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Kumar P, Turati V, Marusyk A. Abstract B032: Deciphering the mechanisms of environmentally mediated Alectinib resistance in ALK+NSCLC. Cancer Res 2022. [DOI: 10.1158/1538-7445.evodyn22-b032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Non-small cell lung cancer (NSCLC) is a devastating disease with a subset containing targetable oncogenic mutations that strongly benefit from targeted therapies. 3-7% of NSCLC patients bear an amplification of the Anaplastic lymphoma kinase (ALK) and Echinoderm microtubule-associated protein like 4 (EML4) fusion gene. These tumors typically show strong durable responses to first line therapy, Alectinib, an ALK tyrosine kinase inhibitors (ALK-TKIs). However, there is a high degree of patient-to-patient variability in the level of response to this drug; with some patients being innately resistant or less sensitive. Moreover, weak initial sensitivity to therapy has been linked to poor long-term responses with early acquisition of resistance. Thus, to improve clinical outcomes, we need to understand the mechanisms that lead to this reduced sensitivity to ALK inhibition. While, historically, reduced sensitivity to ALK TKI was thought to reflect cell intrinsic mechanisms, a growing body of evidence points to the importance of tumor microenvironmentally (TME) mediated mechanisms. We fortuitously encountered an observation of strong environment-mediated desensitization to Alectinib. We found that combining Alectinib with a small molecule inhibitor, Jumonji histone demethylase inhibitor, JIB04 in vitro overcomes tolerance, preventing ALK+NSCLC cells from developing resistance to Alectinib. Surprisingly, our validation experiments in mouse models revealed the opposite effect, where, JIB04 desensitized tumors to ALK inhibition. The disparity in the in vitro versus the in vivo response indicates the contribution of the TME in the reduced Alectinib sensitivity observed in vivo. The resistance phenotype in Alectinib+JIB04 treated mice was strongly associated with extensive inflammation in the tumor proximal tissues, along with higher circulating levels of inflammatory markers, IL6, LIF and monocytes, suggesting that inflammation may play a role in mediating this resistance. This is consistent with the recent findings where the markers of systemic inflammation such as Neutrophil to Lymphocyte ratio (NLR) have been associated with poor prognosis in ALK+NSCLC. While the mechanistic understanding is not well characterized, our model may help us explore the mechanisms of this correlation. Thus, our objective is to understand the underlying microenvironmental mechanism of this resistance to Alectinib. We hypothesize that Alectinib+JIB04 associated inflammation reduces ALK+NSCLC’s sensitivity to Alectinib. We envision two possibilities, either inflammation may directly affect resistance to Alectinib or indirectly where inflammation enhances tumor cell plasticity that then leads to resistance. We posit that the underlying molecular mechanisms of Alectinib+JIB04 mediated resistance are likely to be relevant to a subset of patients with poor initial responses with weak sensitivity or innate resistance to Alectinib observed in the clinics and will improve our knowledge about microenvironmental regulation of resistance.
Citation Format: Pragya Kumar, Virginia Turati, Andriy Marusyk. Deciphering the mechanisms of environmentally mediated Alectinib resistance in ALK+NSCLC [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr B032.
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Affiliation(s)
- Pragya Kumar
- Moffitt Cancer Center, University of South Florida, Tampa, FL,
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Schenck RO, Jakobsen NA, Turati V, Shibata D, Vyas P, Leedham S, Anderson AR. Abstract A019: Mutation agnostic diagnosis of clonal hematopoiesis of indeterminate potential (CHIP) using fluctuating methylation clocks. Cancer Res 2022. [DOI: 10.1158/1538-7445.evodyn22-a019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Clonal hematopoiesis (CH), such as clonal hematopoiesis of indeterminant potential (CHIP), is diagnosed based on somatic genomic alterations in the absence of hematologic malignancy. At present, CHIP is diagnosed using peripheral blood, where putative driver point mutations and small insertions/deletions whose variant allele frequency is greater or equal to two percent. Generally, the prevalence of CH increases as an individual ages and conveys a risk for progression to a malignancy. CH is thought to be driven by the underlying hematopoietic stem cells of an unknown quantity, with estimates in the literature for stem cell numbers differing by orders of magnitude. Previously, we developed a method using fluctuating CpG (fCpG) sites to serve as a fluctuating methylation clock to uncover stem cell dynamics in glandular tissues and orthogonally validated our method using publicly available datasets of human blood from normal cohorts and malignant cohorts. Here we expand on this work by presenting 38 new patients with distinct VAF groups from 1-2% VAF up to greater than 10% VAF for putative drivers with corresponding DNA methylation profiles using the Illumina EPIC array platform. We identify fCpG from our normal and CHIP cohorts to train and validate a machine learning approach that allows us to diagnose CHIP without DNA sequencing. Importantly, our approach allows for the identification of patients who may have CH driven by structural variants such as copy number alterations. We use this method to evaluate two publicly available methylation datasets of reportedly normal patients (n=656 and n=732) showing that evidence of CHIP can be found in 19% and 29% of these datasets, respectively. We then evaluate copy number differences in burden within our CHIP cohort and these newly identified CHIP cohorts. Using a mechanistic model of hematopoietic stem cells containing fCpGs we examine the temporal dynamics of competing founder CHIP drivers and the number of stem cells in the hematopoietic stem cell compartment.
Citation Format: Ryan O. Schenck, Niels Asger Jakobsen, Virginia Turati, Darryl Shibata, Paresh Vyas, Simon Leedham, Alexander R.A. Anderson. Mutation agnostic diagnosis of clonal hematopoiesis of indeterminate potential (CHIP) using fluctuating methylation clocks [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr A019.
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Affiliation(s)
| | | | | | | | - Paresh Vyas
- University of Oxford, Oxford, United Kingdom,
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3
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Litchfield K, Reading JL, Puttick C, Thakkar K, Abbosh C, Bentham R, Watkins TBK, Rosenthal R, Biswas D, Rowan A, Lim E, Al Bakir M, Turati V, Guerra-Assunção JA, Conde L, Furness AJS, Saini SK, Hadrup SR, Herrero J, Lee SH, Van Loo P, Enver T, Larkin J, Hellmann MD, Turajlic S, Quezada SA, McGranahan N, Swanton C. Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition. Cell 2021; 184:596-614.e14. [PMID: 33508232 PMCID: PMC7933824 DOI: 10.1016/j.cell.2021.01.002] [Citation(s) in RCA: 420] [Impact Index Per Article: 140.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/26/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022]
Abstract
Checkpoint inhibitors (CPIs) augment adaptive immunity. Systematic pan-tumor analyses may reveal the relative importance of tumor-cell-intrinsic and microenvironmental features underpinning CPI sensitization. Here, we collated whole-exome and transcriptomic data for >1,000 CPI-treated patients across seven tumor types, utilizing standardized bioinformatics workflows and clinical outcome criteria to validate multivariable predictors of CPI sensitization. Clonal tumor mutation burden (TMB) was the strongest predictor of CPI response, followed by total TMB and CXCL9 expression. Subclonal TMB, somatic copy alteration burden, and histocompatibility leukocyte antigen (HLA) evolutionary divergence failed to attain pan-cancer significance. Dinucleotide variants were identified as a source of immunogenic epitopes associated with radical amino acid substitutions and enhanced peptide hydrophobicity/immunogenicity. Copy-number analysis revealed two additional determinants of CPI outcome supported by prior functional evidence: 9q34 (TRAF2) loss associated with response and CCND1 amplification associated with resistance. Finally, single-cell RNA sequencing (RNA-seq) of clonal neoantigen-reactive CD8 tumor-infiltrating lymphocytes (TILs), combined with bulk RNA-seq analysis of CPI-responding tumors, identified CCR5 and CXCL13 as T-cell-intrinsic markers of CPI sensitivity.
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Affiliation(s)
- Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - James L Reading
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Clare Puttick
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Krupa Thakkar
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Chris Abbosh
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Robert Bentham
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Rachel Rosenthal
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Dhruva Biswas
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Emilia Lim
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Virginia Turati
- Stem Cell Group, Cancer Institute, University College London, London WC1E 6DD, UK
| | - José Afonso Guerra-Assunção
- Bill Lyons Informatics Centre, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Lucia Conde
- Bill Lyons Informatics Centre, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Andrew J S Furness
- Renal and Skin Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Sunil Kumar Saini
- Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Sine R Hadrup
- Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Se-Hoon Lee
- Department of Health Sciences and Technology, Samsung Advanced Institute of Health Sciences and Technology, Sungkyunkwan University, Seoul, South Korea; Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Tariq Enver
- Stem Cell Group, Cancer Institute, University College London, London WC1E 6DD, UK
| | - James Larkin
- Renal and Skin Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Matthew D Hellmann
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, and Parker Center for Cancer Immunotherapy, 885 2nd Avenue, New York, NY 10017, USA
| | - Samra Turajlic
- Renal and Skin Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Cancer Dynamics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK.
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK.
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK.
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4
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Joshi K, de Massy MR, Ismail M, Reading JL, Uddin I, Woolston A, Hatipoglu E, Oakes T, Rosenthal R, Peacock T, Ronel T, Noursadeghi M, Turati V, Furness AJS, Georgiou A, Wong YNS, Ben Aissa A, Sunderland MW, Jamal-Hanjani M, Veeriah S, Birkbak NJ, Wilson GA, Hiley CT, Ghorani E, Guerra-Assunção JA, Herrero J, Enver T, Hadrup SR, Hackshaw A, Peggs KS, McGranahan N, Swanton C, Quezada SA, Chain B. Publisher Correction: Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer. Nat Med 2020; 26:1148. [PMID: 32494063 DOI: 10.1038/s41591-020-0866-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Kroopa Joshi
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Marc Robert de Massy
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Mazlina Ismail
- Division of Infection and Immunity, University College London, London, UK
| | - James L Reading
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Imran Uddin
- Division of Infection and Immunity, University College London, London, UK
| | - Annemarie Woolston
- Division of Infection and Immunity, University College London, London, UK
| | - Emine Hatipoglu
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Theres Oakes
- Division of Infection and Immunity, University College London, London, UK
| | - Rachel Rosenthal
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Thomas Peacock
- Division of Infection and Immunity, University College London, London, UK
- Computation, Mathematics and Physics in the Life Sciences and Experimental Biology, Department of Computer Science, University College London, London, UK
| | - Tahel Ronel
- Division of Infection and Immunity, University College London, London, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | - Virginia Turati
- Department of Cancer Biology, University College London Cancer Institute, London, UK
| | - Andrew J S Furness
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Andrew Georgiou
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Yien Ning Sophia Wong
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Assma Ben Aissa
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mariana Werner Sunderland
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Gareth A Wilson
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Crispin T Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Ehsan Ghorani
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | | | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Tariq Enver
- University College London Cancer Institute, London, UK
| | - Sine R Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Allan Hackshaw
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Karl S Peggs
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, UK.
- Department of Computer Sciences, University College London, London, UK.
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Ghorani E, Reading JL, Henry JY, Massy MRD, Rosenthal R, Turati V, Joshi K, Furness AJS, Ben Aissa A, Saini SK, Ramskov S, Georgiou A, Sunderland MW, Wong YNS, Mucha MVD, Day W, Galvez-Cancino F, Becker PD, Uddin I, Oakes T, Ismail M, Ronel T, Woolston A, Jamal-Hanjani M, Veeriah S, Birkbak NJ, Wilson GA, Litchfield K, Conde L, Guerra-Assunção JA, Blighe K, Biswas D, Salgado R, Lund T, Bakir MA, Moore DA, Hiley CT, Loi S, Sun Y, Yuan Y, AbdulJabbar K, Turajilic S, Herrero J, Enver T, Hadrup SR, Hackshaw A, Peggs KS, McGranahan N, Chain B, Swanton C, Quezada SA. The T cell differentiation landscape is shaped by tumour mutations in lung cancer. Nat Cancer 2020; 1:546-561. [PMID: 32803172 PMCID: PMC7115931 DOI: 10.1038/s43018-020-0066-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/20/2020] [Indexed: 01/06/2023]
Abstract
Tumour mutational burden (TMB) predicts immunotherapy outcome in non-small cell lung cancer (NSCLC), consistent with immune recognition of tumour neoantigens. However, persistent antigen exposure is detrimental for T cell function. How TMB affects CD4 and CD8 T cell differentiation in untreated tumours, and whether this affects patient outcomes is unknown. Here we paired high-dimensional flow cytometry, exome, single-cell and bulk RNA sequencing from patients with resected, untreated NSCLC to examine these relationships. TMB was associated with compartment-wide T cell differentiation skewing, characterized by loss of TCF7-expressing progenitor-like CD4 T cells, and an increased abundance of dysfunctional CD8 and CD4 T cell subsets, with significant phenotypic and transcriptional similarity to neoantigen-reactive CD8 T cells. A gene signature of redistribution from progenitor-like to dysfunctional states associated with poor survival in lung and other cancer cohorts. Single-cell characterization of these populations informs potential strategies for therapeutic manipulation in NSCLC.
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Affiliation(s)
- Ehsan Ghorani
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - James L Reading
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Jake Y Henry
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Marc Robert de Massy
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Rachel Rosenthal
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Virginia Turati
- Department of Cancer Biology, University College London Cancer Institute, London, UK
| | - Kroopa Joshi
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Andrew J S Furness
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Assma Ben Aissa
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sunil Kumar Saini
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Sofie Ramskov
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Andrew Georgiou
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mariana Werner Sunderland
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Yien Ning Sophia Wong
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Maria Vila De Mucha
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - William Day
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Felipe Galvez-Cancino
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Pablo D Becker
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Imran Uddin
- Division of Infection and Immunity, University College London, London, UK
| | - Theres Oakes
- Division of Infection and Immunity, University College London, London, UK
| | - Mazlina Ismail
- Division of Infection and Immunity, University College London, London, UK
| | - Tahel Ronel
- Division of Infection and Immunity, University College London, London, UK
| | - Annemarie Woolston
- Division of Infection and Immunity, University College London, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Lucia Conde
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | | | - Kevin Blighe
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Dhruva Biswas
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | | | - Tom Lund
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - David A Moore
- Department of Pathology, University College London Cancer Institute, London, UK
| | - Crispin T Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Sherene Loi
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | - Yuxin Sun
- Division of Infection and Immunity, University College London, London, UK
| | - Yinyin Yuan
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Khalid AbdulJabbar
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Samra Turajilic
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Tariq Enver
- Department of Cancer Biology, University College London Cancer Institute, London, UK
| | - Sine R Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Allan Hackshaw
- Cancer Research UK and University College London Cancer Trials Centre, London, UK
| | - Karl S Peggs
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, UK
- Department of Computer Sciences, University College London, London, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- University College London Hospitals, London, UK.
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
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6
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Gupta R, Turati V, Brian D, Thrussel C, Wilbourn B, May G, Enver T. Nov/CCN3 Enhances Cord Blood Engraftment by Rapidly Recruiting Latent Human Stem Cell Activity. Cell Stem Cell 2020; 26:527-541.e8. [PMID: 32197066 PMCID: PMC7118368 DOI: 10.1016/j.stem.2020.02.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 01/04/2020] [Accepted: 02/19/2020] [Indexed: 01/13/2023]
Abstract
Umbilical cord blood (UCB) has had considerable impact in pediatric stem cell transplantation, but its wider use is limited in part by unit size. Long-term ex vivo culture offers one approach to increase engraftment capacity by seeking to expand stem and progenitor cells. Here, we show brief incubation (8 h) of UCB CD34+ cells with the matricellular regulator Nov (CCN3) increases the frequency of serially transplantable hematopoietic stem cells (HSCs) 6-fold. This rapid response suggests recruitment rather than expansion of stem cells; accordingly, in single-cell assays, Nov increases the clonogenicity of phenotypic HSCs without increasing their number through cell division. Recruitment is associated with both metabolic and transcriptional changes, and tracing of cell divisions demonstrates that the increased clonogenic activity resides within the undivided fraction of cells. Harnessing latent stem cell potential through recruitment-based approaches will inform understanding of stem cell state transitions with implications for translation to the clinic. NOV rapidly increases the number of functional HSCs in a single cord blood unit This is by direct recruitment without expansion or self-renewal ex vivo NOV reduces C-MYC and ROS but increases glycolytic enzymes in HSCs Manipulating non-dividing stem cells can alter their state and functional potential
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Affiliation(s)
- Rajeev Gupta
- Stem Cell Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK; Manual Blood Sciences, Health Services Laboratories, The Halo Building, 1 Mabledon Place, London WC1H 9AX, UK
| | - Virginia Turati
- Stem Cell Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Duncan Brian
- Stem Cell Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Craig Thrussel
- Stem Cell Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Barry Wilbourn
- Flow Cytometry Core Facility, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Gillian May
- Stem Cell Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Tariq Enver
- Stem Cell Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK.
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7
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Joshi K, de Massy MR, Ismail M, Reading JL, Uddin I, Woolston A, Hatipoglu E, Oakes T, Rosenthal R, Peacock T, Ronel T, Noursadeghi M, Turati V, Furness AJS, Georgiou A, Wong YNS, Ben Aissa A, Sunderland MW, Jamal-Hanjani M, Veeriah S, Birkbak NJ, Wilson GA, Hiley CT, Ghorani E, Guerra-Assunção JA, Herrero J, Enver T, Hadrup SR, Hackshaw A, Peggs KS, McGranahan N, Swanton C, Quezada SA, Chain B. Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer. Nat Med 2019; 25:1549-1559. [PMID: 31591606 PMCID: PMC6890490 DOI: 10.1038/s41591-019-0592-2] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022]
Abstract
Somatic mutations together with immunoediting drive extensive heterogeneity within non-small-cell lung cancer (NSCLC). Herein we examine heterogeneity of the T cell antigen receptor (TCR) repertoire. The number of TCR sequences selectively expanded in tumors varies within and between tumors and correlates with the number of nonsynonymous mutations. Expanded TCRs can be subdivided into TCRs found in all tumor regions (ubiquitous) and those present in a subset of regions (regional). The number of ubiquitous and regional TCRs correlates with the number of ubiquitous and regional nonsynonymous mutations, respectively. Expanded TCRs form part of clusters of TCRs of similar sequence, suggestive of a spatially constrained antigen-driven process. CD8+ tumor-infiltrating lymphocytes harboring ubiquitous TCRs display a dysfunctional tissue-resident phenotype. Ubiquitous TCRs are preferentially detected in the blood at the time of tumor resection as compared to routine follow-up. These findings highlight a noninvasive method to identify and track relevant tumor-reactive TCRs for use in adoptive T cell immunotherapy.
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MESH Headings
- Aged
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/pathology
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/immunology
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Non-Small-Cell Lung/therapy
- Female
- Genetic Heterogeneity
- Humans
- Immunotherapy, Adoptive
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/pathology
- Male
- Middle Aged
- Mutation
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
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Affiliation(s)
- Kroopa Joshi
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Marc Robert de Massy
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Mazlina Ismail
- Division of Infection and Immunity, University College London, London, UK
| | - James L Reading
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Imran Uddin
- Division of Infection and Immunity, University College London, London, UK
| | - Annemarie Woolston
- Division of Infection and Immunity, University College London, London, UK
| | - Emine Hatipoglu
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Theres Oakes
- Division of Infection and Immunity, University College London, London, UK
| | - Rachel Rosenthal
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Thomas Peacock
- Division of Infection and Immunity, University College London, London, UK
- Computation, Mathematics and Physics in the Life Sciences and Experimental Biology, Department of Computer Science, University College London, London, UK
| | - Tahel Ronel
- Division of Infection and Immunity, University College London, London, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | - Virginia Turati
- Department of Cancer Biology, University College London Cancer Institute, London, UK
| | - Andrew J S Furness
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Andrew Georgiou
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Yien Ning Sophia Wong
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Assma Ben Aissa
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mariana Werner Sunderland
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Gareth A Wilson
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Crispin T Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Ehsan Ghorani
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | | | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Tariq Enver
- University College London Cancer Institute, London, UK
| | - Sine R Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Allan Hackshaw
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Karl S Peggs
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, UK.
- Department of Computer Sciences, University College London, London, UK.
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Böiers C, Richardson S, Zriwil A, Laycock E, Turati V, Brown J, Wray J, Wang D, James C, Herrero J, Sitnicka E, Karlsson S, Smith A, Jacobsen SE, Enver T. A human ips model implicates embryonic B-myeloid fate restriction as a developmental susceptibility to ETV6-RUNX1. Exp Hematol 2017. [DOI: 10.1016/j.exphem.2017.06.055] [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: 11/30/2022]
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Turati V, Guerra-Assunção JA, Ambrose J, Brown J, Hubank M, Lynch M, Gaal B, Conde L, Jacobsen SE, Herrero J, Enver T. Single-cell analysis of clonal dynamics of childhood acute lymphoblastic leukaemia. Exp Hematol 2017. [DOI: 10.1016/j.exphem.2017.06.078] [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: 11/30/2022]
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Richardson SE, Böiers C, Zriwil A, Turati V, Brown J, Wang D, Herrero J, Karlsson S, Smith AJH, Jacobsen SE, Enver T. Abstract 2692: ETV6-RUNX1 targets a developmentally restricted embryonic human B-myeloid progenitor. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Childhood acute lymphoblastic leukemia (cALL) is distinct from that in adults with higher incidence, better prognosis and a distinct mutational spectrum. One hypothesis for this difference is that cALL arises in transient cells unique to early human development. We explored this in ETV6-RUNX1 cALL where evidence from twins and neonatal heel prick testing has shown that this mutation arises in utero and is an initiating event. We characterized B cell development in first trimester human fetal liver (FL) to identify compartments vulnerable to ETV6-RUNX1. Using CD19 as a marker of B lineage commitment we found the first CD19+ B cells emerge in the human FL at Carnegie Stage (CS) 17 and were distinct from adult in that the majority expressed surface IL7 receptor. We used IL7R to identify a CD19-IL7R+ B progenitor compartment that produced B cells in vitro, possessed DJH recombination, but also had monocytic potential. Single cell analysis of CS20 IL7R+ progenitors revealed co-expression of lymphoid and myeloid programmes, whereas at CS17 they were strongly myeloid primed indicating that IL7R+ progenitors acquire lymphoid potential in this developmental window. Some co-expression of lymphoid and myeloid programmes also persisted in CS20 FL B cells. We tested whether FL B cell development could be modeled using human pluripotent stem cells (hPSCs). In vitro B cell differentiation of hPSCs produced IL7R expressing pro and preB cells as well as an IL7R+ progenitor that switched from myeloid to B-myeloid priming during culture. At the global transcriptional level the hPSC lymphoid hierarchy mapped closely with FL, with both separating from adult suggesting that hPSCs provide a developmentally relevant model of early FL B lymphopoiesis. We next used CRIPSR-directed homologous recombination to engineer the expression of ETV6-RUNX1 under the endogenous ETV6 promoter. ETV6-RUNX1 hPSCs displayed a partial block in B cell differentiation at the level of the IL7R+ progenitor. ETV6-RUNX1 expressing B cells co-expressed an abnormal B-myeloid gene expression signature akin to that seen in the IL7R+ progenitor. Both the transcriptional and differentiation phenotypes were dependent on ETV6-RUNX1 as demonstrated by their reversion upon cre-mediated excision of the knock-in cassette. Our data support a model where expression of ETV6-RUNX1 inhibits lymphoid specification in an early FL IL7R+ lymphomyeloid progenitor, arresting B lineage differentiation and resulting in the production of myeloid-primed B cells. This may explain the relatively high levels of myeloid antigen expression lineage promiscuity seen in cALL. ETV6-RUNX1 hPSCs will afford the systematic evaluation of the contribution of additional mutations seen in cALL and may offer a tractable platform for drug screening. In conclusion we propose that a novel IL7R+ lymphomyeloid progenitor in the human FL is a candidate target cell for in utero pre-leukemic initiation in cALL.
Citation Format: Simon E. Richardson, Charlotta Böiers, Alya Zriwil, Virginia Turati, John Brown, Dapeng Wang, Javier Herrero, Stefan Karlsson, Andrew J. H. Smith, Sten Erik Jacobsen, Tariq Enver. ETV6-RUNX1 targets a developmentally restricted embryonic human B-myeloid progenitor. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2692.
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Affiliation(s)
| | | | - Alya Zriwil
- 2BMC A12, Gene Therapy, Lund University, Lund, Sweden
| | - Virginia Turati
- 1University College London Cancer Institute, London, United Kingdom
| | - John Brown
- 1University College London Cancer Institute, London, United Kingdom
| | - Dapeng Wang
- 1University College London Cancer Institute, London, United Kingdom
| | - Javier Herrero
- 1University College London Cancer Institute, London, United Kingdom
| | | | - Andrew J. H. Smith
- 3MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Sten Erik Jacobsen
- 4Haematopoietic Stem Cell Laboratory and MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Tariq Enver
- 1University College London Cancer Institute, London, United Kingdom
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Turati V, Mike H, Herrero J, John A, Richardson S, Gaal B, Mark L, Jacobsen S, Enver T. Single cell analysis of intratumour heterogeneity in childhood acute lymphoblastic leukaemia. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)61365-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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