberger M, Whalley J, Witty L, Wray K, Xue L, Yeung HY, Yin Z, Young RK, Youngs J, Zhang P, Zurke YX. A blood atlas of COVID-19 defines hallmarks of disease severity and specificity. Cell 2022; 185:916-938.e58. [PMID: 35216673 PMCID: PMC8776501 DOI: 10.1016/j.cell.2022.01.012] [Citation(s) in RCA: 117] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/16/2021] [Accepted: 01/17/2022] [Indexed: 02/06/2023]
Abstract
Treatment of severe COVID-19 is currently limited by clinical heterogeneity and incomplete description of specific immune biomarkers. We present here a comprehensive multi-omic blood atlas for patients with varying COVID-19 severity in an integrated comparison with influenza and sepsis patients versus healthy volunteers. We identify immune signatures and correlates of host response. Hallmarks of disease severity involved cells, their inflammatory mediators and networks, including progenitor cells and specific myeloid and lymphocyte subsets, features of the immune repertoire, acute phase response, metabolism, and coagulation. Persisting immune activation involving AP-1/p38MAPK was a specific feature of COVID-19. The plasma proteome enabled sub-phenotyping into patient clusters, predictive of severity and outcome. Systems-based integrative analyses including tensor and matrix decomposition of all modalities revealed feature groupings linked with severity and specificity compared to influenza and sepsis. Our approach and blood atlas will support future drug development, clinical trial design, and personalized medicine approaches for COVID-19.
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8
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Peng Y, Felce SL, Dong D, Penkava F, Mentzer AJ, Yao X, Liu G, Yin Z, Chen JL, Lu Y, Wellington D, Wing PAC, Dominey-Foy DCC, Jin C, Wang W, Hamid MA, Fernandes RA, Wang B, Fries A, Zhuang X, Ashley N, Rostron T, Waugh C, Sopp P, Hublitz P, Beveridge R, Tan TK, Dold C, Kwok AJ, Rich-Griffin C, Dejnirattisa W, Liu C, Kurupati P, Nassiri I, Watson RA, Tong O, Taylor CA, Kumar Sharma P, Sun B, Curion F, Revale S, Garner LC, Jansen K, Ferreira RC, Attar M, Fry JW, Russell RA, Stauss HJ, James W, Townsend A, Ho LP, Klenerman P, Mongkolsapaya J, Screaton GR, Dendrou C, Sansom SN, Bashford-Rogers R, Chain B, Smith GL, McKeating JA, Fairfax BP, Bowness P, McMichael AJ, Ogg G, Knight JC, Dong T. An immunodominant NP 105-113-B*07:02 cytotoxic T cell response controls viral replication and is associated with less severe COVID-19 disease. Nat Immunol 2022; 23:50-61. [PMID: 34853448 PMCID: PMC8709787 DOI: 10.1038/s41590-021-01084-z] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/26/2021] [Indexed: 11/11/2022]
Abstract
NP105-113-B*07:02-specific CD8+ T cell responses are considered among the most dominant in SARS-CoV-2-infected individuals. We found strong association of this response with mild disease. Analysis of NP105-113-B*07:02-specific T cell clones and single-cell sequencing were performed concurrently, with functional avidity and antiviral efficacy assessed using an in vitro SARS-CoV-2 infection system, and were correlated with T cell receptor usage, transcriptome signature and disease severity (acute n = 77, convalescent n = 52). We demonstrated a beneficial association of NP105-113-B*07:02-specific T cells in COVID-19 disease progression, linked with expansion of T cell precursors, high functional avidity and antiviral effector function. Broad immune memory pools were narrowed postinfection but NP105-113-B*07:02-specific T cells were maintained 6 months after infection with preserved antiviral efficacy to the SARS-CoV-2 Victoria strain, as well as Alpha, Beta, Gamma and Delta variants. Our data show that NP105-113-B*07:02-specific T cell responses associate with mild disease and high antiviral efficacy, pointing to inclusion for future vaccine design.
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Affiliation(s)
- Yanchun Peng
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
| | - Suet Ling Felce
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Danning Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- CAMS Key Laboratory of Tumor Immunology and Radiation Therapy, Xinjiang Tumor Hospital, Xinjiang Medical University, Urumqi, China
| | - Frank Penkava
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Xuan Yao
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Guihai Liu
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Zixi Yin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ji-Li Chen
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
| | - Yongxu Lu
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Dannielle Wellington
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
| | - Peter A C Wing
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Delaney C C Dominey-Foy
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chen Jin
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wenbo Wang
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Megat Abd Hamid
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ricardo A Fernandes
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Beibei Wang
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anastasia Fries
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Xiaodong Zhuang
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Neil Ashley
- Single Cell Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Timothy Rostron
- Sequencing Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Craig Waugh
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Paul Sopp
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Philip Hublitz
- Genome Engineering Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Ryan Beveridge
- Virus Screening Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Tiong Kit Tan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Christina Dold
- Oxford Vaccine Group, Department of Paediatrics, and NIHR Oxford Biomedical Research Centre, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Andrew J Kwok
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Wanwisa Dejnirattisa
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Prathiba Kurupati
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Isar Nassiri
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Robert A Watson
- Department of Oncology, University of Oxford, Oxford, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Orion Tong
- Department of Oncology, University of Oxford, Oxford, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Chelsea A Taylor
- Department of Oncology, University of Oxford, Oxford, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Piyush Kumar Sharma
- Department of Oncology, University of Oxford, Oxford, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Bo Sun
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Fabiola Curion
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Helmholtz Center Munich-German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | - Santiago Revale
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lucy C Garner
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kathrin Jansen
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | | | - Moustafa Attar
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | | | - Rebecca A Russell
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Hans J Stauss
- Institute of Immunity and Transplantation, University College London, London, UK
| | - William James
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Alain Townsend
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
| | - Ling-Pei Ho
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Dengue Hemorrhagic Fever Research Unit, Office for Research and Development, Faculty of Medicine, Siriaj Hospital, Mahidol Unviversity, Bangkok, Thailand
| | - Gavin R Screaton
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Calliope Dendrou
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stephen N Sansom
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | | | - Benny Chain
- Division of Infection and Immunity, University College London, London, UK
| | | | - Jane A McKeating
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Benjamin P Fairfax
- Department of Oncology, University of Oxford, Oxford, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Paul Bowness
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Andrew J McMichael
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Graham Ogg
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
| | - Julian C Knight
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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9
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Watson RA, Tong O, Cooper R, Taylor CA, Sharma PK, de Los Aires AV, Mahé EA, Ruffieux H, Nassiri I, Middleton MR, Fairfax BP. Immune checkpoint blockade sensitivity and progression-free survival associates with baseline CD8 + T cell clone size and cytotoxicity. Sci Immunol 2021; 6:eabj8825. [PMID: 34597125 DOI: 10.1126/sciimmunol.abj8825] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Robert A Watson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DU, UK.,Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK.,MRC Biostatistics Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0SR, UK
| | - Orion Tong
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DU, UK.,Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Rosalin Cooper
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DU, UK.,Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Chelsea A Taylor
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DU, UK.,Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Piyush K Sharma
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DU, UK.,Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Alba Verge de Los Aires
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DU, UK.,Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Elise A Mahé
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DU, UK.,Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Hélène Ruffieux
- MRC Biostatistics Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0SR, UK
| | - Isar Nassiri
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DU, UK.,Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Mark R Middleton
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK.,Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford OX3 7LE, UK
| | - Benjamin P Fairfax
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DU, UK.,Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK.,Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford OX3 7LE, UK
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10
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Sasson SC, Slevin SM, Cheung VT, Nassiri I, Olsson-Brown A, Fryer E, Ferreira RC, Trzupek D, Gupta T, Al-Hillawi L, Issaias ML, Easton A, Campo L, FitzPatrick ME, Adams J, Chitnis M, Protheroe A, Tuthill M, Coupe N, Simmons A, Payne M, Middleton MR, Travis SP, Fairfax BP, Klenerman P, Brain O. Interferon-Gamma-Producing CD8 + Tissue Resident Memory T Cells Are a Targetable Hallmark of Immune Checkpoint Inhibitor-Colitis. Gastroenterology 2021; 161:1229-1244.e9. [PMID: 34147519 PMCID: PMC8527886 DOI: 10.1053/j.gastro.2021.06.025] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [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: 11/26/2020] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS The pathogenesis of immune checkpoint inhibitor (ICI)-colitis remains incompletely understood. We sought to identify key cellular drivers of ICI-colitis and their similarities to idiopathic ulcerative colitis, and to determine potential novel therapeutic targets. METHODS We used a cross-sectional approach to study patients with ICI-colitis, those receiving ICI without the development of colitis, idiopathic ulcerative colitis, and healthy controls. A subset of patients with ICI-colitis were studied longitudinally. We applied a range of methods, including multiparameter and spectral flow cytometry, spectral immunofluorescence microscopy, targeted gene panels, and bulk and single-cell RNA sequencing. RESULTS We demonstrate CD8+ tissue resident memory T (TRM) cells are the dominant activated T cell subset in ICI-colitis. The pattern of gastrointestinal immunopathology is distinct from ulcerative colitis at both the immune and epithelial-signaling levels. CD8+ TRM cell activation correlates with clinical and endoscopic ICI-colitis severity. Single-cell RNA sequencing analysis confirms activated CD8+ TRM cells express high levels of transcripts for checkpoint inhibitors and interferon-gamma in ICI-colitis. We demonstrate similar findings in both anti-CTLA-4/PD-1 combination therapy and in anti-PD-1 inhibitor-associated colitis. On the basis of our data, we successfully targeted this pathway in a patient with refractory ICI-colitis, using the JAK inhibitor tofacitinib. CONCLUSIONS Interferon gamma-producing CD8+ TRM cells are a pathological hallmark of ICI-colitis and a novel target for therapy.
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Affiliation(s)
- Sarah C. Sasson
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Stephanie M. Slevin
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Vincent T.F. Cheung
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Isar Nassiri
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Anna Olsson-Brown
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom,The Clatterbridge Cancer Centre National Health Service Foundation Trust, Wirral, United Kingdom
| | - Eve Fryer
- Department of Cellular Pathology, Oxford University Hospitals National Health Service Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Ricardo C. Ferreira
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Dominik Trzupek
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Tarun Gupta
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Lulia Al-Hillawi
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Mari-lenna Issaias
- Department of Oncology, University of Oxford and Oxford Cancer Centre, Churchill Hospital, Oxford University Hospitals National Health Service Foundation Trust, Oxford, United Kingdom
| | - Alistair Easton
- Department of Cellular Pathology, Oxford University Hospitals National Health Service Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Leticia Campo
- Translational Histopathology Laboratory, Department of Oncology, University of Oxford, United Kingdom
| | - Michael E.B. FitzPatrick
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Joss Adams
- Berkshire Cancer Centre, Royal Berkshire Hospital, Reading, United Kingdom
| | - Meenali Chitnis
- Department of Oncology, University of Oxford and Oxford Cancer Centre, Churchill Hospital, Oxford University Hospitals National Health Service Foundation Trust, Oxford, United Kingdom
| | - Andrew Protheroe
- Department of Oncology, University of Oxford and Oxford Cancer Centre, Churchill Hospital, Oxford University Hospitals National Health Service Foundation Trust, Oxford, United Kingdom
| | - Mark Tuthill
- Department of Oncology, University of Oxford and Oxford Cancer Centre, Churchill Hospital, Oxford University Hospitals National Health Service Foundation Trust, Oxford, United Kingdom
| | - Nicholas Coupe
- Department of Oncology, University of Oxford and Oxford Cancer Centre, Churchill Hospital, Oxford University Hospitals National Health Service Foundation Trust, Oxford, United Kingdom
| | - Alison Simmons
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Miranda Payne
- Department of Oncology, University of Oxford and Oxford Cancer Centre, Churchill Hospital, Oxford University Hospitals National Health Service Foundation Trust, Oxford, United Kingdom
| | - Mark R. Middleton
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom,Department of Oncology, University of Oxford and Oxford Cancer Centre, Churchill Hospital, Oxford University Hospitals National Health Service Foundation Trust, Oxford, United Kingdom
| | - Simon P.L. Travis
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | | | - Benjamin P. Fairfax
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,Department of Oncology, University of Oxford and Oxford Cancer Centre, Churchill Hospital, Oxford University Hospitals National Health Service Foundation Trust, Oxford, United Kingdom
| | - Paul Klenerman
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Oliver Brain
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom; National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom.
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Cooper R, Nassiri I, Watson R, Taylor C, Tong O, Sharma PK, Verge de los Aires A, Mahé E, Danielli S, Fairfax B. 1761MO Defining subset-wise myeloid responses to immune checkpoint blockade in melanoma. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.1706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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12
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Ruffieux H, Fairfax BP, Nassiri I, Vigorito E, Wallace C, Richardson S, Bottolo L. EPISPOT: An epigenome-driven approach for detecting and interpreting hotspots in molecular QTL studies. Am J Hum Genet 2021; 108:983-1000. [PMID: 33909991 PMCID: PMC8206410 DOI: 10.1016/j.ajhg.2021.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 04/08/2021] [Indexed: 12/27/2022] Open
Abstract
We present EPISPOT, a fully joint framework which exploits large panels of epigenetic annotations as variant-level information to enhance molecular quantitative trait locus (QTL) mapping. Thanks to a purpose-built Bayesian inferential algorithm, EPISPOT accommodates functional information for both cis and trans actions, including QTL hotspot effects. It effectively couples simultaneous QTL analysis of thousands of genetic variants and molecular traits with hypothesis-free selection of biologically interpretable annotations which directly contribute to the QTL effects. This unified, epigenome-aided learning boosts statistical power and sheds light on the regulatory basis of the uncovered hits; EPISPOT therefore marks an essential step toward improving the challenging detection and functional interpretation of trans-acting genetic variants and hotspots. We illustrate the advantages of EPISPOT in simulations emulating real-data conditions and in a monocyte expression QTL study, which confirms known hotspots and finds other signals, as well as plausible mechanisms of action. In particular, by highlighting the role of monocyte DNase-I sensitivity sites from >150 epigenetic annotations, we clarify the mediation effects and cell-type specificity of major hotspots close to the lysozyme gene. Our approach forgoes the daunting and underpowered task of one-annotation-at-a-time enrichment analyses for prioritizing cis and trans QTL hits and is tailored to any transcriptomic, proteomic, or metabolomic QTL problem. By enabling principled epigenome-driven QTL mapping transcriptome-wide, EPISPOT helps progress toward a better functional understanding of genetic regulation.
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Affiliation(s)
- Hélène Ruffieux
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, UK.
| | - Benjamin P Fairfax
- Department of Oncology, MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Isar Nassiri
- Department of Oncology, MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Elena Vigorito
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, UK
| | - Chris Wallace
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Sylvia Richardson
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, UK; The Alan Turing Institute, London NW1 2DB, UK
| | - Leonardo Bottolo
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, UK; The Alan Turing Institute, London NW1 2DB, UK; Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
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13
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Ye W, Olsson-Brown A, Watson RA, Cheung VTF, Morgan RD, Nassiri I, Cooper R, Taylor CA, Akbani U, Brain O, Matin RN, Coupe N, Middleton MR, Coles M, Sacco JJ, Payne MJ, Fairfax BP. Checkpoint-blocker-induced autoimmunity is associated with favourable outcome in metastatic melanoma and distinct T-cell expression profiles. Br J Cancer 2021; 124:1661-1669. [PMID: 33723392 PMCID: PMC8110747 DOI: 10.1038/s41416-021-01310-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/13/2021] [Accepted: 02/03/2021] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Immune checkpoint blockers (ICBs) activate CD8+ T cells, eliciting both anti-cancer activity and immune-related adverse events (irAEs). The relationship of irAEs with baseline parameters and clinical outcome is unclear. METHODS Retrospective evaluation of irAEs on survival was performed across primary (N = 144) and secondary (N = 211) independent cohorts of patients with metastatic melanoma receiving single agent (pembrolizumab/nivolumab-sICB) or combination (nivolumab and ipilimumab-cICB) checkpoint blockade. RNA from pre-treatment and post-treatment CD8+ T cells was sequenced and differential gene expression according to irAE development assessed. RESULTS 58.3% of patients developed early irAEs and this was associated with longer progression-free (PFS) and overall survival (OS) across both cohorts (log-rank test, OS: P < 0.0001). Median survival for patients without irAEs was 16.6 months (95% CI: 10.9-33.4) versus not-reached (P = 2.8 × 10-6). Pre-treatment monocyte and neutrophil counts, but not BMI, were additional predictors of clinical outcome. Differential expression of numerous gene pathway members was observed in CD8+ T cells according to irAE development, and patients not developing irAEs demonstrating upregulated CXCR1 pre- and post-treatment. CONCLUSIONS Early irAE development post-ICB is associated with favourable survival in MM. Development of irAEs is coupled to expression of numerous gene pathways, suggesting irAE development in-part reflects baseline immune activation.
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Affiliation(s)
- Weiyu Ye
- grid.4991.50000 0004 1936 8948Oxford University Clinical Academic Graduate School, University of Oxford, Oxford, UK
| | - Anna Olsson-Brown
- grid.418624.d0000 0004 0614 6369The Clatterbridge Cancer Centre, Wirral, UK ,grid.10025.360000 0004 1936 8470University of Liverpool, Liverpool, UK
| | - Robert A. Watson
- grid.415719.f0000 0004 0488 9484Department of Oncology, Churchill Hospital, Oxford, UK ,grid.4991.50000 0004 1936 8948The MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Vincent T. F. Cheung
- grid.4991.50000 0004 1936 8948Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Robert D. Morgan
- grid.412917.80000 0004 0430 9259Department of Oncology, The Christie NHS Foundation Trust, Manchester, UK
| | - Isar Nassiri
- grid.415719.f0000 0004 0488 9484Department of Oncology, Churchill Hospital, Oxford, UK ,grid.4991.50000 0004 1936 8948The MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Rosalin Cooper
- grid.415719.f0000 0004 0488 9484Department of Oncology, Churchill Hospital, Oxford, UK ,grid.4991.50000 0004 1936 8948The MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Chelsea A. Taylor
- grid.415719.f0000 0004 0488 9484Department of Oncology, Churchill Hospital, Oxford, UK ,grid.4991.50000 0004 1936 8948The MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Umair Akbani
- grid.418624.d0000 0004 0614 6369The Clatterbridge Cancer Centre, Wirral, UK ,grid.10025.360000 0004 1936 8470University of Liverpool, Liverpool, UK
| | - Oliver Brain
- grid.4991.50000 0004 1936 8948Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Rubeta N. Matin
- grid.415719.f0000 0004 0488 9484Department of Oncology, Churchill Hospital, Oxford, UK ,grid.415719.f0000 0004 0488 9484Department of Dermatology, Churchill Hospital, Oxford, UK
| | - Nicholas Coupe
- grid.415719.f0000 0004 0488 9484Department of Oncology, Churchill Hospital, Oxford, UK
| | - Mark R. Middleton
- grid.415719.f0000 0004 0488 9484Department of Oncology, Churchill Hospital, Oxford, UK ,grid.8348.70000 0001 2306 7492NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Mark Coles
- grid.8348.70000 0001 2306 7492NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK ,grid.4991.50000 0004 1936 8948Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Joseph J. Sacco
- grid.418624.d0000 0004 0614 6369The Clatterbridge Cancer Centre, Wirral, UK ,grid.10025.360000 0004 1936 8470University of Liverpool, Liverpool, UK
| | - Miranda J. Payne
- grid.415719.f0000 0004 0488 9484Department of Oncology, Churchill Hospital, Oxford, UK
| | - Benjamin P. Fairfax
- grid.415719.f0000 0004 0488 9484Department of Oncology, Churchill Hospital, Oxford, UK ,grid.4991.50000 0004 1936 8948The MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK ,grid.8348.70000 0001 2306 7492NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
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14
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Watson R, Tong O, Nassiri I, Cooper R, Taylor C, Verge de los Aires A, Middleton M, Fairfax B. 1947P Single cell analysis reveals that CD8+ T cell clone size determines response to immune checkpoint blockade. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.1339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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15
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Nassiri I, Inga A, Meškytė EM, Alessandrini F, Ciribilli Y, Priami C. Regulatory Crosstalk of Doxorubicin, Estradiol and TNFα Combined Treatment in Breast Cancer-derived Cell Lines. Sci Rep 2019; 9:15172. [PMID: 31645610 PMCID: PMC6811586 DOI: 10.1038/s41598-019-51349-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 09/28/2019] [Indexed: 11/10/2022] Open
Abstract
We present a new model of ESR1 network regulation based on analysis of Doxorubicin, Estradiol, and TNFα combination treatment in MCF-7. We used Doxorubicin as a therapeutic agent, TNFα as marker and mediator of an inflammatory microenvironment and 17β-Estradiol (E2) as an agonist of Estrogen Receptors, known predisposing factor for hormone-driven breast cancer, whose pharmacological inhibition reduces the risk of breast cancer recurrence. Based on the results of transcriptomics analysis, we found 71 differentially expressed genes that are specific for the combination treatment with Doxorubicin + Estradiol + TNFα in comparison with single or double treatments. The responsiveness to the triple treatment was examined for seven genes by qPCR, of which six were validated, and then extended to four additional cell lines differing for p53 and/or ER status. The results of differential regulation enrichment analysis highlight the role of the ESR1 network that included 36 of 71 specific differentially expressed genes. We propose that the combined activation of p53 and NF-kB transcription factors significantly influences ligand-dependent, ER-driven transcriptional responses, also of the ESR1 gene itself. These results provide a model of coordinated interaction of TFs to explain the Doxorubicin, E2 and TNFα induced repression mechanisms.
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Affiliation(s)
- Isar Nassiri
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, TN, Italy
| | - Alberto Inga
- Laboratory of Transcriptional Networks, Department CIBIO, University of Trento, 38123, Trento, Italy
| | - Erna Marija Meškytė
- Laboratory of Molecular Cancer Genetics, Department CIBIO, University of Trento, 38123, Trento, Italy.,Department of Biological Models, Life Sciences Centre, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Federica Alessandrini
- Laboratory of Molecular Cancer Genetics, Department CIBIO, University of Trento, 38123, Trento, Italy
| | - Yari Ciribilli
- Laboratory of Molecular Cancer Genetics, Department CIBIO, University of Trento, 38123, Trento, Italy
| | - Corrado Priami
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, TN, Italy. .,Dipartimento di Informatica, Università di Pisa, Pisa, Italy.
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16
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Al-Mossawi H, Yager N, Taylor CA, Lau E, Danielli S, de Wit J, Gilchrist J, Nassiri I, Mahe EA, Lee W, Rizvi L, Makino S, Cheeseman J, Neville M, Knight JC, Bowness P, Fairfax BP. Context-specific regulation of surface and soluble IL7R expression by an autoimmune risk allele. Nat Commun 2019; 10:4575. [PMID: 31594933 PMCID: PMC6783569 DOI: 10.1038/s41467-019-12393-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 09/04/2019] [Indexed: 01/19/2023] Open
Abstract
IL-7 is a key factor in T cell immunity and common variants at IL7R, encoding its receptor, are associated with autoimmune disease susceptibility. IL7R mRNA is induced in stimulated monocytes, yet a function for IL7R in monocyte biology remains unexplored. Here we characterize genetic regulation of IL7R at the protein level in healthy individuals, and find that monocyte surface and soluble IL7R (sIL7R) are markedly induced by lipopolysaccharide. In monocytes, both surface IL7R and sIL7R expression strongly associate with allelic carriage of rs6897932, a disease-associated IL7R polymorphism. Monocytes produce more sIL7R than CD4 + T cells, and the amount is additionally correlated with the expression of DDX39A, encoding a splicing factor. Synovial fluid-derived monocytes from patients with spondyloarthritis are enriched for IL7R+ cells with a unique transcriptional profile that overlaps with IL-7-induced gene sets. Our data thus suggest a previously unappreciated function for monocytes in IL-7 biology and IL7R-associated diseases.
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Affiliation(s)
- Hussein Al-Mossawi
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Nicole Yager
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Chelsea A Taylor
- Department of Oncology, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Evelyn Lau
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sara Danielli
- Department of Oncology, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Jelle de Wit
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - James Gilchrist
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Isar Nassiri
- Department of Oncology, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Elise A Mahe
- Department of Oncology, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Wanseon Lee
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Laila Rizvi
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Seiko Makino
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jane Cheeseman
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Matt Neville
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Paul Bowness
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Benjamin P Fairfax
- Department of Oncology, Weatherall Institute of Molecular Medicine, Oxford, UK.
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17
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Fairfax B, Taylor C, Watson R, Nassiri I, Fang H, Mahe E, Cooper R, Danielli S, Woodcock V, Traill Z, Knight J, Payne M, Middleton M. Early peripheral T-cell responses predict oncological outcome to checkpoint immune blockade in metastatic melanoma. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz253.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Nassiri I, McCall MN. Systematic exploration of cell morphological phenotypes associated with a transcriptomic query. Nucleic Acids Res 2019; 46:e116. [PMID: 30011038 PMCID: PMC6212779 DOI: 10.1093/nar/gky626] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 07/10/2018] [Indexed: 12/23/2022] Open
Abstract
Cell morphological phenotypes, including shape, size, intensity, and texture of cellular compartments have been shown to change in response to perturbation with small molecule compounds. Image-based cell profiling or cell morphological profiling has been used to associate changes of cell morphological features with alterations in cellular function and to infer molecular mechanisms of action. Recently, the Library of Integrated Network-based Cellular Signatures (LINCS) Project has measured gene expression and performed image-based cell profiling on cell lines treated with 9515 unique compounds. These data provide an opportunity to study the interdependence between transcription and cell morphology. Previous methods to investigate cell phenotypes have focused on targeting candidate genes as components of known pathways, RNAi morphological profiling, and cataloging morphological defects; however, these methods do not provide an explicit model to link transcriptomic changes with corresponding alterations in morphology. To address this, we propose a cell morphology enrichment analysis to assess the association between transcriptomic alterations and changes in cell morphology. Additionally, for a new transcriptomic query, our approach can be used to predict associated changes in cellular morphology. We demonstrate the utility of our method by applying it to cell morphological changes in a human bone osteosarcoma cell line.
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Affiliation(s)
- Isar Nassiri
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA.,Department of Oncology, Weatherall Institute for Molecular Medicine, University of Oxford, UK
| | - Matthew N McCall
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA.,Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, USA
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Al-Mossawi H, Yager N, Taylor C, Danielli S, Gilchrist J, Nassiri I, Mahe E, Knight J, Fairfax BP, Bowness P. O32 Ankylosing spondylitis associated polymorphism of the IL7R controls expression surface and soluble IL7R-alpha during in inflammation. Rheumatology (Oxford) 2019. [DOI: 10.1093/rheumatology/kez105.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Hussein Al-Mossawi
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Nicole Yager
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Chelsea Taylor
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Sara Danielli
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - James Gilchrist
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Isar Nassiri
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Elise Mahe
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Benjamin P Fairfax
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Paul Bowness
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
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Gowran A, Kulikova T, Lewis FC, Foldes G, Fuentes L, Viiri LE, Spinelli V, Costa A, Perbellini F, Sid-Otmane C, Bax NAM, Pekkanen-Mattila M, Schiano C, Chaloupka A, Forini F, Sarkozy M, De Jager SCA, Vajen T, Glezeva N, Lee HW, Golovkin A, Kucera T, Musikhina NA, Korzhenkov NP, Santuchi MDEC, Munteanu D, Garcia RG, Ang R, Usui S, Kamilova U, Jumeau C, Aberg M, Kostina DA, Brandt MM, Muntean D, Lindner D, Sadaba R, Bacova B, Nikolov A, Sedmera D, Ryabov V, Neto FP, Lynch M, Portero V, Kui P, Howarth FC, Gualdoni A, Prorok J, Diolaiuti L, Vostarek F, Wagner M, Abela MA, Nebert C, Xiang W, Kloza M, Maslenko A, Grechanyk M, Bhattachariya A, Morawietz H, Babaeva AR, Martinez Sanchez SM, Krychtiuk KA, Starodubova J, Fiorelli S, Rinne P, Ozkaramanli Gur D, Hofbauer T, Starodubova J, Stellos K, Pinon P, Tsoref O, Thaler B, Fraga-Silva RA, Fuijkschot WW, Shaaban MNS, Matthaeus C, Deluyker D, Scardigli M, Zahradnikova A, Dominguez A, Kondrat'eva D, Sosorburam T, Murarikova M, Duerr GD, Griecsova L, Portnichenko VI, Smolina N, Duicu OANAM, Elder JM, Zaglia T, Lorenzon A, Ruperez C, Woudstra L, Suffee N, De Lucia C, Tsoref O, Russell-Hallinan A, Menendez-Montes I, Kapelko VI, Emmens RW, Hetman O, Van Der Laarse WJ, Goncharov S, Adao R, Huisamen B, Sirenko O, Kamilova U, Nassiri I, Tserendavaa SUMIYA, Yushko K, Baldan Martin M, Falcone C, Vigorelli V, Nigro P, Pompilio G, Stepanova O, Valikhov M, Samko A, Masenko V, Tereschenko S, Teoh T, Domenjo-Vila E, Theologou T, Field M, Awad W, Yasin M, Nadal-Ginard B, Ellison-Hughes GM, Hellen N, Vittay O, Harding SE, Gomez-Cid L, Fernandez-Santos ME, Suarez-Sancho S, Plasencia V, Climent A, Sanz-Ruiz R, Hedhammar M, Atienza F, Fernandez-Aviles F, Kiamehr M, Oittinen M, Viiri KM, Kaikkonen M, Aalto-Setala K, Diolaiuti L, Laurino A, Sartiani L, Vona A, Zanardelli M, Cerbai E, Failli P, Hortigon-Vinagre MP, Van Der Heyden M, Burton FL, Smith GL, Watson S, Scigliano M, Tkach S, Alayoubi S, Harding SE, Terracciano CM, Ly HQ, Mauretti A, Van Marion MH, Van Turnhout MC, Van Der Schaft DWJ, Sahlgren CM, Goumans MJ, Bouten CVC, Vuorenpaa H, Penttinen K, Sarkanen R, Ylikomi T, Heinonen T, Aalto-Setala K, Grimaldi V, Aprile M, Esposito R, Maiello C, Soricelli A, Colantuoni V, Costa V, Ciccodicola A, Napoli C, Rowe GC, Johnson K, Arany ZP, Del Monte F, D'aurizio R, Kusmic C, Nicolini G, Baumgart M, Groth M, Ucciferri N, Iervasi G, Pitto L, Pipicz M, Gaspar R, Siska A, Foldesi I, Kiss K, Bencsik P, Thum T, Batkai S, Csont T, Haan JJ, Bosch L, Brans MAD, Van De Weg SM, Deddens JC, Lee SJ, Sluijter JPG, Pasterkamp G, Werner I, Projahn D, Staudt M, Curaj A, Soenmez TT, Simsekyilmaz S, Hackeng TM, Von Hundelshausen P, Koenen RR, Weber C, Liehn EA, Santos-Martinez M, Medina C, Watson C, Mcdonald K, Gilmer J, Ledwidge M, Song SH, Lee MY, Park MH, Choi JC, Ahn JH, Park JS, Oh JH, Choi JH, Lee HC, Cha KS, Hong TJ, Kudryavtsev I, Serebryakova M, Malashicheva A, Shishkova A, Zhiduleva E, Moiseeva O, Durisova M, Blaha M, Melenovsky V, Pirk J, Kautzner J, Petelina TI, Gapon LI, Gorbatenko EA, Potolinskaya YV, Arkhipova EV, Solodenkova KS, Osadchuk MA, Dutra MF, Oliveira FCB, Silva MM, Passos-Silva DG, Goncalves R, Santos RAS, Da Silva RF, Gavrilescu CM, Paraschiv CM, Manea P, Strat LC, Gomez JMG, Merino D, Hurle MA, Nistal JF, Aires A, Cortajarena AL, Villar AV, Abramowitz J, Birnbaumer L, Gourine AV, Tinker A, Takamura M, Takashima S, Inoue O, Misu H, Takamura T, Kaneko S, Alieva TOHIRA, Mougenot N, Dufilho M, Hatem S, Siegbahn A, Kostina AS, Uspensky VE, Moiseeva OM, Kostareva AA, Malashicheva AB, Van Dijk CGM, Chrifi I, Verhaar MC, Duncker DJ, Cheng C, Sturza A, Petrus A, Duicu O, Kiss L, Danila M, Baczko I, Jost N, Gotzhein F, Schon J, Schwarzl M, Hinrichs S, Blankenberg S, Volker U, Hammer E, Westermann D, Martinez-Martinez E, Arrieta V, Fernandez-Celis A, Jimenez-Alfaro L, Melero A, Alvarez-Asiain V, Cachofeiro V, Lopez-Andres N, Tribulova N, Wallukat G, Knezl V, Radosinska J, Barancik M, Tsinlikov I, Tsinlikova I, Nicoloff G, Blazhev A, Pesevski Z, Kvasilova A, Stopkova T, Eckhardt A, Buffinton CM, Nanka O, Kercheva M, Suslova T, Gusakova A, Ryabova T, Markov V, Karpov R, Seemann H, Alcantara TC, Santuchi MDEC, Fonseca SG, Da Silva RF, Barallobre-Barreiro J, Oklu R, Fava M, Baig F, Yin X, Albadawi H, Jahangiri M, Stoughton J, Mayr M, Podliesna SP, Veerman CCV, Verkerk AOV, Klerk MK, Lodder EML, Mengarelli IM, Bezzina CRB, Remme CAR, Takacs H, Polyak A, Morvay N, Lepran I, Tiszlavicz L, Nagy N, Ordog B, Farkas A, Forster T, Varro A, Farkas AS, Jayaprakash P, Parekh K, Ferdous Z, Oz M, Dobrzynski H, Adrian TE, Landi S, Bonzanni M, D'souza A, Boyett M, Bucchi A, Baruscotti M, Difrancesco D, Barbuti A, Kui P, Takacs H, Oravecz K, Hezso T, Polyak A, Levijoki J, Pollesello P, Koskelainen T, Otsomaa L, Farkas AS, Papp JGY, Varro A, Toth A, Acsai K, Dini L, Mazzoni L, Sartiani L, Cerbai E, Mugelli A, Svatunkova J, Sedmera D, Deffge C, Baer C, Weinert S, Braun-Dullaeus RC, Herold J, Cassar AC, Zahra GZ, Pllaha EP, Dingli PD, Montefort SM, Xuereb RGX, Aschacher T, Messner B, Eichmair E, Mohl W, Reglin B, Rong W, Nitzsche B, Maibier M, Guimaraes P, Ruggeri A, Secomb TW, Pries AR, Baranowska-Kuczko M, Karpinska O, Kusaczuk M, Malinowska B, Kozlowska H, Demikhova N, Vynnychenko L, Prykhodko O, Grechanyk N, Kuryata A, Cottrill KA, Du L, Bjorck HM, Maleki S, Franco-Cereceda A, Chan SY, Eriksson P, Giebe S, Cockcroft N, Hewitt K, Brux M, Brunssen C, Tarasov AA, Davidov SI, Reznikova EA, Tapia Abellan A, Angosto Bazarra D, Pelegrin Vivancos P, Montoro Garcia S, Kastl SP, Pongratz T, Goliasch G, Gaspar L, Maurer G, Huber K, Dostal E, Pfaffenberger S, Oravec S, Wojta J, Speidl WS, Osipova I, Sopotova I, Eligini S, Cosentino N, Marenzi G, Tremoli E, Rami M, Ring L, Steffens S, Gur O, Gurkan S, Mangold A, Scherz T, Panzenboeck A, Staier N, Heidari H, Mueller J, Lang IM, Osipova I, Sopotova I, Gatsiou A, Stamatelopoulos K, Perisic L, John D, Lunella FF, Eriksson P, Hedin U, Zeiher A, Dimmeler S, Nunez L, Moure R, Marron-Linares G, Flores X, Aldama G, Salgado J, Calvino R, Tomas M, Bou G, Vazquez N, Hermida-Prieto M, Vazquez-Rodriguez JM, Amit U, Landa N, Kain D, Tyomkin D, David A, Leor J, Hohensinner PJ, Baumgartner J, Krychtiuk KA, Maurer G, Huber K, Baik N, Miles LA, Wojta J, Seeman H, Montecucco F, Da Silva AR, Costa-Fraga FP, Anguenot L, Mach FP, Santos RAS, Stergiopulos N, Da Silva RF, Kupreishvili K, Vonk ABA, Smulders YM, Van Hinsbergh VWM, Stooker W, Niessen HWM, Krijnen PAJ, Ashmawy MM, Salama MA, Elamrosy MZ, Juettner R, Rathjen FG, Bito V, Crocini C, Ferrantini C, Gabbrielli T, Silvestri L, Coppini R, Tesi C, Cerbai E, Poggesi C, Pavone FS, Sacconi L, Mackova K, Zahradnik I, Zahradnikova A, Diaz I, Sanchez De Rojas De Pedro E, Hmadcha K, Calderon Sanchez E, Benitah JP, Gomez AM, Smani T, Ordonez A, Afanasiev SA, Egorova MV, Popov SV, Wu Qing P, Cheng X, Carnicka S, Pancza D, Jasova M, Kancirova I, Ferko M, Ravingerova T, Wu S, Schneider M, Marggraf V, Verfuerth L, Frede S, Boehm O, Dewald O, Baumgarten G, Kim SC, Farkasova V, Gablovsky I, Bernatova I, Ravingerova T, Nosar V, Portnychenko A, Drevytska T, Mankovska I, Gogvadze V, Sejersen T, Kostareva A, Sturza A, Wolf A, Privistirescu A, Danila M, Muntean D, O ' Gara P, Sanchez-Alonso JL, Harding SE, Lyon AR, Prando V, Pianca N, Lo Verso F, Milan G, Pesce P, Sandri M, Mongillo M, Beffagna G, Poloni G, Dazzo E, Sabatelli P, Doliana R, Polishchuk R, Carnevale D, Lembo G, Bonaldo P, Braghetta P, Rampazzo A, Cairo M, Giralt M, Villarroya F, Planavila A, Biesbroek PS, Emmens RWE, Juffermans LJM, Van Der Wall AC, Van Rossum AC, Niessen JWM, Krijnen PAJ, Moor Morris T, Dilanian G, Farahmand P, Puceat M, Hatem S, Gambino G, Petraglia L, Elia A, Komici K, Femminella GD, D'amico ML, Pagano G, Cannavo A, Liccardo D, Koch WJ, Nolano M, Leosco D, Ferrara N, Rengo G, Amit U, Landa N, Kain D, Leor J, Neary R, Shiels L, Watson C, Baugh J, Palacios B, Escobar B, Alonso AV, Guzman G, Ruiz-Cabello J, Jimenez-Borreguero LJ, Martin-Puig S, Lakomkin VL, Lukoshkova EV, Abramov AA, Gramovich VV, Vyborov ON, Ermishkin VV, Undrovinas NA, Shirinsky VP, Smilde BJ, Woudstra L, Fong Hing G, Wouters D, Zeerleder S, Murk JL, Van Ham SM, Heymans S, Juffermans LJM, Van Rossum AC, Niessen JWM, Krijnen PAJ, Krakhmalova O, Van Groen D, Bogaards SJP, Schalij I, Portnichenko GV, Tumanovska LV, Goshovska YV, Lapikova-Bryhinska TU, Nagibin VS, Dosenko VE, Mendes-Ferreira P, Maia-Rocha C, Santos-Ribeiro D, Potus F, Breuils-Bonnet S, Provencher S, Bonnet S, Rademaker M, Leite-Moreira AF, Bras-Silva C, Lopes J, Kuryata O, Lusynets T, Alikulov I, Nourddine M, Azzouzi L, Habbal R, Tserendavaa SUMIYA, Enkhtaivan ODKHUU, Enkhtaivan ODKHUU, Shagdar ZORIGO, Shagdar ZORIGO, Malchinkhuu MUNKHZ, Malchinkhuu MUNLHZ, Koval S, Starchenko T, Mourino-Alvarez L, Gonzalez-Calero L, Sastre-Oliva T, Lopez JA, Vazquez J, Alvarez-Llamas G, Ruilope LUISM, De La Cuesta F, Barderas MG, Bozzini S, D'angelo A, Pelissero G. Poster session 3Cell growth, differentiation and stem cells - Heart511The role of the endocannabinoid system in modelling muscular dystrophy cardiac disease with induced pluripotent stem cells.512An emerging role of T lymphocytes in cardiac regenerative processes in heart failure due to dilated cardiomyopathy513Canonical wnt signaling reverses the ‘aged/senescent’ human endogenous cardiac stem cell phenotype514Hippo signalling modulates survival of human induced pluripotent stem cell-derived cardiomyocytes515Biocompatibility of mesenchymal stem cells with a spider silk matrix and its potential use as scaffold for cardiac tissue regeneration516A snapshot of genome-wide transcription in human induced pluripotent stem cell-derived hepatocyte-like cells (iPSC-HLCs)517Can NOS/sGC/cGK1 pathway trigger the differentiation and maturation of mouse embryonic stem cells (ESCs)?518Introduction of external Ik1 to human-induced pluripotent stem cell-derived cardiomyocytes via Ik1-expressing HEK293519Cell therapy of the heart studied using adult myocardial slices in vitro520Enhancement of the paracrine potential of human adipose derived stem cells when cultured as spheroid bodies521Mechanosensitivity of cardiomyocyte progenitor cells: the strain response in 2D and 3D environments522The effect of the vascular-like network on the maturation of the human induced pluripotent stem cell derived cardiomyocytes.Transcriptional control and RNA species - Heart525Gene expression regulation in heart failure: from pathobiology to bioinformatics526Human transcriptome in idiopathic dilated cardiomyopathy - a novel high throughput screening527A high-throghput approach unveils putative miRNA-mediated mitochondria-targeted cardioprotective circuits activated by T3 in the post ischemia reperfusion setting528The effect of uraemia on the expression of miR-212/132 and the calcineurin pathway in the rat heartCytokines and cellular inflammation - Heart531Lack of growth differentiation factor 15 aggravates adverse cardiac remodeling upon pressure-overload in mice532Blocking heteromerization of platelet chemokines ccl5 and cxcl4 reduces inflammation and preserves heart function after myocardial infarction533Is there an association between low-dose aspirin use and clinical outcome in HFPEF? Implications of modulating monocyte function and inflammatory mediator release534N-terminal truncated intracellular matrix metalloproteinase-2 expression in diabetic heart.535Expression of CD39 and CD73 on peripheral T-cell subsets in calcific aortic stenosis536Mast cells in the atrial myocardium of patients with atrial fibrillation: a comparison with patients in sinus rhythm539Characteristics of the inflammatory response in patients with coronary artery disease and arterial hypertension540Pro-inflammatory cytokines as cardiovascular events predictors in rheumatoid arthritis and asymptomatic atherosclerosis541Characterization of FVB/N murinic bone marrow-derived macrophage polarization into M1 and M2 phenotypes542The biological expression and thoracic anterior pain syndromeSignal transduction - Heart545The association of heat shock protein 90 and TGFbeta receptor I is involved in collagen production during cardiac remodelling in aortic-banded mice546Loss of the inhibitory GalphaO protein in the rostral ventrolateral medulla of the brainstem leads to abnormalities in cardiovascular reflexes and altered ventricular excitablitiy547Selenoprotein P regulates pressure overload-induced cardiac remodeling548Study of adenylyl cyclase activity in erythrocyte membranes in patients with chronic heart failure549Direct thrombin inhibitors inhibit atrial myocardium hypertrophy in a rat model of heart failure and atrial remodeling550Tissue factor / FVIIa transactivates the IGF-1R by a Src-dependent phosphorylation of caveolin-1551Notch signaling is differently altered in endothelial and smooth muscle cells of ascending aortic aneurysm patients552Frizzled 5 expression is essential for endothelial proliferation and migration553Modulation of vascular function and ROS production by novel synthetic benzopyran analogues in diabetes mellitusExtracellular matrix and fibrosis - Heart556Cardiac fibroblasts as inflammatory supporter cells trigger cardiac inflammation in heart failure557A role for galectin-3 in calcific aortic valve stenosis558Omega-3 polyunsaturated fatty acids- can they decrease risk for ventricular fibrillation?559Serum levels of elastin derived peptides and circulating elastin-antielastin immune complexes in sera of patients with coronary artery disease560Endocardial fibroelastosis is secondary to hemodynamic alterations in the chick model of hypoplastic left heart syndrome561Dynamics of serum levels of matrix metalloproteinases in primary anterior STEMI patients564Deletion of the alpha-7 nicotinic acetylcholine receptor changes the vascular remodeling induced by transverse aortic constriction in mice.565Extracellular matrix remodelling in response to venous hypertension: proteomics of human varicose veinsIon channels, ion exchangers and cellular electrophysiology - Heart568Microtubule-associated protein RP/EB family member 1 modulates sodium channel trafficking and cardiac conduction569Investigation of electrophysiological abnormalities in a rabbit athlete's heart model570Upregulation of expression of multiple genes in the atrioventricular node of streptozotocin-induced diabetic rat571miR-1 as a regulator of sinoatrial rhythm in endurance training adaptation572Selective sodium-calcium exchanger inhibition reduces myocardial dysfunction associated with hypokalaemia and ventricular fibrillation573Effect of racemic and levo-methadone on action potential of human ventricular cardiomyocytes574Acute temperature effects on the chick embryonic heart functionVasculogenesis, angiogenesis and arteriogenesis577Clinical improvement and enhanced collateral vessel growth after monocyte transplantation in mice578The role of HIF-1 alpha, VEGF and obstructive sleep apnoea in the development of coronary collateral circulation579Initiating cardiac repair with a trans-coronary sinus catheter intervention in an ischemia/reperfusion porcine animal model580Early adaptation of pre-existing collaterals after acute arteriolar and venular microocclusion: an in vivo study in chick chorioallantoic membraneEndothelium583EDH-type responses to the activator of potassium KCa2.3 and KCa3.1 channels SKA-31 in the small mesenteric artery from spontaneously hypertensive rats584The peculiarities of endothelial dysfunction in patients with chronic renocardial syndrome585Endothelial dysfunction, atherosclerosis of the carotid arteries and level of leptin in patient with coronary heart disease in combination with hepatic steatosis depend from body mass index.586Role of non-coding RNAs in thoracic aortic aneurysm associated with bicuspid aortic valve587Cigarette smoke extract abrogates atheroprotective effects of high laminar flow on endothelial function588The prognostic value of anti-connective tissue antibodies in coronary heart disease and asymptomatic atherosclerosis589Novel potential properties of bioactive peptides from spanish dry-cured ham on the endothelium.Lipids592Intermediate density lipoprotein is associated with monocyte subset distribution in patients with stable atherosclerosis593The characteristics of dyslipidemia in rheumatoid arthritisAtherosclerosis596Macrophages differentiated in vitro are heterogeneous: morphological and functional profile in patients with coronary artery disease597Palmitoylethanolamide promotes anti-inflammatory phenotype of macrophages and attenuates plaque formation in ApoE-/- mice598Amiodarone versus esmolol in the perioperative period: an in vitro study of coronary artery bypass grafts599BMPRII signaling of fibrocytes, a mesenchymal progenitor cell population, is increased in STEMI and dyslipidemia600The characteristics of atherogenesis and systemic inflammation in rheumatoid arthritis601Role of adenosine-to-inosine RNA editing in human atherosclerosis602Presence of bacterial DNA in thrombus aspirates of patients with myocardial infarction603Novel E-selectin binding polymers reduce atherosclerotic lesions in ApoE(-/-) mice604Differential expression of the plasminogen receptor Plg-RKT in monocyte and macrophage subsets - possible functional consequences in atherogenesis605Apelin-13 treatment enhances the stability of atherosclerotic plaques606Mast cells are increased in the media of coronary lesions in patients with myocardial infarction and favor atherosclerotic plaque instability607Association of neutrophil to lymphocyte ratio with presence of isolated coronary artery ectasiaCalcium fluxes and excitation-contraction coupling610The coxsackie- and adenovirus receptor (CAR) regulates calcium homeostasis in the developing heart611HMW-AGEs application acutely reduces ICaL in adult cardiomyocytes612Measuring electrical conductibility of cardiac T-tubular systems613Postnatal development of cardiac excitation-contraction coupling in rats614Role of altered Ca2+ homeostasis during adverse cardiac remodeling after ischemia/reperfusion615Experimental study of sarcoplasmic reticulum dysfunction and energetic metabolism in failing myocardium associated with diabetes mellitusHibernation, stunning and preconditioning618Volatile anesthetic preconditioning attenuates ischemic-reperfusion injury in type II diabetic patients undergoing on-pump heart surgery619The effect of early and delayed phase of remote ischemic preconditioning on ischemia-reperfusion injury in the isolated hearts of healthy and diabetic rats620Post-conditioning with 1668-thioate leads to attenuation of the inflammatory response and remodeling with less fibrosis and better left ventricular function in a murine model of myocardial infarction621Maturation-related changes in response to ischemia-reperfusion injury and in effects of classical ischemic preconditioning and remote preconditioningMitochondria and energetics624Phase changes in myocardial mitochondrial respiration caused by hypoxic preconditioning or periodic hypoxic training625Desmin mutations depress mitochondrial metabolism626Methylene blue modulates mitochondrial function and monoamine oxidases-related ROS production in diabetic rat hearts627Doxorubicin modulates the real-time oxygen consumption rate of freshly isolated adult rat and human ventricular cardiomyocytesCardiomyopathies and fibrosis630Effects of genetic or pharmacologic inhibition of the ubiquitin/proteasome system on myocardial proteostasis and cardiac function631Suppression of Wnt signalling in a desmoglein-2 transgenic mouse model for arrhythmogenic cardiomyopathy632Cold-induced cardiac hypertrophy is reversed after thermo-neutral deacclimatization633CD45 is a sensitive marker to diagnose lymphocytic myocarditis in endomyocardial biopsies of living patients and in autopsies634Atrial epicardial adipose tissue derives from epicardial progenitors635Caloric restriction ameliorates cardiac function, sympathetic cardiac innervation and beta-adrenergic receptor signaling in an experimental model of post-ischemic heart failure636High fat diet improves cardiac remodelling and function after extensive myocardial infarction in mice637Epigenetic therapy reduces cardiac hypertrophy in murine models of heart failure638Imbalance of the VHL/HIF signaling in WT1+ Epicardial Progenitors results in coronary vascular defects, fibrosis and cardiac hypertrophy639Diastolic dysfunction is the first stage of the developing heart failure640Colchicine aggravates coxsackievirus B3 infection in miceArterial and pulmonary hypertension642Osteopontin as a marker of pulmonary hypertension in patients with coronary heart disease combined with chronic obstructive pulmonary disease643Myocardial dynamic stiffness is increased in experimental pulmonary hypertension partly due to incomplete relaxation644Hypotensive effect of quercetin is possibly mediated by down-regulation of immunotroteasome subunits in aorta of spontaneously hypertensive rats645Urocortin-2 improves right ventricular function and attenuates experimental pulmonary arterial hypertension646A preclinical evaluation of the anti-hypertensive properties of an aqueous extract of Agathosma (Buchu)Biomarkers648The adiponectin level in hypertensive females with rheumatoid arthritis and its relationship with subclinical atherosclerosis649Markers for identification of renal dysfunction in the patients with chronic heart failure650cardio-hepatic syndromes in chronic heart failure: North Africa profile651To study other biomarkers that assess during myocardial infarction652Interconnections of apelin levels with parameters of lipid metabolism in hypertension patients653Plasma proteomics in hypertension: prediction and follow-up of albuminuria during chronic renin-angiotensin system suppression654Soluble RAGE levels in plasma of patients with cerebrovascular events. Cardiovasc Res 2016. [DOI: 10.1093/cvr/cvw150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Nassiri I, Masoudi-Nejad A, Jalili M, Moeini A. Discovering dominant pathways and signal-response relationships in signaling networks through nonparametric approaches. Genomics 2013; 102:195-201. [PMID: 23912059 DOI: 10.1016/j.ygeno.2013.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 07/22/2013] [Accepted: 07/26/2013] [Indexed: 11/25/2022]
Abstract
A signaling pathway is a sequence of proteins and passenger molecules that transmits information from the cell surface to target molecules. Understanding signal transduction process requires detailed description of the involved pathways. Several methods and tools resolved this problem by incorporating genomic and proteomic data. However, the difficulty of obtaining prior knowledge of complex signaling networks limited the applicability of these tools. In this study, based on the simulation of signal flow in signaling network, we introduce a method for determining dominant pathways and signal response to stimulations. The model uses topology-weighted transit compartment approach and comprises four main steps which include weighting the edges, simulating signal transduction in the network (weighting the nodes), finding paths between initial and target nodes, and assigning a significance score to each path. We applied the proposed model to eighty-three signaling networks by using biologically derived source and sink molecules. The recovered dominant paths matched many known signaling pathways and suggesting a promising index to analyze the phenotype essentiality of molecule encoding paths. We also modeled the stimulus-response relations in long and short-term synaptic plasticity based on the dominant signaling pathway concept. We showed that the proposed method not only accurately determines dominant signaling pathways, but also identifies effective points of intervention in signal transduction.
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Affiliation(s)
- Isar Nassiri
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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Nassiri I, Masoudi-Nejad A, Jalili M, Moeini A. Nonparametric simulation of signal transduction networks with semi-synchronized update. PLoS One 2012; 7:e39643. [PMID: 22737250 PMCID: PMC3380921 DOI: 10.1371/journal.pone.0039643] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 05/23/2012] [Indexed: 01/20/2023] Open
Abstract
Simulating signal transduction in cellular signaling networks provides predictions of network dynamics by quantifying the changes in concentration and activity-level of the individual proteins. Since numerical values of kinetic parameters might be difficult to obtain, it is imperative to develop non-parametric approaches that combine the connectivity of a network with the response of individual proteins to signals which travel through the network. The activity levels of signaling proteins computed through existing non-parametric modeling tools do not show significant correlations with the observed values in experimental results. In this work we developed a non-parametric computational framework to describe the profile of the evolving process and the time course of the proportion of active form of molecules in the signal transduction networks. The model is also capable of incorporating perturbations. The model was validated on four signaling networks showing that it can effectively uncover the activity levels and trends of response during signal transduction process.
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Affiliation(s)
- Isar Nassiri
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ali Masoudi-Nejad
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
- * E-mail:
| | - Mahdi Jalili
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Ali Moeini
- Department of Algorithms and Computation, College of Engineering, University of Tehran, Tehran, Iran
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Owlia P, Vasei M, Goliaei B, Nassiri I. Normalized impact factor (NIF): An adjusted method for calculating the citation rate of biomedical journals. J Biomed Inform 2011; 44:216-20. [PMID: 21078409 DOI: 10.1016/j.jbi.2010.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Revised: 10/27/2010] [Accepted: 11/04/2010] [Indexed: 10/18/2022]
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Vallian S, Nassiri I. Development of a sensitive deaminated single-strand conformation polymorphism (DSSCP). Appl Biochem Biotechnol 2009; 160:927-31. [PMID: 19333563 DOI: 10.1007/s12010-009-8595-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Accepted: 02/24/2009] [Indexed: 11/28/2022]
Abstract
The single-strand conformation polymorphism (SSCP), accompanied by sequencing, is a useful methods for identifying mutations in a DNA fragment. In this study, we have developed a modified SSCP with the aid of sodium bisulfite treatment. The corresponding PCR products for exon 3 of Hb gene were sequenced and samples with homozygote and heterozygote single nucleotide substitutions were identified. The PCR products were treated with sodium bisulfite, which deaminates all the cytosine residues. The reaction mixture was then analyzed on non-denaturing polyacrylamide gels. The modified method, which is called deaminated SSCP (DSSCP), was applied successfully in analysis of mutations in the beta-globin gene at positions relevant to codon 6. DSSCP is a very effective and reproducible method providing clear results that are easy to interpret without the involvement of radioactivity.
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Affiliation(s)
- Sadeq Vallian
- Division of Genetics, Department of Biology, Faculty of Science, The University of Isfahan, Hezarjerib St., Isfahan, IR, Iran.
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Vallian S, Sedaghat M, Nassiri I, Frazmand A. Methylation status of p16 INK4A tumor suppressor gene in Iranian patients with sporadic breast cancer. J Cancer Res Clin Oncol 2009; 135:991-6. [PMID: 19125298 DOI: 10.1007/s00432-008-0534-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [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: 05/27/2008] [Accepted: 12/08/2008] [Indexed: 11/27/2022]
Abstract
INTRODUCTION p16(INK4A) is a tumor suppressor encoding the Cdk inhibitor protein, which acts to repress Cdk4/6 and pRb phosphorylation. p16(INK4A) gene can be inactivated by a variety of events, including promoter hypermethylation. MATERIALS AND METHODS To investigate the methylation status of the p16(INK4A) gene in Iranian patients with breast carcinoma, promoter methylation was studied by methylation-specific PCR (MSP) and restriction enzyme-related PCR (REP). In addition, p16(INK4A) promoter was analyzed by PCR-SSCP in order to detection of mutation and single nucleotide polymorphisms. RESULTS Analysis of 70 patients by MPS and REP showed hypermethylation of p16(INK4A) promoter in 35.7% (25/70) and 40% (28/70) of samples, respectively. Comparison of the molecular data and pathological information of the samples suggested that p16(INK4A) gene might be inactivated at the early stages in breast cancer. CONCLUSION Therefore, it could be suggested that hypermethylation of p16(INK4A) promoter is one of the epigenetic factors affecting the progress of sporadic breast carcinogenesis in Iranian patients.
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Affiliation(s)
- Sadeq Vallian
- Division of Genetics, Department of Biology, Faculty of Science, The University of Isfahan, Hezarjerib St., Isfahan, Islamic Republic of Iran.
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