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Li J, Kalev‐Zylinska ML. Advances in molecular characterization of pediatric acute megakaryoblastic leukemia not associated with Down syndrome; impact on therapy development. Front Cell Dev Biol 2023; 11:1170622. [PMID: 37325571 PMCID: PMC10267407 DOI: 10.3389/fcell.2023.1170622] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/19/2023] [Indexed: 06/17/2023] Open
Abstract
Acute megakaryoblastic leukemia (AMKL) is a rare subtype of acute myeloid leukemia (AML) in which leukemic blasts have megakaryocytic features. AMKL makes up 4%-15% of newly diagnosed pediatric AML, typically affecting young children (less than 2 years old). AMKL associated with Down syndrome (DS) shows GATA1 mutations and has a favorable prognosis. In contrast, AMKL in children without DS is often associated with recurrent and mutually exclusive chimeric fusion genes and has an unfavorable prognosis. This review mainly summarizes the unique features of pediatric non-DS AMKL and highlights the development of novel therapies for high-risk patients. Due to the rarity of pediatric AMKL, large-scale multi-center studies are needed to progress molecular characterization of this disease. Better disease models are also required to test leukemogenic mechanisms and emerging therapies.
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Affiliation(s)
- Jixia Li
- Blood and Cancer Biology Laboratory, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
- Department of Laboratory Medicine, School of Medicine, Foshan University, Foshan, China
| | - Maggie L. Kalev‐Zylinska
- Blood and Cancer Biology Laboratory, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
- Haematology Laboratory, Department of Pathology and Laboratory Medicine, Auckland City Hospital, Auckland, New Zealand
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2
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Lopes BA, Poubel CP, Teixeira CE, Caye-Eude A, Cavé H, Meyer C, Marschalek R, Boroni M, Emerenciano M. Novel Diagnostic and Therapeutic Options for KMT2A-Rearranged Acute Leukemias. Front Pharmacol 2022; 13:749472. [PMID: 35734412 PMCID: PMC9208280 DOI: 10.3389/fphar.2022.749472] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 05/04/2022] [Indexed: 11/24/2022] Open
Abstract
The KMT2A (MLL) gene rearrangements (KMT2A-r) are associated with a diverse spectrum of acute leukemias. Although most KMT2A-r are restricted to nine partner genes, we have recently revealed that KMT2A-USP2 fusions are often missed during FISH screening of these genetic alterations. Therefore, complementary methods are important for appropriate detection of any KMT2A-r. Here we use a machine learning model to unravel the most appropriate markers for prediction of KMT2A-r in various types of acute leukemia. A Random Forest and LightGBM classifier was trained to predict KMT2A-r in patients with acute leukemia. Our results revealed a set of 20 genes capable of accurately estimating KMT2A-r. The SKIDA1 (AUC: 0.839; CI: 0.799–0.879) and LAMP5 (AUC: 0.746; CI: 0.685–0.806) overexpression were the better markers associated with KMT2A-r compared to CSPG4 (also named NG2; AUC: 0.722; CI: 0.659–0.784), regardless of the type of acute leukemia. Of importance, high expression levels of LAMP5 estimated the occurrence of all KMT2A-USP2 fusions. Also, we performed drug sensitivity analysis using IC50 data from 345 drugs available in the GDSC database to identify which ones could be used to treat KMT2A-r leukemia. We observed that KMT2A-r cell lines were more sensitive to 5-Fluorouracil (5FU), Gemcitabine (both antimetabolite chemotherapy drugs), WHI-P97 (JAK-3 inhibitor), Foretinib (MET/VEGFR inhibitor), SNX-2112 (Hsp90 inhibitor), AZD6482 (PI3Kβ inhibitor), KU-60019 (ATM kinase inhibitor), and Pevonedistat (NEDD8-activating enzyme (NAE) inhibitor). Moreover, IC50 data from analyses of ex-vivo drug sensitivity to small-molecule inhibitors reveals that Foretinib is a promising drug option for AML patients carrying FLT3 activating mutations. Thus, we provide novel and accurate options for the diagnostic screening and therapy of KMT2A-r leukemia, regardless of leukemia subtype.
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Affiliation(s)
- Bruno A. Lopes
- Acute Leukemia RioSearch Group, Division of Clinical Research and Technological Development, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Caroline Pires Poubel
- Acute Leukemia RioSearch Group, Division of Clinical Research and Technological Development, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Cristiane Esteves Teixeira
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Aurélie Caye-Eude
- Département de Génétique, UF de Génétique moléculaire, Assistance Publique des Hópitaux de Paris (AP-HP), Hópital Robert Debré, Paris, France
- INSERM UMR_S1131, Institut de Recherche Saint-Louis, Université de Paris-Cité, Paris, France
| | - Hélène Cavé
- Département de Génétique, UF de Génétique moléculaire, Assistance Publique des Hópitaux de Paris (AP-HP), Hópital Robert Debré, Paris, France
- INSERM UMR_S1131, Institut de Recherche Saint-Louis, Université de Paris-Cité, Paris, France
| | - Claus Meyer
- DCAL/Institute of Pharmaceutical Biology, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Rolf Marschalek
- DCAL/Institute of Pharmaceutical Biology, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Mariana Boroni
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Mariana Emerenciano
- Acute Leukemia RioSearch Group, Division of Clinical Research and Technological Development, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
- *Correspondence: Mariana Emerenciano,
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Watt SM, Hua P, Roberts I. Increasing Complexity of Molecular Landscapes in Human Hematopoietic Stem and Progenitor Cells during Development and Aging. Int J Mol Sci 2022; 23:ijms23073675. [PMID: 35409034 PMCID: PMC8999121 DOI: 10.3390/ijms23073675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 02/05/2023] Open
Abstract
The past five decades have seen significant progress in our understanding of human hematopoiesis. This has in part been due to the unprecedented development of advanced technologies, which have allowed the identification and characterization of rare subsets of human hematopoietic stem and progenitor cells and their lineage trajectories from embryonic through to adult life. Additionally, surrogate in vitro and in vivo models, although not fully recapitulating human hematopoiesis, have spurred on these scientific advances. These approaches have heightened our knowledge of hematological disorders and diseases and have led to their improved diagnosis and therapies. Here, we review human hematopoiesis at each end of the age spectrum, during embryonic and fetal development and on aging, providing exemplars of recent progress in deciphering the increasingly complex cellular and molecular hematopoietic landscapes in health and disease. This review concludes by highlighting links between chronic inflammation and metabolic and epigenetic changes associated with aging and in the development of clonal hematopoiesis.
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Affiliation(s)
- Suzanne M. Watt
- Stem Cell Research, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9BQ, UK
- Myeloma Research Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, North Terrace, Adelaide 5005, Australia
- Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide 5001, Australia
- Correspondence: or ; Tel.: +61-403-393-755
| | - Peng Hua
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China;
| | - Irene Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, and NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK;
- Department of Paediatrics and NIHR Oxford Biomedical Research Centre Haematology Theme, University of Oxford, Oxford OX3 9DU, UK
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The role of reciprocal fusions in MLL-r acute leukemia: studying the chromosomal translocation t(4;11). Oncogene 2021; 40:6093-6102. [PMID: 34489550 PMCID: PMC8530991 DOI: 10.1038/s41388-021-02001-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 02/08/2023]
Abstract
Leukemia patients bearing the t(4;11)(q21;q23) translocations can be divided into two subgroups: those expressing both reciprocal fusion genes, and those that have only the MLL-AF4 fusion gene. Moreover, a recent study has demonstrated that patients expressing both fusion genes have a better outcome than patients that are expressing the MLL-AF4 fusion protein alone. All this may point to a clonal process where the reciprocal fusion gene AF4-MLL could be lost during disease progression, as this loss may select for a more aggressive type of leukemia. Therefore, we were interested in unraveling the decisive role of the AF4-MLL fusion protein at an early timepoint of disease development. We designed an experimental model system where the MLL-AF4 fusion protein was constitutively expressed, while an inducible AF4-MLL fusion gene was induced for only 48 h. Subsequently, we investigated genome-wide changes by RNA- and ATAC-Seq experiments at distinct timepoints. These analyses revealed that the expression of AF4-MLL for only 48 h was sufficient to significantly change the genomic landscape (transcription and chromatin) even on a longer time scale. Thus, we have to conclude that the AF4-MLL fusion protein works through a hit-and-run mechanism, probably necessary to set up pre-leukemic conditions, but being dispensable for later disease progression.
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Heyer EE, Deveson IW, Wooi D, Selinger CI, Lyons RJ, Hayes VM, O'Toole SA, Ballinger ML, Gill D, Thomas DM, Mercer TR, Blackburn J. Diagnosis of fusion genes using targeted RNA sequencing. Nat Commun 2019; 10:1388. [PMID: 30918253 PMCID: PMC6437215 DOI: 10.1038/s41467-019-09374-9] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 02/22/2019] [Indexed: 01/05/2023] Open
Abstract
Fusion genes are a major cause of cancer. Their rapid and accurate diagnosis can inform clinical action, but current molecular diagnostic assays are restricted in resolution and throughput. Here, we show that targeted RNA sequencing (RNAseq) can overcome these limitations. First, we establish that fusion gene detection with targeted RNAseq is both sensitive and quantitative by optimising laboratory and bioinformatic variables using spike-in standards and cell lines. Next, we analyse a clinical patient cohort and improve the overall fusion gene diagnostic rate from 63% with conventional approaches to 76% with targeted RNAseq while demonstrating high concordance for patient samples with previous diagnoses. Finally, we show that targeted RNAseq offers additional advantages by simultaneously measuring gene expression levels and profiling the immune-receptor repertoire. We anticipate that targeted RNAseq will improve clinical fusion gene detection, and its increasing use will provide a deeper understanding of fusion gene biology. Rapid and accurate detection of fusion genes is important in cancer diagnostics. Here, the authors demonstrate that targeted RNA sequencing provides fast, sensitive and quantitative gene fusion detection and overcomes the limitations of approaches currently in clinical use.
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Affiliation(s)
- Erin E Heyer
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Ira W Deveson
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia.,St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia
| | - Danson Wooi
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia.,St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia
| | - Christina I Selinger
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, 2050, NSW, Australia
| | - Ruth J Lyons
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Vanessa M Hayes
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia.,St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia.,Faculty of Health Sciences, University of Limpopo, Turfloop Campus, Mankweng, 0727, South Africa.,School of Health Systems and Public Health, University of Pretoria, Pretoria, 0002, South Africa.,Central Clinical School, University of Sydney, Sydney, 2006, NSW, Australia
| | - Sandra A O'Toole
- St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia.,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, 2050, NSW, Australia.,Central Clinical School, University of Sydney, Sydney, 2006, NSW, Australia.,The Kinghorn Cancer Centre and Cancer Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia.,Australian Clinical Labs, Sydney, 2010, NSW, Australia
| | - Mandy L Ballinger
- The Kinghorn Cancer Centre and Cancer Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Devinder Gill
- Department of Haematology, Princess Alexandra Hospital, Brisbane, 4102, QLD, Australia
| | - David M Thomas
- The Kinghorn Cancer Centre and Cancer Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Tim R Mercer
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia. .,St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia. .,Altius Institute for Biomedical Sciences, Seattle, 98121, WA, USA.
| | - James Blackburn
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia. .,St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia.
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