1
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He J, Munir F, Catueno S, Connors JS, Gibson A, Robusto L, McCall D, Nunez C, Roth M, Tewari P, Garces S, Cuglievan B, Garcia MB. Biological Markers of High-Risk Childhood Acute Lymphoblastic Leukemia. Cancers (Basel) 2024; 16:858. [PMID: 38473221 DOI: 10.3390/cancers16050858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/14/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
Childhood acute lymphoblastic leukemia (ALL) has witnessed substantial improvements in prognosis; however, a subset of patients classified as high-risk continues to face higher rates of relapse and increased mortality. While the National Cancer Institute (NCI) criteria have traditionally guided risk stratification based on initial clinical information, recent advances highlight the pivotal role of biological markers in shaping the prognosis of childhood ALL. This review delves into the emerging understanding of high-risk childhood ALL, focusing on molecular, cytogenetic, and immunophenotypic markers. These markers not only contribute to unraveling the underlying mechanisms of the disease, but also shed light on specific clinical patterns that dictate prognosis. The paradigm shift in treatment strategies, exemplified by the success of tyrosine kinase inhibitors in Philadelphia chromosome-positive leukemia, underscores the importance of recognizing and targeting precise risk factors. Through a comprehensive exploration of high-risk childhood ALL characteristics, this review aims to enhance our comprehension of the disease, offering insights into its molecular landscape and clinical intricacies in the hope of contributing to future targeted and tailored therapies.
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Affiliation(s)
- Jiasen He
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Faryal Munir
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Samanta Catueno
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeremy S Connors
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Amber Gibson
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lindsay Robusto
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David McCall
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cesar Nunez
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael Roth
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Priti Tewari
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sofia Garces
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Branko Cuglievan
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Miriam B Garcia
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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2
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Trinquand A, Betts DR, Harte S, Sills A, Rooney S, Barrett N, Storey L, Malone A, O'Marcaigh A, Smith OP. Adapted risk stratification and intensive chemotherapy abrogate the poor prognosis of pediatric B acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21 (iAMP21): a National cohort analysis. Leuk Lymphoma 2024; 65:279-282. [PMID: 37909291 DOI: 10.1080/10428194.2023.2276061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/23/2023] [Indexed: 11/03/2023]
Affiliation(s)
- Amélie Trinquand
- National Children's Cancer Service, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - David R Betts
- Department of Clinical Genetics, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Shauna Harte
- National Children's Cancer Service, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Aoife Sills
- National Children's Cancer Service, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Sean Rooney
- Haematology Laboratory, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Neil Barrett
- National Children's Cancer Service, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Lorna Storey
- National Children's Cancer Service, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Andrea Malone
- National Children's Cancer Service, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Aengus O'Marcaigh
- National Children's Cancer Service, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Owen P Smith
- National Children's Cancer Service, Children's Health Ireland at Crumlin, Dublin, Ireland
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3
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Hormann FM, Mooij EJ, van de Mheen M, Beverloo HB, den Boer ML, Boer JM. The impact of an additional copy of chromosome 21 in B-cell precursor acute lymphoblastic leukemia. Genes Chromosomes Cancer 2024; 63:e23217. [PMID: 38087879 DOI: 10.1002/gcc.23217] [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: 09/12/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 01/04/2024] Open
Abstract
A common finding in pediatric B-cell precursor acute lymphoblastic leukemia (BCPALL) is that chromosome 21 is never lost and an extra chromosome 21 is often gained. This implies an important role for chromosome 21 in the pathobiology of BCPALL, emphasized by the increased risk of BCPALL in children with Down syndrome. However, model systems of chromosome 21 gain are lacking. We therefore developed a BCPALL cell line (Nalm-6, DUX4-rearranged) with an additional chromosome 21 by means of microcell-mediated chromosome transfer. FISH, PCR, multiplex ligation-dependent probe amplification, and whole exome sequencing showed that an additional chromosome 21 was successfully transferred to the recipient cells. Transcription of some but not all genes on chromosome 21 was increased, indicating tight transcriptional regulation. Nalm-6 cells with an additional chromosome 21 proliferated slightly slower compared with parental Nalm-6 and sensitivity to induction chemotherapeutics was mildly increased. The extra copy of chromosome 21 did not confer sensitivity to targeted signaling inhibitors. In conclusion, a BCPALL cell line with an additional human chromosome 21 was developed, validated, and subjected to functional studies, which showed a minor but potentially relevant effect in vitro. This cell line offers the possibility to study further the role of chromosome 21 in ALL.
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Affiliation(s)
- Femke M Hormann
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Eva J Mooij
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - H Berna Beverloo
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Monique L den Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Judith M Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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4
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Beder T, Hansen BT, Hartmann AM, Zimmermann J, Amelunxen E, Wolgast N, Walter W, Zaliova M, Antić Ž, Chouvarine P, Bartsch L, Barz MJ, Bultmann M, Horns J, Bendig S, Kässens J, Kaleta C, Cario G, Schrappe M, Neumann M, Gökbuget N, Bergmann AK, Trka J, Haferlach C, Brüggemann M, Baldus CD, Bastian L. The Gene Expression Classifier ALLCatchR Identifies B-cell Precursor ALL Subtypes and Underlying Developmental Trajectories Across Age. Hemasphere 2023; 7:e939. [PMID: 37645423 PMCID: PMC10461941 DOI: 10.1097/hs9.0000000000000939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/26/2023] [Indexed: 08/31/2023] Open
Abstract
Current classifications (World Health Organization-HAEM5/ICC) define up to 26 molecular B-cell precursor acute lymphoblastic leukemia (BCP-ALL) disease subtypes by genomic driver aberrations and corresponding gene expression signatures. Identification of driver aberrations by transcriptome sequencing (RNA-Seq) is well established, while systematic approaches for gene expression analysis are less advanced. Therefore, we developed ALLCatchR, a machine learning-based classifier using RNA-Seq gene expression data to allocate BCP-ALL samples to all 21 gene expression-defined molecular subtypes. Trained on n = 1869 transcriptome profiles with established subtype definitions (4 cohorts; 55% pediatric / 45% adult), ALLCatchR allowed subtype allocation in 3 independent hold-out cohorts (n = 1018; 75% pediatric / 25% adult) with 95.7% accuracy (averaged sensitivity across subtypes: 91.1% / specificity: 99.8%). High-confidence predictions were achieved in 83.7% of samples with 98.9% accuracy. Only 1.2% of samples remained unclassified. ALLCatchR outperformed existing tools and identified novel driver candidates in previously unassigned samples. Additional modules provided predictions of samples blast counts, patient's sex, and immunophenotype, allowing the imputation in cases where these information are missing. We established a novel RNA-Seq reference of human B-lymphopoiesis using 7 FACS-sorted progenitor stages from healthy bone marrow donors. Implementation in ALLCatchR enabled projection of BCP-ALL samples to this trajectory. This identified shared proximity patterns of BCP-ALL subtypes to normal lymphopoiesis stages, extending immunophenotypic classifications with a novel framework for developmental comparisons of BCP-ALL. ALLCatchR enables RNA-Seq routine application for BCP-ALL diagnostics with systematic gene expression analysis for accurate subtype allocation and novel insights into underlying developmental trajectories.
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Affiliation(s)
- Thomas Beder
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Björn-Thore Hansen
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Alina M Hartmann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | - Johannes Zimmermann
- Institute of Experimental Medicine, Research Group Medical Systems Biology, Christian-Albrechts-University Kiel, Germany
| | - Eric Amelunxen
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Nadine Wolgast
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | | | - Marketa Zaliova
- Childhood Leukaemia Investigation Prague, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Željko Antić
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Philippe Chouvarine
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Lorenz Bartsch
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Malwine J Barz
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | - Miriam Bultmann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Johanna Horns
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Sonja Bendig
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | - Jan Kässens
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Christoph Kaleta
- Institute of Experimental Medicine, Research Group Medical Systems Biology, Christian-Albrechts-University Kiel, Germany
| | - Gunnar Cario
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
- Department of Pediatrics, University Hospital Schleswig-Holstein Kiel, Germany
| | - Martin Schrappe
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
- Department of Pediatrics, University Hospital Schleswig-Holstein Kiel, Germany
| | - Martin Neumann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | - Nicola Gökbuget
- Department of Medicine II, Hematology/Oncology, Goethe University Hospital, Frankfurt/M., Germany
| | | | - Jan Trka
- Childhood Leukaemia Investigation Prague, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | | | - Monika Brüggemann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | - Claudia D Baldus
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | - Lorenz Bastian
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
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5
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Gao Q, Ryan SL, Iacobucci I, Ghate PS, Cranston RE, Schwab C, Elsayed AH, Shi L, Pounds S, Lei S, Baviskar P, Pei D, Cheng C, Bashton M, Sinclair P, Bentley DR, Ross MT, Kingsbury Z, James T, Roberts KG, Devidas M, Fan Y, Chen W, Chang TC, Wu G, Carroll A, Heerema N, Valentine V, Valentine M, Yang W, Yang JJ, Moorman AV, Harrison CJ, Mullighan CG. The genomic landscape of acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21. Blood 2023; 142:711-723. [PMID: 37216686 PMCID: PMC10460677 DOI: 10.1182/blood.2022019094] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 04/06/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Intrachromosomal amplification of chromosome 21 defines a subtype of high-risk childhood acute lymphoblastic leukemia (iAMP21-ALL) characterized by copy number changes and complex rearrangements of chromosome 21. The genomic basis of iAMP21-ALL and the pathogenic role of the region of amplification of chromosome 21 to leukemogenesis remains incompletely understood. In this study, using integrated whole genome and transcriptome sequencing of 124 patients with iAMP21-ALL, including rare cases arising in the context of constitutional chromosomal aberrations, we identified subgroups of iAMP21-ALL based on the patterns of copy number alteration and structural variation. This large data set enabled formal delineation of a 7.8 Mb common region of amplification harboring 71 genes, 43 of which were differentially expressed compared with non-iAMP21-ALL ones, including multiple genes implicated in the pathogenesis of acute leukemia (CHAF1B, DYRK1A, ERG, HMGN1, and RUNX1). Using multimodal single-cell genomic profiling, including single-cell whole genome sequencing of 2 cases, we documented clonal heterogeneity and genomic evolution, demonstrating that the acquisition of the iAMP21 chromosome is an early event that may undergo progressive amplification during disease ontogeny. We show that UV-mutational signatures and high mutation load are characteristic secondary genetic features. Although the genomic alterations of chromosome 21 are variable, these integrated genomic analyses and demonstration of an extended common minimal region of amplification broaden the definition of iAMP21-ALL for more precise diagnosis using cytogenetic or genomic methods to inform clinical management.
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Affiliation(s)
- Qingsong Gao
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Sarra L Ryan
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, United Kingdom
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Pankaj S Ghate
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Ruth E Cranston
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, United Kingdom
| | - Claire Schwab
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, United Kingdom
| | - Abdelrahman H Elsayed
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Lei Shi
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Shaohua Lei
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
- Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, Memphis, TN
| | | | - Deqing Pei
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Matthew Bashton
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, United Kingdom
| | - Paul Sinclair
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, United Kingdom
| | - David R Bentley
- Illumina Cambridge, Ltd, Illumina Centre, Great Abingdon, Cambridge, United Kingdom
| | - Mark T Ross
- Illumina Cambridge, Ltd, Illumina Centre, Great Abingdon, Cambridge, United Kingdom
| | - Zoya Kingsbury
- Illumina Cambridge, Ltd, Illumina Centre, Great Abingdon, Cambridge, United Kingdom
| | - Terena James
- Illumina Cambridge, Ltd, Illumina Centre, Great Abingdon, Cambridge, United Kingdom
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
- Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, Memphis, TN
| | - Meenakshi Devidas
- Department of Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN
| | - Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN
| | - Andrew Carroll
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Nyla Heerema
- Department of Pathology, The Ohio State University, Columbus, OH
| | - Virginia Valentine
- Cytogenetics Shared Resource, St. Jude Children's Research Hospital, Memphis, TN
| | - Marcus Valentine
- Cytogenetics Shared Resource, St. Jude Children's Research Hospital, Memphis, TN
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Anthony V Moorman
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, United Kingdom
| | - Christine J Harrison
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, United Kingdom
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
- Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, Memphis, TN
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6
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Ryan SL, Peden JF, Kingsbury Z, Schwab CJ, James T, Polonen P, Mijuskovic M, Becq J, Yim R, Cranston RE, Hedges DJ, Roberts KG, Mullighan CG, Vora A, Russell LJ, Bain R, Moorman AV, Bentley DR, Harrison CJ, Ross MT. Whole genome sequencing provides comprehensive genetic testing in childhood B-cell acute lymphoblastic leukaemia. Leukemia 2023; 37:518-528. [PMID: 36658389 PMCID: PMC9991920 DOI: 10.1038/s41375-022-01806-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 01/20/2023]
Abstract
Childhood B-cell acute lymphoblastic leukaemia (B-ALL) is characterised by recurrent genetic abnormalities that drive risk-directed treatment strategies. Using current techniques, accurate detection of such aberrations can be challenging, due to the rapidly expanding list of key genetic abnormalities. Whole genome sequencing (WGS) has the potential to improve genetic testing, but requires comprehensive validation. We performed WGS on 210 childhood B-ALL samples annotated with clinical and genetic data. We devised a molecular classification system to subtype these patients based on identification of key genetic changes in tumour-normal and tumour-only analyses. This approach detected 294 subtype-defining genetic abnormalities in 96% (202/210) patients. Novel genetic variants, including fusions involving genes in the MAP kinase pathway, were identified. WGS results were concordant with standard-of-care methods and whole transcriptome sequencing (WTS). We expanded the catalogue of genetic profiles that reliably classify PAX5alt and ETV6::RUNX1-like subtypes. Our novel bioinformatic pipeline improved detection of DUX4 rearrangements (DUX4-r): a good-risk B-ALL subtype with high survival rates. Overall, we have validated that WGS provides a standalone, reliable genetic test to detect all subtype-defining genetic abnormalities in B-ALL, accurately classifying patients for the risk-directed treatment stratification, while simultaneously performing as a research tool to identify novel disease biomarkers.
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Affiliation(s)
- Sarra L Ryan
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - John F Peden
- Illumina Cambridge Ltd., Granta Park, Great Abington, Cambridge, UK
| | - Zoya Kingsbury
- Illumina Cambridge Ltd., Granta Park, Great Abington, Cambridge, UK
| | - Claire J Schwab
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Terena James
- Illumina Cambridge Ltd., Granta Park, Great Abington, Cambridge, UK
| | - Petri Polonen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Jenn Becq
- Illumina Cambridge Ltd., Granta Park, Great Abington, Cambridge, UK
| | - Richard Yim
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Ruth E Cranston
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Dale J Hedges
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ajay Vora
- Department of Haematology, Great Ormond Street Hospital, London, UK
| | - Lisa J Russell
- Biosciences Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Robert Bain
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Anthony V Moorman
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - David R Bentley
- Illumina Cambridge Ltd., Granta Park, Great Abington, Cambridge, UK
| | - Christine J Harrison
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, UK.
| | - Mark T Ross
- Illumina Cambridge Ltd., Granta Park, Great Abington, Cambridge, UK.
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7
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Sinclair PB, Cranston RE, Raninga P, Cheng J, Hanna R, Hawking Z, Hair S, Ryan SL, Enshaei A, Nakjang S, Rand V, Blair HJ, Moorman AV, Heidenreich O, Harrison CJ. Disruption to the FOXO-PRDM1 axis resulting from deletions of chromosome 6 in acute lymphoblastic leukaemia. Leukemia 2023; 37:636-649. [PMID: 36670235 PMCID: PMC9991907 DOI: 10.1038/s41375-023-01816-0] [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: 08/23/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/22/2023]
Abstract
A common problem in the study of human malignancy is the elucidation of cancer driver mechanisms associated with recurrent deletion of regions containing multiple genes. Taking B-cell acute lymphoblastic leukaemia (B-ALL) and large deletions of 6q [del(6q)] as a model, we integrated analysis of functional cDNA clone tracking assays with patient genomic and transcriptomic data, to identify the transcription factors FOXO3 and PRDM1 as candidate tumour suppressor genes (TSG). Analysis of cell cycle and transcriptomic changes following overexpression of FOXO3 or PRDM1 indicated that they co-operate to promote cell cycle exit at the pre-B cell stage. FOXO1 abnormalities are absent in B-ALL, but like FOXO3, FOXO1 expression suppressed growth of TCF3::PBX1 and ETV6::RUNX1 B-ALL in-vitro. While both FOXOs induced PRDM1 and other genes contributing to late pre-B cell development, FOXO1 alone induced the key transcription factor, IRF4, and chemokine, CXCR4. CRISPR-Cas9 screening identified FOXO3 as a TSG, while FOXO1 emerged as essential for B-ALL growth. We relate this FOXO3-specific leukaemia-protective role to suppression of glycolysis based on integrated analysis of CRISPR-data and gene sets induced or suppressed by FOXO1 and FOXO3. Pan-FOXO agonist Selinexor induced the glycolysis inhibitor TXNIP and suppressed B-ALL growth at low dose (ID50 < 50 nM).
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Affiliation(s)
- Paul B Sinclair
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK.
| | - Ruth E Cranston
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Prahlad Raninga
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Joanna Cheng
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Rebecca Hanna
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Zoe Hawking
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Steven Hair
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Sarra L Ryan
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Amir Enshaei
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Sirintra Nakjang
- Bioinformatics Support Unit, Faculty of Medical Science, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Vikki Rand
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
- School of Health and Life Sciences, Teesside University, Middlesborough, UK
- National Horizons Centre, Teesside University, Darlington, UK
| | - Helen J Blair
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Anthony V Moorman
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Olaf Heidenreich
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK
- Princess Maxima Centre for Paediatric Oncology, Utrecht, The Netherlands
| | - Christine J Harrison
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-Upon-Tyne, UK.
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8
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Das Gupta D, Lohoff M. Puppet masters of B-cell progenitor acute lymphoblastic leukemia: The preB cell receptor and the interleukin 7 receptor α. Eur J Immunol 2023; 53:e2250093. [PMID: 36805963 DOI: 10.1002/eji.202250093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/02/2022] [Accepted: 01/13/2023] [Indexed: 02/23/2023]
Abstract
B-cell progenitor acute lymphoblastic leukemia (BCP-ALL) is enriched for a preB cell phenotype, hinting at a specific vulnerability of this cell stage. Two signaling pathways via the preB cell receptor (preBCR) and the interleukin 7 receptor α (IL-7Rα) chain govern the balance between differentiation and proliferation at this stage and both receptor pathways are routinely altered in human BCP-ALL. Here, we review the immunobiology of both the preBCR as well as the IL-7Rα and analyze the human BCP-ALL spectrum in the light of these signaling complexes. Finally, we present a terminology for preBCR signaling modules that distinguishes a pro-proliferative "phase-I" module from a pro-differentiative "phase-II" module. This terminology might serve as a framework to better address shared oncogenic mechanics of preB cell stage BCP-ALL.
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Affiliation(s)
- Dennis Das Gupta
- Institute for Medical Microbiology & Hospital Hygiene, Philipps University Marburg, Marburg, Germany.,Medical Department II, Hematology and Oncology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Michael Lohoff
- Institute for Medical Microbiology & Hospital Hygiene, Philipps University Marburg, Marburg, Germany
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9
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Hormann FM, Hoogkamer AQ, Boeree A, Sonneveld E, Escherich G, den Boer ML, Boer JM. Integrating copy number data of 64 iAMP21 BCP-ALL patients narrows the common region of amplification to 1.57 Mb. Front Oncol 2023; 13:1128560. [PMID: 36910655 PMCID: PMC9996016 DOI: 10.3389/fonc.2023.1128560] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
Background and purpose Intrachromosomal amplification of chromosome 21 (iAMP21) is a rare subtype of B-cell precursor acute lymphoblastic leukaemia (BCP-ALL). It is unknown how iAMP21 contributes to leukaemia. The currently known commonly amplified region is 5.1 Mb. Methods We aimed to narrow down the common region of amplification by using high resolution techniques. Array comparative genomic hybridization (aCGH) was used to determine copy number aberrations, Affymetrix U133 Plus2 expression arrays were used to determine gene expression. Genome-wide expression correlations were evaluated using Globaltest. Results We narrowed down the common region of amplification by combining copy number data from 12 iAMP21 cases with 52 cases from literature. The combined common region of amplification was 1.57 Mb, located from 36.07 to 37.64 Mb (GRCh38). This region is located telomeric from, but not including, RUNX1, which is the locus commonly used to diagnose iAMP21. This narrow region, which falls inside the Down Syndrome critical region, includes 13 genes of which the expression of eight genes was significantly upregulated compared with 143 non-iAMP21 B-other cases. Among these, transcriptional repressor RIPPLY3 (also known as DSCR6) was the highest overexpressed gene (fold change = 4.2, FDR < 0.001) and most strongly correlated (R = 0.58) with iAMP21-related genome-wide expression changes. Discussion The more precise definition of the common region of amplification could be beneficial in the diagnosis of iAMP21 based on copy number analysis from DNA sequencing or arrays as well as stimulate functional research into the role of the included genes in iAMP21 biology.
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Affiliation(s)
- Femke M Hormann
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands.,Oncode Institute, Utrecht, Netherlands.,Erasmus Medical Center (MC) - Sophia Children's Hospital, Department of Pediatric Oncology and Hematology, Rotterdam, Netherlands
| | - Alex Q Hoogkamer
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands.,Oncode Institute, Utrecht, Netherlands
| | - Aurélie Boeree
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands.,Oncode Institute, Utrecht, Netherlands
| | - Edwin Sonneveld
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands.,Dutch Childhood Oncology Group, Utrecht, Netherlands
| | - Gabriele Escherich
- Cooperative study group for childhood acute lymphoblastic leukaemia (COALL) - German Cooperative Study Group for Childhood Acute Lymphoblastic Leukemia, Hamburg, Germany.,Clinic of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Monique L den Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands.,Oncode Institute, Utrecht, Netherlands.,Erasmus Medical Center (MC) - Sophia Children's Hospital, Department of Pediatric Oncology and Hematology, Rotterdam, Netherlands.,Dutch Childhood Oncology Group, Utrecht, Netherlands
| | - Judith M Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands.,Oncode Institute, Utrecht, Netherlands
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10
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Koleilat A, Smadbeck JB, Zepeda‐Mendoza CJ, Williamson CM, Pitel BA, Golden CL, Xu X, Greipp PT, Ketterling RP, Hoppman NL, Peterson JF, Harrison CJ, Akkari YMN, Tsuchiya KD, Shago M, Baughn LB. Characterization of unusual iAMP21 B-lymphoblastic leukemia (iAMP21-ALL) from the Mayo Clinic and Children's Oncology Group. Genes Chromosomes Cancer 2022; 61:710-719. [PMID: 35771717 PMCID: PMC9549522 DOI: 10.1002/gcc.23084] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/06/2022] [Accepted: 06/27/2022] [Indexed: 01/01/2023] Open
Abstract
Acute lymphoblastic leukemia (B-ALL) with intrachromosomal amplification of chromosome 21 (iAMP21-ALL) represents a recurrent high-risk cytogenetic abnormality and accurate identification is critical for appropriate clinical management. Identification of iAMP21-ALL has historically relied on fluorescence in situ hybridization (FISH) using a RUNX1 probe. Current classification requires ≥ five copies of RUNX1 per cell and ≥ three additional copies of RUNX1 on a single abnormal iAMP21-chromosome. We sought to evaluate the performance of the RUNX1 probe in the identification of iAMP21-ALL. This study was a retrospective evaluation of iAMP21-ALL in the Mayo Clinic and Children's Oncology Group cohorts. Of 207 cases of iAMP21-ALL, 188 (91%) were classified as "typical" iAMP21-ALL, while 19 (9%) cases were classified as "unusual" iAMP21-ALL. The "unusual" iAMP21 cases did not meet the current definition of iAMP21 by FISH but were confirmed to have iAMP21 by chromosomal microarray. Half of the "unusual" iAMP21-ALL cases had less than five RUNX1 signals, while the remainder had ≥ five RUNX1 signals with some located apart from the abnormal iAMP21-chromosome. Nine percent of iAMP21-ALL cases fail to meet the FISH definition of iAMP21-ALL demonstrating that laboratories are at risk of misidentification of iAMP21-ALL when relying only on the RUNX1 FISH probe. Incorporation of chromosomal microarray testing circumvents these risks.
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Affiliation(s)
- Alaa Koleilat
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - James B. Smadbeck
- Division of Computational Biology, Department of Quantitative Health SciencesMayo ClinicRochesterMinnesotaUSA
| | | | - Cynthia M. Williamson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Beth A. Pitel
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Crystal L. Golden
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Xinjie Xu
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Patricia T. Greipp
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Rhett P. Ketterling
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Nicole L. Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Jess F. Peterson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Christine J. Harrison
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research InstituteNewcastle University Centre for CancerNewcastle‐upon‐TyneUK
| | | | - Karen D. Tsuchiya
- Department of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWAUSA
| | - Mary Shago
- Department of Paediatric Laboratory Medicine, The Hospital for Sick ChildrenUniversity of TorontoTorontoOntarioCanada
| | - Linda B. Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
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11
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Xie L, Wu S, He R, Li S, Lai X, Wang Z. Identification of epigenetic dysregulation gene markers and immune landscape in kidney renal clear cell carcinoma by comprehensive genomic analysis. Front Immunol 2022; 13:901662. [PMID: 36059531 PMCID: PMC9433776 DOI: 10.3389/fimmu.2022.901662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/28/2022] [Indexed: 12/24/2022] Open
Abstract
Kidney cancer is one the most lethal cancers of the urinary system, but current treatments are limited and its prognosis is poor. This study focused on kidney renal clear cell carcinoma (KIRC) and analyzed the relationship between epigenetic alterations and KIRC prognosis, and explored the prognostic significance of these findings in KIRC patients. Based on multi-omics data, differentially expressed histone-modified genes were identified using the R package limma package. Gene enhancers were detected from data in the FANTOM5 database. Gene promoters were screened using the R package ChIPseeker, and the Bumphunter in the R package CHAMP was applied to screen differentially methylated regions (DMR). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Gene Ontology (GO) functional enrichment analysis of genes was performed using the R package clusterProfiler. We identified 51 dysregulated epigenetic protein coding genes (epi-PCGs) from 872 epi-PCGs, and categorized three molecular subtypes (C1, C2, and C3) of KIRC samples with significantly different prognosis. Notably, among the three molecular subtypes, we found a markedly differential immune features in immune checkpoints, cytokines, immune signatures, and immune cell distribution. C2 subtype had significantly lower enrichment score of IFNγ, cytotoxic score (CYT), and angiogenesis. In addition, an 8-gene signature containing 8 epi-PCGs (ETV4, SH2B3, FATE1, GRK5, MALL, HRH2, SEMA3G, and SLC10A6) was developed for predicting KIRC prognosis. Prognosis of patients with a high 8-gene signature score was significantly worse than those with a low 8-gene signature score, which was also validated by the independent validation data. The 8-gene signature had a better performance compared with previous signatures of KIRC. Overall, this study highlighted the important role of epigenetic regulation in KIRC development, and explored prognostic epi-PCGs, which may provide a guidance for exploiting further pathological mechanisms of KIRC and for developing novel drug targets.
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Affiliation(s)
- Linli Xie
- Department of Pharmacy, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Shuang Wu
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Rong He
- Department of Pharmacy, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Sisi Li
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xiaodan Lai
- Department of Pharmacy, No. 958 Hospital of Chinese People's Liberation Army (PLA), Chongqing, China
- *Correspondence: Xiaodan Lai, ; Zhe Wang,
| | - Zhe Wang
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- *Correspondence: Xiaodan Lai, ; Zhe Wang,
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12
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Morris R, Butler L, Perkins A, Kershaw NJ, Babon JJ. The Role of LNK (SH2B3) in the Regulation of JAK-STAT Signalling in Haematopoiesis. Pharmaceuticals (Basel) 2021; 15:ph15010024. [PMID: 35056081 PMCID: PMC8781068 DOI: 10.3390/ph15010024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 01/05/2023] Open
Abstract
LNK is a member of the SH2B family of adaptor proteins and is a non-redundant regulator of cytokine signalling. Cytokines are secreted intercellular messengers that bind to specific receptors on the surface of target cells to activate the Janus Kinase-Signal Transducer and Activator of Transcription (JAK-STAT) signalling pathway. Activation of the JAK-STAT pathway leads to proliferative and often inflammatory effects, and so the amplitude and duration of signalling are tightly controlled. LNK binds phosphotyrosine residues to signalling proteins downstream of cytokines and constrains JAK-STAT signalling. Mutations in LNK have been identified in a range of haematological and inflammatory diseases due to increased signalling following the loss of LNK function. Here, we review the regulation of JAK-STAT signalling via the adaptor protein LNK and discuss the role of LNK in haematological diseases.
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Affiliation(s)
- Rhiannon Morris
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (R.M.); (N.J.K.)
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Liesl Butler
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3001, Australia; (L.B.); (A.P.)
- Alfred Health, Melbourne, VIC 3001, Australia
| | - Andrew Perkins
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3001, Australia; (L.B.); (A.P.)
- Alfred Health, Melbourne, VIC 3001, Australia
| | - Nadia J. Kershaw
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (R.M.); (N.J.K.)
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Jeffrey J. Babon
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (R.M.); (N.J.K.)
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
- Correspondence: ; Tel.: +61-3-9345-2960; Fax: +61-3-9347-0852
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13
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Capela de Matos RR, Othman M, Ferreira GM, Monteso K, de Souza MT, Rouxinol M, Melo JB, Carreira IM, Abdelhay E, Liehr T, Ribeiro RC, Silva M. Somatic homozygous loss of SH2B3, and a non-Robertsonian translocation t(15;21)(q25.3;q22.1) with NTRK3 rearrangement, in an adolescent with progenitor B-cell acute lymphoblastic leukemia with the iAMP21. Cancer Genet 2021; 262-263:16-22. [PMID: 34974289 DOI: 10.1016/j.cancergen.2021.12.003] [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: 01/26/2021] [Revised: 11/04/2021] [Accepted: 12/20/2021] [Indexed: 11/18/2022]
Abstract
Intrachromosomal amplification of chromosome 21 (iAMP21) occurs in ∼2% of B-cell acute lymphoblastic leukemia (ALL) and is considered to confer a poor prognosis. The relapse risk is associated with therapy intensity, suggesting that other somatic mutations may influence iAMP21-ALL prognosis. This abnormality is characterized by multiple copies of the RUNX1 gene in chromosome 21 and appears to arise through multiple breakage-fusion bridge cycles and chromothripsis. Rob(15;21) or a ring chromosome 21 have been associated with an increased risk for iAMP21-ALL, suggesting that constitutional genetic abnormalities may also drive leukemogenesis. Here we describe homozygous deletion of the SH2B3 gene, chromothripsis of chromosome 21, and a non-Robertsonian somatic t(15;21)(q25.3;q22.1) with NTRK3 gene rearrangement in an adolescent with iAMP21-B-ALL. Molecular cytogenetic studies detected iAMP21 with aCGH analysis revealing further genomic imbalances. The RT-qPCR analysis detected elevated expression levels of RUNX1 (68-fold) and reduced expression of CDK6 (0.057-fold). Studies with constitutive cells collected from mouth swabs showed that SH2B3 biallelic deletion was a somatic alteration occurring during clonal evolution. The identification of novel secondary genetic changes was valuable to discuss sporadic iAMP21 leukemogenic mechanisms. For the first time, we show a t(15;21)(q25.3;q22.1) with NTRK3 rearrangement in an adolescent with iAMP21-ALL.
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Affiliation(s)
- R R Capela de Matos
- Cytogenetics Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil; Post-Graduate Programme in Oncology, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil
| | - Mak Othman
- Jena University Hospital, Institute of Human Genetics, Jena, Germany
| | - G M Ferreira
- Stem Cells Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil
| | - Kca Monteso
- Cytogenetics Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil; Post-Graduate Programme in Oncology, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil
| | - M T de Souza
- Cytogenetics Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil
| | - M Rouxinol
- Lagoa Federal Hospital, Rio de Janeiro, Brazil
| | - J B Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal; Centre of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - I M Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal; Centre of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - E Abdelhay
- Stem Cells Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil; Post-Graduate Programme in Oncology, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil
| | - T Liehr
- Jena University Hospital, Institute of Human Genetics, Jena, Germany
| | - R C Ribeiro
- Departments of Oncology and Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mlm Silva
- Cytogenetics Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil; Post-Graduate Programme in Oncology, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil.
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14
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Inaba H, Pui CH. Advances in the Diagnosis and Treatment of Pediatric Acute Lymphoblastic Leukemia. J Clin Med 2021; 10:1926. [PMID: 33946897 PMCID: PMC8124693 DOI: 10.3390/jcm10091926] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/20/2021] [Accepted: 04/25/2021] [Indexed: 12/12/2022] Open
Abstract
The outcomes of pediatric acute lymphoblastic leukemia (ALL) have improved remarkably during the last five decades. Such improvements were made possible by the incorporation of new diagnostic technologies, the effective administration of conventional chemotherapeutic agents, and the provision of better supportive care. With the 5-year survival rates now exceeding 90% in high-income countries, the goal for the next decade is to improve survival further toward 100% and to minimize treatment-related adverse effects. Based on genome-wide analyses, especially RNA-sequencing analyses, ALL can be classified into more than 20 B-lineage subtypes and more than 10 T-lineage subtypes with prognostic and therapeutic implications. Response to treatment is another critical prognostic factor, and detailed analysis of minimal residual disease can detect levels as low as one ALL cell among 1 million total cells. Such detailed analysis can facilitate the rational use of molecular targeted therapy and immunotherapy, which have emerged as new treatment strategies that can replace or reduce the use of conventional chemotherapy.
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Affiliation(s)
- Hiroto Inaba
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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15
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Cai S, Lu JX, Wang YP, Shi CJ, Yuan T, Wang XP. SH2B3, Transcribed by STAT1, Promotes Glioblastoma Progression Through Transducing IL-6/gp130 Signaling to Activate STAT3 Signaling. Front Cell Dev Biol 2021; 9:606527. [PMID: 33937225 PMCID: PMC8080264 DOI: 10.3389/fcell.2021.606527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/29/2021] [Indexed: 01/05/2023] Open
Abstract
Glioblastoma (GBM) is the most common and aggressive brain tumor in adults. The aberrant activation of STAT3 commonly occurs in GBM and is a key player in GBM tumorigenesis. Yet, the aberrant activation of STAT3 signaling is not fully understood. Here, we report that SH2B adaptor protein 3 (SH2B3) is highly expressed in GBM and preferentially expressed in GBM stem cells (GSCs). Moreover, SH2B3 high expression predicts worse survival of GBM patients. Targeting SH2B3 considerably impairs GBM cell proliferation, migration, and GSCs' self-renewal in vitro as well as xenograft tumors growth in vivo. Additionally, we provide evidence suggesting that STAT1 directly binds to the promoter of SH2B3 and activates SH2B3 expression in the transcriptional level. Functionally, SH2B3 facilitates GBM progression via physically interacting with gp130 and acting as an adaptor protein to transduce IL-6/gp130/STAT3 signaling. Together, our work firstly uncovers that the STAT1/SH2B3/gp130/STAT3 signaling axis plays critical roles in promoting GBM progression and provides insight into new prognosis marker and therapeutic target in GBM.
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Affiliation(s)
| | | | | | | | | | - Xiang-peng Wang
- Department of Neurosurgery, First Affiliated Hospital of Kunming Medical University, Kunming, China
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16
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Davis L, Khoo KJ, Zhang Y, Maizels N. POLQ suppresses interhomolog recombination and loss of heterozygosity at targeted DNA breaks. Proc Natl Acad Sci U S A 2020; 117:22900-22909. [PMID: 32873648 PMCID: PMC7502765 DOI: 10.1073/pnas.2008073117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Interhomolog recombination (IHR) occurs spontaneously in somatic human cells at frequencies that are low but sufficient to ameliorate some genetic diseases caused by heterozygous mutations or autosomal dominant mutations. Here we demonstrate that DNA nicks or double-strand breaks (DSBs) targeted by CRISPR-Cas9 to both homologs can stimulate IHR and associated copy-neutral loss of heterozygosity (cnLOH) in human cells. The frequency of IHR is 10-fold lower at nicks than at DSBs, but cnLOH is evident in a greater fraction of recombinants. IHR at DSBs occurs predominantly via reciprocal end joining. At DSBs, depletion of POLQ caused a dramatic increase in IHR and in the fraction of recombinants exhibiting cnLOH, suggesting that POLQ promotes end joining in cis, which limits breaks available for recombination in trans These results define conditions that may produce cnLOH as a mutagenic signature in cancer and may, conversely, promote therapeutic correction of both compound heterozygous and dominant negative mutations associated with genetic disease.
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Affiliation(s)
- Luther Davis
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195
| | - Kevin J Khoo
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195
| | - Yinbo Zhang
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195
| | - Nancy Maizels
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195;
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195
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17
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Laurent AP, Kotecha RS, Malinge S. Gain of chromosome 21 in hematological malignancies: lessons from studying leukemia in children with Down syndrome. Leukemia 2020; 34:1984-1999. [PMID: 32433508 PMCID: PMC7387246 DOI: 10.1038/s41375-020-0854-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/22/2020] [Accepted: 04/28/2020] [Indexed: 12/31/2022]
Abstract
Structural and numerical alterations of chromosome 21 are extremely common in hematological malignancies. While the functional impact of chimeric transcripts from fused chromosome 21 genes such as TEL-AML1, AML1-ETO, or FUS-ERG have been extensively studied, the role of gain of chromosome 21 remains largely unknown. Gain of chromosome 21 is a frequently occurring aberration in several types of acute leukemia and can be found in up to 35% of cases. Children with Down syndrome (DS), who harbor constitutive trisomy 21, highlight the link between gain of chromosome 21 and leukemogenesis, with an increased risk of developing acute leukemia compared with other children. Clinical outcomes for DS-associated leukemia have improved over the years through the development of uniform treatment protocols facilitated by international cooperative groups. The genetic landscape has also recently been characterized, providing an insight into the molecular pathogenesis underlying DS-associated leukemia. These studies emphasize the key role of trisomy 21 in priming a developmental stage and cellular context susceptible to transformation, and have unveiled its cooperative function with additional genetic events that occur during leukemia progression. Here, using DS-leukemia as a paradigm, we aim to integrate our current understanding of the role of trisomy 21, of critical dosage-sensitive chromosome 21 genes, and of associated mechanisms underlying the development of hematological malignancies. This review will pave the way for future investigations on the broad impact of gain of chromosome 21 in hematological cancer, with a view to discovering new vulnerabilities and develop novel targeted therapies to improve long term outcomes for DS and non-DS patients.
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Affiliation(s)
- Anouchka P Laurent
- INSERM U1170, Gustave Roussy Institute, Université Paris Saclay, Villejuif, France
- Université Paris Diderot, Paris, France
| | - Rishi S Kotecha
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Western Australia, Australia
- Department of Clinical Haematology, Oncology and Bone Marrow Transplantation, Perth Children's Hospital, Perth, Western Australia, Australia
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Sébastien Malinge
- INSERM U1170, Gustave Roussy Institute, Université Paris Saclay, Villejuif, France.
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia.
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18
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Kou F, Wu L, Ren X, Yang L. Chromosome Abnormalities: New Insights into Their Clinical Significance in Cancer. MOLECULAR THERAPY-ONCOLYTICS 2020; 17:562-570. [PMID: 32637574 PMCID: PMC7321812 DOI: 10.1016/j.omto.2020.05.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chromosomal abnormalities, consisting of numerical and structural chromosome abnormalities, are a common characteristic of cancer. Numerical chromosome abnormalities, mainly including aneuploidy and chromosome instability, are caused by chromosome segregation errors in mitosis, whereas structural chromosome abnormalities are a consequence of DNA damage and comprise focal/arm-level chromosome gain or loss. Recent advances have started to unveil the mechanisms by which chromosomal abnormalities can facilitate tumorigenesis and change the cellular fitness and the expression or function of RNAs and proteins. Accumulating evidence suggests that chromosome abnormalities represent a genomic signature that is linked to cancer prognosis and reaction to chemotherapy and immunotherapy. In this review, we discuss the most recent findings on the role of chromosome abnormalities in tumorigenesis and cancer progression, with a particular emphasis on how aneuploidy and chromosome instability influence cancer therapy and prognosis. We also highlight the distribution and clinical application of the structural chromosome abnormalities in various cancer types. A better understanding of the role of chromosome abnormalities will be beneficial to the development of precision oncology and suggest future directions for the field.
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Affiliation(s)
- Fan Kou
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Lei Wu
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Xiubao Ren
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- Corresponding author: Xiubao Ren, Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Huanhuxi Road, Tiyuanbei, Hexi District, Tianjin 300060, China.
| | - Lili Yang
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Corresponding author: Lili Yang, Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Huanhuxi Road, Tiyuanbei, Hexi District, Tianjin 300060, China.
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19
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Parental origin of monosomic chromosomes in near-haploid acute lymphoblastic leukemia. Blood Cancer J 2020; 10:51. [PMID: 32371983 PMCID: PMC7200744 DOI: 10.1038/s41408-020-0317-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 01/30/2023] Open
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20
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Laurent AP, Siret A, Ignacimouttou C, Panchal K, Diop M, Jenni S, Tsai YC, Roos-Weil D, Aid Z, Prade N, Lagarde S, Plassard D, Pierron G, Daudigeos E, Lecluse Y, Droin N, Bornhauser BC, Cheung LC, Crispino JD, Gaudry M, Bernard OA, Macintyre E, Barin Bonnigal C, Kotecha RS, Geoerger B, Ballerini P, Bourquin JP, Delabesse E, Mercher T, Malinge S. Constitutive Activation of RAS/MAPK Pathway Cooperates with Trisomy 21 and Is Therapeutically Exploitable in Down Syndrome B-cell Leukemia. Clin Cancer Res 2020; 26:3307-3318. [PMID: 32220889 DOI: 10.1158/1078-0432.ccr-19-3519] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 02/20/2020] [Accepted: 03/23/2020] [Indexed: 12/20/2022]
Abstract
PURPOSE Children with Down syndrome (constitutive trisomy 21) that develop acute lymphoblastic leukemia (DS-ALL) have a 3-fold increased likelihood of treatment-related mortality coupled with a higher cumulative incidence of relapse, compared with other children with B-cell acute lymphoblastic leukemia (B-ALL). This highlights the lack of suitable treatment for Down syndrome children with B-ALL. EXPERIMENTAL DESIGN To facilitate the translation of new therapeutic agents into clinical trials, we built the first preclinical cohort of patient-derived xenograft (PDX) models of DS-ALL, comprehensively characterized at the genetic and transcriptomic levels, and have proven its suitability for preclinical studies by assessing the efficacy of drug combination between the MEK inhibitor trametinib and conventional chemotherapy agents. RESULTS Whole-exome and RNA-sequencing experiments revealed a high incidence of somatic alterations leading to RAS/MAPK pathway activation in our cohort of DS-ALL, as well as in other pediatric B-ALL presenting somatic gain of the chromosome 21 (B-ALL+21). In murine and human B-cell precursors, activated KRASG12D functionally cooperates with trisomy 21 to deregulate transcriptional networks that promote increased proliferation and self renewal, as well as B-cell differentiation blockade. Moreover, we revealed that inhibition of RAS/MAPK pathway activation using the MEK1/2 inhibitor trametinib decreased leukemia burden in several PDX models of B-ALL+21, and enhanced survival of DS-ALL PDX in combination with conventional chemotherapy agents such as vincristine. CONCLUSIONS Altogether, using novel and suitable PDX models, this study indicates that RAS/MAPK pathway inhibition represents a promising strategy to improve the outcome of Down syndrome children with B-cell precursor leukemia.
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Affiliation(s)
- Anouchka P Laurent
- INSERM U1170, Gustave Roussy Institute, Université Paris Saclay, Villejuif, France.,Université Paris Diderot, Paris, France
| | - Aurélie Siret
- INSERM U1170, Gustave Roussy Institute, Université Paris Saclay, Villejuif, France
| | - Cathy Ignacimouttou
- INSERM U1170, Gustave Roussy Institute, Université Paris Saclay, Villejuif, France
| | - Kunjal Panchal
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - M'Boyba Diop
- Gustave Roussy Institute Cancer Campus, Department of Pediatric and Adolescent Oncology, INSERM U1015, Equipe Labellisée Ligue Nationale Contre le Cancer, Université Paris-Saclay, Villejuif, France
| | - Silvia Jenni
- Department of Pediatric Oncology, Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
| | - Yi-Chien Tsai
- Department of Pediatric Oncology, Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
| | - Damien Roos-Weil
- INSERM U1170, Gustave Roussy Institute, Université Paris Saclay, Villejuif, France
| | - Zakia Aid
- INSERM U1170, Gustave Roussy Institute, Université Paris Saclay, Villejuif, France
| | - Nais Prade
- Centre of Research on Cancer of Toulouse (CRCT), CHU Toulouse, Université Toulouse III, Toulouse, France
| | - Stephanie Lagarde
- Centre of Research on Cancer of Toulouse (CRCT), CHU Toulouse, Université Toulouse III, Toulouse, France
| | | | | | - Estelle Daudigeos
- Gustave Roussy Institute Cancer Campus, Department of Pediatric and Adolescent Oncology, INSERM U1015, Equipe Labellisée Ligue Nationale Contre le Cancer, Université Paris-Saclay, Villejuif, France
| | - Yann Lecluse
- Gustave Roussy Institute Cancer Campus, Department of Pediatric and Adolescent Oncology, INSERM U1015, Equipe Labellisée Ligue Nationale Contre le Cancer, Université Paris-Saclay, Villejuif, France
| | - Nathalie Droin
- INSERM U1170, Gustave Roussy Institute, Université Paris Saclay, Villejuif, France
| | - Beat C Bornhauser
- Department of Pediatric Oncology, Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
| | - Laurence C Cheung
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, Australia.,School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Australia
| | - John D Crispino
- Division of Hematology/Oncology, Northwestern University, Chicago, Illinois
| | - Muriel Gaudry
- INSERM U1170, Gustave Roussy Institute, Université Paris Saclay, Villejuif, France
| | - Olivier A Bernard
- INSERM U1170, Gustave Roussy Institute, Université Paris Saclay, Villejuif, France
| | - Elizabeth Macintyre
- Hematology, Université de Paris, Institut Necker-Enfants Malades and Assistance Publique-Hopitaux de Paris, Paris, France
| | | | - Rishi S Kotecha
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, Australia.,School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Australia.,Department of Clinical Haematology, Oncology and Bone Marrow Transplantation, Perth Children's Hospital, Perth, Australia
| | - Birgit Geoerger
- Gustave Roussy Institute Cancer Campus, Department of Pediatric and Adolescent Oncology, INSERM U1015, Equipe Labellisée Ligue Nationale Contre le Cancer, Université Paris-Saclay, Villejuif, France
| | - Paola Ballerini
- Laboratoire d'Hématologie, Hôpital Trousseau, APHP, Paris-Sorbonne, Paris, France
| | - Jean-Pierre Bourquin
- Department of Pediatric Oncology, Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
| | - Eric Delabesse
- Centre of Research on Cancer of Toulouse (CRCT), CHU Toulouse, Université Toulouse III, Toulouse, France
| | - Thomas Mercher
- INSERM U1170, Gustave Roussy Institute, Université Paris Saclay, Villejuif, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Sebastien Malinge
- INSERM U1170, Gustave Roussy Institute, Université Paris Saclay, Villejuif, France. .,Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, Australia
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21
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Evidence-based review of genomic aberrations in B-lymphoblastic leukemia/lymphoma: Report from the cancer genomics consortium working group for lymphoblastic leukemia. Cancer Genet 2020; 243:52-72. [PMID: 32302940 DOI: 10.1016/j.cancergen.2020.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 03/04/2020] [Accepted: 03/17/2020] [Indexed: 12/19/2022]
Abstract
Clinical management and risk stratification of B-lymphoblastic leukemia/ lymphoma (B-ALL/LBL) depend largely on identification of chromosomal abnormalities obtained using conventional cytogenetics and Fluorescence In Situ Hybridization (FISH) testing. In the last few decades, testing algorithms have been implemented to support an optimal risk-oriented therapy, leading to a large improvement in overall survival. In addition, large scale genomic studies have identified multiple aberrations of prognostic significance that are not routinely tested by existing modalities. However, as chromosomal microarray analysis (CMA) and next-generation sequencing (NGS) technologies are increasingly used in clinical management of hematologic malignancies, these abnormalities may be more readily detected. In this article, we have compiled a comprehensive, evidence-based review of the current B-ALL literature, focusing on known and published subtypes described to date. More specifically, we describe the role of various testing modalities in the diagnosis, prognosis, and therapeutic relevance. In addition, we propose a testing algorithm aimed at assisting laboratories in the most effective detection of the underlying genomic abnormalities.
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22
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Ntziachristos P. iAMPlified gene expression offers new insights in B cell precursor leukemia subtype. Leuk Lymphoma 2020; 61:501-503. [PMID: 32008406 DOI: 10.1080/10428194.2019.1695055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Simpson Querrey Center for Epigenetics, Chicago, IL, USA
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23
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Zhong ZM, Chen X, Qi X, Wang XM, Li CY, Qin RJ, Wang SQ, Liang J, Zeng MS, Sun CZ. Adaptor protein LNK promotes anaplastic thyroid carcinoma cell growth via 14-3-3 ε/γ binding. Cancer Cell Int 2020; 20:11. [PMID: 31938019 PMCID: PMC6953139 DOI: 10.1186/s12935-019-1090-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 12/28/2019] [Indexed: 01/08/2023] Open
Abstract
Background Rapid progression contributes to treatment failure in anaplastic thyroid carcinoma (ATC) patients. In a preliminary study, we demonstrated that some hematopoietic factors may be involved in the progression of ATC. The adaptor protein LNK, which is a negative regulator of hematopoietic cytokine signalling, has been studied extensively in malignant hematopoietic cells. However, there are few studies on LNK in solid tumours. Methods Real-time PCR, immunohistochemistry (IHC) and western blot analysis of LNK were performed on ATC cells, differentiated thyroid cancer (DTC) cells and normal thyroid cells. In vitro assays (including pull-down, liquid chromatography-mass spectrometry (LC–MS), co-IP, MTT and colony formation) were performed to validate the effect of LNK on ATC progression and elucidate the molecular mechanisms. Results Compared with DTC cells and normal thyroid cells, ATC cells exhibit overexpression of LNK. In addition, LNK overexpression results in increased proliferation of ATC cells. Conversely, LNK knockdown significantly suppresses ATC cell proliferation. LC–MS identified the 14-3-3 ε/γ protein as a LNK binding partner. Finally, the results indicate that LNK overexpression significantly enhances the anti-apoptotic ability of ATC cells via the Akt-NFκB-Bcl-2/Bcl-xL pathway and that the oncogenic effect of LNK largely depends on 14-3-3 ε/γ binding. Conclusions The present study elucidated the important role of LNK in the growth of ATC opposite to its behaviour in the hematopoietic system and indicates that LNK is a potential target for the treatment of ATC.
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Affiliation(s)
- Zhao-Ming Zhong
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, 519 Kunzhou Road, Kunming, China.,2Department of Medical Oncology, The First Affiliated Hospital of Kunming Medical University, 295 Xichang Road, Kunming, China
| | - Xue Chen
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, 519 Kunzhou Road, Kunming, China
| | - Xiao Qi
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, 519 Kunzhou Road, Kunming, China
| | - Xue-Min Wang
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, 519 Kunzhou Road, Kunming, China
| | - Chun-Yan Li
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, 519 Kunzhou Road, Kunming, China
| | - Ru-Jia Qin
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, 519 Kunzhou Road, Kunming, China
| | - Shi-Qi Wang
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, 519 Kunzhou Road, Kunming, China
| | - Jin Liang
- 2Department of Medical Oncology, The First Affiliated Hospital of Kunming Medical University, 295 Xichang Road, Kunming, China
| | - Mu-Sheng Zeng
- 3State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, China
| | - Chuan-Zheng Sun
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, 519 Kunzhou Road, Kunming, China
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24
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Ivanov Öfverholm I, Zachariadis V, Taylan F, Marincevic-Zuniga Y, Tran AN, Saft L, Nilsson D, Syvänen AC, Lönnerholm G, Harila-Saari A, Nordenskjöld M, Heyman M, Nordgren A, Nordlund J, Barbany G. Overexpression of chromatin remodeling and tyrosine kinase genes in iAMP21-positive acute lymphoblastic leukemia. Leuk Lymphoma 2019; 61:604-613. [PMID: 31640433 DOI: 10.1080/10428194.2019.1678153] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Intrachromosomal amplification of chromosome 21 (iAMP21) is a cytogenetic subtype associated with relapse and poor prognosis in pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL). The biology behind the high relapse risk is unknown and the aim of this study was to further characterize the genomic and transcriptional landscape of iAMP21. Using DNA arrays and sequencing, we could identify rearrangements and aberrations characteristic for iAMP21. RNA sequencing revealed that only half of the genes in the minimal region of amplification (20/45) were differentially expressed in iAMP21. Among them were the top overexpressed genes (p < 0.001) in iAMP21 vs. BCP ALL without iAMP21 and three candidate genes could be identified, the tyrosine kinase gene DYRK1A and chromatin remodeling genes CHAF1B and SON. While overexpression of DYRK1A and CHAF1B is associated with poor prognosis in malignant diseases including myeloid leukemia, this is the first study to show significant correlation with iAMP21-positive ALL.
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Affiliation(s)
- Ingegerd Ivanov Öfverholm
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | | | - Fulya Taylan
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Yanara Marincevic-Zuniga
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anh Nhi Tran
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Leonie Saft
- Department of Pathology, Karolinska University Hospital, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, Stockholm, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gudmar Lönnerholm
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Arja Harila-Saari
- Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Mats Heyman
- Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gisela Barbany
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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