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Hultquist H, Rodriguez A, Ferreira JE, Placek A, Miller KP, Wood BL, Bhojwani D, Kapoor N, Raca G, Gaynon P, Kovach AE. Development of second genetically distinct T-lymphoblastic leukemia in a pediatric patient. Pediatr Blood Cancer 2024; 71:e31050. [PMID: 38736199 PMCID: PMC11208117 DOI: 10.1002/pbc.31050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 05/14/2024]
Affiliation(s)
- Haley Hultquist
- Department of Pediatrics, Hematology/Oncology, Children's Hospital Los Angeles, Los Angeles, California, USA
- University of Illinois College of Medicine, Chicago, Illinois, USA
| | - Alyssa Rodriguez
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
- University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Juanita E Ferreira
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Alexandra Placek
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
- Pathology, Queen's Medical Center, Honolulu, Hawaii, USA
| | - Karin P Miller
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Brent L Wood
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Deepa Bhojwani
- Department of Pediatrics, Hematology/Oncology, Children's Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Neena Kapoor
- Department of Pediatrics, Hematology/Oncology, Children's Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Paul Gaynon
- Department of Pediatrics, Hematology/Oncology, Children's Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Alexandra E Kovach
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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3
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Pölönen P, Di Giacomo D, Seffernick AE, Elsayed A, Kimura S, Benini F, Montefiori LE, Wood BL, Xu J, Chen C, Cheng Z, Newman H, Myers J, Iacobucci I, Li E, Sussman J, Hedges D, Hui Y, Diorio C, Uppuluri L, Frank D, Fan Y, Chang Y, Meshinchi S, Ries R, Shraim R, Li A, Bernt KM, Devidas M, Winter SS, Dunsmore KP, Inaba H, Carroll WL, Ramirez NC, Phillips AH, Kriwacki RW, Yang JJ, Vincent TL, Zhao Y, Ghate PS, Wang J, Reilly C, Zhou X, Sanders MA, Takita J, Kato M, Takasugi N, Chang BH, Press RD, Loh M, Rampersaud E, Raetz E, Hunger SP, Tan K, Chang TC, Wu G, Pounds SB, Mullighan CG, Teachey DT. The genomic basis of childhood T-lineage acute lymphoblastic leukaemia. Nature 2024; 632:1082-1091. [PMID: 39143224 PMCID: PMC11611067 DOI: 10.1038/s41586-024-07807-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 07/09/2024] [Indexed: 08/16/2024]
Abstract
T-lineage acute lymphoblastic leukaemia (T-ALL) is a high-risk tumour1 that has eluded comprehensive genomic characterization, which is partly due to the high frequency of noncoding genomic alterations that result in oncogene deregulation2,3. Here we report an integrated analysis of genome and transcriptome sequencing of tumour and remission samples from more than 1,300 uniformly treated children with T-ALL, coupled with epigenomic and single-cell analyses of malignant and normal T cell precursors. This approach identified 15 subtypes with distinct genomic drivers, gene expression patterns, developmental states and outcomes. Analyses of chromatin topology revealed multiple mechanisms of enhancer deregulation that involve enhancers and genes in a subtype-specific manner, thereby demonstrating widespread involvement of the noncoding genome. We show that the immunophenotypically described, high-risk entity of early T cell precursor ALL is superseded by a broader category of 'early T cell precursor-like' leukaemia. This category has a variable immunophenotype and diverse genomic alterations of a core set of genes that encode regulators of hematopoietic stem cell development. Using multivariable outcome models, we show that genetic subtypes, driver and concomitant genetic alterations independently predict treatment failure and survival. These findings provide a roadmap for the classification, risk stratification and mechanistic understanding of this disease.
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Affiliation(s)
- Petri Pölönen
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Danika Di Giacomo
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | | | - Abdelrahman Elsayed
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Shunsuke Kimura
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Francesca Benini
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Rome, Italy
- Department of Pediatric Hematology and Oncology, Bambino Gesù Children's Research Hospital, Rome, Italy
| | | | - Brent L Wood
- Children's Hospital Los Angeles, Laboratory Medicine, Los Angeles, CA, USA
| | - Jason Xu
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Changya Chen
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Zhongshan Cheng
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Haley Newman
- Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jason Myers
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ilaria Iacobucci
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Elizabeth Li
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jonathan Sussman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dale Hedges
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Yawei Hui
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Caroline Diorio
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lahari Uppuluri
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - David Frank
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Yunchao Chang
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Soheil Meshinchi
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA
| | - Rhonda Ries
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA
| | - Rawan Shraim
- Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alexander Li
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kathrin M Bernt
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Meenakshi Devidas
- Global Pediatric Medicine, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Stuart S Winter
- Research Institute and Cancer and Blood Disorders Program, Children's Minnesota, Minneapolis, MN, USA
| | - Kimberly P Dunsmore
- Division of Oncology, University of Virginia Children's Hospital, Charlottesville, VA, USA
| | - Hiroto Inaba
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - William L Carroll
- Division of Pediatric Hematology Oncology, Department of Pediatrics, NYU Langone Health, New York, NY, USA
- Department of Pediatrics and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Nilsa C Ramirez
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Aaron H Phillips
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Tiffaney L Vincent
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yaqi Zhao
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Pankaj S Ghate
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jian Wang
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Colleen Reilly
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Xin Zhou
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Mathijs A Sanders
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine Kyoto University, Kyoto, Japan
| | - Motohiro Kato
- Department of Pediatrics, Tokyo University, Tokyo, Japan
| | - Nao Takasugi
- Department of Pediatrics, Tokyo University, Tokyo, Japan
| | - Bill H Chang
- Department of Pediatrics, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Richard D Press
- Department of Pathology, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Mignon Loh
- Department of Pediatrics and the Ben Towne Center for Childhood Cancer Research, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - Evadnie Rampersaud
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Elizabeth Raetz
- Division of Pediatric Hematology Oncology, Department of Pediatrics, NYU Langone Health, New York, NY, USA
- Department of Pediatrics and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Stephen P Hunger
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kai Tan
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Single Cell Biology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Stanley B Pounds
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles G Mullighan
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - David T Teachey
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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