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Ghobrial IM, Gormley N, Kumar SK, Mateos MV, Bergsagel PL, Chesi M, Dhodapkar MV, Dispenzieri A, Fonseca R, Getz G, Kastritis E, Kristinsson SY, Martinez-Climent JA, Manier S, Marinac CR, Maura F, Morgan GJ, Davies FE, Nadeem O, Nuvolone M, Paiva B, O'Donnell E, Prosper F, Shah UA, Sklavenitis-Pistofidis R, Sperling AS, Vassiliou GS, Munshi NC, Castle PE, Anderson KC, San Miguel JF. Round Table Discussion on Optimal Clinical Trial Design in Precursor Multiple Myeloma. Blood Cancer Discov 2024; 5:146-152. [PMID: 38441243 PMCID: PMC11061588 DOI: 10.1158/2643-3230.bcd-24-0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024] Open
Abstract
SUMMARY While the current approach to precursor hematologic conditions is to "watch and wait," this may change with the development of therapies that are safe and extend survival or delay the onset of symptomatic disease. The goal of future therapies in precursor hematologic conditions is to improve survival and prevent or delay the development of symptomatic disease while maximizing safety. Clinical trial considerations in this field include identifying an appropriate at-risk population, safety assessments, dose selection, primary and secondary trial endpoints including surrogate endpoints, control arms, and quality-of-life metrics, all of which may enable more precise benefit-risk assessment.
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Affiliation(s)
| | - Nicole Gormley
- Division of Hematology, Food and Drug Administration, Silver Spring, Maryland
| | - Shaji K. Kumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Maria-Victoria Mateos
- Hospital Universitario de Salamanca, Instituto de Investigacion Biomedica de Salamanca (IBSAL), Centro de Investigación del Cancer (IBMCC-USAL, CSIC), CIBER-ONC number CB16/12/00233, Salamanca, Spain
| | | | - Marta Chesi
- Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | | | - Angela Dispenzieri
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Rafael Fonseca
- Division of Hematology/Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Efstathios Kastritis
- Department of Clinical Therapeutics, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Jose Angel Martinez-Climent
- Cancer Center Clinica Universidad de Navarra (CCUN), Centro de Investigacion Medica Aplicada (CIMA), Instituto de Investigacion Sanitaria de Navarra (IDISNA), CIBER-ONC numbers CB16/12/00369, CB16/12/00489, Pamplona, Spain
| | - Salomon Manier
- Hematology Department, CHU Lille, Lille University, INSERM UMR-S1277, Lille, France
| | | | - Francesco Maura
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Gareth J. Morgan
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, New York
| | - Faith E. Davies
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, New York
| | - Omar Nadeem
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mario Nuvolone
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Bruno Paiva
- Cancer Center Clinica Universidad de Navarra (CCUN), Centro de Investigacion Medica Aplicada (CIMA), Instituto de Investigacion Sanitaria de Navarra (IDISNA), CIBER-ONC numbers CB16/12/00369, CB16/12/00489, Pamplona, Spain
| | | | - Felipe Prosper
- Hematology Service and Cell Therapy Unit and Program of Hematology-Oncology CIMA, Clinica Universidad de Navarra, Cancer Center Clínica Universidad de Navarra (CCUN) and Instituto de Investigación Sanitaria de Navarra (IdISNA), Pamplona, Spain
- Centro de Investigación Biomedica en Red Cancer (CIBERONC) and RICORS TERAV, Madrid, Spain
| | - Urvi A. Shah
- Department of Medicine, Myeloma Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | - George S. Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | | | - Philip E. Castle
- Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland
| | | | - Jesus F. San Miguel
- Cancer Center Clinica Universidad de Navarra (CCUN), Centro de Investigacion Medica Aplicada (CIMA), Instituto de Investigacion Sanitaria de Navarra (IDISNA), CIBER-ONC numbers CB16/12/00369, CB16/12/00489, Pamplona, Spain
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2
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Rocco JM, Zhou Y, Liu NS, Laidlaw E, Galindo F, Anderson MV, Rupert A, Lucena Lage S, Ortega-Villa AM, Yu S, Lisco A, Manion M, Vassiliou GS, Dunbar CE, Sereti I. Clonal hematopoiesis in people with advanced HIV and associated inflammatory syndromes. JCI Insight 2024:e174783. [PMID: 38564303 DOI: 10.1172/jci.insight.174783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
People with HIV (PWH) have a higher age-adjusted mortality due to chronic immune activation and age-related comorbidities. PWH also have higher rates of clonal hematopoiesis (CH) than age-matched non-HIV cohorts, however, risk factors influencing the development and expansion of CH in PWH remain incompletely explored. We investigated the relationship between CH, immune biomarkers, and HIV-associated risk factors (CD4, CD8 T-cells, nadir CD4 count, opportunistic infections [OIs], and immune reconstitution inflammatory syndrome [IRIS]) in a diverse cohort of 197-PWH with median age of 42-years, using a 56-gene panel. Seventy-nine percent had a CD4 nadir < 200, 58.9% had prior OIs, and 34.5% had a history of IRIS. The prevalence of CH was high (27.4%), even in younger individuals, and CD8 T-cells and nadir CD4 counts strongly associated with CH after controlling for age. A history of IRIS was associated with CH in a subgroup analysis of ≥ 35-years-old patients. Inflammatory biomarkers were higher in CH carriers compared to non-carriers supporting a dysregulated immune state. These findings suggest PWH with low nadir CD4 and/or inflammatory complications may be at high risk of CH regardless of age and represent a high-risk group that could benefit from risk reduction and potentially targeted immunomodulation.
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Affiliation(s)
- Joseph M Rocco
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, United States of America
| | - Yifan Zhou
- Translational Stem Cell Biology Branch, National Heart, Lung and Blood Inst, NIH, Bethesda, United States of America
| | - Nicholas S Liu
- Translational Stem Cell Biology Branch, National Heart, Lung and Blood Inst, NIH, Bethesda, United States of America
| | - Elizabeth Laidlaw
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, United States of America
| | - Frances Galindo
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, United States of America
| | - Megan V Anderson
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, United States of America
| | - Adam Rupert
- Leidos Biomedical Research Core, Frederick, United States of America
| | - Silvia Lucena Lage
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, United States of America
| | - Ana M Ortega-Villa
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, United States of America
| | - Shiqin Yu
- Translational Stem Cell Biology Branch, National Heart, Lung and Blood Inst, NIH, Bethesda, United States of America
| | - Andrea Lisco
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, United States of America
| | - Maura Manion
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, United States of America
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Cynthia E Dunbar
- Translational Stem Cell Biology Branch, National Heart, Lung and Blood Inst, NIH, Bethesda, United States of America
| | - Irini Sereti
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, United States of America
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3
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Fabre MA, Vassiliou GS. The lifelong natural history of clonal hematopoiesis and its links to myeloid neoplasia. Blood 2024; 143:573-581. [PMID: 37992214 DOI: 10.1182/blood.2023019964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/26/2023] [Accepted: 11/13/2023] [Indexed: 11/24/2023] Open
Abstract
ABSTRACT The study of somatic mutations and the associated clonal mosaicism across the human body has transformed our understanding of aging and its links to cancer. In proliferative human tissues, stem cells compete for dominance, and those with an advantage expand clonally to outgrow their peers. In the hematopoietic system, such expansion is termed clonal hematopoiesis (CH). The forces driving competition, namely heterogeneity of the hematopoietic stem cell (HSC) pool and attrition of their environment, become increasingly prominent with age. As a result, CH becomes progressively more common through life to the point of becoming essentially ubiquitous. We are beginning to unravel the specific intracellular and extracellular factors underpinning clonal behavior, with somatic mutations in specific driver genes, inflammation, telomere maintenance, extraneous exposures, and inherited genetic variation among the important players. The inevitability of CH with age combined with its unequivocal links to myeloid cancers poses a scientific and clinical challenge. Specifically, we need to decipher the factors determining clonal behavior and develop prognostic tools to identify those at high risk of malignant progression, for whom preventive interventions may be warranted. Here, we discuss how recent advances in our understanding of the natural history of CH have provided important insights into these processes and helped define future avenues of investigation.
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Affiliation(s)
- Margarete A Fabre
- Department of Haematology, Cambridge University Hospitals National Health Service Trust, Cambridge, United Kingdom
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals Research & Development, AstraZeneca, Cambridge, United Kingdom
| | - George S Vassiliou
- Department of Haematology, Cambridge University Hospitals National Health Service Trust, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
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4
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Guo J, Walter K, Quiros PM, Gu M, Baxter EJ, Danesh J, Di Angelantonio E, Roberts D, Guglielmelli P, Harrison CN, Godfrey AL, Green AR, Vassiliou GS, Vuckovic D, Nangalia J, Soranzo N. Inherited polygenic effects on common hematological traits influence clonal selection on JAK2 V617F and the development of myeloproliferative neoplasms. Nat Genet 2024; 56:273-280. [PMID: 38233595 PMCID: PMC10864174 DOI: 10.1038/s41588-023-01638-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 12/01/2023] [Indexed: 01/19/2024]
Abstract
Myeloproliferative neoplasms (MPNs) are chronic cancers characterized by overproduction of mature blood cells. Their causative somatic mutations, for example, JAK2V617F, are common in the population, yet only a minority of carriers develop MPN. Here we show that the inherited polygenic loci that underlie common hematological traits influence JAK2V617F clonal expansion. We identify polygenic risk scores (PGSs) for monocyte count and plateletcrit as new risk factors for JAK2V617F positivity. PGSs for several hematological traits influenced the risk of different MPN subtypes, with low PGSs for two platelet traits also showing protective effects in JAK2V617F carriers, making them two to three times less likely to have essential thrombocythemia than carriers with high PGSs. We observed that extreme hematological PGSs may contribute to an MPN diagnosis in the absence of somatic driver mutations. Our study showcases how polygenic backgrounds underlying common hematological traits influence both clonal selection on somatic mutations and the subsequent phenotype of cancer.
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Affiliation(s)
- Jing Guo
- Wellcome Sanger Institute, Hinxton, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
| | | | - Pedro M Quiros
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Muxin Gu
- Wellcome Sanger Institute, Hinxton, UK
| | - E Joanna Baxter
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - John Danesh
- Wellcome Sanger Institute, Hinxton, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Emanuele Di Angelantonio
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Fondazione Human Technopole, Milan, Italy
| | - David Roberts
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant-Oxford Centre, John Radcliffe Hospital and Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Paola Guglielmelli
- Department of Experimental and Clinical Medicine, Center for Research and Innovation of Myeloproliferative Neoplasms (CRIMM), AOU Careggi, University of Florence, Florence, Italy
| | - Claire N Harrison
- Department of Haematology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | - Anthony R Green
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Dragana Vuckovic
- Wellcome Sanger Institute, Hinxton, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- Department of Epidemiology and Biostatistics, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
| | - Jyoti Nangalia
- Wellcome Sanger Institute, Hinxton, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
- Cambridge University Hospitals NHS Trust, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
| | - Nicole Soranzo
- Wellcome Sanger Institute, Hinxton, UK.
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK.
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK.
- Fondazione Human Technopole, Milan, Italy.
- Department of Haematology, University of Cambridge, Cambridge, UK.
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5
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Isobe T, Kucinski I, Barile M, Wang X, Hannah R, Bastos HP, Chabra S, Vijayabaskar M, Sturgess KH, Williams MJ, Giotopoulos G, Marando L, Li J, Rak J, Gozdecka M, Prins D, Shepherd MS, Watcham S, Green AR, Kent DG, Vassiliou GS, Huntly BJ, Wilson NK, Göttgens B. Preleukemic single-cell landscapes reveal mutation-specific mechanisms and gene programs predictive of AML patient outcomes. Cell Genom 2023; 3:100426. [PMID: 38116120 PMCID: PMC10726426 DOI: 10.1016/j.xgen.2023.100426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/13/2023] [Accepted: 09/29/2023] [Indexed: 12/21/2023]
Abstract
Acute myeloid leukemia (AML) and myeloid neoplasms develop through acquisition of somatic mutations that confer mutation-specific fitness advantages to hematopoietic stem and progenitor cells. However, our understanding of mutational effects remains limited to the resolution attainable within immunophenotypically and clinically accessible bulk cell populations. To decipher heterogeneous cellular fitness to preleukemic mutational perturbations, we performed single-cell RNA sequencing of eight different mouse models with driver mutations of myeloid malignancies, generating 269,048 single-cell profiles. Our analysis infers mutation-driven perturbations in cell abundance, cellular lineage fate, cellular metabolism, and gene expression at the continuous resolution, pinpointing cell populations with transcriptional alterations associated with differentiation bias. We further develop an 11-gene scoring system (Stem11) on the basis of preleukemic transcriptional signatures that predicts AML patient outcomes. Our results demonstrate that a single-cell-resolution deep characterization of preleukemic biology has the potential to enhance our understanding of AML heterogeneity and inform more effective risk stratification strategies.
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Affiliation(s)
- Tomoya Isobe
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Iwo Kucinski
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Melania Barile
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Xiaonan Wang
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Rebecca Hannah
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Hugo P. Bastos
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Shirom Chabra
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - M.S. Vijayabaskar
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Katherine H.M. Sturgess
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Matthew J. Williams
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - George Giotopoulos
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Ludovica Marando
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Juan Li
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Justyna Rak
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
- Hematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Malgorzata Gozdecka
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
- Hematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Daniel Prins
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Mairi S. Shepherd
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Sam Watcham
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Anthony R. Green
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - David G. Kent
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - George S. Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
- Hematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Brian J.P. Huntly
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Nicola K. Wilson
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
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6
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Stelmach P, Richter S, Sauer S, Fabre MA, Gu M, Rohde C, Janssen M, Liebers N, Proynova R, Weinhold N, Raab MS, Goldschmidt H, Besenbeck B, Pavel P, Laier S, Trumpp A, Dietrich S, Vassiliou GS, Müller-Tidow C. Clonal hematopoiesis with DNMT3A and PPM1D mutations impairs regeneration in autologous stem cell transplant recipients. Haematologica 2023; 108:3308-3320. [PMID: 37381752 PMCID: PMC10690900 DOI: 10.3324/haematol.2023.282992] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023] Open
Abstract
Clonal hematopoiesis (CH) is an age-related condition driven by stem and progenitor cells harboring recurrent mutations linked to myeloid neoplasms. Currently, potential effects on hematopoiesis, stem cell function and regenerative potential under stress conditions are unknown. We performed targeted DNA sequencing of 457 hematopoietic stem cell grafts collected for autologous stem cell transplantation (ASCT) in myeloma patients and correlated our findings with high-dimensional longitudinal clinical and laboratory data (26,510 data points for blood cell counts/serum values in 25 days around transplantation). We detected CHrelated mutations in 152 patients (33.3%). Since many patients (n=54) harbored multiple CH mutations in one or more genes, we applied a non-negative matrix factorization (NMF) clustering algorithm to identify genes that are commonly co-mutated in an unbiased approach. Patients with CH were assigned to one of three clusters (C1-C3) and compared to patients without CH (C0) in a gene specific manner. To study the dynamics of blood cell regeneration following ASCT, we developed a time-dependent linear mixed effect model to validate differences in blood cell count trajectories amongst different clusters. The results demonstrated that C2, composed of patients with DNMT3A and PPM1D single and co-mutated CH, correlated with reduced stem cell yields and delayed platelet count recovery following ASCT. Also, the benefit of maintenance therapy was particularly strong in C2 patients. Taken together, these data indicate an impaired regenerative potential of hematopoietic stem cell grafts harboring CH with DNMT3A and PPM1D mutations.
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Affiliation(s)
- Patrick Stelmach
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany; Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM, gGmbH), Heidelberg
| | - Sarah Richter
- Department of Medicine V, Heidelberg University Hospital, Heidelberg
| | - Sandra Sauer
- Department of Medicine V, Heidelberg University Hospital, Heidelberg
| | - Margarete A Fabre
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R/D, AstraZeneca, Cambridge
| | - Muxin Gu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge
| | - Christian Rohde
- Department of Medicine V, Heidelberg University Hospital, Heidelberg
| | - Maike Janssen
- Department of Medicine V, Heidelberg University Hospital, Heidelberg
| | - Nora Liebers
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany; National Center for Tumor Diseases (NCT), Heidelberg
| | - Rumyana Proynova
- Department of Medicine V, Heidelberg University Hospital, Heidelberg
| | - Niels Weinhold
- Department of Medicine V, Heidelberg University Hospital, Heidelberg
| | - Marc S Raab
- Department of Medicine V, Heidelberg University Hospital, Heidelberg
| | | | - Birgit Besenbeck
- Department of Medicine V, Heidelberg University Hospital, Heidelberg
| | - Petra Pavel
- Stem Cell Laboratory, Institute of Clinical Transfusion Medicine and Cell Therapy Heidelberg GmbH, Heidelberg
| | - Sascha Laier
- Stem Cell Laboratory, Institute of Clinical Transfusion Medicine and Cell Therapy Heidelberg GmbH, Heidelberg
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM, gGmbH), Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg
| | - Sascha Dietrich
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany; Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), Heidelberg
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge
| | - Carsten Müller-Tidow
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany; National Center for Tumor Diseases (NCT), Heidelberg, Germany; Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), Heidelberg.
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7
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Cheloor Kovilakam S, Gu M, Dunn WG, Marando L, Barcena C, Nik-Zainal S, Mohorianu I, Kar SP, Fabre MA, Quiros PM, Vassiliou GS. Prevalence and significance of DDX41 gene variants in the general population. Blood 2023; 142:1185-1192. [PMID: 37506341 DOI: 10.1182/blood.2023020209] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 02/28/2023] [Revised: 06/26/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Germ line variants in the DDX41 gene have been linked to myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) development. However, the risks associated with different variants remain unknown, as do the basis of their leukemogenic properties, impact on steady-state hematopoiesis, and links to other cancers. Here, we investigate the frequency and significance of DDX41 variants in 454 792 United Kingdom Biobank (UKB) participants and identify 452 unique nonsynonymous DNA variants in 3538 (1/129) individuals. Many were novel, and the prevalence of most varied markedly by ancestry. Among the 1059 individuals with germ line pathogenic variants (DDX41-GPV) 34 developed MDS/AML (odds ratio, 12.3 vs noncarriers). Of these, 7 of 218 had start-lost, 22 of 584 had truncating, and 5 of 257 had missense (odds ratios: 12.9, 15.1, and 7.5, respectively). Using multivariate logistic regression, we found significant associations of DDX41-GPV with MDS, AML, and family history of leukemia but not lymphoma, myeloproliferative neoplasms, or other cancers. We also report that DDX41-GPV carriers do not have an increased prevalence of clonal hematopoiesis (CH). In fact, CH was significantly more common before sporadic vs DDX41-mutant MDS/AML, revealing distinct evolutionary paths. Furthermore, somatic mutation rates did not differ between sporadic and DDX41-mutant AML genomes, ruling out genomic instability as a driver of the latter. Finally, we found that higher mean red cell volume (MCV) and somatic DDX41 mutations in blood DNA identify DDX41-GPV carriers at increased MDS/AML risk. Collectively, our findings give new insights into the prevalence and cognate risks associated with DDX41 variants, as well as the clonal evolution and early detection of DDX41-mutant MDS/AML.
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Affiliation(s)
- Sruthi Cheloor Kovilakam
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Muxin Gu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - William G Dunn
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
| | - Ludovica Marando
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Clea Barcena
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry and Molecular Biology, Universidad de Oviedo, Oviedo, Spain
| | - Serena Nik-Zainal
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Irina Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Siddhartha P Kar
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Section of Translational Epidemiology, Division of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Margarete A Fabre
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals Research and Development, AstraZeneca, Cambridge, United Kingdom
| | - Pedro M Quiros
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
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8
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Gu M, Kovilakam SC, Dunn WG, Marando L, Barcena C, Mohorianu I, Smith A, Kar SP, Fabre MA, Gerstung M, Cargo CA, Malcovati L, Quiros PM, Vassiliou GS. Author Correction: Multiparameter prediction of myeloid neoplasia risk. Nat Genet 2023; 55:1777. [PMID: 37726541 PMCID: PMC10562208 DOI: 10.1038/s41588-023-01532-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Affiliation(s)
- Muxin Gu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Sruthi Cheloor Kovilakam
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - William G Dunn
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Ludovica Marando
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Clea Barcena
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Biochemistry and Molecular Biology, Universidad de Oviedo, Oviedo, Spain
| | - Irina Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Alexandra Smith
- Epidemiology and Cancer Statistics Group, University of York, York, UK
| | - Siddhartha P Kar
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Section of Translational Epidemiology, Division of Population Health Sciences, Bristol, Medical School, University of Bristol, Bristol, UK
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Margarete A Fabre
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Moritz Gerstung
- Division of Artificial Intelligence in Oncology, DKFZ, Heidelberg, Germany
| | - Catherine A Cargo
- Haematological Malignancy Diagnostic Service, St James's Hospital, Leeds, UK
- Department of Haematology, Leeds Teaching Hospitals, Leeds, UK
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Hematology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Pedro M Quiros
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain.
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, UK.
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9
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Gu M, Kovilakam SC, Dunn WG, Marando L, Barcena C, Mohorianu I, Smith A, Kar SP, Fabre MA, Gerstung M, Cargo CA, Malcovati L, Quiros PM, Vassiliou GS. Multiparameter prediction of myeloid neoplasia risk. Nat Genet 2023; 55:1523-1530. [PMID: 37620601 PMCID: PMC10484784 DOI: 10.1038/s41588-023-01472-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 01/19/2023] [Accepted: 07/11/2023] [Indexed: 08/26/2023]
Abstract
The myeloid neoplasms encompass acute myeloid leukemia, myelodysplastic syndromes and myeloproliferative neoplasms. Most cases arise from the shared ancestor of clonal hematopoiesis (CH). Here we analyze data from 454,340 UK Biobank participants, of whom 1,808 developed a myeloid neoplasm 0-15 years after recruitment. We describe the differences in CH mutational landscapes and hematology/biochemistry test parameters among individuals that later develop myeloid neoplasms (pre-MN) versus controls, finding that disease-specific changes are detectable years before diagnosis. By analyzing differences between 'pre-MN' and controls, we develop and validate Cox regression models quantifying the risk of progression to each myeloid neoplasm subtype. We construct 'MN-predict', a web application that generates time-dependent predictions with the input of basic blood tests and genetic data. Our study demonstrates that many individuals that develop myeloid neoplasms can be identified years in advance and provides a framework for disease-specific prognostication that will be of substantial use to researchers and physicians.
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Affiliation(s)
- Muxin Gu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Sruthi Cheloor Kovilakam
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - William G Dunn
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Ludovica Marando
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Clea Barcena
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Biochemistry and Molecular Biology, Universidad de Oviedo, Oviedo, Spain
| | - Irina Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Alexandra Smith
- Epidemiology and Cancer Statistics Group, University of York, York, UK
| | - Siddhartha P Kar
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Section of Translational Epidemiology, Division of Population Health Sciences, Bristol, Medical School, University of Bristol, Bristol, UK
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Margarete A Fabre
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Moritz Gerstung
- Division of Artificial Intelligence in Oncology, DKFZ, Heidelberg, Germany
| | - Catherine A Cargo
- Haematological Malignancy Diagnostic Service, St James's Hospital, Leeds, UK
- Department of Haematology, Leeds Teaching Hospitals, Leeds, UK
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Hematology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Pedro M Quiros
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain.
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, UK.
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10
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Quiros PM, Vassiliou GS. Genetic Predisposition to Clonal Hematopoiesis. Hemasphere 2023; 7:e947. [PMID: 37600859 PMCID: PMC10438798 DOI: 10.1097/hs9.0000000000000947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023] Open
Affiliation(s)
- Pedro M. Quiros
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
| | - George S. Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, United Kingdom
- Department of Hematology, University of Cambridge, United Kingdom
- Department of Hematology, Cambridge University Hospitals NHS Trust, United Kingdom
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11
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Wang M, Brandt LTL, Wang X, Russell H, Mitchell E, Kamimae-Lanning AN, Brown JM, Dingler FA, Garaycoechea JI, Isobe T, Kinston SJ, Gu M, Vassiliou GS, Wilson NK, Göttgens B, Patel KJ. Genotoxic aldehyde stress prematurely ages hematopoietic stem cells in a p53-driven manner. Mol Cell 2023; 83:2417-2433.e7. [PMID: 37348497 PMCID: PMC7614878 DOI: 10.1016/j.molcel.2023.05.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 04/18/2023] [Accepted: 05/25/2023] [Indexed: 06/24/2023]
Abstract
Aged hematopoietic stem cells (HSCs) display diminished self-renewal and a myeloid differentiation bias. However, the drivers and mechanisms that underpin this fundamental switch are not understood. HSCs produce genotoxic formaldehyde that requires protection by the detoxification enzymes ALDH2 and ADH5 and the Fanconi anemia (FA) DNA repair pathway. We find that the HSCs in young Aldh2-/-Fancd2-/- mice harbor a transcriptomic signature equivalent to aged wild-type HSCs, along with increased epigenetic age, telomere attrition, and myeloid-biased differentiation quantified by single HSC transplantation. In addition, the p53 response is vigorously activated in Aldh2-/-Fancd2-/- HSCs, while p53 deletion rescued this aged HSC phenotype. To further define the origins of the myeloid differentiation bias, we use a GFP genetic reporter to find a striking enrichment of Vwf+ myeloid and megakaryocyte-lineage-biased HSCs. These results indicate that metabolism-derived formaldehyde-DNA damage stimulates the p53 response in HSCs to drive accelerated aging.
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Affiliation(s)
- Meng Wang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
| | - Laura T L Brandt
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Xiaonan Wang
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK; School of Public Health, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Holly Russell
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Emily Mitchell
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Hinxton, UK
| | - Ashley N Kamimae-Lanning
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Jill M Brown
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Felix A Dingler
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Juan I Garaycoechea
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands
| | - Tomoya Isobe
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Sarah J Kinston
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Muxin Gu
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Nicola K Wilson
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Ketan J Patel
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
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12
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de Almeida JG, Gudgin E, Besser M, Dunn WG, Cooper J, Haferlach T, Vassiliou GS, Gerstung M. Computational analysis of peripheral blood smears detects disease-associated cytomorphologies. Nat Commun 2023; 14:4378. [PMID: 37474506 PMCID: PMC10359268 DOI: 10.1038/s41467-023-39676-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/22/2023] [Indexed: 07/22/2023] Open
Abstract
Many hematological diseases are characterized by altered abundance and morphology of blood cells and their progenitors. Myelodysplastic syndromes (MDS), for example, are a group of blood cancers characterised by cytopenias, dysplasia of hematopoietic cells and blast expansion. Examination of peripheral blood slides (PBS) in MDS often reveals changes such as abnormal granulocyte lobulation or granularity and altered red blood cell (RBC) morphology; however, some of these features are shared with conditions such as haematinic deficiency anemias. Definitive diagnosis of MDS requires expert cytomorphology analysis of bone marrow smears and complementary information such as blood counts, karyotype and molecular genetics testing. Here, we present Haemorasis, a computational method that detects and characterizes white blood cells (WBC) and RBC in PBS. Applied to over 300 individuals with different conditions (SF3B1-mutant and SF3B1-wildtype MDS, megaloblastic anemia, and iron deficiency anemia), Haemorasis detected over half a million WBC and millions of RBC and characterized their morphology. These large sets of cell morphologies can be used in diagnosis and disease subtyping, while identifying novel associations between computational morphotypes and disease. We find that hypolobulated neutrophils and large RBC are characteristic of SF3B1-mutant MDS. Additionally, while prevalent in both iron deficiency and megaloblastic anemia, hyperlobulated neutrophils are larger in the latter. By integrating cytomorphological features using machine learning, Haemorasis was able to distinguish SF3B1-mutant MDS from other MDS using cytomorphology and blood counts alone, with high predictive performance. We validate our findings externally, showing that they generalize to other centers and scanners. Collectively, our work reveals the potential for the large-scale incorporation of automated cytomorphology into routine diagnostic workflows.
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Affiliation(s)
- José Guilherme de Almeida
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- Champalimaud Foundation-Centre for the Unknown, Lisbon, Portugal
| | - Emma Gudgin
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Martin Besser
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - William G Dunn
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Jonathan Cooper
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - George S Vassiliou
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.
- Division of AI in Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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13
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Mikutis S, Rebelo M, Yankova E, Gu M, Tang C, Coelho AR, Yang M, Hazemi ME, Pires de Miranda M, Eleftheriou M, Robertson M, Vassiliou GS, Adams DJ, Simas JP, Corzana F, Schneekloth JS, Tzelepis K, Bernardes GJL. Proximity-Induced Nucleic Acid Degrader (PINAD) Approach to Targeted RNA Degradation Using Small Molecules. ACS Cent Sci 2023; 9:892-904. [PMID: 37252343 PMCID: PMC10214512 DOI: 10.1021/acscentsci.3c00015] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Indexed: 05/31/2023]
Abstract
Nature has evolved intricate machinery to target and degrade RNA, and some of these molecular mechanisms can be adapted for therapeutic use. Small interfering RNAs and RNase H-inducing oligonucleotides have yielded therapeutic agents against diseases that cannot be tackled using protein-centered approaches. Because these therapeutic agents are nucleic acid-based, they have several inherent drawbacks which include poor cellular uptake and stability. Here we report a new approach to target and degrade RNA using small molecules, proximity-induced nucleic acid degrader (PINAD). We have utilized this strategy to design two families of RNA degraders which target two different RNA structures within the genome of SARS-CoV-2: G-quadruplexes and the betacoronaviral pseudoknot. We demonstrate that these novel molecules degrade their targets using in vitro, in cellulo, and in vivo SARS-CoV-2 infection models. Our strategy allows any RNA binding small molecule to be converted into a degrader, empowering RNA binders that are not potent enough to exert a phenotypic effect on their own. PINAD raises the possibility of targeting and destroying any disease-related RNA species, which can greatly expand the space of druggable targets and diseases.
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Affiliation(s)
- Sigitas Mikutis
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Maria Rebelo
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Eliza Yankova
- Wellcome-MRC
Cambridge Stem Cell Institute, University
of Cambridge, Cambridge CB2 0AW, U.K.
- Milner
Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, U.K.
| | - Muxin Gu
- Wellcome-MRC
Cambridge Stem Cell Institute, University
of Cambridge, Cambridge CB2 0AW, U.K.
| | - Cong Tang
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Ana R. Coelho
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Mo Yang
- Chemical
Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Madoka E. Hazemi
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Marta Pires de Miranda
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Maria Eleftheriou
- Wellcome-MRC
Cambridge Stem Cell Institute, University
of Cambridge, Cambridge CB2 0AW, U.K.
- Milner
Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, U.K.
| | - Max Robertson
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - George S. Vassiliou
- Wellcome-MRC
Cambridge Stem Cell Institute, University
of Cambridge, Cambridge CB2 0AW, U.K.
| | - David J. Adams
- Experimental
Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, U.K.
| | - J. Pedro Simas
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
- Católica
Biomedical Research and Católica Medical School, Universidade Católica Portuguesa, 1649-023 Lisboa, Portugal
| | - Francisco Corzana
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - John S. Schneekloth
- Chemical
Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Konstantinos Tzelepis
- Wellcome-MRC
Cambridge Stem Cell Institute, University
of Cambridge, Cambridge CB2 0AW, U.K.
- Milner
Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, U.K.
| | - Gonçalo J. L. Bernardes
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
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14
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Woodley K, Dillingh LS, Giotopoulos G, Madrigal P, Rattigan KM, Philippe C, Dembitz V, Magee AMS, Asby R, van de Lagemaat LN, Mapperley C, James SC, Prehn JHM, Tzelepis K, Rouault-Pierre K, Vassiliou GS, Kranc KR, Helgason GV, Huntly BJP, Gallipoli P. Mannose metabolism inhibition sensitizes acute myeloid leukaemia cells to therapy by driving ferroptotic cell death. Nat Commun 2023; 14:2132. [PMID: 37059720 PMCID: PMC10104861 DOI: 10.1038/s41467-023-37652-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 03/24/2023] [Indexed: 04/16/2023] Open
Abstract
Resistance to standard and novel therapies remains the main obstacle to cure in acute myeloid leukaemia (AML) and is often driven by metabolic adaptations which are therapeutically actionable. Here we identify inhibition of mannose-6-phosphate isomerase (MPI), the first enzyme in the mannose metabolism pathway, as a sensitizer to both cytarabine and FLT3 inhibitors across multiple AML models. Mechanistically, we identify a connection between mannose metabolism and fatty acid metabolism, that is mediated via preferential activation of the ATF6 arm of the unfolded protein response (UPR). This in turn leads to cellular accumulation of polyunsaturated fatty acids, lipid peroxidation and ferroptotic cell death in AML cells. Our findings provide further support to the role of rewired metabolism in AML therapy resistance, unveil a connection between two apparently independent metabolic pathways and support further efforts to achieve eradication of therapy-resistant AML cells by sensitizing them to ferroptotic cell death.
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Affiliation(s)
- Keith Woodley
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Laura S Dillingh
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - George Giotopoulos
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Pedro Madrigal
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, CB10 1SD, UK
| | - Kevin M Rattigan
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Céline Philippe
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Vilma Dembitz
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Aoife M S Magee
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Ryan Asby
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Louie N van de Lagemaat
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Christopher Mapperley
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Sophie C James
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Jochen H M Prehn
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin, Ireland
| | - Konstantinos Tzelepis
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Kevin Rouault-Pierre
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - George S Vassiliou
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Kamil R Kranc
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - G Vignir Helgason
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Brian J P Huntly
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Paolo Gallipoli
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK.
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15
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Agrawal-Singh S, Bagri J, Giotopoulos G, Azazi DMA, Horton SJ, Lopez CK, Anand S, Bach AS, Stedham F, Antrobus R, Houghton JW, Vassiliou GS, Sasca D, Yun H, Whetton AD, Huntly BJP. HOXA9 forms a repressive complex with nuclear matrix-associated protein SAFB to maintain acute myeloid leukemia. Blood 2023; 141:1737-1754. [PMID: 36577137 PMCID: PMC10113176 DOI: 10.1182/blood.2022016528] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 11/07/2022] [Accepted: 11/28/2022] [Indexed: 12/29/2022] Open
Abstract
HOXA9 is commonly upregulated in acute myeloid leukemia (AML), in which it confers a poor prognosis. Characterizing the protein interactome of endogenous HOXA9 in human AML, we identified a chromatin complex of HOXA9 with the nuclear matrix attachment protein SAFB. SAFB perturbation phenocopied HOXA9 knockout to decrease AML proliferation, increase differentiation and apoptosis in vitro, and prolong survival in vivo. Integrated genomic, transcriptomic, and proteomic analyses further demonstrated that the HOXA9-SAFB (H9SB)-chromatin complex associates with nucleosome remodeling and histone deacetylase (NuRD) and HP1γ to repress the expression of factors associated with differentiation and apoptosis, including NOTCH1, CEBPδ, S100A8, and CDKN1A. Chemical or genetic perturbation of NuRD and HP1γ-associated catalytic activity also triggered differentiation, apoptosis, and the induction of these tumor-suppressive genes. Importantly, this mechanism is operative in other HOXA9-dependent AML genotypes. This mechanistic insight demonstrates the active HOXA9-dependent differentiation block as a potent mechanism of disease maintenance in AML that may be amenable to therapeutic intervention by targeting the H9SB interface and/or NuRD and HP1γ activity.
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Affiliation(s)
- Shuchi Agrawal-Singh
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Jaana Bagri
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - George Giotopoulos
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Dhoyazan M A Azazi
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Sarah J Horton
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Cecile K Lopez
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Shubha Anand
- Cancer Molecular Diagnostics Laboratory, Cancer Research UK Cambridge Centre, Cambridge, United Kingdom
| | - Anne-Sophie Bach
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Frances Stedham
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Jack W Houghton
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - George S Vassiliou
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Daniel Sasca
- Department of Hematology, Oncology and Pneumology, University Medical Center Mainz, Mainz, Germany
| | - Haiyang Yun
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Anthony D Whetton
- School of Veterinary Medicine, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - Brian J P Huntly
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
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16
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Fischer A, Lersch R, de Andrade Krätzig N, Strong A, Friedrich MJ, Weber J, Engleitner T, Öllinger R, Yen HY, Kohlhofer U, Gonzalez-Menendez I, Sailer D, Kogan L, Lahnalampi M, Laukkanen S, Kaltenbacher T, Klement C, Rezaei M, Ammon T, Montero JJ, Schneider G, Mayerle J, Heikenwälder M, Schmidt-Supprian M, Quintanilla-Martinez L, Steiger K, Liu P, Cadiñanos J, Vassiliou GS, Saur D, Lohi O, Heinäniemi M, Conte N, Bradley A, Rad L, Rad R. In vivo interrogation of regulatory genomes reveals extensive quasi-insufficiency in cancer evolution. Cell Genom 2023; 3:100276. [PMID: 36950387 PMCID: PMC10025556 DOI: 10.1016/j.xgen.2023.100276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 09/05/2022] [Accepted: 02/08/2023] [Indexed: 03/10/2023]
Abstract
In contrast to mono- or biallelic loss of tumor-suppressor function, effects of discrete gene dysregulations, as caused by non-coding (epi)genome alterations, are poorly understood. Here, by perturbing the regulatory genome in mice, we uncover pervasive roles of subtle gene expression variation in cancer evolution. Genome-wide screens characterizing 1,450 tumors revealed that such quasi-insufficiency is extensive across entities and displays diverse context dependencies, such as distinct cell-of-origin associations in T-ALL subtypes. We compile catalogs of non-coding regions linked to quasi-insufficiency, show their enrichment with human cancer risk variants, and provide functional insights by engineering regulatory alterations in mice. As such, kilo-/megabase deletions in a Bcl11b-linked non-coding region triggered aggressive malignancies, with allele-specific tumor spectra reflecting gradual gene dysregulations through modular and cell-type-specific enhancer activities. Our study constitutes a first survey toward a systems-level understanding of quasi-insufficiency in cancer and gives multifaceted insights into tumor evolution and the tissue-specific effects of non-coding mutations.
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Affiliation(s)
- Anja Fischer
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Robert Lersch
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Niklas de Andrade Krätzig
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Alexander Strong
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
| | - Mathias J. Friedrich
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Julia Weber
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Hsi-Yu Yen
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Comparative Experimental Pathology, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Ursula Kohlhofer
- Institute of Pathology and Comprehensive Cancer Center, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Irene Gonzalez-Menendez
- Institute of Pathology and Comprehensive Cancer Center, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - David Sailer
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Liz Kogan
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Mari Lahnalampi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Saara Laukkanen
- Faculty of Medicine and Health Technology, Tampere Center for Child, Adolescent and Maternal Health Research and Tays Cancer Center, Tampere University, Tampere, Finland
| | - Thorsten Kaltenbacher
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Christine Klement
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Majdaddin Rezaei
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Tim Ammon
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- Institute of Experimental Hematology, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Juan J. Montero
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Günter Schneider
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Julia Mayerle
- Medical Department II, University Hospital, LMU Munich, Munich, Germany
| | - Mathias Heikenwälder
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marc Schmidt-Supprian
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute of Experimental Hematology, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Leticia Quintanilla-Martinez
- Institute of Pathology and Comprehensive Cancer Center, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Katja Steiger
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Comparative Experimental Pathology, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Pentao Liu
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
- Li Ka Shing Faculty of Medicine, Stem Cell and Regenerative Medicine Consortium, School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), 33193 Oviedo, Spain
| | - George S. Vassiliou
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge CB2 0PT, UK
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Institute for Experimental Cancer Therapy, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Olli Lohi
- Faculty of Medicine and Health Technology, Tampere Center for Child, Adolescent and Maternal Health Research and Tays Cancer Center, Tampere University, Tampere, Finland
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Nathalie Conte
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Lena Rad
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- Institute for Experimental Cancer Therapy, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, 81675 Munich, Germany
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17
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Shin TH, Zhou Y, Chen S, Cordes S, Grice MZ, Fan X, Lee BC, Aljanahi AA, Hong SG, Vaughan KL, Mattison JA, Kohama SG, Fabre MA, Uchida N, Demirci S, Corat MA, Métais JY, Calvo KR, Buscarlet M, Natanson H, McGraw KL, List AF, Busque L, Tisdale JF, Vassiliou GS, Yu KR, Dunbar CE. A macaque clonal hematopoiesis model demonstrates expansion of TET2-disrupted clones and utility for testing interventions. Blood 2022; 140:1774-1789. [PMID: 35714307 PMCID: PMC9837449 DOI: 10.1182/blood.2021014875] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 11/22/2021] [Accepted: 05/26/2022] [Indexed: 01/21/2023] Open
Abstract
Individuals with age-related clonal hematopoiesis (CH) are at greater risk for hematologic malignancies and cardiovascular diseases. However, predictive preclinical animal models to recapitulate the spectrum of human CH are lacking. Through error-corrected sequencing of 56 human CH/myeloid malignancy genes, we identified natural CH driver mutations in aged rhesus macaques matching genes somatically mutated in human CH, with DNMT3A mutations being the most frequent. A CH model in young adult macaques was generated via autologous transplantation of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9-mediated gene-edited hematopoietic stem and progenitor cells (HSPCs), targeting the top human CH genes with loss-of-function (LOF) mutations. Long-term follow-up revealed reproducible and significant expansion of multiple HSPC clones with heterozygous TET2 LOF mutations, compared with minimal expansion of clones bearing other mutations. Although the blood counts of these CH macaques were normal, their bone marrows were hypercellular and myeloid-predominant. TET2-disrupted myeloid colony-forming units isolated from these animals showed a distinct hyperinflammatory gene expression profile compared with wild type. In addition, mature macrophages purified from the CH macaques showed elevated NLRP3 inflammasome activity and increased interleukin-1β (IL-1β) and IL-6 production. The model was used to test the impact of IL-6 blockage by tocilizumab, documenting a slowing of TET2-mutated expansion, suggesting that interruption of the IL-6 axis may remove the selective advantage of mutant HSPCs. These findings provide a model for examining the pathophysiology of CH and give insights into potential therapeutic interventions.
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Affiliation(s)
- Tae-Hoon Shin
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
| | - Yifan Zhou
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- Wellcome-Medical Research Council (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Shirley Chen
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - Stefan Cordes
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - Max Z. Grice
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - Xing Fan
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - Byung-Chul Lee
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - Aisha A. Aljanahi
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - So Gun Hong
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - Kelli L. Vaughan
- Translational Gerontology Branch, National Institute on Aging, NIH Animal Center, Dickerson, MD
| | - Julie A. Mattison
- Translational Gerontology Branch, National Institute on Aging, NIH Animal Center, Dickerson, MD
| | - Steven G. Kohama
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR
| | - Margarete A. Fabre
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- Wellcome-Medical Research Council (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Naoya Uchida
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
| | - Selami Demirci
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
| | - Marcus A.F. Corat
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Multidisciplinary Center for Biological Research, University of Campinas, Campinas, Brazil
| | - Jean-Yves Métais
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN
| | - Katherine R. Calvo
- Hematology Section, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, MD
| | - Manuel Buscarlet
- Hôpital Maisonneuve-Rosemont, Universite de Montreal, Montreal, QC, Canada
| | - Hannah Natanson
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - Kathy L. McGraw
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | | | - Lambert Busque
- Hôpital Maisonneuve-Rosemont, Universite de Montreal, Montreal, QC, Canada
| | - John F. Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
| | - George S. Vassiliou
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- Wellcome-Medical Research Council (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Kyung-Rok Yu
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Cynthia E. Dunbar
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
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18
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Zhou Y, Shalhoub R, Rogers SN, Yu S, Gu M, Fabre MA, Quiros PM, Shin TH, Diangson A, Deng W, Anand S, Lu W, Cullen M, Godfrey AL, Preller J, Hadjadj J, Jouanguy E, Cobat A, Abel L, Rieux-Laucat F, Terrier B, Fischer A, Novik L, Gordon IJ, Strom L, Gaudinski MR, Lisco A, Sereti I, Gniadek TJ, Biondi A, Bonfanti P, Imberti L, Dalgard CL, Zhang Y, Dobbs K, Su HC, Notarangelo LD, Wu CO, Openshaw PJ, Semple MG, Mallat Z, Baillie K, Dunbar CE, Vassiliou GS. Clonal hematopoiesis is not significantly associated with COVID-19 disease severity. Blood 2022; 140:1650-1655. [PMID: 35839449 PMCID: PMC9293387 DOI: 10.1182/blood.2022015721] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/28/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Yifan Zhou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ruba Shalhoub
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
| | - Stephanie N. Rogers
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Shiqin Yu
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - Muxin Gu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Margarete A. Fabre
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Pedro M. Quiros
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tae-Hoon Shin
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
| | - Arch Diangson
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
| | - Wenhan Deng
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
| | - Shubha Anand
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
| | - Wenhua Lu
- East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Matthew Cullen
- East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Anna L. Godfrey
- Haematopathology and Oncology Diagnostics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jacobus Preller
- John Farman Intensive Care Unit, Cambridge University Hospital, Cambridge, UK
| | - Jerome Hadjadj
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, Assistance Publique-Hôpitaux de Paris, APHP.CUP, Hôpital Cochin, Paris Cité University, Paris, France
| | - Emmanuelle Jouanguy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Frederic Rieux-Laucat
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université de Paris, Institut Imagine, INSERM UMR 1163, Paris, France
| | - Benjamin Terrier
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, Assistance Publique-Hôpitaux de Paris, APHP.CUP, Hôpital Cochin, Paris Cité University, Paris, France
| | - Alain Fischer
- Université de Paris, Institut Imagine, and Paediatric Immuno-Haematology and Rheumatology Department, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Collège de France, Paris, France
| | - Lara Novik
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Ingelise J. Gordon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Larisa Strom
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Martin R. Gaudinski
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Andrea Lisco
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Irini Sereti
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Thomas J. Gniadek
- Department of Pathology and Laboratory Medicine, NorthShore University Health System, Evanston, IL
| | - Andrea Biondi
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, Italy
| | - Paolo Bonfanti
- Department of Infectious Diseases, San Gerardo Hospital-University of Milano-Bicocca, Monza, Italy
| | - Luisa Imberti
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Clifton L. Dalgard
- Primer, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Kerry Dobbs
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Helen C. Su
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Luigi D. Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - COVID-STORM Clinicians
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
- East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Haematopathology and Oncology Diagnostics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- John Farman Intensive Care Unit, Cambridge University Hospital, Cambridge, UK
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, Assistance Publique-Hôpitaux de Paris, APHP.CUP, Hôpital Cochin, Paris Cité University, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université de Paris, Institut Imagine, INSERM UMR 1163, Paris, France
- Université de Paris, Institut Imagine, and Paediatric Immuno-Haematology and Rheumatology Department, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Collège de France, Paris, France
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, NorthShore University Health System, Evanston, IL
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, Italy
- Department of Infectious Diseases, San Gerardo Hospital-University of Milano-Bicocca, Monza, Italy
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
- Primer, Uniformed Services University of the Health Sciences, Bethesda, MD
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- National Heart and Lung Institute, Imperial College London, Chelsea, London, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
- INSERM U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - NIAID Immune Response to COVID Group
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
- East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Haematopathology and Oncology Diagnostics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- John Farman Intensive Care Unit, Cambridge University Hospital, Cambridge, UK
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, Assistance Publique-Hôpitaux de Paris, APHP.CUP, Hôpital Cochin, Paris Cité University, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université de Paris, Institut Imagine, INSERM UMR 1163, Paris, France
- Université de Paris, Institut Imagine, and Paediatric Immuno-Haematology and Rheumatology Department, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Collège de France, Paris, France
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, NorthShore University Health System, Evanston, IL
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, Italy
- Department of Infectious Diseases, San Gerardo Hospital-University of Milano-Bicocca, Monza, Italy
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
- Primer, Uniformed Services University of the Health Sciences, Bethesda, MD
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- National Heart and Lung Institute, Imperial College London, Chelsea, London, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
- INSERM U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - The ISARIC4C Investigators
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
- East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Haematopathology and Oncology Diagnostics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- John Farman Intensive Care Unit, Cambridge University Hospital, Cambridge, UK
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, Assistance Publique-Hôpitaux de Paris, APHP.CUP, Hôpital Cochin, Paris Cité University, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université de Paris, Institut Imagine, INSERM UMR 1163, Paris, France
- Université de Paris, Institut Imagine, and Paediatric Immuno-Haematology and Rheumatology Department, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Collège de France, Paris, France
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, NorthShore University Health System, Evanston, IL
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, Italy
- Department of Infectious Diseases, San Gerardo Hospital-University of Milano-Bicocca, Monza, Italy
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
- Primer, Uniformed Services University of the Health Sciences, Bethesda, MD
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- National Heart and Lung Institute, Imperial College London, Chelsea, London, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
- INSERM U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Colin O. Wu
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
| | - Peter J.M. Openshaw
- National Heart and Lung Institute, Imperial College London, Chelsea, London, UK
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Ziad Mallat
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
- INSERM U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Cynthia E. Dunbar
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - George S. Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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19
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Li J, Williams MJ, Park HJ, Bastos HP, Wang X, Prins D, Wilson NK, Johnson C, Sham K, Wantoch M, Watcham S, Kinston SJ, Pask DC, Hamilton TL, Sneade R, Waller AK, Ghevaert C, Vassiliou GS, Laurenti E, Kent DG, Göttgens B, Green AR. STAT1 is essential for HSC function and maintains MHCIIhi stem cells that resist myeloablation and neoplastic expansion. Blood 2022; 140:1592-1606. [PMID: 35767701 PMCID: PMC7614316 DOI: 10.1182/blood.2021014009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 04/21/2022] [Indexed: 02/02/2023] Open
Abstract
Adult hematopoietic stem cells (HSCs) are predominantly quiescent and can be activated in response to acute stress such as infection or cytotoxic insults. STAT1 is a pivotal downstream mediator of interferon (IFN) signaling and is required for IFN-induced HSC proliferation, but little is known about the role of STAT1 in regulating homeostatic hematopoietic stem/progenitor cells (HSPCs). Here, we show that loss of STAT1 altered the steady state HSPC landscape, impaired HSC function in transplantation assays, delayed blood cell regeneration following myeloablation, and disrupted molecular programs that protect HSCs, including control of quiescence. Our results also reveal STAT1-dependent functional HSC heterogeneity. A previously unrecognized subset of homeostatic HSCs with elevated major histocompatibility complex class II (MHCII) expression (MHCIIhi) displayed molecular features of reduced cycling and apoptosis and was refractory to 5-fluorouracil-induced myeloablation. Conversely, MHCIIlo HSCs displayed increased megakaryocytic potential and were preferentially expanded in CALR mutant mice with thrombocytosis. Similar to mice, high MHCII expression is a feature of human HSCs residing in a deeper quiescent state. Our results therefore position STAT1 at the interface of stem cell heterogeneity and the interplay between stem cells and the adaptive immune system, areas of broad interest in the wider stem cell field.
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Affiliation(s)
- Juan Li
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Matthew J. Williams
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Hyun Jung Park
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Hugo P. Bastos
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Xiaonan Wang
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Daniel Prins
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Nicola K. Wilson
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Carys Johnson
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Kendig Sham
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Michelle Wantoch
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Sam Watcham
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Sarah J. Kinston
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Dean C. Pask
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Tina L. Hamilton
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Rachel Sneade
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Amie K. Waller
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Cedric Ghevaert
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - George S. Vassiliou
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Elisa Laurenti
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - David G. Kent
- Department of Biology, University of York, York, United Kingdom
| | - Berthold Göttgens
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Anthony R. Green
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
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20
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Gupta S, Dovey OM, Domingues AF, Cyran OW, Cash CM, Giotopoulos G, Rak J, Cooper J, Gozdecka M, Dijkhuis L, Asby RJ, Al-Jabery N, Hernandez-Hernandez V, Prabakaran S, Huntly BJ, Vassiliou GS, Pina C. Transcriptional variability accelerates preleukemia by cell diversification and perturbation of protein synthesis. Sci Adv 2022; 8:eabn4886. [PMID: 35921412 PMCID: PMC9348803 DOI: 10.1126/sciadv.abn4886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Transcriptional variability facilitates stochastic cell diversification and can in turn underpin adaptation to stress or injury. We hypothesize that it may analogously facilitate progression of premalignancy to cancer. To investigate this, we initiated preleukemia in mouse cells with enhanced transcriptional variability due to conditional disruption of the histone lysine acetyltransferase gene Kat2a. By combining single-cell RNA sequencing of preleukemia with functional analysis of transformation, we show that Kat2a loss results in global variegation of cell identity and accumulation of preleukemic cells. Leukemia progression is subsequently facilitated by destabilization of ribosome biogenesis and protein synthesis, which confer a transient transformation advantage. The contribution of transcriptional variability to early cancer evolution reflects a generic role in promoting cell fate transitions, which, in the case of well-adapted malignancies, contrastingly differentiates and depletes cancer stem cells. That is, transcriptional variability confers forward momentum to cell fate systems, with differential multistage impact throughout cancer evolution.
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Affiliation(s)
- Shikha Gupta
- Department of Genetics, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Oliver M. Dovey
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Ana Filipa Domingues
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Oliwia W. Cyran
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Caitlin M. Cash
- College of Health, Medicine and Life Sciences - Division of Biosciences, Brunel University London, Uxbridge, UK
| | - George Giotopoulos
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Justyna Rak
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Jonathan Cooper
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Malgorzata Gozdecka
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Liza Dijkhuis
- College of Health, Medicine and Life Sciences - Division of Biosciences, Brunel University London, Uxbridge, UK
| | - Ryan J. Asby
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Noor Al-Jabery
- College of Health, Medicine and Life Sciences - Division of Biosciences, Brunel University London, Uxbridge, UK
| | - Victor Hernandez-Hernandez
- College of Health, Medicine and Life Sciences - Division of Biosciences, Brunel University London, Uxbridge, UK
- Centre for Genome Engineering and Maintenance, Brunel University London, Uxbridge, UB8 3PH, UK
| | | | - Brian J. Huntly
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - George S. Vassiliou
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Cristina Pina
- College of Health, Medicine and Life Sciences - Division of Biosciences, Brunel University London, Uxbridge, UK
- Centre for Genome Engineering and Maintenance, Brunel University London, Uxbridge, UB8 3PH, UK
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21
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Kar SP, Quiros PM, Gu M, Jiang T, Mitchell J, Langdon R, Iyer V, Barcena C, Vijayabaskar MS, Fabre MA, Carter P, Petrovski S, Burgess S, Vassiliou GS. Genome-wide analyses of 200,453 individuals yield new insights into the causes and consequences of clonal hematopoiesis. Nat Genet 2022; 54:1155-1166. [PMID: 35835912 PMCID: PMC9355874 DOI: 10.1038/s41588-022-01121-z] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 06/06/2022] [Indexed: 12/14/2022]
Abstract
Clonal hematopoiesis (CH), the clonal expansion of a blood stem cell and its progeny driven by somatic driver mutations, affects over a third of people, yet remains poorly understood. Here we analyze genetic data from 200,453 UK Biobank participants to map the landscape of inherited predisposition to CH, increasing the number of germline associations with CH in European-ancestry populations from 4 to 14. Genes at new loci implicate DNA damage repair (PARP1, ATM, CHEK2), hematopoietic stem cell migration/homing (CD164) and myeloid oncogenesis (SETBP1). Several associations were CH-subtype-specific including variants at TCL1A and CD164 that had opposite associations with DNMT3A- versus TET2-mutant CH, the two most common CH subtypes, proposing key roles for these two loci in CH development. Mendelian randomization analyses showed that smoking and longer leukocyte telomere length are causal risk factors for CH and that genetic predisposition to CH increases risks of myeloproliferative neoplasia, nonhematological malignancies, atrial fibrillation and blood epigenetic ageing.
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Affiliation(s)
- Siddhartha P Kar
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Section of Translational Epidemiology, Division of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Pedro M Quiros
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.
| | - Muxin Gu
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tao Jiang
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Cambridge, UK
| | - Jonathan Mitchell
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Ryan Langdon
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Section of Translational Epidemiology, Division of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Vivek Iyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Clea Barcena
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - M S Vijayabaskar
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Margarete A Fabre
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Paul Carter
- Division of Cardiovascular Medicine, Department of Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Stephen Burgess
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Cambridge, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - George S Vassiliou
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
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22
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Meyer AE, Stelloh C, Pulakanti K, Burns R, Fisher JB, Heimbruch KE, Tarima S, Furumo Q, Brennan J, Zheng Y, Viny AD, Vassiliou GS, Rao S. Combinatorial genetics reveals the Dock1-Rac2 axis as a potential target for the treatment of NPM1;Cohesin mutated AML. Leukemia 2022; 36:2032-2041. [PMID: 35778533 PMCID: PMC9357218 DOI: 10.1038/s41375-022-01632-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 02/03/2023]
Abstract
Acute myeloid leukemia (AML) is driven by mutations that occur in numerous combinations. A better understanding of how mutations interact with one another to cause disease is critical to developing targeted therapies. Approximately 50% of patients that harbor a common mutation in NPM1 (NPM1cA) also have a mutation in the cohesin complex. As cohesin and Npm1 are known to regulate gene expression, we sought to determine how cohesin mutation alters the transcriptome in the context of NPM1cA. We utilized inducible Npm1cAflox/+ and core cohesin subunit Smc3flox/+ mice to examine AML development. While Npm1cA/+;Smc3Δ/+ mice developed AML with a similar latency and penetrance as Npm1cA/+ mice, RNA-seq suggests that the Npm1cA/+; Smc3Δ/+ mutational combination uniquely alters the transcriptome. We found that the Rac1/2 nucleotide exchange factor Dock1 was specifically upregulated in Npm1cA/+;Smc3Δ/+ HSPCs. Knockdown of Dock1 resulted in decreased growth and adhesion and increased apoptosis only in Npm1cA/+;Smc3Δ/+ AML. Higher Rac activity was also observed in Npm1cA/+;Smc3Δ/+ vs. Npm1cA/+ AMLs. Importantly, the Dock1/Rac pathway is targetable in Npm1cA/+;Smc3Δ/+ AMLs. Our results suggest that Dock1/Rac represents a potential target for the treatment of patients harboring NPM1cA and cohesin mutations and supports the use of combinatorial genetics to identify novel precision oncology targets.
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Affiliation(s)
| | - Cary Stelloh
- Blood Research Institute, Versiti, Milwaukee, WI, USA
| | | | - Robert Burns
- Blood Research Institute, Versiti, Milwaukee, WI, USA
| | - Joseph B Fisher
- Department of Natural Sciences, Concordia University Wisconsin, Mequon, WI, USA
| | - Katelyn E Heimbruch
- Blood Research Institute, Versiti, Milwaukee, WI, USA
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Sergey Tarima
- Department of Biostatistics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Quinlan Furumo
- Department of Biology, Boston College, Chestnut Hill, MA, USA
| | - John Brennan
- Department of Pathology and Lab Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Yongwei Zheng
- Guangzhou Bio-gene Technology Co., Ltd., Guangzhou, China
| | - Aaron D Viny
- Department of Medicine, Division of Hematology and Oncology and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - George S Vassiliou
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Sridhar Rao
- Blood Research Institute, Versiti, Milwaukee, WI, USA.
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA.
- Department of Pediatrics, Division of Hematology, Oncology, and Bone Marrow Transplantation, Medical College of Wisconsin, Milwaukee, WI, USA.
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23
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Fabre MA, de Almeida JG, Fiorillo E, Mitchell E, Damaskou A, Rak J, Orrù V, Marongiu M, Chapman MS, Vijayabaskar MS, Baxter J, Hardy C, Abascal F, Williams N, Nangalia J, Martincorena I, Campbell PJ, McKinney EF, Cucca F, Gerstung M, Vassiliou GS. The longitudinal dynamics and natural history of clonal haematopoiesis. Nature 2022; 606:335-342. [PMID: 35650444 PMCID: PMC9177423 DOI: 10.1038/s41586-022-04785-z] [Citation(s) in RCA: 117] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 04/19/2022] [Indexed: 12/13/2022]
Abstract
Clonal expansions driven by somatic mutations become pervasive across human tissues with age, including in the haematopoietic system, where the phenomenon is termed clonal haematopoiesis1-4. The understanding of how and when clonal haematopoiesis develops, the factors that govern its behaviour, how it interacts with ageing and how these variables relate to malignant progression remains limited5,6. Here we track 697 clonal haematopoiesis clones from 385 individuals 55 years of age or older over a median of 13 years. We find that 92.4% of clones expanded at a stable exponential rate over the study period, with different mutations driving substantially different growth rates, ranging from 5% (DNMT3A and TP53) to more than 50% per year (SRSF2P95H). Growth rates of clones with the same mutation differed by approximately ±5% per year, proportionately affecting slow drivers more substantially. By combining our time-series data with phylogenetic analysis of 1,731 whole-genome sequences of haematopoietic colonies from 7 individuals from an older age group, we reveal distinct patterns of lifelong clonal behaviour. DNMT3A-mutant clones preferentially expanded early in life and displayed slower growth in old age, in the context of an increasingly competitive oligoclonal landscape. By contrast, splicing gene mutations drove expansion only later in life, whereas TET2-mutant clones emerged across all ages. Finally, we show that mutations driving faster clonal growth carry a higher risk of malignant progression. Our findings characterize the lifelong natural history of clonal haematopoiesis and give fundamental insights into the interactions between somatic mutation, ageing and clonal selection.
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Affiliation(s)
- Margarete A Fabre
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - José Guilherme de Almeida
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Cambridge, UK
| | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Lanusei, Italy
| | - Emily Mitchell
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Aristi Damaskou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Justyna Rak
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Valeria Orrù
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Lanusei, Italy
| | - Michele Marongiu
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Lanusei, Italy
| | - Michael Spencer Chapman
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - M S Vijayabaskar
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Joanna Baxter
- Cambridge Blood and Stem Cell Biobank, Department of Haematology, University of Cambridge, Cambridge, UK
| | - Claire Hardy
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Federico Abascal
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Nicholas Williams
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Jyoti Nangalia
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | | | - Peter J Campbell
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Eoin F McKinney
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Lanusei, Italy
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Cambridge, UK.
- Division of AI in Oncology, German Cancer Research Centre DKFZ, Heidelberg, Germany.
| | - George S Vassiliou
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
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24
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Mitchell E, Spencer Chapman M, Williams N, Dawson KJ, Mende N, Calderbank EF, Jung H, Mitchell T, Coorens THH, Spencer DH, Machado H, Lee-Six H, Davies M, Hayler D, Fabre MA, Mahbubani K, Abascal F, Cagan A, Vassiliou GS, Baxter J, Martincorena I, Stratton MR, Kent DG, Chatterjee K, Parsy KS, Green AR, Nangalia J, Laurenti E, Campbell PJ. Clonal dynamics of haematopoiesis across the human lifespan. Nature 2022; 606:343-350. [PMID: 35650442 PMCID: PMC9177428 DOI: 10.1038/s41586-022-04786-y] [Citation(s) in RCA: 128] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 04/19/2022] [Indexed: 12/11/2022]
Abstract
Age-related change in human haematopoiesis causes reduced regenerative capacity1, cytopenias2, immune dysfunction3 and increased risk of blood cancer4-6, but the reason for such abrupt functional decline after 70 years of age remains unclear. Here we sequenced 3,579 genomes from single cell-derived colonies of haematopoietic cells across 10 human subjects from 0 to 81 years of age. Haematopoietic stem cells or multipotent progenitors (HSC/MPPs) accumulated a mean of 17 mutations per year after birth and lost 30 base pairs per year of telomere length. Haematopoiesis in adults less than 65 years of age was massively polyclonal, with high clonal diversity and a stable population of 20,000-200,000 HSC/MPPs contributing evenly to blood production. By contrast, haematopoiesis in individuals aged over 75 showed profoundly decreased clonal diversity. In each of the older subjects, 30-60% of haematopoiesis was accounted for by 12-18 independent clones, each contributing 1-34% of blood production. Most clones had begun their expansion before the subject was 40 years old, but only 22% had known driver mutations. Genome-wide selection analysis estimated that between 1 in 34 and 1 in 12 non-synonymous mutations were drivers, accruing at constant rates throughout life, affecting more genes than identified in blood cancers. Loss of the Y chromosome conferred selective benefits in males. Simulations of haematopoiesis, with constant stem cell population size and constant acquisition of driver mutations conferring moderate fitness benefits, entirely explained the abrupt change in clonal structure in the elderly. Rapidly decreasing clonal diversity is a universal feature of haematopoiesis in aged humans, underpinned by pervasive positive selection acting on many more genes than currently identified.
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Affiliation(s)
- Emily Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | | | | | | | - Nicole Mende
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
| | - Emily F Calderbank
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
| | | | | | | | - David H Spencer
- Department of Medicine, McDonnell Genome Institute, Washington University, St Louis, MO, USA
| | | | | | - Megan Davies
- Cambridge Molecular Diagnostics, Milton Road, Cambridge, UK
| | - Daniel Hayler
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
| | - Margarete A Fabre
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Krishnaa Mahbubani
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge Biorepository for Translational Medicine, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | | | | | - George S Vassiliou
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Joanna Baxter
- Department of Haematology, University of Cambridge, Cambridge, UK
| | | | | | - David G Kent
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - Krishna Chatterjee
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Kourosh Saeb Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge Biorepository for Translational Medicine, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Anthony R Green
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Jyoti Nangalia
- Wellcome Sanger Institute, Hinxton, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
| | - Elisa Laurenti
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
| | - Peter J Campbell
- Wellcome Sanger Institute, Hinxton, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK.
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25
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Quiros PM, Gu M, Barcena C, Iyer V, Vassiliou GS. NPM1 gene mutations can be confidently identified in blood DNA months before de novo AML onset. Blood Adv 2022; 6:2409-2413. [PMID: 34920452 PMCID: PMC9006299 DOI: 10.1182/bloodadvances.2021005927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/10/2021] [Indexed: 11/20/2022] Open
Affiliation(s)
- Pedro M. Quiros
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain; and
| | - Muxin Gu
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Clea Barcena
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Vivek Iyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - George S. Vassiliou
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Department of Haematology, Cambridge University Hospitals National Health Service Trust, Cambridge, United Kingdom
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26
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Teng YHF, Quah HS, Suteja L, Dias JML, Mupo A, Bashford-Rogers RJM, Vassiliou GS, Chua MLK, Tan DSW, Lim DWT, Iyer NG. Analysis of T cell receptor clonotypes in tumor microenvironment identifies shared cancer-type-specific signatures. Cancer Immunol Immunother 2022; 71:989-998. [PMID: 34580764 PMCID: PMC8476067 DOI: 10.1007/s00262-021-03047-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 08/25/2021] [Indexed: 12/02/2022]
Abstract
Despite the conventional view that a truly random V(D)J recombination process should generate a highly diverse immune repertoire, emerging reports suggest that there is a certain bias toward the generation of shared/public immune receptor chains. These studies were performed in viral diseases where public T cell receptors (TCR) appear to confer better protective responses. Selective pressures generating common TCR clonotypes are currently not well understood, but it is believed that they confer a growth advantage. As very little is known about public TCR clonotypes in cancer, here we set out to determine the extent of shared TCR clonotypes in the intra-tumor microenvironments of virus- and non-virus-driven head and neck cancers using TCR sequencing. We report that tumor-infiltrating T cell clonotypes were indeed shared across individuals with the same cancer type, where the majority of shared sequences were specific to the cancer type (i.e., viral versus non-viral). These shared clonotypes were not particularly enriched in EBV-associated nasopharynx cancer but, in both cancers, exhibited distinct characteristics, namely shorter CDR3 lengths, restricted V- and J-gene usages, and also demonstrated convergent V(D)J recombination. Many of these shared TCRs were expressed in patients with a shared HLA background. Pattern recognition of CDR3 amino acid sequences revealed strong convergence to specific pattern motifs, and these motifs were uniquely found to each cancer type. This suggests that they may be enriched for specificity to common antigens found in the tumor microenvironment of different cancers. The identification of shared TCRs in infiltrating tumor T cells not only adds to our understanding of the tumor-adaptive immune recognition but could also serve as disease-specific biomarkers and guide the development of future immunotherapies.
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Affiliation(s)
- Yvonne H. F. Teng
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Hong Sheng Quah
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Lisda Suteja
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - João M. L. Dias
- Hutchison/MRC Research Centre, MRC Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ UK
| | | | | | - George S. Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge, CB2 0AW UK
| | - Melvin L. K. Chua
- Duke-NUS Medical School, Singapore, Singapore
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Daniel S. W. Tan
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Darren W. T. Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Institute of Molecular and Cell Biology, A-STAR, Singapore, Singapore
| | - N. Gopalakrishna Iyer
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Department of Head and Neck Surgery, National Cancer Centre Singapore, Singapore, Singapore
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27
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Dunn WG, Gu MS, Fabre MA, Cooper J, Nomdedeu JF, Koumas L, Nicolaou K, Chi J, Costeas P, Vassiliou GS. The PML-RARA fusion is not detectable in historical blood samples of acute promyelocytic leukaemia patients. Ann Hematol 2022; 101:443-445. [PMID: 33650061 PMCID: PMC8742812 DOI: 10.1007/s00277-021-04472-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 10/28/2022]
Affiliation(s)
- William G Dunn
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, UK
| | - Muxin S Gu
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Margarete A Fabre
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jonathan Cooper
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Josep F Nomdedeu
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Department of Haematology, Hospital de la Santa Creu I Sant Pau, Barcelona, Spain
| | - Laura Koumas
- Center for the Study of Haematological Malignancies, Karaiskakio Foundation, Nicosia, Cyprus
| | - Katerina Nicolaou
- Center for the Study of Haematological Malignancies, Karaiskakio Foundation, Nicosia, Cyprus
| | - Jiangxiang Chi
- Center for the Study of Haematological Malignancies, Karaiskakio Foundation, Nicosia, Cyprus
| | - Paul Costeas
- Center for the Study of Haematological Malignancies, Karaiskakio Foundation, Nicosia, Cyprus.
- Cyprus Cancer Research Institute, Nicosia, Cyprus.
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK.
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
- Center for the Study of Haematological Malignancies, Karaiskakio Foundation, Nicosia, Cyprus.
- Cyprus Cancer Research Institute, Nicosia, Cyprus.
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28
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Lafage-Pochitaloff M, Gerby B, Baccini V, Largeaud L, Fregona V, Prade N, Juvin PY, Jamrog L, Bories P, Hébrard S, Lagarde S, Mansat-De Mas V, Dovey OM, Yusa K, Vassiliou GS, Jansen JH, Tekath T, Rombaut D, Ameye G, Barin C, Bidet A, Boudjarane J, Collonge-Rame MA, Gervais C, Ittel A, Lefebvre C, Luquet I, Michaux L, Nadal N, Poirel HA, Radford-Weiss I, Ribourtout B, Richebourg S, Struski S, Terré C, Tigaud I, Penther D, Eclache V, Fontenay M, Broccardo C, Delabesse, E. The CADM1 tumor suppressor gene is a major candidate gene in MDS with deletion of the long arm of chromosome 11. Blood Adv 2022; 6:386-398. [PMID: 34638130 PMCID: PMC8791575 DOI: 10.1182/bloodadvances.2021005311] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/10/2021] [Indexed: 11/24/2022] Open
Abstract
Myelodysplastic syndromes (MDS) represent a heterogeneous group of clonal hematopoietic stem cell disorders characterized by ineffective hematopoiesis leading to peripheral cytopenias and in a substantial proportion of cases to acute myeloid leukemia. The deletion of the long arm of chromosome 11, del(11q), is a rare but recurrent clonal event in MDS. Here, we detail the largest series of 113 cases of MDS and myelodysplastic syndromes/myeloproliferative neoplasms (MDS/MPN) harboring a del(11q) analyzed at clinical, cytological, cytogenetic, and molecular levels. Female predominance, a survival prognosis similar to other MDS, a low monocyte count, and dysmegakaryopoiesis were the specific clinical and cytological features of del(11q) MDS. In most cases, del(11q) was isolated, primary and interstitial encompassing the 11q22-23 region containing ATM, KMT2A, and CBL genes. The common deleted region at 11q23.2 is centered on an intergenic region between CADM1 (also known as Tumor Suppressor in Lung Cancer 1) and NXPE2. CADM1 was expressed in all myeloid cells analyzed in contrast to NXPE2. At the functional level, the deletion of Cadm1 in murine Lineage-Sca1+Kit+ cells modifies the lymphoid-to-myeloid ratio in bone marrow, although not altering their multilineage hematopoietic reconstitution potential after syngenic transplantation. Together with the frequent simultaneous deletions of KMT2A, ATM, and CBL and mutations of ASXL1, SF3B1, and CBL, we show that CADM1 may be important in the physiopathology of the del(11q) MDS, extending its role as tumor-suppressor gene from solid tumors to hematopoietic malignancies.
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Affiliation(s)
- Marina Lafage-Pochitaloff
- Groupe Francophone de Cytogénétique Hématologique (GFCH)
- Laboratoire de Cytogénétique Hématologique, Centre Hospitalier Universitaire (CHU) de Marseille, Aix-Marseille University, Marseille, France
| | - Bastien Gerby
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Team 16, Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France
| | - Véronique Baccini
- Groupe Francophone d’Hématologie Cellulaire (GFHC) and
- Laboratoire d’hématologie, CHU de Guadeloupe, Inserm Unité Mixte de Recherche 1134, Pointe à Pitre, France
| | - Laetitia Largeaud
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Team 16, Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France
- Laboratoire d’Hématologie, Institut Universitaire de Cancérologie de Toulouse, CHU Toulouse, France
- Department of Hematology, University Toulouse III, Toulouse, France
| | - Vincent Fregona
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Team 16, Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France
| | - Naïs Prade
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Team 16, Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France
- Laboratoire d’Hématologie, Institut Universitaire de Cancérologie de Toulouse, CHU Toulouse, France
| | - Pierre-Yves Juvin
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Team 16, Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France
| | - Laura Jamrog
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Team 16, Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France
| | - Pierre Bories
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Team 16, Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France
| | - Sylvie Hébrard
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Team 16, Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France
| | - Stéphanie Lagarde
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Team 16, Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France
- Laboratoire d’Hématologie, Institut Universitaire de Cancérologie de Toulouse, CHU Toulouse, France
| | - Véronique Mansat-De Mas
- Laboratoire d’Hématologie, Institut Universitaire de Cancérologie de Toulouse, CHU Toulouse, France
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Team 8, Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France
| | - Oliver M. Dovey
- Gene Editing, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Kosuke Yusa
- Stem Cell Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - George S. Vassiliou
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, Cambridge University Hospitals National Health Service Trust, Cambridge, UK
- Wellcome-Medical Research Council Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Joop H. Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tobias Tekath
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - David Rombaut
- Institut Cochin, Université de Paris, Inserm U1016, Centre National de la Recherche Scientifique UMR8104, Paris, France
| | - Geneviève Ameye
- Groupe Francophone de Cytogénétique Hématologique (GFCH)
- Belgium Cancer Registry, Brussels, Belgium
- Department of Human Genetics, Katholieke Universiteit Leuven and Universitair Ziekenhuis, Leuven, Belgium
| | - Carole Barin
- Groupe Francophone de Cytogénétique Hématologique (GFCH)
- Laboratoire de Cytogénétique, CHU de Tours, France
| | - Audrey Bidet
- Groupe Francophone de Cytogénétique Hématologique (GFCH)
- Laboratoire d’Hématologie, CHU de Bordeaux, Bordeaux, France
| | - John Boudjarane
- Laboratoire de Cytogénétique Hématologique, Centre Hospitalier Universitaire (CHU) de Marseille, Aix-Marseille University, Marseille, France
| | - Marie-Agnès Collonge-Rame
- Groupe Francophone de Cytogénétique Hématologique (GFCH)
- Laboratoire de Cytogénétique, CHU de Besançon, Besançon, France
| | - Carine Gervais
- Groupe Francophone de Cytogénétique Hématologique (GFCH)
- Laboratoire de Cytogénétique, CHU de Strasbourg, Strasbourg, France
| | - Antoine Ittel
- Groupe Francophone de Cytogénétique Hématologique (GFCH)
- Département de Biopathologie, Institut Paoli-Calmettes, Marseille, France
| | - Christine Lefebvre
- Groupe Francophone de Cytogénétique Hématologique (GFCH)
- Laboratoire de Cytogénétique, CHU de Grenoble, Grenoble, France
| | - Isabelle Luquet
- Groupe Francophone de Cytogénétique Hématologique (GFCH)
- Laboratoire d’Hématologie, Institut Universitaire de Cancérologie de Toulouse, CHU Toulouse, France
- Laboratoire de Cytogénétique, CHU de Reims, Reims, France
| | - Lucienne Michaux
- Groupe Francophone de Cytogénétique Hématologique (GFCH)
- Department of Human Genetics, Katholieke Universiteit Leuven and Universitair Ziekenhuis, Leuven, Belgium
| | - Nathalie Nadal
- Groupe Francophone de Cytogénétique Hématologique (GFCH)
- Laboratoire de Cytogénétique, CHU de Saint-Etienne, Saint-Etienne, France
| | - Hélène A. Poirel
- Groupe Francophone de Cytogénétique Hématologique (GFCH)
- Belgium Cancer Registry, Brussels, Belgium
| | - Isabelle Radford-Weiss
- Groupe Francophone de Cytogénétique Hématologique (GFCH)
- Laboratoire de Cytogénétique, CHU de Paris-Necker, Paris, France
| | - Bénédicte Ribourtout
- Groupe Francophone de Cytogénétique Hématologique (GFCH)
- Laboratoire d'Hématologie, CHU d'Angers, Angers, France
| | - Steven Richebourg
- Groupe Francophone de Cytogénétique Hématologique (GFCH)
- Laboratoire de Cytogénétique, CHU de Nantes, Nantes, France
| | - Stéphanie Struski
- Groupe Francophone de Cytogénétique Hématologique (GFCH)
- Laboratoire d’Hématologie, Institut Universitaire de Cancérologie de Toulouse, CHU Toulouse, France
| | - Christine Terré
- Groupe Francophone de Cytogénétique Hématologique (GFCH)
- Laboratoire de Cytogénétique, CH de Versailles, Le Chesnay, France
| | - Isabelle Tigaud
- Groupe Francophone de Cytogénétique Hématologique (GFCH)
- Laboratoire de Cytogénétique, CHU de Lyon, Lyon, France
| | - Dominique Penther
- Groupe Francophone de Cytogénétique Hématologique (GFCH)
- Laboratoire de Cytogénétique, Centre Henri-Becquerel, Rouen, France
| | - Virginie Eclache
- Groupe Francophone de Cytogénétique Hématologique (GFCH)
- Laboratoire d’Hématologie, CHU Avicenne, Bobigny, France
- Groupe Francophone des Myélodysplasies (GFM); and
| | - Michaela Fontenay
- Institut Cochin, Université de Paris, Inserm U1016, Centre National de la Recherche Scientifique UMR8104, Paris, France
- Groupe Francophone des Myélodysplasies (GFM); and
- Laboratoire d’hématologie, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Centre-Université de Paris, Paris, France
| | - Cyril Broccardo
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Team 16, Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France
| | - Eric Delabesse,
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Team 16, Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France
- Laboratoire d’Hématologie, Institut Universitaire de Cancérologie de Toulouse, CHU Toulouse, France
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29
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Teng YHF, Quah HS, Suteja L, Dias JML, Mupo A, Bashford-Rogers RJM, Vassiliou GS, Chua MLK, Tan DSW, Lim DWT, Iyer NG. Correction to: Analysis of T cell receptor clonotypes in tumor microenvironment identifies shared cancer-type-specific signatures. Cancer Immunol Immunother 2021; 71:999. [PMID: 34677648 PMCID: PMC9119220 DOI: 10.1007/s00262-021-03086-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Yvonne H F Teng
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore
| | - Hong Sheng Quah
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Duke-NUS Medical School, Singapore, Singapore
| | - Lisda Suteja
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - João M L Dias
- Hutchison/MRC Research Centre, MRC Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Annalisa Mupo
- Babraham Research Institute, Cambridge, CB22 3AT, UK
| | - Rachael J M Bashford-Rogers
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Dr, Headington, Oxford, OX3 7BN, UK
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Melvin L K Chua
- Duke-NUS Medical School, Singapore, Singapore.,Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Daniel S W Tan
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore
| | - Darren W T Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore.,Institute of Molecular and Cell Biology, A-STAR, Singapore, Singapore
| | - N Gopalakrishna Iyer
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore. .,Duke-NUS Medical School, Singapore, Singapore. .,Department of Head and Neck Surgery, National Cancer Centre Singapore, Singapore, Singapore.
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30
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Yun H, Narayan N, Vohra S, Giotopoulos G, Mupo A, Madrigal P, Sasca D, Lara-Astiaso D, Horton SJ, Agrawal-Singh S, Meduri E, Basheer F, Marando L, Gozdecka M, Dovey OM, Castillo-Venzor A, Wang X, Gallipoli P, Müller-Tidow C, Osborne CS, Vassiliou GS, Huntly BJP. Mutational synergy during leukemia induction remodels chromatin accessibility, histone modifications and three-dimensional DNA topology to alter gene expression. Nat Genet 2021; 53:1443-1455. [PMID: 34556857 PMCID: PMC7611829 DOI: 10.1038/s41588-021-00925-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/28/2021] [Indexed: 02/08/2023]
Abstract
Altered transcription is a cardinal feature of acute myeloid leukemia (AML); however, exactly how mutations synergize to remodel the epigenetic landscape and rewire three-dimensional DNA topology is unknown. Here, we apply an integrated genomic approach to a murine allelic series that models the two most common mutations in AML: Flt3-ITD and Npm1c. We then deconvolute the contribution of each mutation to alterations of the epigenetic landscape and genome organization, and infer how mutations synergize in the induction of AML. Our studies demonstrate that Flt3-ITD signals to chromatin to alter the epigenetic environment and synergizes with mutations in Npm1c to alter gene expression and drive leukemia induction. These analyses also allow the identification of long-range cis-regulatory circuits, including a previously unknown superenhancer of Hoxa locus, as well as larger and more detailed gene-regulatory networks, driven by transcription factors including PU.1 and IRF8, whose importance we demonstrate through perturbation of network members.
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MESH Headings
- Animals
- Base Sequence
- Chromatin Assembly and Disassembly/genetics
- DNA, Neoplasm/chemistry
- Disease Models, Animal
- Enhancer Elements, Genetic/genetics
- Gene Expression Regulation, Leukemic
- Gene Regulatory Networks
- Genetic Loci
- Histones/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Mice, Inbred C57BL
- Mutation/genetics
- Nuclear Proteins/metabolism
- Nucleophosmin
- Principal Component Analysis
- Protein Processing, Post-Translational
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Transcription, Genetic
- fms-Like Tyrosine Kinase 3/metabolism
- Mice
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Affiliation(s)
- Haiyang Yun
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Nisha Narayan
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Shabana Vohra
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - George Giotopoulos
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Annalisa Mupo
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Pedro Madrigal
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Daniel Sasca
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Hematology, Oncology and Pneumology, University Medical Center Mainz, Mainz, Germany
| | - David Lara-Astiaso
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Sarah J Horton
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Shuchi Agrawal-Singh
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Eshwar Meduri
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Faisal Basheer
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Ludovica Marando
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Malgorzata Gozdecka
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Oliver M Dovey
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | | | - Xiaonan Wang
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Paolo Gallipoli
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Carsten Müller-Tidow
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Cameron S Osborne
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - George S Vassiliou
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Brian J P Huntly
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
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31
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Maifrede S, Le BV, Nieborowska-Skorska M, Golovine K, Sullivan-Reed K, Dunuwille WMB, Nacson J, Hulse M, Keith K, Madzo J, Caruso LB, Gazze Z, Lian Z, Padella A, Chitrala KN, Bartholdy BA, Matlawska-Wasowska K, Di Marcantonio D, Simonetti G, Greiner G, Sykes SM, Valent P, Paietta EM, Tallman MS, Fernandez HF, Litzow MR, Minden MD, Huang J, Martinelli G, Vassiliou GS, Tempera I, Piwocka K, Johnson N, Challen GA, Skorski T. TET2 and DNMT3A Mutations Exert Divergent Effects on DNA Repair and Sensitivity of Leukemia Cells to PARP Inhibitors. Cancer Res 2021; 81:5089-5101. [PMID: 34215619 PMCID: PMC8487956 DOI: 10.1158/0008-5472.can-20-3761] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/15/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022]
Abstract
Somatic variants in TET2 and DNMT3A are founding mutations in hematological malignancies that affect the epigenetic regulation of DNA methylation. Mutations in both genes often co-occur with activating mutations in genes encoding oncogenic tyrosine kinases such as FLT3ITD, BCR-ABL1, JAK2V617F , and MPLW515L , or with mutations affecting related signaling pathways such as NRASG12D and CALRdel52 . Here, we show that TET2 and DNMT3A mutations exert divergent roles in regulating DNA repair activities in leukemia cells expressing these oncogenes. Malignant TET2-deficient cells displayed downregulation of BRCA1 and LIG4, resulting in reduced activity of BRCA1/2-mediated homologous recombination (HR) and DNA-PK-mediated non-homologous end-joining (D-NHEJ), respectively. TET2-deficient cells relied on PARP1-mediated alternative NHEJ (Alt-NHEJ) for protection from the toxic effects of spontaneous and drug-induced DNA double-strand breaks. Conversely, DNMT3A-deficient cells favored HR/D-NHEJ owing to downregulation of PARP1 and reduction of Alt-NHEJ. Consequently, malignant TET2-deficient cells were sensitive to PARP inhibitor (PARPi) treatment in vitro and in vivo, whereas DNMT3A-deficient cells were resistant. Disruption of TET2 dioxygenase activity or TET2-Wilms' tumor 1 (WT1)-binding ability was responsible for DNA repair defects and sensitivity to PARPi associated with TET2 deficiency. Moreover, mutation or deletion of WT1 mimicked the effect of TET2 mutation on DSB repair activity and sensitivity to PARPi. Collectively, these findings reveal that TET2 and WT1 mutations may serve as biomarkers of synthetic lethality triggered by PARPi, which should be explored therapeutically. SIGNIFICANCE: TET2 and DNMT3A mutations affect distinct DNA repair mechanisms and govern the differential sensitivities of oncogenic tyrosine kinase-positive malignant hematopoietic cells to PARP inhibitors.
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Affiliation(s)
- Silvia Maifrede
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Bac Viet Le
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
- Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Margaret Nieborowska-Skorska
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Konstantin Golovine
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Katherine Sullivan-Reed
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Wangisa M B Dunuwille
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, Missouri
| | - Joseph Nacson
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Michael Hulse
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Kelsey Keith
- Coriell Institute for Medical Research, Camden, New Jersey
| | - Jozef Madzo
- Coriell Institute for Medical Research, Camden, New Jersey
| | - Lisa Beatrice Caruso
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Zachary Gazze
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Zhaorui Lian
- Coriell Institute for Medical Research, Camden, New Jersey
| | - Antonella Padella
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori," Meldola, Italy
| | - Kumaraswamy N Chitrala
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Boris A Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York
| | - Ksenia Matlawska-Wasowska
- Division of Hematology-Oncology, Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Daniela Di Marcantonio
- Research Institute of Fox Chase Cancer Center, Immune Cell Development and Host Defense, Philadelphia, Pennsylvania
| | - Giorgia Simonetti
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori," Meldola, Italy
| | - Georg Greiner
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Stephen M Sykes
- Research Institute of Fox Chase Cancer Center, Immune Cell Development and Host Defense, Philadelphia, Pennsylvania
| | - Peter Valent
- Division of Hematology and Hemostaseology and Ludwig-Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Elisabeth M Paietta
- Albert Einstein College of Medicine-Montefiore Medical Center, Bronx, New York
| | - Martin S Tallman
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hugo F Fernandez
- Moffitt Malignant Hematology and Cellular Therapy at Memorial Healthcare System, Pembroke Pines, Florida
| | - Mark R Litzow
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Mark D Minden
- Princess Margaret Cancer Center, Ontario Cancer Institute, Toronto, Ontario, Canada
| | - Jian Huang
- Coriell Institute for Medical Research, Camden, New Jersey
| | - Giovanni Martinelli
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori," Meldola, Italy
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Italo Tempera
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | | | - Neil Johnson
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Grant A Challen
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, Missouri.
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania.
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32
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Orellana EA, Liu Q, Yankova E, Pirouz M, De Braekeleer E, Zhang W, Lim J, Aspris D, Sendinc E, Garyfallos DA, Gu M, Ali R, Gutierrez A, Mikutis S, Bernardes GJL, Fischer ES, Bradley A, Vassiliou GS, Slack FJ, Tzelepis K, Gregory RI. METTL1-mediated m 7G modification of Arg-TCT tRNA drives oncogenic transformation. Mol Cell 2021; 81:3323-3338.e14. [PMID: 34352207 PMCID: PMC8380730 DOI: 10.1016/j.molcel.2021.06.031] [Citation(s) in RCA: 141] [Impact Index Per Article: 47.0] [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: 05/27/2020] [Revised: 02/02/2021] [Accepted: 06/27/2021] [Indexed: 02/07/2023]
Abstract
The emerging "epitranscriptomics" field is providing insights into the biological and pathological roles of different RNA modifications. The RNA methyltransferase METTL1 catalyzes N7-methylguanosine (m7G) modification of tRNAs. Here we find METTL1 is frequently amplified and overexpressed in cancers and is associated with poor patient survival. METTL1 depletion causes decreased abundance of m7G-modified tRNAs and altered cell cycle and inhibits oncogenicity. Conversely, METTL1 overexpression induces oncogenic cell transformation and cancer. Mechanistically, we find increased abundance of m7G-modified tRNAs, in particular Arg-TCT-4-1, and increased translation of mRNAs, including cell cycle regulators that are enriched in the corresponding AGA codon. Accordingly, Arg-TCT expression is elevated in many tumor types and is associated with patient survival, and strikingly, overexpression of this individual tRNA induces oncogenic transformation. Thus, METTL1-mediated tRNA modification drives oncogenic transformation through a remodeling of the mRNA "translatome" to increase expression of growth-promoting proteins and represents a promising anti-cancer target.
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Affiliation(s)
- Esteban A Orellana
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Qi Liu
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Eliza Yankova
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Milner Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Storm Therapeutics Ltd., Moneta Building (B280), Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Mehdi Pirouz
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Etienne De Braekeleer
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Wencai Zhang
- Department of Pathology, Cancer Center, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Jihoon Lim
- Department of Pathology, Cancer Center, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Demetrios Aspris
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Karaiskakio Foundation, Nicandrou Papamina Avenue, 2032 Nicosia, Cyprus
| | - Erdem Sendinc
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Dimitrios A Garyfallos
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Muxin Gu
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Raja Ali
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Alejandro Gutierrez
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Sigitas Mikutis
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Eric S Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Allan Bradley
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - George S Vassiliou
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Karaiskakio Foundation, Nicandrou Papamina Avenue, 2032 Nicosia, Cyprus; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Frank J Slack
- Department of Pathology, Cancer Center, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
| | - Konstantinos Tzelepis
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Milner Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK.
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Harvard Initiative for RNA Medicine, Boston, MA 02115, USA.
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33
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Pacharne S, Dovey OM, Cooper JL, Gu M, Friedrich MJ, Rajan SS, Barenboim M, Collord G, Vijayabaskar MS, Ponstingl H, De Braekeleer E, Bautista R, Mazan M, Rad R, Tzelepis K, Wright P, Gozdecka M, Vassiliou GS. SETBP1 overexpression acts in the place of class-defining mutations to drive FLT3-ITD-mutant AML. Blood Adv 2021; 5:2412-2425. [PMID: 33956058 PMCID: PMC8114559 DOI: 10.1182/bloodadvances.2020003443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 09/18/2020] [Accepted: 01/25/2021] [Indexed: 12/23/2022] Open
Abstract
Advances in cancer genomics have revealed genomic classes of acute myeloid leukemia (AML) characterized by class-defining mutations, such as chimeric fusion genes or in genes such as NPM1, MLL, and CEBPA. These class-defining mutations frequently synergize with internal tandem duplications in FLT3 (FLT3-ITDs) to drive leukemogenesis. However, ∼20% of FLT3-ITD-positive AMLs bare no class-defining mutations, and mechanisms of leukemic transformation in these cases are unknown. To identify pathways that drive FLT3-ITD mutant AML in the absence of class-defining mutations, we performed an insertional mutagenesis (IM) screening in Flt3-ITD mice, using Sleeping Beauty transposons. All mice developed acute leukemia (predominantly AML) after a median of 73 days. Analysis of transposon insertions in 38 samples from Flt3-ITD/IM leukemic mice identified recurrent integrations at 22 loci, including Setbp1 (20/38), Ets1 (11/38), Ash1l (8/38), Notch1 (8/38), Erg (7/38), and Runx1 (5/38). Insertions at Setbp1 led exclusively to AML and activated a transcriptional program similar, but not identical, to those of NPM1-mutant and MLL-rearranged AMLs. Guide RNA targeting of Setbp1 was highly detrimental to Flt3ITD/+/Setbp1IM+, but not to Flt3ITD/+/Npm1cA/+, AMLs. Also, analysis of RNA-sequencing data from hundreds of human AMLs revealed that SETBP1 expression is significantly higher in FLT3-ITD AMLs lacking class-defining mutations. These findings propose that SETBP1 overexpression collaborates with FLT3-ITD to drive a subtype of human AML. To identify genetic vulnerabilities of these AMLs, we performed genome-wide CRISPR-Cas9 screening in Flt3ITD/+/Setbp1IM+ AMLs and identified potential therapeutic targets, including Kdm1a, Brd3, Ezh2, and Hmgcr. Our study gives new insights into epigenetic pathways that can drive AMLs lacking class-defining mutations and proposes therapeutic approaches against such cases.
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Affiliation(s)
- Suruchi Pacharne
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Wellcome-Medical Research Center (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Oliver M Dovey
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Jonathan L Cooper
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Muxin Gu
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Wellcome-Medical Research Center (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Mathias J Friedrich
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Sandeep S Rajan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- United Kingdom Dementia Research Institute, University of Cambridge, Cambridge, United Kingdom
| | - Maxim Barenboim
- Department of Pediatrics and Children's Cancer Research Center, Klinikum Rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Grace Collord
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Wellcome-Medical Research Center (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - M S Vijayabaskar
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Wellcome-Medical Research Center (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Hannes Ponstingl
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Etienne De Braekeleer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Wellcome-Medical Research Center (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Ruben Bautista
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Milena Mazan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Research and Development Department, Selvita S.A., Krakow, Poland
| | - Roland Rad
- Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany; and
| | - Konstantinos Tzelepis
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Gurdon Institute
- Department of Pathology, and
| | | | - Malgorzata Gozdecka
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Wellcome-Medical Research Center (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - George S Vassiliou
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Wellcome-Medical Research Center (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, Cambridge University Hospitals National Health Service (NHS) Trust, Cambridge, United Kingdom
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34
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Yankova E, Blackaby W, Albertella M, Rak J, De Braekeleer E, Tsagkogeorga G, Pilka ES, Aspris D, Leggate D, Hendrick AG, Webster NA, Andrews B, Fosbeary R, Guest P, Irigoyen N, Eleftheriou M, Gozdecka M, Dias JML, Bannister AJ, Vick B, Jeremias I, Vassiliou GS, Rausch O, Tzelepis K, Kouzarides T. Small-molecule inhibition of METTL3 as a strategy against myeloid leukaemia. Nature 2021; 593:597-601. [PMID: 33902106 PMCID: PMC7613134 DOI: 10.1038/s41586-021-03536-w] [Citation(s) in RCA: 459] [Impact Index Per Article: 153.0] [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: 12/18/2020] [Accepted: 04/12/2021] [Indexed: 12/22/2022]
Abstract
N6-methyladenosine (m6A) is an abundant internal RNA modification1,2 that is catalysed predominantly by the METTL3-METTL14 methyltransferase complex3,4. The m6A methyltransferase METTL3 has been linked to the initiation and maintenance of acute myeloid leukaemia (AML), but the potential of therapeutic applications targeting this enzyme remains unknown5-7. Here we present the identification and characterization of STM2457, a highly potent and selective first-in-class catalytic inhibitor of METTL3, and a crystal structure of STM2457 in complex with METTL3-METTL14. Treatment of tumours with STM2457 leads to reduced AML growth and an increase in differentiation and apoptosis. These cellular effects are accompanied by selective reduction of m6A levels on known leukaemogenic mRNAs and a decrease in their expression consistent with a translational defect. We demonstrate that pharmacological inhibition of METTL3 in vivo leads to impaired engraftment and prolonged survival in various mouse models of AML, specifically targeting key stem cell subpopulations of AML. Collectively, these results reveal the inhibition of METTL3 as a potential therapeutic strategy against AML, and provide proof of concept that the targeting of RNA-modifying enzymes represents a promising avenue for anticancer therapy.
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Affiliation(s)
- Eliza Yankova
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
- Storm Therapeutics Ltd, Cambridge, UK
| | | | | | - Justyna Rak
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Etienne De Braekeleer
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Georgia Tsagkogeorga
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
- Storm Therapeutics Ltd, Cambridge, UK
| | | | - Demetrios Aspris
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
- The Center for the Study of Hematological Malignancies/Karaiskakio Foundation, Nicosia, Cyprus
| | | | | | | | | | | | | | - Nerea Irigoyen
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Maria Eleftheriou
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Malgorzata Gozdecka
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Joao M L Dias
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, UK
| | - Andrew J Bannister
- The Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK
| | - Binje Vick
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
- German Consortium for Translational Cancer Research (DKTK), Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
- German Consortium for Translational Cancer Research (DKTK), Munich, Germany
- Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig Maximilians University München, Munich, Germany
| | - George S Vassiliou
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- The Center for the Study of Hematological Malignancies/Karaiskakio Foundation, Nicosia, Cyprus
| | | | - Konstantinos Tzelepis
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK.
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Tony Kouzarides
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK.
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35
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Mikutis S, Gu M, Sendinc E, Hazemi ME, Kiely-Collins H, Aspris D, Vassiliou GS, Shi Y, Tzelepis K, Bernardes GJL. meCLICK-Seq, a Substrate-Hijacking and RNA Degradation Strategy for the Study of RNA Methylation. ACS Cent Sci 2020; 6:2196-2208. [PMID: 33376781 PMCID: PMC7760485 DOI: 10.1021/acscentsci.0c01094] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Indexed: 06/01/2023]
Abstract
The fates of RNA species in a cell are controlled by ribonucleases, which degrade them by exploiting the universal structural 2'-OH group. This phenomenon plays a key role in numerous transformative technologies, for example, RNA interference and CRISPR/Cas13-based RNA editing systems. These approaches, however, are genetic or oligomer-based and so have inherent limitations. This has led to interest in the development of small molecules capable of degrading nucleic acids in a targeted manner. Here we describe click-degraders, small molecules that can be covalently attached to RNA species through click-chemistry and can degrade them, that are akin to ribonucleases. By using these molecules, we have developed the meCLICK-Seq (methylation CLICK-degradation Sequencing) a method to identify RNA modification substrates with high resolution at intronic and intergenic regions. The method hijacks RNA methyltransferase activity to introduce an alkyne, instead of a methyl, moiety on RNA. Subsequent copper(I)-catalyzed azide-alkyne cycloaddition reaction with the click-degrader leads to RNA cleavage and degradation exploiting a mechanism used by endogenous ribonucleases. Focusing on N6-methyladenosine (m6A), meCLICK-Seq identifies methylated transcripts, determines RNA methylase specificity, and reliably maps modification sites in intronic and intergenic regions. Importantly, we show that METTL16 deposits m6A to intronic polyadenylation (IPA) sites, which suggests a potential role for METTL16 in IPA and, in turn, splicing. Unlike other methods, the readout of meCLICK-Seq is depletion, not enrichment, of modified RNA species, which allows a comprehensive and dynamic study of RNA modifications throughout the transcriptome, including regions of low abundance. The click-degraders are highly modular and so may be exploited to study any RNA modification and design new technologies that rely on RNA degradation.
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Affiliation(s)
- Sigitas Mikutis
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Muxin Gu
- Haematological
Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10
1SA, U.K.
| | - Erdem Sendinc
- Boston
Childrens’ Hospital, Harvard Medical
School, 300 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Madoka E. Hazemi
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Hannah Kiely-Collins
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Demetrios Aspris
- Haematological
Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10
1SA, U.K.
- The
Center for the Study of Haematological Malignancies, Karaiskakio Foundation, Nicandrou Papamina Avenue, 2032 Nicosia, Cyprus
| | - George S. Vassiliou
- Haematological
Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10
1SA, U.K.
- The
Center for the Study of Haematological Malignancies, Karaiskakio Foundation, Nicandrou Papamina Avenue, 2032 Nicosia, Cyprus
- Wellcome-MRC
Cambridge Stem Cell Institute, University
of Cambridge, Puddicombe Way, Cambridge CB2 0AW, U.K.
| | - Yang Shi
- Boston
Childrens’ Hospital, Harvard Medical
School, 300 Longwood Avenue, Boston, Massachusetts 02115, United States
- Ludwig
Institute for Cancer Research, Oxford University, Old Road Campus Research Build,
Roosevelt Dr., Oxford OX3
7DQ, U.K.
| | - Konstantinos Tzelepis
- Haematological
Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10
1SA, U.K.
- Boston
Childrens’ Hospital, Harvard Medical
School, 300 Longwood Avenue, Boston, Massachusetts 02115, United States
- Milner Therapeutics
Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, U.K.
| | - Gonçalo J. L. Bernardes
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
- Instituto
de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
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36
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Nguyen CH, Schlerka A, Grandits AM, Koller E, van der Kouwe E, Vassiliou GS, Staber PB, Heller G, Wieser R. IL2RA Promotes Aggressiveness and Stem Cell-Related Properties of Acute Myeloid Leukemia. Cancer Res 2020; 80:4527-4539. [PMID: 32873636 DOI: 10.1158/0008-5472.can-20-0531] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 02/15/2020] [Revised: 07/14/2020] [Accepted: 08/26/2020] [Indexed: 11/16/2022]
Abstract
Overexpression of IL2RA, which encodes the alpha chain of the IL2 receptor, is associated with chemotherapy resistance and poor outcome in acute myeloid leukemia (AML). The clinical potential of anti-IL2RA therapy is, therefore, being explored in early-stage clinical trials. Notwithstanding, only very limited information regarding the biological function of IL2RA in AML is available. Using genetic manipulation of IL2RA expression as well as antibody-mediated inhibition of IL2RA in human cell lines, mouse models, and primary patient samples, we investigated the effects of IL2RA on AML cell proliferation and apoptosis, and on pertinent signaling pathways. The impact of IL2RA on the properties of leukemic stem cells (LSC) and on leukemogenesis were queried. IL2RA promoted proliferation and cell-cycle activity and inhibited apoptosis in human AML cell lines and primary cells. These phenotypes were accompanied by corresponding alterations in cell-cycle machinery and in pathways associated with cell survival and apoptosis. The biological roles of IL2RA were confirmed in two genetically distinct AML mouse models, revealing that IL2RA inhibits differentiation, promotes stem cell-related properties, and is required for leukemogenesis. IL2RA antibodies inhibited leukemic, but not normal, hematopoietic cells and synergized with other antileukemic agents in this regard. Collectively, these data show for the first time that IL2RA plays key biological roles in AML and underscore its value as a potential therapeutic target in this disease. SIGNIFICANCE: This study identifies IL2RA as a potential therapeutic target in AML, where it is shown to regulate proliferation, differentiation, apoptosis, stem cell-related properties, and leukemogenesis.
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MESH Headings
- Animals
- Antibodies, Monoclonal/pharmacology
- Apoptosis/genetics
- Case-Control Studies
- Cell Line, Tumor
- Cell Proliferation/genetics
- Female
- Gene Expression Regulation, Leukemic
- Humans
- Interleukin-2 Receptor alpha Subunit/genetics
- Interleukin-2 Receptor alpha Subunit/immunology
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/pathology
- Mice, Inbred C57BL
- Prognosis
- Stem Cells/pathology
- fms-Like Tyrosine Kinase 3/genetics
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Affiliation(s)
- Chi Huu Nguyen
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria.
- Comprehensive Cancer Center, Vienna, Austria
| | - Angela Schlerka
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Vienna, Austria
| | - Alexander M Grandits
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Vienna, Austria
| | | | - Emiel van der Kouwe
- Division of Hematology and Hemostaseology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - George S Vassiliou
- Wellcome Medical Research Council Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Philipp B Staber
- Division of Hematology and Hemostaseology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Gerwin Heller
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Vienna, Austria
| | - Rotraud Wieser
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria.
- Comprehensive Cancer Center, Vienna, Austria
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37
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Nguyen CH, Grandits AM, Vassiliou GS, Staber PB, Heller G, Wieser R. Evi1 Counteracts Anti-Leukemic and Stem Cell Inhibitory Effects of All-Trans Retinoic Acid on Flt3-ITD/ Npm1c-Driven Acute Myeloid Leukemia Cells. Biomedicines 2020; 8:E385. [PMID: 32998330 PMCID: PMC7600968 DOI: 10.3390/biomedicines8100385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/18/2020] [Accepted: 09/24/2020] [Indexed: 12/15/2022] Open
Abstract
All-trans retinoic acid (atRA) has a dramatic impact on the survival of patients with acute promyelocytic leukemia, but its therapeutic value in other types of acute myeloid leukemia (AML) has so far remained unclear. Given that AML is a stem cell-driven disease, recent studies have addressed the effects of atRA on leukemic stem cells (LSCs). atRA promoted stemness of MLL-AF9-driven AML in an Evi1-dependent manner but had the opposite effect in Flt3-ITD/Nup98-Hoxd13-driven AML. Overexpression of the stem cell-associated transcription factor EVI1 predicts a poor prognosis in AML, and is observed in different genetic subtypes, including cytogenetically normal AML. Here, we therefore investigated the effects of Evi1 in a mouse model for cytogenetically normal AML, which rests on the combined activity of Flt3-ITD and Npm1c mutations. Experimental expression of Evi1 on this background strongly promoted disease aggressiveness. atRA inhibited leukemia cell viability and stem cell-related properties, and these effects were counteracted by overexpression of Evi1. These data further underscore the complexity of the responsiveness of AML LSCs to atRA and point out the need for additional investigations which may lay a foundation for a precision medicine-based use of retinoids in AML.
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Affiliation(s)
- Chi Huu Nguyen
- Division of Oncology, Department of Medicine I, Medical University of Vienna, 1090 Vienna, Austria; (C.H.N.); (A.M.G.); (G.H.)
- Comprehensive Cancer Center, 1090 Vienna, Austria
| | - Alexander M. Grandits
- Division of Oncology, Department of Medicine I, Medical University of Vienna, 1090 Vienna, Austria; (C.H.N.); (A.M.G.); (G.H.)
- Comprehensive Cancer Center, 1090 Vienna, Austria
| | - George S. Vassiliou
- Wellcome Medical Research Council Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK;
| | - Philipp B. Staber
- Division of Hematology and Hemostaseology, Department of Medicine I, Medical University of Vienna, 1090 Vienna, Austria;
| | - Gerwin Heller
- Division of Oncology, Department of Medicine I, Medical University of Vienna, 1090 Vienna, Austria; (C.H.N.); (A.M.G.); (G.H.)
- Comprehensive Cancer Center, 1090 Vienna, Austria
| | - Rotraud Wieser
- Division of Oncology, Department of Medicine I, Medical University of Vienna, 1090 Vienna, Austria; (C.H.N.); (A.M.G.); (G.H.)
- Comprehensive Cancer Center, 1090 Vienna, Austria
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38
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Gu M, Zwiebel M, Ong SH, Boughton N, Nomdedeu J, Basheer F, Nannya Y, Quiros PM, Ogawa S, Cazzola M, Rad R, Butler AP, Vijayabaskar MS, Vassiliou GS. RNAmut: robust identification of somatic mutations in acute myeloid leukemia using RNA-sequencing. Haematologica 2020; 105:e290-e293. [PMID: 31649132 PMCID: PMC7271607 DOI: 10.3324/haematol.2019.230821] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Muxin Gu
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Maximillian Zwiebel
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
- German Consortium for Translational Cancer Research (DKTK), Partnering Site, Munich, Germany
| | - Swee Hoe Ong
- Cancer Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Nick Boughton
- Core Software Services, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Josep Nomdedeu
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Hospital de la Santa Creu I Sant Pau, Barcelona, Spain
| | - Faisal Basheer
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, UK
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Pedro M Quiros
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mario Cazzola
- Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Roland Rad
- German Consortium for Translational Cancer Research (DKTK), Partnering Site, Munich, Germany
| | - Adam P Butler
- Cancer Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - M S Vijayabaskar
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - George S Vassiliou
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, UK
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39
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40
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Basilico S, Wang X, Kennedy A, Tzelepis K, Giotopoulos G, Kinston SJ, Quiros PM, Wong K, Adams DJ, Carnevalli LS, Huntly BJP, Vassiliou GS, Calero-Nieto FJ, Göttgens B. Dissecting the early steps of MLL induced leukaemogenic transformation using a mouse model of AML. Nat Commun 2020; 11:1407. [PMID: 32179751 PMCID: PMC7075888 DOI: 10.1038/s41467-020-15220-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/17/2020] [Indexed: 12/18/2022] Open
Abstract
Leukaemogenic mutations commonly disrupt cellular differentiation and/or enhance proliferation, thus perturbing the regulatory programs that control self-renewal and differentiation of stem and progenitor cells. Translocations involving the Mll1 (Kmt2a) gene generate powerful oncogenic fusion proteins, predominantly affecting infant and paediatric AML and ALL patients. The early stages of leukaemogenic transformation are typically inaccessible from human patients and conventional mouse models. Here, we take advantage of cells conditionally blocked at the multipotent haematopoietic progenitor stage to develop a MLL-r model capturing early cellular and molecular consequences of MLL-ENL expression based on a clear clonal relationship between parental and leukaemic cells. Through a combination of scRNA-seq, ATAC-seq and genome-scale CRISPR-Cas9 screening, we identify pathways and genes likely to drive the early phases of leukaemogenesis. Finally, we demonstrate the broad utility of using matched parental and transformed cells for small molecule inhibitor studies by validating both previously known and other potential therapeutic targets.
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MESH Headings
- Animals
- Cell Transformation, Neoplastic
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Disease Models, Animal
- Female
- Hematopoietic Stem Cells/metabolism
- Histone-Lysine N-Methyltransferase/genetics
- Histone-Lysine N-Methyltransferase/metabolism
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/physiopathology
- Mice
- Mice, Inbred C57BL
- Myeloid-Lymphoid Leukemia Protein/genetics
- Myeloid-Lymphoid Leukemia Protein/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Transcription Factors/genetics
- Transcription Factors/metabolism
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Affiliation(s)
- Silvia Basilico
- Wellcome and MRC Cambridge Stem Cell Institute and University of Cambridge Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Xiaonan Wang
- Wellcome and MRC Cambridge Stem Cell Institute and University of Cambridge Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Alison Kennedy
- Wellcome and MRC Cambridge Stem Cell Institute and University of Cambridge Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Konstantinos Tzelepis
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Milner Therapeutics Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - George Giotopoulos
- Wellcome and MRC Cambridge Stem Cell Institute and University of Cambridge Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Sarah J Kinston
- Wellcome and MRC Cambridge Stem Cell Institute and University of Cambridge Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Pedro M Quiros
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Kim Wong
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - David J Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Brian J P Huntly
- Wellcome and MRC Cambridge Stem Cell Institute and University of Cambridge Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - George S Vassiliou
- Wellcome and MRC Cambridge Stem Cell Institute and University of Cambridge Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Fernando J Calero-Nieto
- Wellcome and MRC Cambridge Stem Cell Institute and University of Cambridge Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK.
| | - Berthold Göttgens
- Wellcome and MRC Cambridge Stem Cell Institute and University of Cambridge Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK.
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41
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Lange S, Engleitner T, Mueller S, Maresch R, Zwiebel M, González-Silva L, Schneider G, Banerjee R, Yang F, Vassiliou GS, Friedrich MJ, Saur D, Varela I, Rad R. Analysis pipelines for cancer genome sequencing in mice. Nat Protoc 2020; 15:266-315. [PMID: 31907453 DOI: 10.1038/s41596-019-0234-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 01/31/2019] [Accepted: 08/27/2019] [Indexed: 12/14/2022]
Abstract
Mouse models of human cancer have transformed our ability to link genetics, molecular mechanisms and phenotypes. Both reverse and forward genetics in mice are currently gaining momentum through advances in next-generation sequencing (NGS). Methodologies to analyze sequencing data were, however, developed for humans and hence do not account for species-specific differences in genome structures and experimental setups. Here, we describe standardized computational pipelines specifically tailored to the analysis of mouse genomic data. We present novel tools and workflows for the detection of different alteration types, including single-nucleotide variants (SNVs), small insertions and deletions (indels), copy-number variations (CNVs), loss of heterozygosity (LOH) and complex rearrangements, such as in chromothripsis. Workflows have been extensively validated and cross-compared using multiple methodologies. We also give step-by-step guidance on the execution of individual analysis types, provide advice on data interpretation and make the complete code available online. The protocol takes 2-7 d, depending on the desired analyses.
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Affiliation(s)
- Sebastian Lange
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Sebastian Mueller
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Roman Maresch
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Maximilian Zwiebel
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Laura González-Silva
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC, Santander, Spain
| | - Günter Schneider
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany
| | | | | | - George S Vassiliou
- The Wellcome Trust Sanger Institute, Cambridge, UK
- Wellcome Trust-MRC Stem Cell Institute, Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cam bridge, UK
| | - Mathias J Friedrich
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Dieter Saur
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute for Experimental Cancer Therapy, School of Medicine, Technische Universität München, Munich, Germany
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC, Santander, Spain
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany.
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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42
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Uckelmann HJ, Kim SM, Wong EM, Hatton C, Giovinazzo H, Gadrey JY, Krivtsov AV, Rücker FG, Döhner K, McGeehan GM, Levine RL, Bullinger L, Vassiliou GS, Armstrong SA. Therapeutic targeting of preleukemia cells in a mouse model of NPM1 mutant acute myeloid leukemia. Science 2020; 367:586-590. [PMID: 32001657 PMCID: PMC7754791 DOI: 10.1126/science.aax5863] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [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: 04/23/2019] [Accepted: 12/27/2019] [Indexed: 12/15/2022]
Abstract
The initiating mutations that contribute to cancer development are sometimes present in premalignant cells. Whether therapies targeting these mutations can eradicate premalignant cells is unclear. Acute myeloid leukemia (AML) is an attractive system for investigating the effect of preventative treatment because this disease is often preceded by a premalignant state (clonal hematopoiesis or myelodysplastic syndrome). In Npm1c/Dnmt3a mutant knock-in mice, a model of AML development, leukemia is preceded by a period of extended myeloid progenitor cell proliferation and self-renewal. We found that this self-renewal can be reversed by oral administration of a small molecule (VTP-50469) that targets the MLL1-Menin chromatin complex. These preclinical results support the hypothesis that individuals at high risk of developing AML might benefit from targeted epigenetic therapy in a preventative setting.
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Affiliation(s)
- Hannah J Uckelmann
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston, MA, USA
- Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Stephanie M Kim
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston, MA, USA
- Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Eric M Wong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston, MA, USA
- Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Charles Hatton
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston, MA, USA
- Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hugh Giovinazzo
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston, MA, USA
- Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jayant Y Gadrey
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston, MA, USA
- Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Andrei V Krivtsov
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston, MA, USA
- Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Frank G Rücker
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | | | - Ross L Levine
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lars Bullinger
- Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine, Berlin, Germany
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston, MA, USA.
- Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
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43
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Fabre MA, McKerrell T, Zwiebel M, Vijayabaskar MS, Park N, Wells PM, Rad R, Deloukas P, Small K, Steves CJ, Vassiliou GS. Concordance for clonal hematopoiesis is limited in elderly twins. Blood 2020; 135:269-273. [PMID: 31697828 PMCID: PMC6978156 DOI: 10.1182/blood.2019001807] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [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: 05/28/2019] [Accepted: 10/06/2019] [Indexed: 12/14/2022] Open
Abstract
Although acquisition of leukemia-associated somatic mutations by 1 or more hematopoietic stem cells is inevitable with advancing age, its consequences are highly variable, ranging from clinically silent clonal hematopoiesis (CH) to leukemic progression. To investigate the influence of heritable factors on CH, we performed deep targeted sequencing of blood DNA from 52 monozygotic (MZ) and 27 dizygotic (DZ) twin pairs (aged 70-99 years). Using this highly sensitive approach, we identified CH (variant allele frequency ≥0.5%) in 62% of individuals. We did not observe higher concordance for CH within MZ twin pairs as compared with that within DZ twin pairs, or to that expected by chance. However, we did identify 2 MZ pairs in which both twins harbored identical rare somatic mutations, suggesting a shared cell of origin. Finally, in 3 MZ twin pairs harboring mutations in the same driver genes, serial blood samples taken 4 to 5 years apart showed substantial twin-to-twin variability in clonal trajectories. Our findings propose that the inherited genome does not exert a dominant influence on the behavior of adult CH and provide evidence that CH mutations may be acquired in utero.
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Affiliation(s)
- Margarete A Fabre
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome-Medical Research Council (MRC) Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, Cambridge University Hospitals National Health Service (NHS) Trust, Cambridge, United Kingdom
| | - Thomas McKerrell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome-Medical Research Council (MRC) Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, Cambridge University Hospitals National Health Service (NHS) Trust, Cambridge, United Kingdom
| | - Maximillian Zwiebel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- German Consortium for Translational Cancer Research (DKTK), Partnering Site Munich, Munich, Germany
| | - M S Vijayabaskar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome-Medical Research Council (MRC) Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - Naomi Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Philippa M Wells
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, United Kingdom; and
| | - Roland Rad
- German Consortium for Translational Cancer Research (DKTK), Partnering Site Munich, Munich, Germany
| | - Panagiotis Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Kerrin Small
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, United Kingdom; and
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, United Kingdom; and
| | - George S Vassiliou
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome-Medical Research Council (MRC) Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, Cambridge University Hospitals National Health Service (NHS) Trust, Cambridge, United Kingdom
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44
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Paubelle E, Zylbersztejn F, Maciel TT, Carvalho C, Mupo A, Cheok M, Lieben L, Sujobert P, Decroocq J, Yokoyama A, Asnafi V, Macintyre E, Tamburini J, Bardet V, Castaigne S, Preudhomme C, Dombret H, Carmeliet G, Bouscary D, Ginzburg YZ, de Thé H, Benhamou M, Monteiro RC, Vassiliou GS, Hermine O, Moura IC. Vitamin D Receptor Controls Cell Stemness in Acute Myeloid Leukemia and in Normal Bone Marrow. Cell Rep 2020; 30:739-754.e4. [PMID: 31968250 DOI: 10.1016/j.celrep.2019.12.055] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 09/10/2015] [Revised: 02/24/2019] [Accepted: 12/16/2019] [Indexed: 02/06/2023] Open
Abstract
Vitamin D (VD) is a known differentiating agent, but the role of VD receptor (VDR) is still incompletely described in acute myeloid leukemia (AML), whose treatment is based mostly on antimitotic chemotherapy. Here, we present an unexpected role of VDR in normal hematopoiesis and in leukemogenesis. Limited VDR expression is associated with impaired myeloid progenitor differentiation and is a new prognostic factor in AML. In mice, the lack of Vdr results in increased numbers of hematopoietic and leukemia stem cells and quiescent hematopoietic stem cells. In addition, malignant transformation of Vdr-/- cells results in myeloid differentiation block and increases self-renewal. Vdr promoter is methylated in AML as in CD34+ cells, and demethylating agents induce VDR expression. Association of VDR agonists with hypomethylating agents promotes leukemia stem cell exhaustion and decreases tumor burden in AML mouse models. Thus, Vdr functions as a regulator of stem cell homeostasis and leukemic propagation.
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Affiliation(s)
- Etienne Paubelle
- INSERM UMR 1163, Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, 75015 Paris, France; Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France; CNRS ERL 8254, Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, 75015 Paris, France; Department of Clinical Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker, 75015 Paris, France.
| | - Florence Zylbersztejn
- INSERM UMR 1163, Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, 75015 Paris, France; Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France; CNRS ERL 8254, Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, 75015 Paris, France
| | - Thiago Trovati Maciel
- INSERM UMR 1163, Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, 75015 Paris, France
| | - Caroline Carvalho
- INSERM UMR 1163, Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, 75015 Paris, France
| | - Annalisa Mupo
- Haematological Cancer Genetics, Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK
| | - Meyling Cheok
- Centre of Research Jean-Pierre Aubert, INSERM UMR 837, 59000 Lille, France
| | - Liesbet Lieben
- Laboratory of Experimental Medicine and Endocrinology, KU Leuven 3000, Belgium
| | - Pierre Sujobert
- Institut Cochin, Département d'Immuno-Hématologie, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 8104, INSERM U1016 Paris, France; Université Paris Descartes, Faculté de Médecine Sorbonne Paris Cité, Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris, France
| | - Justine Decroocq
- INSERM UMR 1163, Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, 75015 Paris, France; Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France; CNRS ERL 8254, Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, 75015 Paris, France
| | - Akihiko Yokoyama
- National Cancer Center Research Institute, Chiba 277-8577, Japan
| | - Vahid Asnafi
- Department of Biological Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker, 75015 Paris, France
| | - Elizabeth Macintyre
- Department of Biological Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker, 75015 Paris, France
| | - Jérôme Tamburini
- Institut Cochin, Département d'Immuno-Hématologie, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 8104, INSERM U1016 Paris, France; Université Paris Descartes, Faculté de Médecine Sorbonne Paris Cité, Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris, France
| | - Valérie Bardet
- INSERM UMR 1163, Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, 75015 Paris, France; Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France; CNRS ERL 8254, Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, 75015 Paris, France
| | - Sylvie Castaigne
- Department of Hematology, Hôpital Mignot, 78150 Le Chesnay, France
| | - Claude Preudhomme
- Centre of Research Jean-Pierre Aubert, INSERM UMR 837, 59000 Lille, France
| | - Hervé Dombret
- Department of Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, 75010 Paris, France
| | - Geert Carmeliet
- Laboratory of Experimental Medicine and Endocrinology, KU Leuven 3000, Belgium
| | - Didier Bouscary
- Institut Cochin, Département d'Immuno-Hématologie, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 8104, INSERM U1016 Paris, France; Université Paris Descartes, Faculté de Médecine Sorbonne Paris Cité, Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris, France
| | - Yelena Z Ginzburg
- Erythropoiesis Laboratory, LFKRI, New York Blood Center, New York, NY, USA
| | - Hughes de Thé
- Molecular Virology and Pathology, INSERM UMR 944, 75010 Paris, France; Molecular Virology and Pathology, CNRS 7212, 75010 Paris, France
| | - Marc Benhamou
- INSERM U1149, Center for Research on Inflammation, 75018 Paris, France
| | - Renato C Monteiro
- INSERM U1149, Center for Research on Inflammation, 75018 Paris, France
| | - George S Vassiliou
- Haematological Cancer Genetics, Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK
| | - Olivier Hermine
- INSERM UMR 1163, Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, 75015 Paris, France; Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France; CNRS ERL 8254, Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, 75015 Paris, France; Department of Clinical Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker, 75015 Paris, France; Laboratory of Excellence GR-Ex, 75015 Paris, France.
| | - Ivan C Moura
- INSERM UMR 1163, Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, 75015 Paris, France; Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France; CNRS ERL 8254, Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, 75015 Paris, France; Laboratory of Excellence GR-Ex, 75015 Paris, France
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45
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MacPherson L, Anokye J, Yeung MM, Lam EYN, Chan YC, Weng CF, Yeh P, Knezevic K, Butler MS, Hoegl A, Chan KL, Burr ML, Gearing LJ, Willson T, Liu J, Choi J, Yang Y, Bilardi RA, Falk H, Nguyen N, Stupple PA, Peat TS, Zhang M, de Silva M, Carrasco-Pozo C, Avery VM, Khoo PS, Dolezal O, Dennis ML, Nuttall S, Surjadi R, Newman J, Ren B, Leaver DJ, Sun Y, Baell JB, Dovey O, Vassiliou GS, Grebien F, Dawson SJ, Street IP, Monahan BJ, Burns CJ, Choudhary C, Blewitt ME, Voss AK, Thomas T, Dawson MA. HBO1 is required for the maintenance of leukaemia stem cells. Nature 2020; 577:266-270. [PMID: 31827282 DOI: 10.1038/s41586-019-1835-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [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: 09/05/2018] [Accepted: 11/12/2019] [Indexed: 02/07/2023]
Abstract
Acute myeloid leukaemia (AML) is a heterogeneous disease characterized by transcriptional dysregulation that results in a block in differentiation and increased malignant self-renewal. Various epigenetic therapies aimed at reversing these hallmarks of AML have progressed into clinical trials, but most show only modest efficacy owing to an inability to effectively eradicate leukaemia stem cells (LSCs)1. Here, to specifically identify novel dependencies in LSCs, we screened a bespoke library of small hairpin RNAs that target chromatin regulators in a unique ex vivo mouse model of LSCs. We identify the MYST acetyltransferase HBO1 (also known as KAT7 or MYST2) and several known members of the HBO1 protein complex as critical regulators of LSC maintenance. Using CRISPR domain screening and quantitative mass spectrometry, we identified the histone acetyltransferase domain of HBO1 as being essential in the acetylation of histone H3 at K14. H3 acetylated at K14 (H3K14ac) facilitates the processivity of RNA polymerase II to maintain the high expression of key genes (including Hoxa9 and Hoxa10) that help to sustain the functional properties of LSCs. To leverage this dependency therapeutically, we developed a highly potent small-molecule inhibitor of HBO1 and demonstrate its mode of activity as a competitive analogue of acetyl-CoA. Inhibition of HBO1 phenocopied our genetic data and showed efficacy in a broad range of human cell lines and primary AML cells from patients. These biological, structural and chemical insights into a therapeutic target in AML will enable the clinical translation of these findings.
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Affiliation(s)
- Laura MacPherson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Juliana Anokye
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Miriam M Yeung
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Enid Y N Lam
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Yih-Chih Chan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Chen-Fang Weng
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Paul Yeh
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kathy Knezevic
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Miriam S Butler
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Annabelle Hoegl
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kah-Lok Chan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Marian L Burr
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Linden J Gearing
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tracy Willson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Joy Liu
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Jarny Choi
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Yuqing Yang
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Rebecca A Bilardi
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Hendrik Falk
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
| | - Nghi Nguyen
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Paul A Stupple
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Thomas S Peat
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Ming Zhang
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
| | - Melanie de Silva
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
| | - Catalina Carrasco-Pozo
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Vicky M Avery
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Poh Sim Khoo
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Children's Cancer Institute, Kensington, New South Wales, Australia
| | - Olan Dolezal
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Matthew L Dennis
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Stewart Nuttall
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Regina Surjadi
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Janet Newman
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Bin Ren
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - David J Leaver
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Yuxin Sun
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Jonathan B Baell
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Oliver Dovey
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Cambridge, UK
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Ian P Street
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
| | - Brendon J Monahan
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
| | - Christopher J Burns
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Anne K Voss
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tim Thomas
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia.
- Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
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Caeser R, Di Re M, Krupka JA, Gao J, Lara-Chica M, Dias JML, Cooke SL, Fenner R, Usheva Z, Runge HFP, Beer PA, Eldaly H, Pak HK, Park CS, Vassiliou GS, Huntly BJP, Mupo A, Bashford-Rogers RJM, Hodson DJ. Genetic modification of primary human B cells to model high-grade lymphoma. Nat Commun 2019; 10:4543. [PMID: 31586074 PMCID: PMC6778131 DOI: 10.1038/s41467-019-12494-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 09/11/2019] [Indexed: 12/03/2022] Open
Abstract
Sequencing studies of diffuse large B cell lymphoma (DLBCL) have identified hundreds of recurrently altered genes. However, it remains largely unknown whether and how these mutations may contribute to lymphomagenesis, either individually or in combination. Existing strategies to address this problem predominantly utilize cell lines, which are limited by their initial characteristics and subsequent adaptions to prolonged in vitro culture. Here, we describe a co-culture system that enables the ex vivo expansion and viral transduction of primary human germinal center B cells. Incorporation of CRISPR/Cas9 technology enables high-throughput functional interrogation of genes recurrently mutated in DLBCL. Using a backbone of BCL2 with either BCL6 or MYC, we identify co-operating genetic alterations that promote growth or even full transformation into synthetically engineered DLBCL models. The resulting tumors can be expanded and sequentially transplanted in vivo, providing a scalable platform to test putative cancer genes and to create mutation-directed, bespoke lymphoma models.
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Affiliation(s)
- Rebecca Caeser
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Miriam Di Re
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Joanna A Krupka
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, UK
| | - Jie Gao
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Maribel Lara-Chica
- Cancer Molecular Diagnostics Laboratory (CMDL), Department of Haematology, University of Cambridge, Cambridge, UK
| | - João M L Dias
- Cancer Molecular Diagnostics Laboratory (CMDL), Department of Haematology, University of Cambridge, Cambridge, UK
| | - Susanna L Cooke
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Glasgow, UK
| | - Rachel Fenner
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Zelvera Usheva
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Hendrik F P Runge
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Philip A Beer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CA, CB10 1SA, UK
| | - Hesham Eldaly
- Department of Pathology, Cambridge University Hospitals, Cambridge, UK
- Department of Clinical Pathology, Cairo University, Giza, Egypt
| | - Hyo-Kyung Pak
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Centre, Seoul, Korea
| | - Chan-Sik Park
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Centre, Seoul, Korea
| | - George S Vassiliou
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CA, CB10 1SA, UK
| | - Brian J P Huntly
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Annalisa Mupo
- Cancer Molecular Diagnostics Laboratory (CMDL), Department of Haematology, University of Cambridge, Cambridge, UK
| | | | - Daniel J Hodson
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
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Rudorf A, Müller TA, Klingeberg C, Kreutmair S, Poggio T, Gorantla SP, Rückert T, Schmitt-Graeff A, Gengenbacher A, Paschka P, Baldus C, Zeiser R, Vassiliou GS, Bradley A, Duyster J, Illert AL. NPM1c alters FLT3-D835Y localization and signaling in acute myeloid leukemia. Blood 2019; 134:383-388. [PMID: 31186273 PMCID: PMC6659255 DOI: 10.1182/blood.2018883140] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 10/30/2018] [Accepted: 04/19/2019] [Indexed: 11/20/2022] Open
Abstract
Activating mutations in FMS-like tyrosine kinase receptor-3 (FLT3) and Nucleophosmin-1 (NPM1) are most frequent alterations in acute myeloid leukemia (AML), and are often coincidental. The mutational status of NPM1 has strong prognostic relevance to patients with point mutations of the FLT3 tyrosine kinase domain (TKD), but the biological mechanism underlying this effect remains unclear. In the present study, we investigated the effect of the coincidence of NPM1c and FLT3-TKD. Although expression of FLT3-TKD is not sufficient to induce a disease in mice, coexpression with NPM1c rapidly leads to an aggressive myeloproliferative disease in mice with a latency of 31.5 days. Mechanistically, we could show that FLT3-TKD is able to activate the downstream effector molecule signal transducer and activator of transcription 5 (STAT5) exclusively in the presence of mutated NPM1c. Moreover, NPM1c alters the cellular localization of FLT3-TKD from the cell surface to the endoplasmic reticulum, which might thereby lead to the aberrant STAT5 activation. Importantly, aberrant STAT5 activation occurs not only in primary murine cells but also in patients with AML with combined FLT3-TKD and NPM1c mutations. Thus, our data indicate a new mechanism, how NPM1c mislocalizes FLT3-TKD and changes its signal transduction ability.
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Affiliation(s)
- Alina Rudorf
- Department of Hematology and Oncology, Freiburg University Medical Center, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
- German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
- Faculty of Biology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Tony Andreas Müller
- Department of Hematology and Oncology, Freiburg University Medical Center, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Cathrin Klingeberg
- Department of Hematology and Oncology, Freiburg University Medical Center, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Stefanie Kreutmair
- Department of Hematology and Oncology, Freiburg University Medical Center, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Teresa Poggio
- Department of Hematology and Oncology, Freiburg University Medical Center, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Sivahari Prasad Gorantla
- Department of Hematology and Oncology, Freiburg University Medical Center, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Tamina Rückert
- Department of Hematology and Oncology, Freiburg University Medical Center, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Annette Schmitt-Graeff
- Department for Pathology, Freiburg University Medical Center, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Anina Gengenbacher
- Department of Hematology and Oncology, Freiburg University Medical Center, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Peter Paschka
- Department of Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Claudia Baldus
- Second Medical Department, University Hospital Schleswig-Holstein, Kiel, Germany; and
| | - Robert Zeiser
- Department of Hematology and Oncology, Freiburg University Medical Center, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
- German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
| | - George S Vassiliou
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Allan Bradley
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Justus Duyster
- Department of Hematology and Oncology, Freiburg University Medical Center, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
- German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
| | - Anna Lena Illert
- Department of Hematology and Oncology, Freiburg University Medical Center, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
- German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
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Dzama MM, Taubert MC, Kunz K, Rausch J, Chen CW, Mupo A, Theobald M, Kindler T, Koche RP, Vassiliou GS, Armstrong SA, Kühn MW. Abstract 3841: Therapeutic targeting of FLT3 mutations in AML via menin-MLL1 and FLT3 inhibition. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3841] [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
Acute myeloid leukemias (AML) that are driven by MLL1 (KMT2A)-fusion proteins (MLL-f) or NPM1 mutations (NPM1mut) are both associated with aberrant expression of HOX and MEIS1 transcription factors and commonly harbor mutations in the gene encoding the receptor tyrosine kinase FLT3. Inhibition of the menin-MLL1 interaction has been shown to be a therapeutic opportunity in MLL-f driven leukemias and we recently demonstrated that this interaction is a dependency in NPM1mut AML. MI503 a specific small molecule menin-MLL1 inhibitor reduces dramatically cell growth and reverses leukemogenic gene expression including MEIS1 and FLT3. To determine global transcriptional changes associated with menin inhibition we performed RNA sequencing upon MI503 treatment in NPM1mut OCI-AML3 and MLL-f driven MV411 cells. MEIS1 and its putative target gene FLT3 were found to be among the most significantly downregulated genes. MEIS1 and FLT3 were consistently downregulated in various human and murine leukemia cell lines driven by MLL-f or NPM1mut. Allele specific qPCR confirmed profound downregulation of the mutant FLT3 allele in the MLL-f driven MV411 and MOLM13 cells as well as murine Npm1mut/+Flt3ITD/+ cells that all harbor a FLT3-ITD mutation. FLT3 surface expression was also substantially reduced upon MI503 treatment as assessed by FACS. Next, we assessed combinatorial menin- and FLT3 tyrosine kinase inhibition using MI503 and the 2nd generation FLT3 inhibitor AC220. The two drugs worked in a synergistic way to promote growth inhibition and enhanced apoptosis compared to single drug treatment or vehicle alone in MOLM13 and MV411 cells. HL60 and NB4 AML cells lacking NPM1mut, MLL-f, or FLT3-ITD showed no response. Drug synergism was also observed in the murine NPM1mut/+FLT3ITD/+ AML cells when combining MI503 with ponatinib a tyrosine kinase inhibitor with activity against the FLT3-ITD F692L resistance mutation that has been described in these cells. Of interest, ectopic expression of Hoxa9-Meis1 resulted in upregulation of Flt3 and rescued the antiproliferative effect of combined menin- and FLT3-inhibition. Combined menin- and FLT3 inhibition reduced FLT3 phosphorylation more than AC220 or MI503 alone most likely reflecting the joint effect of AC220 mediated inhibition of FLT3 phosphorylation and transcriptional FLT3 suppression via MI503. Transcriptional profiling revealed substantial silencing of FLT3 downstream signature genes including MYC upon combinatorial treatment. In vivo treatment of leukemic MV411 xenografts with combined MI503 and AC220 resulted in significantly enhanced reduction of leukemia burden that was observed with single drug treatment compared to vehicle controls. Altogether, our data show that simultaneous menin- and FLT3 inhibition has a synergistic effect against leukemogenic FLT3 signaling and may represent a novel therapeutic concept for MLL-f and NPM1mut driven AML with concomitant FLT3-ITD.
Citation Format: Margarita M. Dzama, Martha C. Taubert, Kerstin Kunz, Johanna Rausch, Chun-Wei Chen, Annalisa Mupo, Matthias Theobald, Thomas Kindler, Richard P. Koche, George S. Vassiliou, Scott A. Armstrong, Michael W. Kühn. Therapeutic targeting of FLT3 mutations in AML via menin-MLL1 and FLT3 inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3841.
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