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Rodriguez-Meira A, Norfo R, Wen S, Chédeville AL, Rahman H, O'Sullivan J, Wang G, Louka E, Kretzschmar WW, Paterson A, Brierley C, Martin JE, Demeule C, Bashton M, Sousos N, Moralli D, Subha Meem L, Carrelha J, Wu B, Hamblin A, Guermouche H, Pasquier F, Marzac C, Girodon F, Vainchenker W, Drummond M, Harrison C, Chapman JR, Plo I, Jacobsen SEW, Psaila B, Thongjuea S, Antony-Debré I, Mead AJ. Single-cell multi-omics identifies chronic inflammation as a driver of TP53-mutant leukemic evolution. Nat Genet 2023; 55:1531-1541. [PMID: 37666991 PMCID: PMC10484789 DOI: 10.1038/s41588-023-01480-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 02/18/2022] [Accepted: 07/20/2023] [Indexed: 09/06/2023]
Abstract
Understanding the genetic and nongenetic determinants of tumor protein 53 (TP53)-mutation-driven clonal evolution and subsequent transformation is a crucial step toward the design of rational therapeutic strategies. Here we carry out allelic resolution single-cell multi-omic analysis of hematopoietic stem/progenitor cells (HSPCs) from patients with a myeloproliferative neoplasm who transform to TP53-mutant secondary acute myeloid leukemia (sAML). All patients showed dominant TP53 'multihit' HSPC clones at transformation, with a leukemia stem cell transcriptional signature strongly predictive of adverse outcomes in independent cohorts, across both TP53-mutant and wild-type (WT) AML. Through analysis of serial samples, antecedent TP53-heterozygous clones and in vivo perturbations, we demonstrate a hitherto unrecognized effect of chronic inflammation, which suppressed TP53 WT HSPCs while enhancing the fitness advantage of TP53-mutant cells and promoted genetic evolution. Our findings will facilitate the development of risk-stratification, early detection and treatment strategies for TP53-mutant leukemia, and are of broad relevance to other cancer types.
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Affiliation(s)
- Alba Rodriguez-Meira
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK.
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA.
- Broad Institute, Cambridge, MA, USA.
| | - Ruggiero Norfo
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- Centre for Regenerative Medicine 'Stefano Ferrari', Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Sean Wen
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- Medical Research Council Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Agathe L Chédeville
- INSERM, UMR 1287, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris Saclay, Gif-sur-Yvette, France
- Université Paris Cité, Paris, France
| | - Haseeb Rahman
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Jennifer O'Sullivan
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Guanlin Wang
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- Medical Research Council Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Eleni Louka
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Warren W Kretzschmar
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Karolinska University Hospital, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Aimee Paterson
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Charlotte Brierley
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- Center for Hematological Malignancies, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Jean-Edouard Martin
- INSERM, UMR 1287, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris Saclay, Gif-sur-Yvette, France
- Université Paris Cité, Paris, France
| | | | - Matthew Bashton
- The Hub for Biotechnology in the Built Environment, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Nikolaos Sousos
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | | | | | - Joana Carrelha
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Bishan Wu
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Angela Hamblin
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Helene Guermouche
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, AP-HP, Hôpital Saint-Antoine, Service d'hématologie biologique, Paris, France
| | - Florence Pasquier
- INSERM, UMR 1287, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris Saclay, Gif-sur-Yvette, France
- Département d'Hématologie, Gustave Roussy, Villejuif, France
| | - Christophe Marzac
- INSERM, UMR 1287, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris Saclay, Gif-sur-Yvette, France
- Laboratoire d'Immuno-Hématologie, Gustave Roussy, Villejuif, France
| | - François Girodon
- Laboratoire d'Hématologie, CHU Dijon, Dijon, France
- INSERM, UMR 1231, Centre de Recherche, Dijon, France
| | - William Vainchenker
- INSERM, UMR 1287, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris Saclay, Gif-sur-Yvette, France
| | | | | | - J Ross Chapman
- Genome Integrity Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Isabelle Plo
- INSERM, UMR 1287, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris Saclay, Gif-sur-Yvette, France
| | - Sten Eirik W Jacobsen
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Karolinska University Hospital, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Bethan Psaila
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Supat Thongjuea
- Medical Research Council Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Iléana Antony-Debré
- INSERM, UMR 1287, Villejuif, France.
- Gustave Roussy, Villejuif, France.
- Université Paris Saclay, Gif-sur-Yvette, France.
| | - Adam J Mead
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK.
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2
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Pervaiz O, Louka E, Willan J. Neutrophilic erythrophagocytosis in a child with paroxysmal cold hamoglobinuria. EJHaem 2022; 3:1394-1395. [PMID: 36467843 PMCID: PMC9713226 DOI: 10.1002/jha2.596] [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] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 06/17/2023]
Affiliation(s)
- Omer Pervaiz
- Department of HaematologyOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Eleni Louka
- Department of HaematologyOxford University Hospitals NHS Foundation TrustOxfordUK
| | - John Willan
- Department of HaematologyOxford University Hospitals NHS Foundation TrustOxfordUK
- Department of HaematologyWexham Park Hospital part of Frimley Health NHS Foundation TrustSloughUK
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3
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Sousos N, Ní Leathlobhair M, Simoglou Karali C, Louka E, Bienz N, Royston D, Clark SA, Hamblin A, Howard K, Mathews V, George B, Roy A, Psaila B, Wedge DC, Mead AJ. In utero origin of myelofibrosis presenting in adult monozygotic twins. Nat Med 2022; 28:1207-1211. [PMID: 35637336 PMCID: PMC9205768 DOI: 10.1038/s41591-022-01793-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 03/22/2022] [Indexed: 12/11/2022]
Abstract
The latency between acquisition of an initiating somatic driver mutation by a single-cell and clinical presentation with cancer is largely unknown. We describe a remarkable case of monozygotic twins presenting with CALR mutation-positive myeloproliferative neoplasms (MPNs) (aged 37 and 38 years), with a clinical phenotype of primary myelofibrosis. The CALR mutation was absent in T cells and dermal fibroblasts, confirming somatic acquisition. Whole-genome sequencing lineage tracing revealed a common clonal origin of the CALR-mutant MPN clone, which occurred in utero followed by twin-to-twin transplacental transmission and subsequent similar disease latency. Index sorting and single-colony genotyping revealed phenotypic hematopoietic stem cells (HSCs) as the likely MPN-propagating cell. Furthermore, neonatal blood spot analysis confirmed in utero origin of the JAK2V617F mutation in a patient presenting with polycythemia vera (aged 34 years). These findings provide a unique window into the prolonged evolutionary dynamics of MPNs and fitness advantage exerted by MPN-associated driver mutations in HSCs.
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Affiliation(s)
- Nikolaos Sousos
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
- Cancer and Haematology Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Máire Ní Leathlobhair
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Christina Simoglou Karali
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Eleni Louka
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Nicola Bienz
- Haematology Service, Wexham Park Hospital, Frimley Health NHS Foundation Trust, Slough, UK
| | - Daniel Royston
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sally-Ann Clark
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Angela Hamblin
- Cancer and Haematology Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Kieran Howard
- National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Vikram Mathews
- Department of Haematology, Christian Medical College, Vellore, India
| | - Biju George
- Department of Haematology, Christian Medical College, Vellore, India
| | - Anindita Roy
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
- Department of Paediatrics, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Bethan Psaila
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
- Cancer and Haematology Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - David C Wedge
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK.
| | - Adam J Mead
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK.
- Cancer and Haematology Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
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4
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Rodriguez-Meira A, Norfo R, Wen W, Chedeville A, Rahman H, O'Sullivan J, Wang G, Louka E, Kretzschmar W, Paterson A, Brierley C, Martin JE, Demeule C, Bashton M, Sousos N, Hamblin A, Guermouche H, Pasquier F, Marzac C, Girodon F, Drummond M, Harrison C, Plo I, Jacobsen SE, Psaila B, Thongjuea S, Antony-Debré I, Mead A. 3170 – SINGLE-CELL MULTI-OMICS RESOLVES THE EVOLUTION OF TP53-MUTANT LEUKEMIA. Exp Hematol 2022. [DOI: 10.1016/j.exphem.2022.07.226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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5
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Louka E, Povinelli B, Rodriguez-Meira A, Buck G, Wen WX, Wang G, Sousos N, Ashley N, Hamblin A, Booth CAG, Roy A, Elliott N, Iskander D, de la Fuente J, Fordham N, O'Byrne S, Inglott S, Norfo R, Salio M, Thongjuea S, Rao A, Roberts I, Mead AJ. Heterogeneous disease-propagating stem cells in juvenile myelomonocytic leukemia. J Exp Med 2021; 218:211665. [PMID: 33416891 PMCID: PMC7802370 DOI: 10.1084/jem.20180853] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 05/08/2018] [Revised: 09/01/2020] [Accepted: 11/12/2020] [Indexed: 11/22/2022] Open
Abstract
Juvenile myelomonocytic leukemia (JMML) is a poor-prognosis childhood leukemia usually caused by RAS-pathway mutations. The cellular hierarchy in JMML is poorly characterized, including the identity of leukemia stem cells (LSCs). FACS and single-cell RNA sequencing reveal marked heterogeneity of JMML hematopoietic stem/progenitor cells (HSPCs), including an aberrant Lin−CD34+CD38−CD90+CD45RA+ population. Single-cell HSPC index-sorting and clonogenic assays show that (1) all somatic mutations can be backtracked to the phenotypic HSC compartment, with RAS-pathway mutations as a “first hit,” (2) mutations are acquired with both linear and branching patterns of clonal evolution, and (3) mutant HSPCs are present after allogeneic HSC transplant before molecular/clinical evidence of relapse. Stem cell assays reveal interpatient heterogeneity of JMML LSCs, which are present in, but not confined to, the phenotypic HSC compartment. RNA sequencing of JMML LSC reveals up-regulation of stem cell and fetal genes (HLF, MEIS1, CNN3, VNN2, and HMGA2) and candidate therapeutic targets/biomarkers (MTOR, SLC2A1, and CD96), paving the way for LSC-directed disease monitoring and therapy in this disease.
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Affiliation(s)
- Eleni Louka
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Benjamin Povinelli
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Alba Rodriguez-Meira
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Gemma Buck
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,Department of Paediatrics, University of Oxford, Oxford, UK
| | - Wei Xiong Wen
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,MRC WIMM Centre for Computational Biology, University of Oxford, Oxford, UK
| | - Guanlin Wang
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,MRC WIMM Centre for Computational Biology, University of Oxford, Oxford, UK
| | - Nikolaos Sousos
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Neil Ashley
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Angela Hamblin
- National Institute of Health Research Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Christopher A G Booth
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Anindita Roy
- Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,Department of Paediatrics, University of Oxford, Oxford, UK
| | - Natalina Elliott
- Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,Department of Paediatrics, University of Oxford, Oxford, UK
| | - Deena Iskander
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Josu de la Fuente
- Department of Paediatric Haematology and Bone Marrow Transplantation, St Mary's Hospital, Imperial College London, London, UK
| | - Nicholas Fordham
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Sorcha O'Byrne
- Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sarah Inglott
- Department of Haematology, Great Ormond Street Hospital National Health Service Foundation Trust, London, UK
| | - Ruggiero Norfo
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Mariolina Salio
- MRC Human Immunology Unit, WIMM, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Supat Thongjuea
- MRC WIMM Centre for Computational Biology, University of Oxford, Oxford, UK
| | - Anupama Rao
- Department of Haematology, Great Ormond Street Hospital National Health Service Foundation Trust, London, UK
| | - Irene Roberts
- Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,Department of Paediatrics, University of Oxford, Oxford, UK.,National Institute of Health Research Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Adam J Mead
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,National Institute of Health Research Biomedical Research Centre, Churchill Hospital, Oxford, UK
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6
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Djebbari F, Hubenov H, Neelakantan P, Wolf J, Offer M, Khera A, Louka E, Vallance G, Kothari J, Moore S, Ramasamy K. Carfilzomib therapy for relapsed myeloma: results of a UK multicentre experience. Br J Haematol 2019; 188:e57-e60. [PMID: 31792927 DOI: 10.1111/bjh.16324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Faouzi Djebbari
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Huben Hubenov
- Department of Haematology, Wycombe General Hospital, High Wycombe, UK
| | - Pratap Neelakantan
- Department of Haematology, Royal Berkshire Hospital NHS Foundation Trust, Reading, UK
| | - Julia Wolf
- Department of Haematology, Great Western Hospital, Swindon, UK
| | - Mark Offer
- Department of Haematology, Wexham Park Hospital, Slough, UK
| | - Akhil Khera
- Department of Haematology, Milton Keynes Hospital, Milton Keynes, UK
| | - Eleni Louka
- Department of Haematology, Frimley Park Hospital, Frimley, UK
| | - Grant Vallance
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jaimal Kothari
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sally Moore
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Karthik Ramasamy
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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7
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Rodriguez-Meira A, Buck G, Clark SA, Povinelli BJ, Alcolea V, Louka E, McGowan S, Hamblin A, Sousos N, Barkas N, Giustacchini A, Psaila B, Jacobsen SEW, Thongjuea S, Mead AJ. Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing. Mol Cell 2019; 73:1292-1305.e8. [PMID: 30765193 PMCID: PMC6436961 DOI: 10.1016/j.molcel.2019.01.009] [Citation(s) in RCA: 171] [Impact Index Per Article: 34.2] [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: 04/13/2018] [Revised: 11/07/2018] [Accepted: 01/07/2019] [Indexed: 12/29/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for resolving transcriptional heterogeneity. However, its application to studying cancerous tissues is currently hampered by the lack of coverage across key mutation hotspots in the vast majority of cells; this lack of coverage prevents the correlation of genetic and transcriptional readouts from the same single cell. To overcome this, we developed TARGET-seq, a method for the high-sensitivity detection of multiple mutations within single cells from both genomic and coding DNA, in parallel with unbiased whole-transcriptome analysis. Applying TARGET-seq to 4,559 single cells, we demonstrate how this technique uniquely resolves transcriptional and genetic tumor heterogeneity in myeloproliferative neoplasms (MPN) stem and progenitor cells, providing insights into deregulated pathways of mutant and non-mutant cells. TARGET-seq is a powerful tool for resolving the molecular signatures of genetically distinct subclones of cancer cells.
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Affiliation(s)
- Alba Rodriguez-Meira
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Gemma Buck
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Sally-Ann Clark
- Flow Cytometry Facility, Medical Research Council, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Benjamin J Povinelli
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Veronica Alcolea
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Eleni Louka
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Simon McGowan
- Medical Research Council Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Angela Hamblin
- National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Nikolaos Sousos
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Nikolaos Barkas
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Alice Giustacchini
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Bethan Psaila
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Sten Eirik W Jacobsen
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Department of Cell and Molecular Biology, Wallenberg Institute for Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden; Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Supat Thongjuea
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Adam J Mead
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK.
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Rodriguez-Meira A, Buck G, Clark S, Louka E, Povinelli B, Barkas N, McGowan S, Sousos N, Giustacchini A, Hamblin A, Jacobsen S, Thongjuea S, Mead A. Single Cell Analysis Resolves Genetic and Transcriptional Heterogeneity in Myeloproliferative Neoplasms. Exp Hematol 2018. [DOI: 10.1016/j.exphem.2018.06.131] [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: 11/27/2022]
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Whitworth J, Smith PS, Martin JE, West H, Luchetti A, Rodger F, Clark G, Carss K, Stephens J, Stirrups K, Penkett C, Mapeta R, Ashford S, Megy K, Shakeel H, Ahmed M, Adlard J, Barwell J, Brewer C, Casey RT, Armstrong R, Cole T, Evans DG, Fostira F, Greenhalgh L, Hanson H, Henderson A, Hoffman J, Izatt L, Kumar A, Kwong A, Lalloo F, Ong KR, Paterson J, Park SM, Chen-Shtoyerman R, Searle C, Side L, Skytte AB, Snape K, Woodward ER, Tischkowitz MD, Maher ER, Aitman T, Alachkar H, Ali S, Allen L, Allsup D, Ambegaonkar G, Anderson J, Antrobus R, Armstrong R, Arno G, Arumugakani G, Ashford S, Astle W, Attwood A, Austin S, Bacchelli C, Bakchoul T, Bariana TK, Baxendale H, Bennett D, Bethune C, Bibi S, Bitner-Glindzicz M, Bleda M, Boggard H, Bolton-Maggs P, Booth C, Bradley JR, Brady A, Brown M, Browning M, Bryson C, Burns S, Calleja P, Canham N, Carmichael J, Carss K, Caulfield M, Chalmers E, Chandra A, Chinnery P, Chitre M, Church C, Clement E, Clements-Brod N, Clowes V, Coghlan G, Collins P, Cookson V, Cooper N, Corris P, Creaser-Myers A, DaCosta R, Daugherty L, Davies S, Davis J, De Vries M, Deegan P, Deevi SV, Deshpande C, Devlin L, Dewhurst E, Dixon P, Doffinger R, Dormand N, Drewe E, Edgar D, Egner W, Erber WN, Erwood M, Erwood M, Everington T, Favier R, Firth H, Fletcher D, Flinter F, Frary A, Freson K, Furie B, Furnell A, Gale D, Gardham A, Gattens M, Ghali N, Ghataorhe PK, Ghurye R, Gibbs S, Gilmour K, Gissen P, Goddard S, Gomez K, Gordins P, Graf S, Gräf S, Greene D, Greenhalgh A, Greinacher A, Grigoriadou S, Grozeva D, Hackett S, Hadinnapola C, Hague R, Haimel M, Halmagyi C, Hammerton T, Hart D, Hayman G, Heemskerk JW, Henderson R, Hensiek A, Henskens Y, Herwadkar A, Holden S, Holder M, Holder S, Hu F, Huis in’t Veld A, Huissoon A, Humbert M, Hurst J, James R, Jolles S, Josifova D, Kazmi R, Keeling D, Kelleher P, Kelly AM, Kennedy F, Kiely D, Kingston N, Koziell A, Krishnakumar D, Kuijpers TW, Kuijpers T, Kumararatne D, Kurian M, Laffan MA, Lambert MP, Allen HL, Lango-Allen H, Lawrie A, Lear S, Lees M, Lentaigne C, Liesner R, Linger R, Longhurst H, Lorenzo L, Louka E, Machado R, Ross RM, MacLaren R, Maher E, Maimaris J, Mangles S, Manson A, Mapeta R, Markus HS, Martin J, Masati L, Mathias M, Matser V, Maw A, McDermott E, McJannet C, Meacham S, Meehan S, Megy K, Mehta S, Michaelides M, Millar CM, Moledina S, Moore A, Morrell N, Mumford A, Murng S, Murphy E, Nejentsev S, Noorani S, Nurden P, Oksenhendler E, Othman S, Ouwehand WH, Ouwehand WH, Papadia S, Park SM, Parker A, Pasi J, Patch C, Paterson J, Payne J, Peacock A, Peerlinck K, Penkett CJ, Pepke-Zaba J, Perry D, Perry DJ, Pollock V, Polwarth G, Ponsford M, Qasim W, Quinti I, Rankin S, Rankin J, Raymond FL, Rayner-Matthews P, Rehnstrom K, Reid E, Rhodes CJ, Richards M, Richardson S, Richter A, Roberts I, Rondina M, Rosser E, Roughley C, Roy N, Rue-Albrecht K, Samarghitean C, Sanchis-Juan A, Sandford R, Santra S, Sargur R, Savic S, Schotte G, Schulman S, Schulze H, Scott R, Scully M, Seneviratne S, Sewell C, Shamardina O, Shipley D, Simeoni I, Sivapalaratnam S, Smith KG, Sohal A, Southgate L, Staines S, Staples E, Stark H, Stauss H, Stein P, Stephens J, Stirrups K, Stock S, Suntharalingam J, Talks K, Tan Y, Thachil J, Thaventhiran J, Thomas E, Thomas M, Thompson D, Thrasher A, Tischkowitz M, Titterton C, Toh CH, Toshner M, Treacy C, Trembath R, Tuna S, Turek W, Turro E, Van Geet C, Veltman M, Vogt J, von Ziegenweldt J, Vonk Noordegraaf A, Wakeling E, Wanjiku I, Warner TQ, Wassmer E, Watkins H, Watt C, Webster N, Welch S, Westbury S, Wharton J, Whitehorn D, Wilkins M, Willcocks L, Williamson C, Woods G, Woods G, Wort J, Yeatman N, Yong P, Young T, Yu P. Comprehensive Cancer-Predisposition Gene Testing in an Adult Multiple Primary Tumor Series Shows a Broad Range of Deleterious Variants and Atypical Tumor Phenotypes. Am J Hum Genet 2018; 103:3-18. [PMID: 29909963 PMCID: PMC6037202 DOI: 10.1016/j.ajhg.2018.04.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [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: 12/06/2017] [Accepted: 04/25/2018] [Indexed: 12/17/2022] Open
Abstract
Multiple primary tumors (MPTs) affect a substantial proportion of cancer survivors and can result from various causes, including inherited predisposition. Currently, germline genetic testing of MPT-affected individuals for variants in cancer-predisposition genes (CPGs) is mostly targeted by tumor type. We ascertained pre-assessed MPT individuals (with at least two primary tumors by age 60 years or at least three by 70 years) from genetics centers and performed whole-genome sequencing (WGS) on 460 individuals from 440 families. Despite previous negative genetic assessment and molecular investigations, pathogenic variants in moderate- and high-risk CPGs were detected in 67/440 (15.2%) probands. WGS detected variants that would not be (or were not) detected by targeted resequencing strategies, including low-frequency structural variants (6/440 [1.4%] probands). In most individuals with a germline variant assessed as pathogenic or likely pathogenic (P/LP), at least one of their tumor types was characteristic of variants in the relevant CPG. However, in 29 probands (42.2% of those with a P/LP variant), the tumor phenotype appeared discordant. The frequency of individuals with truncating or splice-site CPG variants and at least one discordant tumor type was significantly higher than in a control population (χ2 = 43.642; p ≤ 0.0001). 2/67 (3%) probands with P/LP variants had evidence of multiple inherited neoplasia allele syndrome (MINAS) with deleterious variants in two CPGs. Together with variant detection rates from a previous series of similarly ascertained MPT-affected individuals, the present results suggest that first-line comprehensive CPG analysis in an MPT cohort referred to clinical genetics services would detect a deleterious variant in about a third of individuals.
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