RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia

Peter Campbell, Mel Greaves and colleagues use exome and whole-genome sequencing to characterize somatic mutations in childhood acute lymphoblastic leukemias with the ETV6 - RUNX1 fusion gene. They find that RAG-mediated deletions are the dominant mutational process. The ETV6 - RUNX1 fusion gene, fo...

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Published in	Nature genetics Vol. 46; no. 2; pp. 116 - 125
Main Authors	Papaemmanuil, Elli, Rapado, Inmaculada, Li, Yilong, Potter, Nicola E, Wedge, David C, Tubio, Jose, Alexandrov, Ludmil B, Van Loo, Peter, Cooke, Susanna L, Marshall, John, Martincorena, Inigo, Hinton, Jonathan, Gundem, Gunes, van Delft, Frederik W, Nik-Zainal, Serena, Jones, David R, Ramakrishna, Manasa, Titley, Ian, Stebbings, Lucy, Leroy, Catherine, Menzies, Andrew, Gamble, John, Robinson, Ben, Mudie, Laura, Raine, Keiran, O'Meara, Sarah, Teague, Jon W, Butler, Adam P, Cazzaniga, Giovanni, Biondi, Andrea, Zuna, Jan, Kempski, Helena, Muschen, Markus, Ford, Anthony M, Stratton, Michael R, Greaves, Mel, Campbell, Peter J
Format	Journal Article
Language	English
Published	New York Nature Publishing Group US 01.02.2014 Nature Publishing Group
Subjects	45/23 45/62 631/208/514/1948 692/699/1541/1990/283/2125 Acute lymphocytic leukemia Agriculture Animal Genetics and Genomics Base Sequence Basic Helix-Loop-Helix Transcription Factors - genetics Bioinformatics Biomedicine Cancer Cancer Research Cell differentiation Core Binding Factor Alpha 2 Subunit - genetics Deoxyribonucleic acid DNA DNA Copy Number Variations - genetics Experiments Gene Expression Regulation, Neoplastic - genetics Gene Function Gene Library Gene Rearrangement - genetics Genes Genes, Tumor Suppressor Genetic aspects Genetic recombination Genetic Variation Genomes Homeodomain Proteins - genetics Human Genetics Humans Leukemia Methods Molecular Sequence Data Mutation Oncogene Proteins, Fusion - genetics Precursor B-Cell Lymphoblastic Leukemia-Lymphoma - genetics Recombination, Genetic - genetics Repressor Proteins Risk factors Sequence Analysis, DNA Sequence Deletion - genetics Studies Transcription Factors - genetics Twins V(D)J Recombination - genetics United Kingdom
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Abstract	Peter Campbell, Mel Greaves and colleagues use exome and whole-genome sequencing to characterize somatic mutations in childhood acute lymphoblastic leukemias with the ETV6 - RUNX1 fusion gene. They find that RAG-mediated deletions are the dominant mutational process. The ETV6 - RUNX1 fusion gene, found in 25% of childhood acute lymphoblastic leukemia (ALL) cases, is acquired in utero but requires additional somatic mutations for overt leukemia. We used exome and low-coverage whole-genome sequencing to characterize secondary events associated with leukemic transformation. RAG-mediated deletions emerge as the dominant mutational process, characterized by recombination signal sequence motifs near breakpoints, incorporation of non-templated sequence at junctions, ∼30-fold enrichment at promoters and enhancers of genes actively transcribed in B cell development and an unexpectedly high ratio of recurrent to non-recurrent structural variants. Single-cell tracking shows that this mechanism is active throughout leukemic evolution, with evidence of localized clustering and reiterated deletions. Integration of data on point mutations and rearrangements identifies ATF7IP and MGA as two new tumor-suppressor genes in ALL. Thus, a remarkably parsimonious mutational process transforms ETV6 - RUNX1 –positive lymphoblasts, targeting the promoters, enhancers and first exons of genes that normally regulate B cell differentiation.
AbstractList	The ETV6-RUNX1 fusion gene, found in 25% of childhood acute lymphoblastic leukemia (ALL), is acquired in utero but requires additional somatic mutations for overt leukemia. We used exome and low-coverage whole-genome sequencing to characterize secondary events associated with leukemic transformation. RAG-mediated deletions emerge as the dominant mutational process, characterized by recombination signal sequence motifs near the breakpoints; incorporation of non-templated sequence at the junction; ~30-fold enrichment at promoters and enhancers of genes actively transcribed in B-cell development and an unexpectedly high ratio of recurrent to non-recurrent structural variants. Single cell tracking shows that this mechanism is active throughout leukemic evolution with evidence of localized clustering and re-iterated deletions. Integration of point mutation and rearrangement data identifies ATF7IP and MGA as two new tumor suppressor genes in ALL. Thus, a remarkably parsimonious mutational process transforms ETV6-RUNX1 lymphoblasts, targeting the promoters, enhancers and first exons of genes that normally regulate B-cell differentiation. The ETV6-RUNX1 fusion gene, found in 25% of childhood acute lymphoblastic leukemia (ALL) cases, is acquired in utero but requires additional somatic mutations for overt leukemia. We used exome and low-coverage whole-genome sequencing to characterize secondary events associated with leukemic transformation. RAG-mediated deletions emerge as the dominant mutational process, characterized by recombination signal sequence motifs near breakpoints, incorporation of non-templated sequence at junctions, ∼30-fold enrichment at promoters and enhancers of genes actively transcribed in B cell development and an unexpectedly high ratio of recurrent to non-recurrent structural variants. Single-cell tracking shows that this mechanism is active throughout leukemic evolution, with evidence of localized clustering and reiterated deletions. Integration of data on point mutations and rearrangements identifies ATF7IP and MGA as two new tumor-suppressor genes in ALL. Thus, a remarkably parsimonious mutational process transforms ETV6-RUNX1-positive lymphoblasts, targeting the promoters, enhancers and first exons of genes that normally regulate B cell differentiation. The ETV6-RUNX1 fusion gene, found in 25% of childhood acute lymphoblastic leukemia (ALL) cases, is acquired in utero but requires additional somatic mutations for overt leukemia. We used exome and low-coverage whole-genome sequencing to characterize secondary events associated with leukemic transformation. RAG-mediated deletions emerge as the dominant mutational process, characterized by recombination signal sequence motifs near breakpoints, incorporation of non-templated sequence at junctions, 30-fold enrichment at promoters and enhancers of genes actively transcribed in B cell development and an unexpectedly high ratio of recurrent to non-recurrent structural variants. Single-cell tracking shows that this mechanism is active throughout leukemic evolution, with evidence of localized clustering and reiterated deletions. Integration of data on point mutations and rearrangements identifies ATF7IP and MGA as two new tumor-suppressor genes in ALL. Thus, a remarkably parsimonious mutational process transforms ETV6-RUNX1-positive lymphoblasts, targeting the promoters, enhancers and first exons of genes that normally regulate B cell differentiation. The ETV6-RUNX1 fusion gene, found in 25% of childhood acute lymphoblastic leukemia (ALL) cases, is acquired in utero but requires additional somatic mutations for overt leukemia. We used exome and low-coverage whole-genome sequencing to characterize secondary events associated with leukemic transformation. RAG-mediated deletions emerge as the dominant mutational process, characterized by recombination signal sequence motifs near breakpoints, incorporation of non-templated sequence at junctions, ~30-fold enrichment at promoters and enhancers of genes actively transcribed in B cell development and an unexpectedly high ratio of recurrent to non-recurrent structural variants. Single-cell tracking shows that this mechanism is active throughout leukemic evolution, with evidence of localized clustering and reiterated deletions. Integration of data on point mutations and rearrangements identifies ATF7IP and MGA as two new tumor-suppressor genes in ALL. Thus, a remarkably parsimonious mutational process transforms ETV6-RUNX1-positive lymphoblasts, targeting the promoters, enhancers and first exons of genes that normally regulate B cell differentiation. [PUBLICATION ABSTRACT] Peter Campbell, Mel Greaves and colleagues use exome and whole-genome sequencing to characterize somatic mutations in childhood acute lymphoblastic leukemias with the ETV6 - RUNX1 fusion gene. They find that RAG-mediated deletions are the dominant mutational process. The ETV6 - RUNX1 fusion gene, found in 25% of childhood acute lymphoblastic leukemia (ALL) cases, is acquired in utero but requires additional somatic mutations for overt leukemia. We used exome and low-coverage whole-genome sequencing to characterize secondary events associated with leukemic transformation. RAG-mediated deletions emerge as the dominant mutational process, characterized by recombination signal sequence motifs near breakpoints, incorporation of non-templated sequence at junctions, ∼30-fold enrichment at promoters and enhancers of genes actively transcribed in B cell development and an unexpectedly high ratio of recurrent to non-recurrent structural variants. Single-cell tracking shows that this mechanism is active throughout leukemic evolution, with evidence of localized clustering and reiterated deletions. Integration of data on point mutations and rearrangements identifies ATF7IP and MGA as two new tumor-suppressor genes in ALL. Thus, a remarkably parsimonious mutational process transforms ETV6 - RUNX1 –positive lymphoblasts, targeting the promoters, enhancers and first exons of genes that normally regulate B cell differentiation.
Audience	Academic
Author	van Delft, Frederik W Stebbings, Lucy Gundem, Gunes Menzies, Andrew Tubio, Jose O'Meara, Sarah Li, Yilong Stratton, Michael R Robinson, Ben Zuna, Jan Gamble, John Mudie, Laura Campbell, Peter J Wedge, David C Ramakrishna, Manasa Titley, Ian Rapado, Inmaculada Muschen, Markus Martincorena, Inigo Potter, Nicola E Jones, David R Leroy, Catherine Nik-Zainal, Serena Greaves, Mel Marshall, John Teague, Jon W Hinton, Jonathan Papaemmanuil, Elli Biondi, Andrea Raine, Keiran Cooke, Susanna L Kempski, Helena Cazzaniga, Giovanni Ford, Anthony M Butler, Adam P Van Loo, Peter Alexandrov, Ludmil B
AuthorAffiliation	2 Hospital Universitario 12 de Octubre, Madrid, Spain 9 Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 4 Department of Human Genetics, VIB and University of Leuven, Leuven, Belgium 7 CLIP, Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University Prague and University Hospital Motol, Prague, Czech Republic 11 University of Cambridge, Cambridge, UK 1 Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK 5 Northern Institute for Cancer Research, University of Newcastle, Newcastle upon Tyne, UK 3 Institute for Cancer Research, Sutton, London, UK 6 Centro Ricerca Tettamanti, Hospital San Gerardo, Via Pergolesi, 33, 20052 Monza (Mi), Italy 8 Paediatric Malignancy Unit, CBL Level 2, Molecular Haematology & Cancer Biology Unit, Camelia Botnar Laboratories, Level 2, Great Ormond Street Hospital for Children & UCL Institute of Child Health, Great Ormond Street, London WC1N 3JH 10 Addenbrooke’s NHS Foundation
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BackLink	https://www.ncbi.nlm.nih.gov/pubmed/24413735$$D View this record in MEDLINE/PubMed
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Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 AUTHOR CONTRIBUTIONS EP, MG and PJC designed study, and wrote the manuscript. EP designed experiments, performed experiments, analyzed the sequencing data, performed and reviewed bioinformatic and statistical analysis. IR performed sample preparation, validation experiments and evaluation of the sequencing data. YL performed bioinformatic and statististical analysis and wrote the manuscript. DW, LA, IM, and PVL performed statistical analysis. NP, IT, FVD, AMF performed experiments. GG, SLC, JM, JH, AM, KR, SNZ, MR, LS, DRJ, APB, JG and JWT support variant calling algorithms and sequencing analysis platforms. LM, SO, performed sample preparation and experiments. JZ, HK, GC, AB provided and prepared samples and experimental materials. All authors reviewed the manuscript during its preparation.
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Snippet	Peter Campbell, Mel Greaves and colleagues use exome and whole-genome sequencing to characterize somatic mutations in childhood acute lymphoblastic leukemias... The ETV6-RUNX1 fusion gene, found in 25% of childhood acute lymphoblastic leukemia (ALL) cases, is acquired in utero but requires additional somatic mutations... The ETV6-RUNX1 fusion gene, found in 25% of childhood acute lymphoblastic leukemia (ALL), is acquired in utero but requires additional somatic mutations for...
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SubjectTerms	45/23 45/62 631/208/514/1948 692/699/1541/1990/283/2125 Acute lymphocytic leukemia Agriculture Animal Genetics and Genomics Base Sequence Basic Helix-Loop-Helix Transcription Factors - genetics Bioinformatics Biomedicine Cancer Cancer Research Cell differentiation Core Binding Factor Alpha 2 Subunit - genetics Deoxyribonucleic acid DNA DNA Copy Number Variations - genetics Experiments Gene Expression Regulation, Neoplastic - genetics Gene Function Gene Library Gene Rearrangement - genetics Genes Genes, Tumor Suppressor Genetic aspects Genetic recombination Genetic Variation Genomes Homeodomain Proteins - genetics Human Genetics Humans Leukemia Methods Molecular Sequence Data Mutation Oncogene Proteins, Fusion - genetics Precursor B-Cell Lymphoblastic Leukemia-Lymphoma - genetics Recombination, Genetic - genetics Repressor Proteins Risk factors Sequence Analysis, DNA Sequence Deletion - genetics Studies Transcription Factors - genetics Twins V(D)J Recombination - genetics
Title	RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia
URI	https://link.springer.com/article/10.1038/ng.2874 https://www.ncbi.nlm.nih.gov/pubmed/24413735 https://www.proquest.com/docview/1503088816 https://search.proquest.com/docview/1554953270 https://pubmed.ncbi.nlm.nih.gov/PMC3960636
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