1
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Balachandar S, Graves TJ, Shimonty A, Kerr K, Kilner J, Xiao S, Slade R, Sroya M, Alikian M, Curetean E, Thomas E, McConnell VPM, McKee S, Boardman-Pretty F, Devereau A, Fowler TA, Caulfield MJ, Alton EW, Ferguson T, Redhead J, McKnight AJ, Thomas GA, Aldred MA, Shovlin CL. Identification and validation of a novel pathogenic variant in GDF2 (BMP9) responsible for hereditary hemorrhagic telangiectasia and pulmonary arteriovenous malformations. Am J Med Genet A 2022; 188:959-964. [PMID: 34904380 PMCID: PMC9939255 DOI: 10.1002/ajmg.a.62584] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [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: 08/01/2021] [Accepted: 11/02/2021] [Indexed: 01/14/2023]
Abstract
Hereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant multisystemic vascular dysplasia, characterized by arteriovenous malformations (AVMs), mucocutaneous telangiectasia and nosebleeds. HHT is caused by a heterozygous null allele in ACVRL1, ENG, or SMAD4, which encode proteins mediating bone morphogenetic protein (BMP) signaling. Several missense and stop-gain variants identified in GDF2 (encoding BMP9) have been reported to cause a vascular anomaly syndrome similar to HHT, however none of these patients met diagnostic criteria for HHT. HHT families from UK NHS Genomic Medicine Centres were recruited to the Genomics England 100,000 Genomes Project. Whole genome sequencing and tiering protocols identified a novel, heterozygous GDF2 sequence variant in all three affected members of one HHT family who had previously screened negative for ACVRL1, ENG, and SMAD4. All three had nosebleeds and typical HHT telangiectasia, and the proband also had severe pulmonary AVMs from childhood. In vitro studies showed the mutant construct expressed the proprotein but lacked active mature BMP9 dimer, suggesting the mutation disrupts correct cleavage of the protein. Plasma BMP9 levels in the patients were significantly lower than controls. In conclusion, we propose that this heterozygous GDF2 variant is a rare cause of HHT associated with pulmonary AVMs.
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Affiliation(s)
- Srimmitha Balachandar
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Tamara J. Graves
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Anika Shimonty
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Katie Kerr
- School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, UK
| | - Jill Kilner
- School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, UK
| | - Sihao Xiao
- National Heart and Lung Institute, Imperial College London, London, UK,Genomics England Respiratory Clinical Interpretation Partnership (GeCIP), London, UK
| | - Richard Slade
- National Heart and Lung Institute, Imperial College London, London, UK,Genomics England Respiratory Clinical Interpretation Partnership (GeCIP), London, UK
| | - Manveer Sroya
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Mary Alikian
- Genomics England Respiratory Clinical Interpretation Partnership (GeCIP), London, UK,West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, UK
| | - Emanuel Curetean
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, UK
| | - Ellen Thomas
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, UK,Genomics England, London, UK
| | | | - Shane McKee
- Regional Genetics Service, Belfast Health and Social Care Trust, Belfast, UK
| | | | | | - Tom A. Fowler
- Genomics England, London, UK,William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Mark J. Caulfield
- Genomics England, London, UK,William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Eric W. Alton
- National Heart and Lung Institute, Imperial College London, London, UK,Genomics England Respiratory Clinical Interpretation Partnership (GeCIP), London, UK
| | - Teena Ferguson
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, UK
| | - Julian Redhead
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, UK
| | - Amy J. McKnight
- School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, UK,Genomics England Respiratory Clinical Interpretation Partnership (GeCIP), London, UK
| | | | | | - Micheala A. Aldred
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA,Genomics England Respiratory Clinical Interpretation Partnership (GeCIP), London, UK
| | - Claire L. Shovlin
- National Heart and Lung Institute, Imperial College London, London, UK,Genomics England Respiratory Clinical Interpretation Partnership (GeCIP), London, UK,West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, UK
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2
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Gliddon HD, Kaforou M, Alikian M, Habgood-Coote D, Zhou C, Oni T, Anderson ST, Brent AJ, Crampin AC, Eley B, Heyderman R, Kern F, Langford PR, Ottenhoff THM, Hibberd ML, French N, Wright VJ, Dockrell HM, Coin LJ, Wilkinson RJ, Levin M. Identification of Reduced Host Transcriptomic Signatures for Tuberculosis Disease and Digital PCR-Based Validation and Quantification. Front Immunol 2021; 12:637164. [PMID: 33763081 PMCID: PMC7982854 DOI: 10.3389/fimmu.2021.637164] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/03/2021] [Indexed: 12/18/2022] Open
Abstract
Recently, host whole blood gene expression signatures have been identified for diagnosis of tuberculosis (TB). Absolute quantification of the concentrations of signature transcripts in blood have not been reported, but would facilitate diagnostic test development. To identify minimal transcript signatures, we applied a transcript selection procedure to microarray data from African adults comprising 536 patients with TB, other diseases (OD) and latent TB (LTBI), divided into training and test sets. Signatures were further investigated using reverse transcriptase (RT)-digital PCR (dPCR). A four-transcript signature (GBP6, TMCC1, PRDM1, and ARG1) measured using RT-dPCR distinguished TB patients from those with OD (area under the curve (AUC) 93.8% (CI95% 82.2-100%). A three-transcript signature (FCGR1A, ZNF296, and C1QB) differentiated TB from LTBI (AUC 97.3%, CI95%: 93.3-100%), regardless of HIV. These signatures have been validated across platforms and across samples offering strong, quantitative support for their use as diagnostic biomarkers for TB.
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Affiliation(s)
- Harriet D Gliddon
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom.,National Public Health Speciality Training Programme, South West, United Kingdom
| | - Myrsini Kaforou
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Mary Alikian
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom.,Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Dominic Habgood-Coote
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Chenxi Zhou
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Tolu Oni
- School of Public Health and Family Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Suzanne T Anderson
- Brighton and Sussex Medical School, Brighton, United Kingdom.,Brighton and Malawi Liverpool Wellcome Trust Unit, Blantyre, Malawi
| | - Andrew J Brent
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Amelia C Crampin
- Malawi Epidemiology and Intervention Research Unit, Chilumba, Malawi.,London School of Hygiene & Tropical Medicine, London, United Kingdom.,Karonga Prevention Study, Chilumba, Malawi
| | - Brian Eley
- Paediatric Infectious Diseases Unit, Red Cross War Memorial Children's Hospital, Cape Town, South Africa.,Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Robert Heyderman
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Florian Kern
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom.,Brighton and Sussex University Hospitals National Health Service (NHS) Trust, Brighton, United Kingdom
| | - Paul R Langford
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Martin L Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Neil French
- Tropical and Infectious Disease Unit, Royal Liverpool and Broadgreen University Hospitals National Health Service (NHS) Trust, Liverpool, United Kingdom.,Centre for Global Vaccine Research, Institute of Infection & Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Victoria J Wright
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Hazel M Dockrell
- Department of Immunology and Infection, and Tuberculosis (TB) Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Lachlan J Coin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Robert J Wilkinson
- The Francis Crick Institute, London, United Kingdom.,Department of Medicine, Imperial College London, London, United Kingdom.,Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Michael Levin
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
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3
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Clarke JM, Alikian M, Xiao S, Kasperaviciute D, Thomas E, Turbin I, Olupona K, Cifra E, Curetean E, Ferguson T, Redhead J, Shovlin CL. Low grade mosaicism in hereditary haemorrhagic telangiectasia identified by bidirectional whole genome sequencing reads through the 100,000 Genomes Project clinical diagnostic pipeline. J Med Genet 2020; 57:859-862. [PMID: 32303606 PMCID: PMC7691802 DOI: 10.1136/jmedgenet-2019-106794] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/08/2020] [Accepted: 02/10/2020] [Indexed: 11/04/2022]
Affiliation(s)
- Jessica M Clarke
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, UK.,Genomics England Respiratory Clinical Interpretation Partnership (GeCIP), London, UK
| | - Mary Alikian
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, UK.,Genomics England Respiratory Clinical Interpretation Partnership (GeCIP), London, UK
| | - Sihao Xiao
- Genomics England Respiratory Clinical Interpretation Partnership (GeCIP), London, UK.,NHLI Cardiovascular Sciences, Imperial College London, London, UK
| | | | - Ellen Thomas
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, UK.,Genomics England, London, UK
| | - Isobel Turbin
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, UK.,NHLI Cardiovascular Sciences, Imperial College London, London, UK
| | - Kike Olupona
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, UK
| | - Elna Cifra
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, UK
| | - Emanuel Curetean
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, UK
| | - Teena Ferguson
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, UK
| | - Julian Redhead
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, UK
| | | | - Claire L Shovlin
- West London Genomic Medicine Centre, Imperial College Healthcare NHS Trust, London, UK .,Genomics England Respiratory Clinical Interpretation Partnership (GeCIP), London, UK.,NHLI Cardiovascular Sciences, Imperial College London, London, UK
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4
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Garrett A, Callaway A, Durkie M, Cubuk C, Alikian M, Burghel GJ, Robinson R, Izatt L, Talukdar S, Side L, Cranston T, Palmer-Smith S, Baralle D, Berry IR, Drummond J, Wallace AJ, Norbury G, Eccles DM, Ellard S, Lalloo F, Evans DG, Woodward E, Tischkowitz M, Hanson H, Turnbull C. Cancer Variant Interpretation Group UK (CanVIG-UK): an exemplar national subspecialty multidisciplinary network. J Med Genet 2020; 57:829-834. [PMID: 32170000 PMCID: PMC7691806 DOI: 10.1136/jmedgenet-2019-106759] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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: 12/04/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 12/14/2022]
Abstract
Advances in technology have led to a massive expansion in the capacity for genomic analysis, with a commensurate fall in costs. The clinical indications for genomic testing have evolved markedly; the volume of clinical sequencing has increased dramatically; and the range of clinical professionals involved in the process has broadened. There is general acceptance that our early dichotomous paradigms of variants being pathogenic–high risk and benign–no risk are overly simplistic. There is increasing recognition that the clinical interpretation of genomic data requires significant expertise in disease–gene-variant associations specific to each disease area. Inaccurate interpretation can lead to clinical mismanagement, inconsistent information within families and misdirection of resources. It is for this reason that ‘national subspecialist multidisciplinary meetings’ (MDMs) for genomic interpretation have been articulated as key for the new NHS Genomic Medicine Service, of which Cancer Variant Interpretation Group UK (CanVIG-UK) is an early exemplar. CanVIG-UK was established in 2017 and now has >100 UK members, including at least one clinical diagnostic scientist and one clinical cancer geneticist from each of the 25 regional molecular genetics laboratories of the UK and Ireland. Through CanVIG-UK, we have established national consensus around variant interpretation for cancer susceptibility genes via monthly national teleconferenced MDMs and collaborative data sharing using a secure online portal. We describe here the activities of CanVIG-UK, including exemplar outputs and feedback from the membership.
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Affiliation(s)
- Alice Garrett
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Alison Callaway
- Wessex Regional Genetics Laboratory, Salisbury Hospital NHS Foundation Trust, Salisbury, UK.,Human Genetics and Genomic Medicin, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Miranda Durkie
- Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Cankut Cubuk
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK.,William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Mary Alikian
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Rachel Robinson
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Louise Izatt
- Department of Clinical Genetics, Guy's and Saint Thomas' NHS Foundation Trust, London, UK
| | - Sabrina Talukdar
- Department of Clinical Genetics, Saint George's University Hospitals NHS Foundation Trust, London, UK
| | - Lucy Side
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Treena Cranston
- Oxford Molecular Genetics Laboratory, Churchill Hospital, Oxford, UK
| | | | - Diana Baralle
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Ian R Berry
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - James Drummond
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Andrew J Wallace
- Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Gail Norbury
- Regional Genetics Service, Guy's and Saint Thomas' NHS Foundation Trust, London, UK
| | - Diana M Eccles
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sian Ellard
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub, Manchester University NHS Foundation Trust, Manchester, UK.,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Emma Woodward
- Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub, Manchester University NHS Foundation Trust, Manchester, UK.,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health, Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Helen Hanson
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK.,Department of Clinical Genetics, Saint George's University Hospitals NHS Foundation Trust, London, UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK .,Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
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5
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Iskander D, Roberts I, Rees C, Szydlo R, Alikian M, Neale M, Harrington Y, Kelleher P, Karadimitris A, de la Fuente J. Impaired cellular and humoral immunity is a feature of Diamond-Blackfan anaemia; experience of 107 unselected cases in the United Kingdom. Br J Haematol 2019; 186:321-326. [PMID: 30980390 DOI: 10.1111/bjh.15915] [Citation(s) in RCA: 5] [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: 01/21/2019] [Accepted: 02/25/2019] [Indexed: 11/30/2022]
Abstract
Diamond-Blackfan anaemia (DBA) is a rare bone marrow failure syndrome characterised by anaemia, congenital anomalies and cancer predisposition. Although infections are the second leading cause of mortality in non-transplanted patients, immune function is largely unexplored. We identified quantitative deficits in serum immunoglobulins and/or circulating T, natural killer and B lymphocytes in 59 of 107 unselected patients (55·1%) attending our centre over a 7-year period. Immune abnormalities were independent of ribosomal protein genotype and arose in both steroid-treated and steroid-untreated patients. In summary, these data highlight the high prevalence and spectrum of infections and immune defects in DBA.
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Affiliation(s)
- Deena Iskander
- Centre for Haematology, Department of Medicine, Hammersmith Hospital, Imperial College London, London, UK
| | - Irene Roberts
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | - Clare Rees
- Centre for Haematology, Department of Medicine, Hammersmith Hospital, Imperial College London, London, UK
| | - Richard Szydlo
- Centre for Haematology, Department of Medicine, Hammersmith Hospital, Imperial College London, London, UK
| | - Mary Alikian
- Centre for Haematology, Department of Medicine, Hammersmith Hospital, Imperial College London, London, UK
- Imperial Molecular Pathology Laboratory, Imperial College Healthcare NHS Trust and Academic Health Sciences Centre, Hammersmith Hospital, London, UK
| | - Michael Neale
- Centre for Haematology, Department of Medicine, Hammersmith Hospital, Imperial College London, London, UK
| | - Yvonne Harrington
- Paediatric Haematology and Bone Marrow Transplant, Department of Paediatrics, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Peter Kelleher
- Centre for Immunology and Vaccinology, Department of Medicine, Chelsea & Westminster Hospital, Imperial College London, London, UK
| | - Anastasios Karadimitris
- Centre for Haematology, Department of Medicine, Hammersmith Hospital, Imperial College London, London, UK
| | - Josu de la Fuente
- Centre for Haematology, Department of Medicine, Hammersmith Hospital, Imperial College London, London, UK
- Paediatric Haematology and Bone Marrow Transplant, Department of Paediatrics, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
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6
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Nteliopoulos G, Bazeos A, Claudiani S, Gerrard G, Curry E, Szydlo R, Alikian M, Foong HE, Nikolakopoulou Z, Loaiza S, Khorashad JS, Milojkovic D, Perrotti D, Gale RP, Foroni L, Apperley JF. Somatic variants in epigenetic modifiers can predict failure of response to imatinib but not to second-generation tyrosine kinase inhibitors. Haematologica 2019; 104:2400-2409. [PMID: 31073075 PMCID: PMC6959189 DOI: 10.3324/haematol.2018.200220] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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: 06/20/2018] [Accepted: 05/06/2019] [Indexed: 11/09/2022] Open
Abstract
There are no validated molecular biomarkers to identify newly-diagnosed individuals with chronic-phase chronic myeloid leukemia likely to respond poorly to imatinib and who might benefit from first-line treatment with a more potent second-generation tyrosine kinase inhibitor. Our inability to predict these ‘high-risk’ individuals reflects the poorly understood heterogeneity of the disease. To investigate the potential of genetic variants in epigenetic modifiers as biomarkers at diagnosis, we used Ion Torrent next-generation sequencing of 71 candidate genes for predicting response to tyrosine kinase inhibitors and probability of disease progression. A total of 124 subjects with newly-diagnosed chronic-phase chronic myeloid leukemia began with imatinib (n=62) or second-generation tyrosine kinase inhibitors (n=62) and were classified as responders or non-responders based on the BCRABL1 transcript levels within the first year and the European LeukemiaNet criteria for failure. Somatic variants affecting 21 genes (e.g. ASXL1, IKZF1, DNMT3A, CREBBP) were detected in 30% of subjects, most of whom were non-responders (41% non-responders, 18% responders to imatinib, 38% non-responders, 25% responders to second-generation tyrosine kinase inhibitors). The presence of variants predicted the rate of achieving a major molecular response, event-free survival, progression-free survival and chronic myeloid leukemia-related survival in the imatinib but not the second-generation tyrosine kinase inhibitors cohort. Rare germline variants had no prognostic significance irrespective of treatment while some pre-leukemia variants suggest a multi-step development of chronic myeloid leukemia. Our data suggest that identification of somatic variants at diagnosis facilitates stratification into imatinib responders/non-responders, thereby allowing earlier use of second-generation tyrosine kinase inhibitors, which, in turn, may overcome the negative impact of such variants on disease progression.
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Affiliation(s)
| | - Alexandra Bazeos
- Centre for Haematology, Department of Medicine, Imperial College, London, UK
| | - Simone Claudiani
- Centre for Haematology, Department of Medicine, Imperial College, London, UK.,Imperial College Healthcare NHS Trust, London, UK
| | - Gareth Gerrard
- Centre for Haematology, Department of Medicine, Imperial College, London, UK.,Sarah Cannon Molecular Diagnostics, HCA Healthcare UK, London, UK
| | - Edward Curry
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College, London, UK
| | - Richard Szydlo
- Centre for Haematology, Department of Medicine, Imperial College, London, UK
| | - Mary Alikian
- Centre for Haematology, Department of Medicine, Imperial College, London, UK.,Imperial College Healthcare NHS Trust, London, UK
| | - Hui En Foong
- Imperial College Healthcare NHS Trust, London, UK
| | - Zacharoula Nikolakopoulou
- Centre for Haematology, Department of Medicine, Imperial College, London, UK.,Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Sandra Loaiza
- Centre for Haematology, Department of Medicine, Imperial College, London, UK.,Imperial College Healthcare NHS Trust, London, UK
| | - Jamshid S Khorashad
- Centre for Haematology, Department of Medicine, Imperial College, London, UK.,Imperial College Healthcare NHS Trust, London, UK
| | - Dragana Milojkovic
- Centre for Haematology, Department of Medicine, Imperial College, London, UK.,Imperial College Healthcare NHS Trust, London, UK
| | - Danilo Perrotti
- Centre for Haematology, Department of Medicine, Imperial College, London, UK.,Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore MD, USA
| | - Robert Peter Gale
- Centre for Haematology, Department of Medicine, Imperial College, London, UK
| | - Letizia Foroni
- Centre for Haematology, Department of Medicine, Imperial College, London, UK
| | - Jane F Apperley
- Centre for Haematology, Department of Medicine, Imperial College, London, UK.,Imperial College Healthcare NHS Trust, London, UK
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7
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Menter T, Juskevicius D, Alikian M, Steiger J, Dirnhofer S, Tzankov A, Naresh KN. Mutational landscape of B-cell post-transplant lymphoproliferative disorders. Br J Haematol 2017; 178:48-56. [PMID: 28419429 DOI: 10.1111/bjh.14633] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [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: 10/05/2016] [Accepted: 12/31/2016] [Indexed: 12/14/2022]
Abstract
It is currently unclear whether post-transplant diffuse large B-cell lymphomas (PT-DLBCL) display a similar genomic landscape as DLBCL in immunocompetent patients (IC-DLBCL). We investigated 50 post-transplant lymphoproliferative disorders (PTLDs) including 37 PT-DLBCL samples for somatic mutations frequently observed in IC-DLBCL. Targeted Next Generation Sequencing (NGS) using the Ion Torrent platform and a customized panel of 68 genes was performed on genomic DNA. Non-tumoural tissue was sequenced to exclude germline variants in cases where available. A control cohort of 76 IC-DLBCL was available for comparative analyses. In comparison to IC-DLBCLs, PT-DLBCL showed more frequent mutations of TP53 (P = 0·004), and absence of ATM and B2M mutations (P = 0·004 and P = 0·016, respectively). In comparison to IC-DLBCLs, Epstein-Barr virus (EBV)+ PT-DLBCL had fewer mutated genes (P = 0·007) and particularly fewer mutations in nuclear factor-κB pathway-related genes (P = 0·044). TP53 mutations were more frequent in EBV- PT-DLBCL as compared to IC-DLBCL (P = 0·001). Germinal centre B cell (GCB) subtype of PT-DLBCL had fewer mutations and mutated genes than GCB-IC-DLBCLs (P = 0·048 and 0·04 respectively). Polymorphic PTLD displayed fewer mutations as compared to PT-DLBCL (P = 0·001). PT-DLBCL differs from IC-DLBCL with respect to mutations in genes related to DNA damage control and immune-surveillance, and EBV association is likely to have a bearing on the mutational pattern.
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Affiliation(s)
- Thomas Menter
- Department of Cellular and Molecular Pathology, Hammersmith Hospital Campus, Imperial College Healthcare NHS Trust, London, UK.,Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | | | - Mary Alikian
- Department of Cellular and Molecular Pathology, Hammersmith Hospital Campus, Imperial College Healthcare NHS Trust, London, UK
| | - Juerg Steiger
- Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
| | - Stephan Dirnhofer
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Alexandar Tzankov
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Kikkeri N Naresh
- Department of Cellular and Molecular Pathology, Hammersmith Hospital Campus, Imperial College Healthcare NHS Trust, London, UK
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8
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Alikian M, Gale RP, Apperley JF, Foroni L. Molecular techniques for the personalised management of patients with chronic myeloid leukaemia. Biomol Detect Quantif 2017; 11:4-20. [PMID: 28331814 PMCID: PMC5348117 DOI: 10.1016/j.bdq.2017.01.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 12/28/2016] [Accepted: 01/18/2017] [Indexed: 12/25/2022]
Abstract
Chronic myeloid leukemia (CML) is the paradigm for targeted cancer therapy. RT-qPCR is the gold standard for monitoring response to tyrosine kinase-inhibitor (TKI) therapy based on the reduction of blood or bone marrow BCR-ABL1. Some patients with CML and very low or undetectable levels of BCR-ABL1 transcripts can stop TKI-therapy without CML recurrence. However, about 60 percent of patients discontinuing TKI-therapy have rapid leukaemia recurrence. This has increased the need for more sensitive and specific techniques to measure residual CML cells. The clinical challenge is to determine when it is safe to stop TKI-therapy. In this review we describe and critically evaluate the current state of CML clinical management, different technologies used to monitor measurable residual disease (MRD) focus on comparingRT-qPCR and new methods entering clinical practice. We discuss advantages and disadvantages of new methods.
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Key Words
- ABL1, Abelson murine leukaemia virus
- ALL, acute lymphoblastic leukaemia
- AP, accelerated phase
- ARQ, armored RNA Quant
- ATP, adenosine triphosphate
- BC, blast crisis
- BCR, breakpoint cluster region
- BM, bone marrow
- BMT, bone marrow transplantation
- Bp, base pair
- CAP, College of American Pathology
- CES, capillary electrophoresis sequencing
- CML
- CML, chronic myeloid leukaemia
- CMR, complete molecular response/remission
- CP, chronic phase
- DESTINY, De-Escalation and Stopping Treatment of Imatinib, Nilotinib or sprYcel in Chronic Myeloid Leukaemia
- DNA, deoxyribonucleic acid
- EAC, Europe Against Cancer
- ELN, European Leukaemia Net
- EURO-SKI, European Stop Tyrosine Kinase Inhibitor Study
- GUSB, glucuronidase beta gene
- IC, inhibotory concentration
- IRIS, interferon and cytarabine versus STI571
- IS, International Scale
- InDels, insertions and deletions
- KDa, Kilo Dalton
- Kbp, Kilo Base Pairs
- LPC, leukemic progenitor cells
- LSC, leukemic stem cell
- LoD, limit of detection
- LoQ, limit of quantification
- M-bcr, major-breakpoint cluster region
- MMR, major molecular response/remission
- MR, deep molecular response/remission
- MRD
- MRD, minimal residual disease
- Mbp, mega base pair
- Molecular monitoring
- NCCN, National Comprehensive Cancer Network
- NEQAS, National External Quality Assessement Service
- NGS
- NGS, next generation sequencing
- NTC, No Template Control
- PB, Peripheral Blood
- PCR, Polymerase Chain Reaction
- PFS, Progression Free Survival
- Ph, Philadelpia
- Q-PCR, quantitative polymerase chain reaction
- QC, Quality Control
- RT, reverse transcription
- RT-dPCR, reverse transcription-digital polymerase chain reaction
- RT-qPCR, reverse transcription-quantitative polymerase chain reaction
- SCT, stem cell transplant
- SMRT, single-molecule real-time sequencing
- STIM, stop imatinib
- TKD, tyrosine kinase domain
- TKI, tyrosine kinase inhibitor
- WHO, World Health Organisation
- ZMW, zero-mode wave-guided
- allo-SCT, Allogeneic Stem Cell Transplantation
- cDNA, coding or complimentary DNA
- dMIQE, Minimum Information for Publication of Quantitative Digital PCR Experiments
- dPCR
- dPCR, digital polymerase chain reaction
- emPCR, emulsion PCR
- gDNA, genomic deoxyribonucleic acid
- m-bcr, minor-breakpoint cluster region
- mRNA, messenger RNA
- nM, manomolar
- μ-bcr, micro-breakpoint cluster region
- μg, microgram
- μl, microliter
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Affiliation(s)
- Mary Alikian
- Centre for Haematology, Department of Medicine, Imperial College London Hammersmith Hospital, London UK; Imperial Molecular Pathology, Imperial College Healthcare Trust, Hammersmith Hospital, London, UK
| | - Robert Peter Gale
- Centre for Haematology, Department of Medicine, Imperial College London Hammersmith Hospital, London UK
| | - Jane F Apperley
- Centre for Haematology, Department of Medicine, Imperial College London Hammersmith Hospital, London UK
| | - Letizia Foroni
- Centre for Haematology, Department of Medicine, Imperial College London Hammersmith Hospital, London UK
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Alikian M, Whale AS, Akiki S, Piechocki K, Torrado C, Myint T, Cowen S, Griffiths M, Reid AG, Apperley J, White H, Huggett JF, Foroni L. RT-qPCR and RT-Digital PCR: A Comparison of Different Platforms for the Evaluation of Residual Disease in Chronic Myeloid Leukemia. Clin Chem 2017; 63:525-531. [PMID: 27979961 DOI: 10.1373/clinchem.2016.262824] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 11/09/2016] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Tyrosine kinase inhibitors (TKIs) are the cornerstone of successful clinical management of patients with chronic myeloid leukemia (CML). Quantitative monitoring of the percentage of the fusion transcript BCR-ABL1 (breakpoint cluster region–c-abl oncogene 1, non-receptor tyrosine kinase) BCR-ABL1IS (%BCR-ABL1IS) by reverse transcription–quantitative PCR (RT-qPCR) is the gold standard strategy for evaluating patient response to TKIs and classification into prognostic subgroups. However, this approach can be challenging to perform in a reproducible manner. Reverse-transcription digital PCR (RT-dPCR) is an adaptation of this method that could provide the robust and standardized workflow needed for truly standardized patient stratification.
METHODS
BCR-ABL1 and ABL1 transcript copy numbers were quantified in a total of 102 samples; 70 CML patients undergoing TKI therapy and 32 non-CML individuals. 3 commercially available digital PCR platforms (QS3D, QX200 and Raindrop) were compared with the platform routinely used in the clinic for RT-qPCR using the EAC (Europe Against Cancer) assay.
RESULTS
Measurements on all instruments correlated well when the %BCR-ABL1IS was ≥0.1%. In patients with residual disease below this level, greater variations were measured both within and between instruments limiting comparable performance to a 4 log dynamic range.
CONCLUSIONS
RT-dPCR was able to quantify low-level BCR-ABL1 transcript copies but was unable to improve sensitivity below the level of detection achieved by RT-qPCR. However, RT-dPCR was able to perform these sensitive measurements without use of a calibration curve. Adaptions to the protocol to increase the amount of RNA measured are likely to be necessary to improve the analytical sensitivity of BCR-ABL testing on a dPCR platform.
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Affiliation(s)
- Mary Alikian
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, UK
- Centre for Haematology, Faculty of Medicine, Imperial College London, London, UK
| | | | - Susanna Akiki
- West Midlands Regional Genetics Laboratories, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Kim Piechocki
- West Midlands Regional Genetics Laboratories, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Celia Torrado
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, UK
| | - Thet Myint
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, UK
| | - Simon Cowen
- Statistics Team, LGC, Queens Road, Teddington, UK
| | - Michael Griffiths
- West Midlands Regional Genetics Laboratories, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Alistair G Reid
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, UK
- Centre for Haematology, Faculty of Medicine, Imperial College London, London, UK
| | - Jane Apperley
- Centre for Haematology, Faculty of Medicine, Imperial College London, London, UK
- Clinical Haematology, Imperial College Healthcare NHS Trust, London, UK
| | - Helen White
- National Genetics Reference Laboratory (Wessex), Salisbury District Hospital, Salisbury, UK
| | - Jim F Huggett
- Molecular and Cell Biology Team, LGC, Queens Road, Teddington, UK
- School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, UK
| | - Letizia Foroni
- Centre for Haematology, Faculty of Medicine, Imperial College London, London, UK
- Clinical Haematology, Imperial College Healthcare NHS Trust, London, UK
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Gerrard G, Foong HE, Mudge K, Alikian M, Apperley JF, Foroni L. Cepheid xpert monitor platform for the confirmation of BCR-ABL1 IS conversion factors for the molecular monitoring of chronic myeloid leukaemia. Leuk Res 2016; 49:47-50. [DOI: 10.1016/j.leukres.2016.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 07/21/2016] [Accepted: 08/12/2016] [Indexed: 10/21/2022]
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Preuner S, Barna A, Frommlet F, Czurda S, Konstantin B, Alikian M, Machova Polakova K, Sacha T, Richter J, Lion T, Gabriel C. Quantitative Analysis of Mutant Subclones in Chronic Myeloid Leukemia: Comparison of Different Methodological Approaches. Int J Mol Sci 2016; 17:ijms17050642. [PMID: 27136541 PMCID: PMC4881468 DOI: 10.3390/ijms17050642] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/20/2016] [Accepted: 04/25/2016] [Indexed: 12/17/2022] Open
Abstract
Identification and quantitative monitoring of mutant BCR-ABL1 subclones displaying resistance to tyrosine kinase inhibitors (TKIs) have become important tasks in patients with Ph-positive leukemias. Different technologies have been established for patient screening. Various next-generation sequencing (NGS) platforms facilitating sensitive detection and quantitative monitoring of mutations in the ABL1-kinase domain (KD) have been introduced recently, and are expected to become the preferred technology in the future. However, broad clinical implementation of NGS methods has been hampered by the limited accessibility at different centers and the current costs of analysis which may not be regarded as readily affordable for routine diagnostic monitoring. It is therefore of interest to determine whether NGS platforms can be adequately substituted by other methodological approaches. We have tested three different techniques including pyrosequencing, LD (ligation-dependent)-PCR and NGS in a series of peripheral blood specimens from chronic myeloid leukemia (CML) patients carrying single or multiple mutations in the BCR-ABL1 KD. The proliferation kinetics of mutant subclones in serial specimens obtained during the course of TKI-treatment revealed similar profiles via all technical approaches, but individual specimens showed statistically significant differences between NGS and the other methods tested. The observations indicate that different approaches to detection and quantification of mutant subclones may be applicable for the monitoring of clonal kinetics, but careful calibration of each method is required for accurate size assessment of mutant subclones at individual time points.
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Affiliation(s)
- Sandra Preuner
- Children's Cancer Research Institute (CCRI), Zimmermannplatz 10, A-1090 Vienna, Austria.
| | - Agnes Barna
- Red Cross Transfusion Service for Upper Austria, A-4017 Linz, Austria.
| | - Florian Frommlet
- Department for Medical Statistics, Medical University of Vienna, A-1090 Vienna, Austria.
| | - Stefan Czurda
- Children's Cancer Research Institute (CCRI), Zimmermannplatz 10, A-1090 Vienna, Austria.
| | - Byrgazov Konstantin
- Children's Cancer Research Institute (CCRI), Zimmermannplatz 10, A-1090 Vienna, Austria.
| | - Mary Alikian
- Imperial Molecular Pathology Laboratory, Hammersmith Hospital, Imperial College Healthcare National Health Service (NHS) Trust, London W12 0HS, UK.
| | | | - Tomasz Sacha
- Hematology Department, Jagiellonian University, 31-501 Krakow, Poland.
| | - Johan Richter
- Section for Hematology, Department of Medicine, University Hospital of Lund, 221 00 Lund, Sweden.
| | - Thomas Lion
- Children's Cancer Research Institute (CCRI), Zimmermannplatz 10, A-1090 Vienna, Austria.
- Department of Pediatrics, Medical University Vienna, A-1090 Vienna, Austria.
| | - Christian Gabriel
- Red Cross Transfusion Service for Upper Austria, A-4017 Linz, Austria.
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Alikian M, Ellery P, Forbes M, Gerrard G, Kasperaviciute D, Sosinsky A, Mueller M, Whale AS, Milojkovic D, Apperley J, Huggett JF, Foroni L, Reid AG. Next-Generation Sequencing-Assisted DNA-Based Digital PCR for a Personalized Approach to the Detection and Quantification of Residual Disease in Chronic Myeloid Leukemia Patients. J Mol Diagn 2016; 18:176-89. [PMID: 26857065 DOI: 10.1016/j.jmoldx.2015.09.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 08/31/2015] [Accepted: 09/17/2015] [Indexed: 01/06/2023] Open
Abstract
Recent studies indicate that 40% of chronic myeloid leukemia patients who achieve sustained undetectable BCR-ABL1 transcripts on tyrosine kinase inhibitor therapy remain disease-free after drug discontinuation. In contrast, 60% experience return of detectable disease and have to restart treatment, thus highlighting the need for an improved method of identifying patients with the lowest likelihood of relapse. Here we describe the validation of a personalized DNA-based digital PCR (dPCR) approach for quantifying very low levels of residual disease, which involves the rapid identification of t(9;22) fusion junctions using targeted next-generation sequencing coupled with the use of a dPCR platform. t(9;22) genomic breakpoints were successfully mapped in samples from 32 of 32 patients with early stage disease. Disease quantification by DNA-based dPCR was performed using the Fluidigm BioMark platform on 46 follow-up samples from 6 of the 32 patients, including 36 samples that were in deep molecular remission. dPCR detected persistent disease in 81% of molecular-remission samples, outperforming both RT-dPCR (25%) and DNA-based quantitative PCR (19%). We conclude that dPCR for BCR-ABL1 DNA is the most sensitive available method of residual-disease detection in chronic myeloid leukemia and may prove useful in the management of tyrosine kinase inhibitor withdrawal.
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Affiliation(s)
- Mary Alikian
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom; Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom.
| | - Peter Ellery
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom
| | - Martin Forbes
- Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Gareth Gerrard
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom; Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Dalia Kasperaviciute
- Clinical Genome Informatics Facility, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Alona Sosinsky
- Clinical Genome Informatics Facility, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Michael Mueller
- Clinical Genome Informatics Facility, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Alexandra S Whale
- Molecular & Cell Biology, LGC Limited, Queens Road, Teddington, United Kingdom
| | - Dragana Milojkovic
- Clinical Haematology, Imperial College Healthcare National Health Institute Trust, London, United Kingdom
| | - Jane Apperley
- Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jim F Huggett
- Molecular & Cell Biology, LGC Limited, Queens Road, Teddington, United Kingdom
| | - Letizia Foroni
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom; Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Alistair G Reid
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom; Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom
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13
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Alonso-Dominguez JM, Grinfeld J, Alikian M, Marin D, Reid A, Daghistani M, Hedgley C, O'Brien S, Clark RE, Apperley J, Foroni L, Gerrard G. PTCH1 expression at diagnosis predicts imatinib failure in chronic myeloid leukaemia patients in chronic phase. Am J Hematol 2015; 90:20-6. [PMID: 25250944 DOI: 10.1002/ajh.23857] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 09/17/2014] [Indexed: 11/06/2022]
Abstract
The tyrosine kinase inhibitor (TKI) imatinib has revolutionized the management of chronic myeloid leukaemia (CML). However, around 25% of patients fail to sustain an adequate response. We sought to identify gene-expression biomarkers that could be used to predict imatinib response. The expression of 29 genes, previously implicated in CML pathogenesis, were measured by TaqMan Low Density Array in 73 CML patient samples. Patients were divided into low and high expression for each gene and imatinib failure (IF), probability of achieving CCyR, progression free survival and CML related OS were compared by Kaplan-Meier and log-rank. Results were validated in a second cohort of 56 patients, with a further technical validation using custom gene-expression assays in a conventional RT-qPCR in a sub-cohort of 37 patients. Patients with low PTCH1 expression showed a worse clinical response for all variables in all cohorts. PTCH1 was the most significant predictor in the multivariate analysis compared with Sokal, age and EUTOS. PTCH1 expression assay showed the adequate sensitivity, specificity and predictive values to predict for IF. Given the different treatments available for CML, measuring PTCH1 expression at diagnosis may help establish who will benefit best from imatinib and who is better selected for second generation TKI.
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Affiliation(s)
| | - Jacob Grinfeld
- Centre for Haematology; Department of Medicine; Imperial College London; London United Kingdom
- Department of Medicine; Imperial College Healthcare NHS Trust, Hammersmith Hospital; London United Kingdom
| | - Mary Alikian
- Centre for Haematology; Department of Medicine; Imperial College London; London United Kingdom
| | - David Marin
- Centre for Haematology; Department of Medicine; Imperial College London; London United Kingdom
- Department of Medicine; Imperial College Healthcare NHS Trust, Hammersmith Hospital; London United Kingdom
| | - Alistair Reid
- Centre for Haematology; Department of Medicine; Imperial College London; London United Kingdom
- Department of Medicine; Imperial College Healthcare NHS Trust, Hammersmith Hospital; London United Kingdom
| | - Mustafa Daghistani
- Centre for Haematology; Department of Medicine; Imperial College London; London United Kingdom
| | - Corinne Hedgley
- Academic Haematology; Northern Institute for Cancer Research, Newcastle University Medical School; Newcastle Upon Tyne United Kingdom
| | - Stephen O'Brien
- Academic Haematology; Northern Institute for Cancer Research, Newcastle University Medical School; Newcastle Upon Tyne United Kingdom
| | - Richard E. Clark
- Department of Haematology; Royal Liverpool University Hospital, University of Liverpool; Liverpool United Kingdom
| | - Jane Apperley
- Centre for Haematology; Department of Medicine; Imperial College London; London United Kingdom
- Department of Medicine; Imperial College Healthcare NHS Trust, Hammersmith Hospital; London United Kingdom
| | - Letizia Foroni
- Centre for Haematology; Department of Medicine; Imperial College London; London United Kingdom
- Department of Medicine; Imperial College Healthcare NHS Trust, Hammersmith Hospital; London United Kingdom
| | - Gareth Gerrard
- Centre for Haematology; Department of Medicine; Imperial College London; London United Kingdom
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Grinfeld J, Gerrard G, Alikian M, Alonso-Dominguez J, Ale S, Valgañon M, Nteliopoulos G, White D, Marin D, Hedgley C, O'Brien S, Clark R, Goldman JM, Milojkovic D, Apperley JF, Foroni L. A common novel splice variant ofSLC22A1(OCT1)is associated with impaired responses to imatinib in patients with chronic myeloid leukaemia. Br J Haematol 2013; 163:631-9. [DOI: 10.1111/bjh.12591] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/14/2013] [Indexed: 12/20/2022]
Affiliation(s)
- Jacob Grinfeld
- Department of Haematology; Imperial College Healthcare NHS Trust; London UK
| | - Gareth Gerrard
- Department of Haematology; Imperial College Healthcare NHS Trust; London UK
| | - Mary Alikian
- Department of Haematology; Imperial College Healthcare NHS Trust; London UK
| | | | - Sakuntala Ale
- Department of Haematology; Imperial College Healthcare NHS Trust; London UK
| | - Mikel Valgañon
- Department of Haematology; Imperial College Healthcare NHS Trust; London UK
| | | | - Deborah White
- Department of Haematology; Centre for Cancer Biology/SA Pathology; Universities of South Australia and Adelaide; Adelaide Australia
| | - David Marin
- Department of Haematology; Imperial College Healthcare NHS Trust; London UK
| | - Corinne Hedgley
- Northern Institute for Cancer Research; Newcastle University Medical School; Newcastle Upon Tyne UK
| | - Stephen O'Brien
- Northern Institute for Cancer Research; Newcastle University Medical School; Newcastle Upon Tyne UK
| | - Richard Clark
- Department of Haematology; Royal Liverpool University Hospital; University of Liverpool; Liverpool UK
| | - John M. Goldman
- Department of Haematology; Imperial College Healthcare NHS Trust; London UK
| | - Dragana Milojkovic
- Department of Haematology; Imperial College Healthcare NHS Trust; London UK
| | - Jane F. Apperley
- Department of Haematology; Imperial College Healthcare NHS Trust; London UK
| | - Letizia Foroni
- Department of Haematology; Imperial College Healthcare NHS Trust; London UK
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Gerrard G, Mudge K, Foskett P, Stevens D, Alikian M, White HE, Cross NCP, Apperley J, Foroni L. Fast-mode duplex qPCR for BCR-ABL1 molecular monitoring: innovation, automation, and harmonization. Am J Hematol 2012; 87:717-20. [PMID: 22566190 DOI: 10.1002/ajh.23212] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Reverse transcription quantitative polymerase chain reaction (RTqPCR)is currently the most sensitive tool available for the routine monitoring of disease level in patients undergoing treatment for BCRABL1 associated malignancies. Considerable effort has been invested at both the local and international levels to standardise the methodology and reporting criteria used to assess this critical metric. In an effort to accommodate the demands of increasing sample throughput and greater standardization, we adapted the current best-practice guidelines to encompass automation platforms and improved multiplex RT-qPCR technology.
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Affiliation(s)
- Gareth Gerrard
- Imperial Molecular Pathology, Imperial College Academic Health Science Centre, London, United Kingdom.
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16
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Alikian M, Gerrard G, Subramanian PG, Mudge K, Foskett P, Khorashad JS, Lim AC, Marin D, Milojkovic D, Reid A, Rezvani K, Goldman J, Apperley J, Foroni L. BCR-ABL1 kinase domain mutations: methodology and clinical evaluation. Am J Hematol 2012; 87:298-304. [PMID: 22231203 DOI: 10.1002/ajh.22272] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 11/24/2011] [Accepted: 12/01/2011] [Indexed: 12/31/2022]
Abstract
The introduction of tyrosine kinase inhibitors (TKIs), starting with imatinib and followed by second and third generation TKIs, has significantly changed the clinical management of patients with chronic myeloid leukemia (CML). Despite their unprecedented clinical success, a proportion of patients fail to achieve complete cytogenetic remission by 12 months of treatment (primary resistance) while others experience progressive resistance after an initial response (secondary resistance). BCR-ABL1 kinase domain (KD) mutations have been detected in a proportion of patients at the time of treatment failure, and therefore their identification and monitoring plays an important role in therapeutic decisions particularly when switching TKIs. When monitoring KD mutations in a clinical laboratory, the choice of method should take into account turnaround time, cost, sensitivity, specificity, and ability to accurately quantify the size of the mutant clone. In this article, we describe in a "manual" style the methods most widely used in our laboratory to monitor KD mutations in patients with CML including direct sequencing, D-HPLC, and pyrosequencing. Advantages, disadvantages, interpretation of results, and their clinical applications are reviewed for each method.
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MESH Headings
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Chromatography, High Pressure Liquid/methods
- DNA Mutational Analysis/methods
- Drug Resistance, Neoplasm/genetics
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/genetics
- Genes, abl
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/enzymology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Mutation
- Polymerase Chain Reaction/methods
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/therapeutic use
- Protein Structure, Tertiary/genetics
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Protein-Tyrosine Kinases/genetics
- Quality Control
- RNA, Messenger/genetics
- RNA, Messenger/isolation & purification
- RNA, Neoplasm/genetics
- RNA, Neoplasm/isolation & purification
- Sequence Analysis, DNA/methods
- Specimen Handling
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Affiliation(s)
- Mary Alikian
- Imperial Molecular Pathology Laboratory, Imperial College NHS Trust and Academic Science Centre, Hammersmith Hospital, London W12 OHS, United Kingdom
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Heathcote DA, Patel H, Kroll SHB, Hazel P, Periyasamy M, Alikian M, Kanneganti SK, Jogalekar AS, Scheiper B, Barbazanges M, Blum A, Brackow J, Siwicka A, Pace RDM, Fuchter MJ, Snyder JP, Liotta DC, Freemont PS, Aboagye EO, Coombes RC, Barrett AGM, Ali S. A novel pyrazolo[1,5-a]pyrimidine is a potent inhibitor of cyclin-dependent protein kinases 1, 2, and 9, which demonstrates antitumor effects in human tumor xenografts following oral administration. J Med Chem 2010; 53:8508-22. [PMID: 21080703 DOI: 10.1021/jm100732t] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cyclin-dependent protein kinases (CDKs) are central to the appropriate regulation of cell proliferation, apoptosis, and gene expression. Abnormalities in CDK activity and regulation are common features of cancer, making CDK family members attractive targets for the development of anticancer drugs. Here, we report the identification of a pyrazolo[1,5-a]pyrimidine derived compound, 4k (BS-194), as a selective and potent CDK inhibitor, which inhibits CDK2, CDK1, CDK5, CDK7, and CDK9 (IC₅₀= 3, 30, 30, 250, and 90 nmol/L, respectively). Cell-based studies showed inhibition of the phosphorylation of CDK substrates, Rb and the RNA polymerase II C-terminal domain, down-regulation of cyclins A, E, and D1, and cell cycle block in the S and G₂/M phases. Consistent with these findings, 4k demonstrated potent antiproliferative activity in 60 cancer cell lines tested (mean GI₅₀= 280 nmol/L). Pharmacokinetic studies showed that 4k is orally bioavailable, with an elimination half-life of 178 min following oral dosing in mice. When administered at a concentration of 25 mg/kg orally, 4k inhibited human tumor xenografts and suppressed CDK substrate phosphorylation. These findings identify 4k as a novel, potent CDK selective inhibitor with potential for oral delivery in cancer patients.
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Affiliation(s)
- Dean A Heathcote
- Dept of Oncology, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, England
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Owen C, Virappane P, Alikian M, Stasevich I, Summers K, Lillington D, Bonnet D, Burnett A, Mills K, Lister TA, Fitzgibbon J. WTX is rarely mutated in acute myeloid leukemia. Haematologica 2008; 93:947-8. [DOI: 10.3324/haematol.12509] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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