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Lysenkova Wiklander M, Arvidsson G, Bunikis I, Lundmark A, Raine A, Marincevic-Zuniga Y, Gezelius H, Bremer A, Feuk L, Ameur A, Nordlund J. A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing. Life Sci Alliance 2024; 7:e202302481. [PMID: 38777370 PMCID: PMC11111970 DOI: 10.26508/lsa.202302481] [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: 11/14/2023] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
The B-cell acute lymphoblastic leukemia (ALL) cell line REH, with the t(12;21) ETV6::RUNX1 translocation, is known to have a complex karyotype defined by a series of large-scale chromosomal rearrangements. Taken from a 15-yr-old at relapse, the cell line offers a practical model for the study of pediatric B-ALL. In recent years, short- and long-read DNA and RNA sequencing have emerged as a complement to karyotyping techniques in the resolution of structural variants in an oncological context. Here, we explore the integration of long-read PacBio and Oxford Nanopore whole-genome sequencing, IsoSeq RNA sequencing, and short-read Illumina sequencing to create a detailed genomic and transcriptomic characterization of the REH cell line. Whole-genome sequencing clarified the molecular traits of disrupted ALL-associated genes including CDKN2A, PAX5, BTG1, VPREB1, and TBL1XR1, as well as the glucocorticoid receptor NR3C1 Meanwhile, transcriptome sequencing identified seven fusion genes within the genomic breakpoints. Together, our extensive whole-genome investigation makes high-quality open-source data available to the leukemia genomics community.
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Affiliation(s)
- Mariya Lysenkova Wiklander
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Gustav Arvidsson
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Anders Lundmark
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Amanda Raine
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Yanara Marincevic-Zuniga
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Henrik Gezelius
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Anna Bremer
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/01apvbh93 Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Lars Feuk
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Adam Ameur
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
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Edsjö A, Gisselsson D, Staaf J, Holmquist L, Fioretos T, Cavelier L, Rosenquist R. Current and emerging sequencing-based tools for precision cancer medicine. Mol Aspects Med 2024; 96:101250. [PMID: 38330674 DOI: 10.1016/j.mam.2024.101250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024]
Abstract
Current precision cancer medicine is dependent on the analyses of a plethora of clinically relevant genomic aberrations. During the last decade, next-generation sequencing (NGS) has gradually replaced most other methods for precision cancer diagnostics, spanning from targeted tumor-informed assays and gene panel sequencing to global whole-genome and whole-transcriptome sequencing analyses. The shift has been impelled by a clinical need to assess an increasing number of genomic alterations with diagnostic, prognostic and predictive impact, including more complex biomarkers (e.g. microsatellite instability, MSI, and homologous recombination deficiency, HRD), driven by the parallel development of novel targeted therapies and enabled by the rapid reduction in sequencing costs. This review focuses on these sequencing-based methods, puts their emergence in a historic perspective, highlights their clinical utility in diagnostics and decision-making in pediatric and adult cancer, as well as raises challenges for their clinical implementation. Finally, the importance of applying sensitive tools for longitudinal monitoring of treatment response and detection of measurable residual disease, as well as future avenues in the rapidly evolving field of sequencing-based methods are discussed.
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Affiliation(s)
- Anders Edsjö
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden; Division of Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden.
| | - David Gisselsson
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden; Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Johan Staaf
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, Lund, Sweden
| | - Louise Holmquist
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Thoas Fioretos
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden; Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Lucia Cavelier
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden; Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
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Chen F, Zhang Y, Chandrashekar DS, Varambally S, Creighton CJ. Global impact of somatic structural variation on the cancer proteome. Nat Commun 2023; 14:5637. [PMID: 37704602 PMCID: PMC10499989 DOI: 10.1038/s41467-023-41374-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/01/2023] [Indexed: 09/15/2023] Open
Abstract
Both proteome and transcriptome data can help assess the relevance of non-coding somatic mutations in cancer. Here, we combine mass spectrometry-based proteomics data with whole genome sequencing data across 1307 human tumors spanning various tissues to determine the extent somatic structural variant (SV) breakpoint patterns impact protein expression of nearby genes. We find that about 25% of the hundreds of genes with SV-associated cis-regulatory alterations at the mRNA level are similarly associated at the protein level. SVs associated with enhancer hijacking, retrotransposon translocation, altered DNA methylation, or fusion transcripts are implicated in protein over-expression. SVs combined with altered protein levels considerably extend the numbers of patients with tumors somatically altered for critical pathways. We catalog both SV breakpoint patterns involving patient survival and genes with nearby SV breakpoints associated with increased cell dependency in cancer cell lines. Pan-cancer proteogenomics identifies targetable non-coding alterations, by virtue of the associated deregulated genes.
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Affiliation(s)
- Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA
| | - Darshan S Chandrashekar
- Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
- Genomic Diagnostics and Bioinformatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Sooryanarayana Varambally
- Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
- The Informatics Institute, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
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Robbe P, Schuh A. Genomic Stratification of Hematological Malignancies. Hemasphere 2023; 7:e902. [PMID: 37251914 PMCID: PMC10219718 DOI: 10.1097/hs9.0000000000000902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023] Open
Affiliation(s)
- Pauline Robbe
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Anna Schuh
- Department of Oncology, University of Oxford, United Kingdom
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Cuppen E, Elemento O, Rosenquist R, Nikic S, IJzerman M, Zaleski ID, Frederix G, Levin LÅ, Mullighan CG, Buettner R, Pugh TJ, Grimmond S, Caldas C, Andre F, Custers I, Campo E, van Snellenberg H, Schuh A, Nakagawa H, von Kalle C, Haferlach T, Fröhling S, Jobanputra V. Implementation of Whole-Genome and Transcriptome Sequencing Into Clinical Cancer Care. JCO Precis Oncol 2022; 6:e2200245. [PMID: 36480778 PMCID: PMC10166391 DOI: 10.1200/po.22.00245] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/30/2022] [Accepted: 09/21/2022] [Indexed: 12/13/2022] Open
Abstract
PURPOSE The combination of whole-genome and transcriptome sequencing (WGTS) is expected to transform diagnosis and treatment for patients with cancer. WGTS is a comprehensive precision diagnostic test that is starting to replace the standard of care for oncology molecular testing in health care systems around the world; however, the implementation and widescale adoption of this best-in-class testing is lacking. METHODS Here, we address the barriers in integrating WGTS for cancer diagnostics and treatment selection and answer questions regarding utility in different cancer types, cost-effectiveness and affordability, and other practical considerations for WGTS implementation. RESULTS We review the current studies implementing WGTS in health care systems and provide a synopsis of the clinical evidence and insights into practical considerations for WGTS implementation. We reflect on regulatory, costs, reimbursement, and incidental findings aspects of this test. CONCLUSION WGTS is an appropriate comprehensive clinical test for many tumor types and can replace multiple, cascade testing approaches currently performed. Decreasing sequencing cost, increasing number of clinically relevant aberrations and discovery of more complex biomarkers of treatment response, should pave the way for health care systems and laboratories in implementing WGTS into clinical practice, to transform diagnosis and treatment for patients with cancer.
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Affiliation(s)
- Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, the Netherlands
- Center for Molecular Medicine and Oncode Institute, University Medical Center, Utrecht, the Netherlands
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
| | - Svetlana Nikic
- Illumina Productos de España, S.L.U., Plaza Pablo Ruiz Picasso, Madrid, Spain
| | - Maarten IJzerman
- Erasmus School of Health Policy & Management, Erasmus University, Rotterdam, the Netherlands
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Isabelle Durand Zaleski
- Université de Paris, CRESS, INSERM, INRA, URCEco, AP-HP, Hôpital de l'Hôtel Dieu, Paris, France
| | - Geert Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Center, Utrecht, the Netherlands
| | - Lars-Åke Levin
- Department of Health, Medicine and Caring Sciences (HMV), Linköping University, Linköping, Sweden
| | | | | | - Trevor J. Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sean Grimmond
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | | | | | - Elias Campo
- Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red, Cáncer (CIBERONC), Madrid, Spain
- Hematopathology Unit, Hospital Clínic of Barcelona, Barcelona, Spain
- University of Barcelona, Barcelona, Spain
| | | | - Anna Schuh
- University of Oxford, Oxford, United Kingdom
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Christof von Kalle
- Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Clinical Study Center, Berlin, Germany
| | | | - Stefan Fröhling
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Vaidehi Jobanputra
- New York Genome Center; Department of Pathology, Columbia University Irving Medical Center, New York, NY
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Rosenquist R, Fröhling S, Stamatopoulos K. Precision Medicine in Cancer - A Paradigm Shift. Semin Cancer Biol 2022; 84:1-2. [PMID: 35597437 DOI: 10.1016/j.semcancer.2022.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Solna, Sweden.
| | - Stefan Fröhling
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kostas Stamatopoulos
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
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Berglund E, Barbany G, Orsmark-Pietras C, Fogelstrand L, Abrahamsson J, Golovleva I, Hallböök H, Höglund M, Lazarevic V, Levin LÅ, Nordlund J, Norèn-Nyström U, Palle J, Thangavelu T, Palmqvist L, Wirta V, Cavelier L, Fioretos T, Rosenquist R. A Study Protocol for Validation and Implementation of Whole-Genome and -Transcriptome Sequencing as a Comprehensive Precision Diagnostic Test in Acute Leukemias. Front Med (Lausanne) 2022; 9:842507. [PMID: 35402448 PMCID: PMC8987911 DOI: 10.3389/fmed.2022.842507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/17/2022] [Indexed: 12/11/2022] Open
Abstract
Background Whole-genome sequencing (WGS) and whole-transcriptome sequencing (WTS), with the ability to provide comprehensive genomic information, have become the focal point of research interest as novel techniques that can support precision diagnostics in routine clinical care of patients with various cancer types, including hematological malignancies. This national multi-center study, led by Genomic Medicine Sweden, aims to evaluate whether combined application of WGS and WTS (WGTS) is technically feasible and can be implemented as an efficient diagnostic tool in patients with acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). In addition to clinical impact assessment, a health-economic evaluation of such strategy will be performed. Methods and Analysis The study comprises four phases (i.e., retrospective, prospective, real-time validation, and follow-up) including approximately 700 adult and pediatric Swedish AML and ALL patients. Results of WGS for tumor (90×) and normal/germline (30×) samples as well as WTS for tumors only will be compared to current standard of care diagnostics. Primary study endpoints are diagnostic efficiency and improved diagnostic yield. Secondary endpoints are technical and clinical feasibility for routine implementation, clinical utility, and health-economic impact. Discussion Data from this national multi-center study will be used to evaluate clinical performance of the integrated WGTS diagnostic workflow compared with standard of care. The study will also elucidate clinical and health-economic impacts of a combined WGTS strategy when implemented in routine clinical care. Clinical Trial Registration [https://doi.org/10.1186/ISRCTN66987142], identifier [ISRCTN66987142].
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Affiliation(s)
- Eva Berglund
- Department of Immunology, Genetics and Pathology, Clinical Genomics Uppsala, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gisela Barbany
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
| | - Christina Orsmark-Pietras
- Department of Clinical Genetics and Pathology, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Linda Fogelstrand
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Clinical Genomics Gothenburg, Science for Life Laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Jonas Abrahamsson
- Clinical Sciences, Queen Silvias Childrens Hospital, Gothenburg, Sweden
| | - Irina Golovleva
- Department of Medical Biosciences, University of Umeå, Umeå, Sweden
| | - Helene Hallböök
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Martin Höglund
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Vladimir Lazarevic
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Lars-Åke Levin
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Josefine Palle
- Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Tharshini Thangavelu
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
| | - Lars Palmqvist
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Clinical Genomics Gothenburg, Science for Life Laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Valtteri Wirta
- Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Stockholm, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Lucia Cavelier
- Department of Immunology, Genetics and Pathology, Clinical Genomics Uppsala, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Thoas Fioretos
- Department of Clinical Genetics and Pathology, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
- *Correspondence: Richard Rosenquist,
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Iacobucci I, Kimura S, Mullighan CG. Biologic and Therapeutic Implications of Genomic Alterations in Acute Lymphoblastic Leukemia. J Clin Med 2021; 10:3792. [PMID: 34501239 PMCID: PMC8432032 DOI: 10.3390/jcm10173792] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/13/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most successful paradigm of how risk-adapted therapy and detailed understanding of the genetic alterations driving leukemogenesis and therapeutic response may dramatically improve treatment outcomes, with cure rates now exceeding 90% in children. However, ALL still represents a leading cause of cancer-related death in the young, and the outcome for older adolescents and young adults with ALL remains poor. In the past decade, next generation sequencing has enabled critical advances in our understanding of leukemogenesis. These include the identification of risk-associated ALL subtypes (e.g., those with rearrangements of MEF2D, DUX4, NUTM1, ZNF384 and BCL11B; the PAX5 P80R and IKZF1 N159Y mutations; and genomic phenocopies such as Ph-like ALL) and the genomic basis of disease evolution. These advances have been complemented by the development of novel therapeutic approaches, including those that are of mutation-specific, such as tyrosine kinase inhibitors, and those that are mutation-agnostic, including antibody and cellular immunotherapies, and protein degradation strategies such as proteolysis-targeting chimeras. Herein, we review the genetic taxonomy of ALL with a focus on clinical implications and the implementation of genomic diagnostic approaches.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Pathology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA;
| | - Shunsuke Kimura
- Department of Pathology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA;
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA;
- Comprehensive Cancer Center, Hematological Malignancies Program, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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