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Ling RE, Cross JW, Roy A. Aberrant stem cell and developmental programs in pediatric leukemia. Front Cell Dev Biol 2024; 12:1372899. [PMID: 38601080 PMCID: PMC11004259 DOI: 10.3389/fcell.2024.1372899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/11/2024] [Indexed: 04/12/2024] Open
Abstract
Hematopoiesis is a finely orchestrated process, whereby hematopoietic stem cells give rise to all mature blood cells. Crucially, they maintain the ability to self-renew and/or differentiate to replenish downstream progeny. This process starts at an embryonic stage and continues throughout the human lifespan. Blood cancers such as leukemia occur when normal hematopoiesis is disrupted, leading to uncontrolled proliferation and a block in differentiation of progenitors of a particular lineage (myeloid or lymphoid). Although normal stem cell programs are crucial for tissue homeostasis, these can be co-opted in many cancers, including leukemia. Myeloid or lymphoid leukemias often display stem cell-like properties that not only allow proliferation and survival of leukemic blasts but also enable them to escape treatments currently employed to treat patients. In addition, some leukemias, especially in children, have a fetal stem cell profile, which may reflect the developmental origins of the disease. Aberrant fetal stem cell programs necessary for leukemia maintenance are particularly attractive therapeutic targets. Understanding how hijacked stem cell programs lead to aberrant gene expression in place and time, and drive the biology of leukemia, will help us develop the best treatment strategies for patients.
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Affiliation(s)
- Rebecca E. Ling
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Joe W. Cross
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Anindita Roy
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Department of Haematology, Great Ormond Street Hospital for Children, London, United Kingdom
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2
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Bueno C, Torres-Ruiz R, Velasco-Hernandez T, Molina O, Petazzi P, Martinez A, Rodriguez V, Vinyoles M, Cantilena S, Williams O, Vega-Garcia N, Rodriguez-Perales S, Segovia JC, Quintana-Bustamante O, Roy A, Meyer C, Marschalek R, Smith AL, Milne TA, Fraga MF, Tejedor JR, Menéndez P. A human genome editing-based MLL::AF4 ALL model recapitulates key cellular and molecular leukemogenic features. Blood 2023; 142:1752-1756. [PMID: 37756522 DOI: 10.1182/blood.2023020858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/20/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Cellular ontogeny and MLL breakpoint site influence the capacity of MLL-edited CD34+ hematopoietic cells to initiate and recapitulate infant patients' features in pro-B-cell acute lymphoblastic leukemia (B-ALL). We provide key insights into the leukemogenic determinants of MLL-AF4+ infant B-ALL.
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Affiliation(s)
- Clara Bueno
- Stem Cell Biology, Immunotherapy and Developmental Leukemia Laboratory. Josep Carreras Leukemia Research Institute, Barcelona, Spain
- Spanish Network for Advanced Therapies, Carlos III Health Institute, Barcelona, Spain
- Spanish Collaborative Cancer Network, Carlos III Health Institute, Barcelona, Spain
| | - Raul Torres-Ruiz
- Stem Cell Biology, Immunotherapy and Developmental Leukemia Laboratory. Josep Carreras Leukemia Research Institute, Barcelona, Spain
- Division of Hematopoietic Innovative Therapies, Biomedical Innovation Unit, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, Madrid, Spain
- Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncologicas, Madrid, Spain
| | - Talia Velasco-Hernandez
- Stem Cell Biology, Immunotherapy and Developmental Leukemia Laboratory. Josep Carreras Leukemia Research Institute, Barcelona, Spain
- Spanish Network for Advanced Therapies, Carlos III Health Institute, Barcelona, Spain
| | - Oscar Molina
- Stem Cell Biology, Immunotherapy and Developmental Leukemia Laboratory. Josep Carreras Leukemia Research Institute, Barcelona, Spain
- Spanish Network for Advanced Therapies, Carlos III Health Institute, Barcelona, Spain
| | - Paolo Petazzi
- Stem Cell Biology, Immunotherapy and Developmental Leukemia Laboratory. Josep Carreras Leukemia Research Institute, Barcelona, Spain
| | - Alba Martinez
- Stem Cell Biology, Immunotherapy and Developmental Leukemia Laboratory. Josep Carreras Leukemia Research Institute, Barcelona, Spain
- Spanish Network for Advanced Therapies, Carlos III Health Institute, Barcelona, Spain
| | - Virginia Rodriguez
- Stem Cell Biology, Immunotherapy and Developmental Leukemia Laboratory. Josep Carreras Leukemia Research Institute, Barcelona, Spain
- Spanish Network for Advanced Therapies, Carlos III Health Institute, Barcelona, Spain
| | - Meritxell Vinyoles
- Stem Cell Biology, Immunotherapy and Developmental Leukemia Laboratory. Josep Carreras Leukemia Research Institute, Barcelona, Spain
- Spanish Network for Advanced Therapies, Carlos III Health Institute, Barcelona, Spain
| | - Sandra Cantilena
- Development Biology Cancer Program, Cancer Section, UCLGOS Institute of Child Health, London, United Kingdom
| | - Owen Williams
- Development Biology Cancer Program, Cancer Section, UCLGOS Institute of Child Health, London, United Kingdom
| | - Nerea Vega-Garcia
- Hematology Laboratory, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
- Developmental Tumors Biology Group, Leukemia, and other Pediatric Hemopathies, Pediatric Cancer Center Barcelona, Institut de Recerca, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Sandra Rodriguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncologicas, Madrid, Spain
| | - Jose C Segovia
- Division of Hematopoietic Innovative Therapies, Biomedical Innovation Unit, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, Madrid, Spain
- Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
| | - Oscar Quintana-Bustamante
- Division of Hematopoietic Innovative Therapies, Biomedical Innovation Unit, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, Madrid, Spain
- Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
| | - Anindita Roy
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford Biomedical Research Center Hematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Pediatrics and National Institute for Health and Care Research Oxford Biomedical Research Centre Hematology Theme, University of Oxford, Oxford, United Kingdom
| | - Claus Meyer
- Diagnostic Center of Acute Leukemia-Institute of Pharmaceutical Biology, Goethe-University, Frankfurt/Main, Germany
| | - Rolf Marschalek
- Diagnostic Center of Acute Leukemia-Institute of Pharmaceutical Biology, Goethe-University, Frankfurt/Main, Germany
| | - Alastair L Smith
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford Biomedical Research Center Hematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Thomas A Milne
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford Biomedical Research Center Hematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Mario F Fraga
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center, El Entrego, Spain
- Health Research Institute of Asturias, Institute of Oncology of Asturias and Department of Organisms and Systems Biology, University of Oviedo, Oviedo, Spain
| | - Juan Ramón Tejedor
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center, El Entrego, Spain
- Health Research Institute of Asturias, Institute of Oncology of Asturias and Department of Organisms and Systems Biology, University of Oviedo, Oviedo, Spain
| | - Pablo Menéndez
- Stem Cell Biology, Immunotherapy and Developmental Leukemia Laboratory. Josep Carreras Leukemia Research Institute, Barcelona, Spain
- Spanish Network for Advanced Therapies, Carlos III Health Institute, Barcelona, Spain
- Spanish Collaborative Cancer Network, Carlos III Health Institute, Barcelona, Spain
- Department of Biomedicine, University of Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
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3
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Sugur HS, Rao S, Sravya P, Athul Menon K, Arivazhagan A, Mehta B, Santosh V. IRX1 is a novel gene, overexpressed in high-grade IDH-mutant astrocytomas. Pathol Res Pract 2023; 245:154464. [PMID: 37116364 DOI: 10.1016/j.prp.2023.154464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/09/2023] [Accepted: 04/10/2023] [Indexed: 04/30/2023]
Abstract
BACKGROUND IDH-mutant astrocytomas include CNS WHO grade 2 (A2), grade 3 (A3) and grade 4 (A4), of which A3 and A4 are high-grade. A3 has a heterogenous clinical outcome that cannot be explained entirely by the existing molecular biomarkers. We comprehensively studied the transcriptome profile of A3 to determine clinical significance. METHODS TCGA mRNA-sequencing data of A3 was analyzed to derive differentially expressed genes (DEG), which were short-listed using various approaches. mRNA expression of the short-listed genes was validated using NanoString platform on a uniformly treated and molecularly characterized A3 cohort. Protein expression of one prognostically significant gene, Iroquois-class homeodomain (IRX1) was assessed by immunohistochemistry and correlated with patient survival and tumor recurrence. IRX1 expression was also studied in different grades of astrocytoma. Since DNA methyltransferase 3 alpha (DNMT3A) influences IRX1 expression, its mutations were evaluated in a subset of tumors. RESULTS TCGA analysis identified 96 DEG in A3 tumours. 57 genes were short-listed and finally narrowed down to 14 genes. mRNA values of 12/14 genes validated in our cohort. On multiple-variable analysis, IRX1 was the most prognostically relevant gene, with respect to progression free survival of patients. Further, IRX1 immunoexpression was significantly higher in A3 and A4 when compared to A2 and glioblastoma. Higher IRX1 immunoexpression correlated with poor prognosis in patients with A3 tumours. Also, a higher IRX1 expression was associated with DNMT3A mutation. CONCLUSION Our study identifies IRX1 as a novel biomarker overexpressed in high-grade IDH-mutant astrocytomas with prognostic significance in A3. DNMT3A mutation probably modulates IRX1 expression.
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Affiliation(s)
- Harsha S Sugur
- Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, Karnataka 560029, India
| | - Shilpa Rao
- Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, Karnataka 560029, India
| | - Palavalasa Sravya
- Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, Karnataka 560029, India
| | - K Athul Menon
- Theracues Innovations Pvt. Ltd, Sahakar Nagar, Bangalore, Karnataka 560092, India
| | - Arimappamagan Arivazhagan
- Department of Neurosurgery, National Institute of Mental Health and Neuro Sciences, Bangalore 560029, India
| | - Bhupesh Mehta
- Department of Biophysics, National Institute of Mental Health and Neuro Sciences, Bangalore, Karnataka 560029, India
| | - Vani Santosh
- Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, Karnataka 560029, India.
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4
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Nagel S. The Role of IRX Homeobox Genes in Hematopoietic Progenitors and Leukemia. Genes (Basel) 2023; 14:genes14020297. [PMID: 36833225 PMCID: PMC9957183 DOI: 10.3390/genes14020297] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
IRX genes are members of the TALE homeobox gene class and encode six related transcription factors (IRX1-IRX6) controlling development and cell differentiation of several tissues in humans. Classification of TALE homeobox gene expression patterns for the hematopoietic compartment, termed TALE-code, has revealed exclusive IRX1 activity in pro-B-cells and megakaryocyte erythroid progenitors (MEPs), highlighting its specific contribution to developmental processes at these early stages of hematopoietic lineage differentiation. Moreover, aberrant expression of IRX homeobox genes IRX1, IRX2, IRX3 and IRX5 has been detected in hematopoietic malignancies, including B-cell precursor acute lymphoblastic leukemia (BCP-ALL), T-cell ALL, and some subtypes of acute myeloid leukemia (AML). Expression analyses of patient samples and experimental studies using cell lines and mouse models have revealed oncogenic functions in cell differentiation arrest and upstream and downstream genes, thus, revealing normal and aberrant regulatory networks. These studies have shown how IRX genes play key roles in the development of both normal blood and immune cells, and hematopoietic malignancies. Understanding their biology serves to illuminate developmental gene regulation in the hematopoietic compartment, and may improve diagnostic classification of leukemias in the clinic and reveal new therapeutic targets and strategies.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Cultures, Leibniz-Institute DSMZ, 38124 Braunschweig, Germany
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5
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Külp M, Siemund AL, Larghero P, Dietz A, Alten J, Cario G, Eckert C, Caye-Eude A, Cavé H, Bardini M, Cazzaniga G, De Lorenzo P, Valsecchi MG, Diehl L, Bonig H, Meyer C, Marschalek R. The immune checkpoint ICOSLG is a relapse-predicting biomarker and therapeutic target in infant t(4;11) acute lymphoblastic leukemia. iScience 2022; 25:104613. [PMID: 35800767 PMCID: PMC9253708 DOI: 10.1016/j.isci.2022.104613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/14/2022] [Accepted: 06/01/2022] [Indexed: 11/23/2022] Open
Abstract
The most frequent genetic aberration leading to infant ALL (iALL) is the chromosomal translocation t(4;11), generating the fusion oncogenes KMT2A:AFF1 and AFF1:KMT2A, respectively. KMT2A-r iALL displays a dismal prognosis through high relapse rates and relapse-associated mortality. Relapse occurs frequently despite ongoing chemotherapy and without the accumulation of secondary mutations. A rational explanation for the observed chemo-resistance and satisfactory treatment options remain to be elucidated. We found that elevated ICOSLG expression level at diagnosis was associated with inferior event free survival (EFS) in a cohort of 43 patients with t(4;-11) iALL and that a cohort of 18 patients with iALL at relapse displayed strongly increased ICOSLG expression. Furthermore, co-culturing t(4;11) ALL cells (ICOSLGhi) with primary T-cells resulted in the development of Tregs. This was impaired through treatment with a neutralizing ICOSLG antibody. These findings imply ICOSLG (1) as a relapse-predicting biomarker, and (2) as a therapeutic target involved in a potential immune evasion relapse-mechanism of infant t(4;11) ALL. Early growth response 3 (EGR3) is a direct transactivator of the immune checkpoint gene ICOSLG high ICOSLG expression at diagnosis is predictive for ALL relapse EGR3 and ICOSLG expressions are relapse-associated expression of ICOSLG on t(4;11) ALL cells leads to the rapid expansion of Tregs
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6
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The Hematopoietic TALE-Code Shows Normal Activity of IRX1 in Myeloid Progenitors and Reveals Ectopic Expression of IRX3 and IRX5 in Acute Myeloid Leukemia. Int J Mol Sci 2022; 23:ijms23063192. [PMID: 35328612 PMCID: PMC8952210 DOI: 10.3390/ijms23063192] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 12/10/2022] Open
Abstract
Homeobox genes encode transcription factors that control basic developmental decisions. Knowledge of their hematopoietic activities casts light on normal and malignant immune cell development. Recently, we constructed the so-called lymphoid TALE-code that codifies expression patterns of all active TALE class homeobox genes in early hematopoiesis and lymphopoiesis. Here, we present the corresponding myeloid TALE-code to extend this gene signature, covering the entire hematopoietic system. The collective data showed expression patterns for eleven TALE homeobox genes and highlighted the exclusive expression of IRX1 in megakaryocyte-erythroid progenitors (MEPs), implicating this TALE class member in a specific myeloid differentiation process. Analysis of public profiling data from acute myeloid leukemia (AML) patients revealed aberrant activity of IRX1 in addition to IRX3 and IRX5, indicating an oncogenic role for these TALE homeobox genes when deregulated. Screening of RNA-seq data from 100 leukemia/lymphoma cell lines showed overexpression of IRX1, IRX3, and IRX5 in megakaryoblastic and myelomonocytic AML cell lines, chosen as suitable models for studying the regulation and function of these homeo-oncogenes. Genomic copy number analysis of IRX-positive cell lines demonstrated chromosomal amplification of the neighboring IRX3 and IRX5 genes at position 16q12 in MEGAL, underlying their overexpression in this cell line model. Comparative gene expression analysis of these cell lines revealed candidate upstream factors and target genes, namely the co-expression of GATA1 and GATA2 together with IRX1, and of BMP2 and HOXA10 with IRX3/IRX5. Subsequent knockdown and stimulation experiments in AML cell lines confirmed their activating impact in the corresponding IRX gene expression. Furthermore, we demonstrated that IRX1 activated KLF1 and TAL1, while IRX3 inhibited GATA1, GATA2, and FST. Accordingly, we propose that these regulatory relationships may represent major physiological and oncogenic activities of IRX factors in normal and malignant myeloid differentiation, respectively. Finally, the established myeloid TALE-code is a useful tool for evaluating TALE homeobox gene activities in AML.
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Genome-wide aberrant methylation in primary metastatic UM and their matched metastases. Sci Rep 2022; 12:42. [PMID: 34997020 PMCID: PMC8742000 DOI: 10.1038/s41598-021-03964-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/01/2021] [Indexed: 12/20/2022] Open
Abstract
Uveal melanoma (UM) is an aggressive intra-ocular cancer with a strong tendency to metastasize. Metastatic UM is associated with mutations in BAP1 and SF3B1, however only little is known about the epigenetic modifications that arise in metastatic UM. In this study we aim to unravel epigenetic changes contributing to UM metastasis using a new genome-wide methylation analysis technique that covers over 50% of all CpG’s. We identified aberrant methylation contributing to BAP1 and SF3B1-mediated UM metastasis. The methylation data was integrated with expression data and surveyed in matched UM metastases from the liver, skin and bone. UM metastases showed no commonly shared novel epigenetic modifications, implying that epigenetic changes contributing to metastatic spreading and colonization in distant tissues occur early in the development of UM and epigenetic changes that occur after metastasis are mainly patient-specific. Our findings reveal a plethora of epigenetic modifications in metastatic UM and its metastases, which could subsequently result in aberrant repression or activation of many tumor-related genes. This observation points towards additional layers of complexity at the level of gene expression regulation, which may explain the low mutational burden of UM.
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Rice S, Jackson T, Crump NT, Fordham N, Elliott N, O'Byrne S, Fanego MDML, Addy D, Crabb T, Dryden C, Inglott S, Ladon D, Wright G, Bartram J, Ancliff P, Mead AJ, Halsey C, Roberts I, Milne TA, Roy A. A human fetal liver-derived infant MLL-AF4 acute lymphoblastic leukemia model reveals a distinct fetal gene expression program. Nat Commun 2021; 12:6905. [PMID: 34824279 PMCID: PMC8616957 DOI: 10.1038/s41467-021-27270-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 11/08/2021] [Indexed: 11/24/2022] Open
Abstract
Although 90% of children with acute lymphoblastic leukemia (ALL) are now cured, the prognosis for infant-ALL remains dismal. Infant-ALL is usually caused by a single genetic hit that arises in utero: an MLL/KMT2A gene rearrangement (MLL-r). This is sufficient to induce a uniquely aggressive and treatment-refractory leukemia compared to older children. The reasons for disparate outcomes in patients of different ages with identical driver mutations are unknown. Using the most common MLL-r in infant-ALL, MLL-AF4, as a disease model, we show that fetal-specific gene expression programs are maintained in MLL-AF4 infant-ALL but not in MLL-AF4 childhood-ALL. We use CRISPR-Cas9 gene editing of primary human fetal liver hematopoietic cells to produce a t(4;11)/MLL-AF4 translocation, which replicates the clinical features of infant-ALL and drives infant-ALL-specific and fetal-specific gene expression programs. These data support the hypothesis that fetal-specific gene expression programs cooperate with MLL-AF4 to initiate and maintain the distinct biology of infant-ALL.
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Affiliation(s)
- Siobhan Rice
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas Jackson
- Department of Paediatrics and NIHR Oxford Biomedical Research Centre Haematology Theme, University of Oxford, Oxford, UK
| | - Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas Fordham
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Natalina Elliott
- Department of Paediatrics and NIHR Oxford Biomedical Research Centre Haematology Theme, University of Oxford, Oxford, UK
| | - Sorcha O'Byrne
- Department of Paediatrics and NIHR Oxford Biomedical Research Centre Haematology Theme, University of Oxford, Oxford, UK
| | | | - Dilys Addy
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK
| | - Trisevgeni Crabb
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK
| | - Carryl Dryden
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK
| | - Sarah Inglott
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK
| | - Dariusz Ladon
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK
| | - Gary Wright
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK
| | - Jack Bartram
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK
| | - Philip Ancliff
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK
| | - Adam J Mead
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Christina Halsey
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Department of Paediatric Haematology, Royal Hospital for Children, Glasgow, UK
| | - Irene Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Department of Paediatrics and NIHR Oxford Biomedical Research Centre Haematology Theme, University of Oxford, Oxford, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Anindita Roy
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
- Department of Paediatrics and NIHR Oxford Biomedical Research Centre Haematology Theme, University of Oxford, Oxford, UK.
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9
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de Barrios O, Parra M. Epigenetic Control of Infant B Cell Precursor Acute Lymphoblastic Leukemia. Int J Mol Sci 2021; 22:ijms22063127. [PMID: 33803872 PMCID: PMC8003172 DOI: 10.3390/ijms22063127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 11/16/2022] Open
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a highly aggressive malignancy, with poorer prognosis in infants than in adults. A genetic signature has been associated with this outcome but, remarkably, leukemogenesis is commonly triggered by genetic alterations of embryonic origin that involve the deregulation of chromatin remodelers. This review considers in depth how the alteration of epigenetic profiles (at DNA and histone levels) induces an aberrant phenotype in B lymphocyte progenitors by modulating the oncogenic drivers and tumor suppressors involved in key cancer hallmarks. DNA methylation patterns have been widely studied in BCP-ALL and their correlation with survival has been established. However, the effect of methylation on histone residues can be very different. For instance, methyltransferase KMT2A gene participates in chromosomal rearrangements with several partners, imposing an altered pattern of methylated H3K4 and H3K79 residues, enhancing oncogene promoter activation, and conferring a worse outcome on affected infants. In parallel, acetylation processes provide an additional layer of epigenetic regulation and can alter the chromatin conformation, enabling the binding of regulatory factors. Therefore, an integrated knowledge of all epigenetic disorders is essential to understand the molecular basis of BCP-ALL and to identify novel entry points that can be exploited to improve therapeutic options and disease prognosis.
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Affiliation(s)
- Oriol de Barrios
- Correspondence: (O.d.B.); (M.P.); Tel.: +34-93-557-28-00 (ext. 4222) (O.d.B.); +34-93-557-28-00 (ext. 4210) (M.P.)
| | - Maribel Parra
- Correspondence: (O.d.B.); (M.P.); Tel.: +34-93-557-28-00 (ext. 4222) (O.d.B.); +34-93-557-28-00 (ext. 4210) (M.P.)
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10
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Küster MM, Schneider MA, Richter AM, Richtmann S, Winter H, Kriegsmann M, Pullamsetti SS, Stiewe T, Savai R, Muley T, Dammann RH. Epigenetic Inactivation of the Tumor Suppressor IRX1 Occurs Frequently in Lung Adenocarcinoma and Its Silencing Is Associated with Impaired Prognosis. Cancers (Basel) 2020; 12:E3528. [PMID: 33256112 PMCID: PMC7760495 DOI: 10.3390/cancers12123528] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/18/2020] [Accepted: 11/24/2020] [Indexed: 12/19/2022] Open
Abstract
Iroquois homeobox (IRX) encodes members of homeodomain containing genes which are involved in development and differentiation. Since it has been reported that the IRX1 gene is localized in a lung cancer susceptibility locus, the epigenetic regulation and function of IRX1 was investigated in lung carcinogenesis. We observed frequent hypermethylation of the IRX1 promoter in non-small cell lung cancer (NSCLC) compared to small cell lung cancer (SCLC). Aberrant IRX1 methylation was significantly correlated with reduced IRX1 expression. In normal lung samples, the IRX1 promoter showed lower median DNA methylation levels (<10%) compared to primary adenocarcinoma (ADC, 22%) and squamous cell carcinoma (SQCC, 14%). A significant hypermethylation and downregulation of IRX1 was detected in ADC and SQCC compared to matching normal lung samples (p < 0.0001). Low IRX1 expression was significantly correlated with impaired prognosis of ADC patients (p = 0.001). Reduced survival probability was also associated with higher IRX1 promoter methylation (p = 0.02). Inhibition of DNA methyltransferase (DNMT) activity reactivated IRX1 expression in human lung cancer cell lines. Induced DNMT3A and EZH2 expression was correlated with downregulation of IRX1. On the cellular level, IRX1 exhibits nuclear localization and expression of IRX1 induced fragmented nuclei in cancer cells. Localization of IRX1 and induction of aberrant nuclei were dependent on the presence of the homeobox of IRX1. By data mining, we showed that IRX1 is negatively correlated with oncogenic pathways and IRX1 expression induces the proapoptotic regulator BAX. In conclusion, we report that IRX1 expression is significantly associated with improved survival probability of ADC patients. IRX1 hypermethylation may serve as molecular biomarker for ADC diagnosis and prognosis. Our data suggest that IRX1 acts as an epigenetically regulated tumor suppressor in the pathogenesis of lung cancer.
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Affiliation(s)
- Miriam M. Küster
- Faculty of Biology, Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany; (M.M.K.); (A.M.R.)
| | - Marc A. Schneider
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany; (M.A.S.); (S.R.); (T.M.)
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
| | - Antje M. Richter
- Faculty of Biology, Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany; (M.M.K.); (A.M.R.)
| | - Sarah Richtmann
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany; (M.A.S.); (S.R.); (T.M.)
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
| | - Hauke Winter
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
- Department of Surgery, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany
| | - Mark Kriegsmann
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
- Department of Pathology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Soni S. Pullamsetti
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Thorsten Stiewe
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
- Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University, 35032 Marburg, Germany
| | - Rajkumar Savai
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Thomas Muley
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany; (M.A.S.); (S.R.); (T.M.)
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
| | - Reinhard H. Dammann
- Faculty of Biology, Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany; (M.M.K.); (A.M.R.)
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
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11
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The reciprocal world of MLL fusions: A personal view. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194547. [PMID: 32294539 DOI: 10.1016/j.bbagrm.2020.194547] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/12/2020] [Accepted: 03/22/2020] [Indexed: 01/28/2023]
Abstract
Over the last 15 years the Diagnostic Center of Acute Leukemia (DCAL) at the Frankfurt University has diagnosed and elucidated the Mixed Lineage Leukemia (MLL) recombinome with >100 MLL fusion partners. When analyzing all these different events, balanced chromosomal translocations were found to comprise the majority of these cases (~70%), while other types of genetic rearrangements (3-way-translocations, spliced fusions, 11q inversions, interstitial deletions or insertion of chromosomal fragments into other chromosomes) account for about 30%. In nearly all those complex cases, functional fusion proteins can be produced by transcription, splicing and translation. With a few exceptions (10 out of 102 fusion genes which were per se out-of-frame), all these genetic rearrangements produced a direct MLL fusion gene, and in 94% of cases an additional reciprocal fusion gene. So far, 114 patients (out of 2454 = ~5%) have been diagnosed only with the reciprocal fusion allele, displaying no MLL-X allele. The fact that so many MLL rearrangements bear at least two fusion alleles, but also our findings that several direct MLL fusions were either out-of-frame fusions or missing, raises the question about the function and importance of reciprocal MLL fusions. Recent findings also demonstrate the presence of reciprocal MLL fusions in sarcoma patients. Here, we want to discuss the role of reciprocal MLL fusion proteins for leukemogenesis and beyond.
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12
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Prognostic value of Iroquois homeobox 1 methylation in non-small cell lung cancers. Genes Genomics 2020; 42:571-579. [PMID: 32200543 DOI: 10.1007/s13258-020-00925-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/10/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) poses a great threat to human health. DNA methylation abnormalities play a central role in the development and outcome of most human malignancies, providing potential biomarkers for diagnosis and prognosis. Iroquois homeobox 1 (IRX1) can act as a tumor suppressor or promoter depending on the tumor microenvironment, and its role in lung cancer is still controversial. OBJECTIVE The purpose of this study was to investigate the biological role and prognostic value of IRX1 in NSCLC. METHODS We examined the methylation status of IRX1 promoter in 146 tumors from patients with NSCLC using pyrosequencing and analyzed the association between methylation status and overall patient survival. RESULTS A total of 37 cases (25.3%) showed IRX1 methylation-positive tumors when compared with matched normal tissues. No association between IRX1 expression level and methylation status was found in lung cancer cell lines. IRX1 methylation significantly correlated with smoking status and TP53 mutation. Patients with IRX1 methylation showed significantly longer survival than patients without methylation (log-rank P = 0.011). In a multivariate analysis of prognostic factors, IRX1 methylation in tumor samples was an independent prognostic factor (adjusted hazard ratio = 0.35, 95% confidence interval 0.17-0.73, P = 0.005). CONCLUSION These results suggest that IRX1 promoter methylation may be a tumor-associated event and an independent predictor of survival advantage in patients with NSCLC. Further large-scale studies are needed to confirm these findings.
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13
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Affiliation(s)
- Rolf Marschalek
- Institute of Pharmaceutical Biology / Diagnostic Center of Acute Leukemia, University of Frankfurt, Frankfurt/Main, Germany
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14
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Bueno C, Calero-Nieto FJ, Wang X, Valdés-Mas R, Gutiérrez-Agüera F, Roca-Ho H, Ayllon V, Real PJ, Arambilet D, Espinosa L, Torres-Ruiz R, Agraz-Doblas A, Varela I, de Boer J, Bigas A, Gottgens B, Marschalek R, Menendez P. Enhanced hemato-endothelial specification during human embryonic differentiation through developmental cooperation between AF4-MLL and MLL-AF4 fusions. Haematologica 2019; 104:1189-1201. [PMID: 30679325 PMCID: PMC6545840 DOI: 10.3324/haematol.2018.202044] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 01/21/2019] [Indexed: 12/18/2022] Open
Abstract
The t(4;11)(q21;q23) translocation is associated with high-risk infant pro-B-cell acute lymphoblastic leukemia and arises prenatally during embryonic/fetal hematopoiesis. The developmental/pathogenic contribution of the t(4;11)-resulting MLL-AF4 (MA4) and AF4-MLL (A4M) fusions remains unclear; MA4 is always expressed in patients with t(4;11)+ B-cell acute lymphoblastic leukemia, but the reciprocal fusion A4M is expressed in only half of the patients. Because prenatal leukemogenesis manifests as impaired early hematopoietic differentiation, we took advantage of well-established human embryonic stem cell-based hematopoietic differentiation models to study whether the A4M fusion cooperates with MA4 during early human hematopoietic development. Co-expression of A4M and MA4 strongly promoted the emergence of hemato-endothelial precursors, both endothelial- and hemogenic-primed. Double fusion-expressing hemato-endothelial precursors specified into significantly higher numbers of both hematopoietic and endothelial-committed cells, irrespective of the differentiation protocol used and without hijacking survival/proliferation. Functional analysis of differentially expressed genes and differentially enriched H3K79me3 genomic regions by RNA-sequencing and H3K79me3 chromatin immunoprecipitation-sequencing, respectively, confirmed a hematopoietic/endothelial cell differentiation signature in double fusion-expressing hemato-endothelial precursors. Importantly, chromatin immunoprecipitation-sequencing analysis revealed a significant enrichment of H3K79 methylated regions specifically associated with HOX-A cluster genes in double fusion-expressing differentiating hematopoietic cells. Overall, these results establish a functional and molecular cooperation between MA4 and A4M fusions during human hematopoietic development.
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Affiliation(s)
- Clara Bueno
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
| | - Fernando J Calero-Nieto
- Department of Hematology, Cambridge Institute for Medical Research and Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, UK
| | - Xiaonan Wang
- Department of Hematology, Cambridge Institute for Medical Research and Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, UK
| | | | - Francisco Gutiérrez-Agüera
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Spain
| | - Heleia Roca-Ho
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Spain
| | - Veronica Ayllon
- GENyO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government and University of Granada, Department of Biochemistry and Molecular Biology, Granada, Spain
| | - Pedro J Real
- GENyO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government and University of Granada, Department of Biochemistry and Molecular Biology, Granada, Spain
| | - David Arambilet
- Programa de Cáncer, Instituto Hospital del Mar de Investigaciones Médicas. Barcelona. Spain
| | - Lluis Espinosa
- Programa de Cáncer, Instituto Hospital del Mar de Investigaciones Médicas. Barcelona. Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
| | - Raul Torres-Ruiz
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Spain
| | - Antonio Agraz-Doblas
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Spain
- Instituto de Biomedicina y Biotecnología de Cantabria (CSIC-UC-Sodercan), Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria (CSIC-UC-Sodercan), Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Jasper de Boer
- Cancer Section, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Anna Bigas
- Programa de Cáncer, Instituto Hospital del Mar de Investigaciones Médicas. Barcelona. Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
| | - Bertie Gottgens
- Department of Hematology, Cambridge Institute for Medical Research and Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, UK
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology, Goethe-University, Frankfurt, Germany
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
- Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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15
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Agraz-Doblas A, Bueno C, Bashford-Rogers R, Roy A, Schneider P, Bardini M, Ballerini P, Cazzaniga G, Moreno T, Revilla C, Gut M, Valsecchi MG, Roberts I, Pieters R, De Lorenzo P, Varela I, Menendez P, Stam RW. Unraveling the cellular origin and clinical prognostic markers of infant B-cell acute lymphoblastic leukemia using genome-wide analysis. Haematologica 2019; 104:1176-1188. [PMID: 30679323 PMCID: PMC6545849 DOI: 10.3324/haematol.2018.206375] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/20/2018] [Indexed: 02/06/2023] Open
Abstract
B-cell acute lymphoblastic leukemia is the commonest childhood cancer. In infants, B-cell acute lymphoblastic leukemia remains fatal, especially in patients with t(4;11), present in ~80% of cases. The pathogenesis of t(4;11)/KMT2A-AFF1+ (MLL-AF4+) infant B-cell acute lymphoblastic leukemia remains difficult to model, and the pathogenic contribution in cancer of the reciprocal fusions resulting from derivative translocated-chromosomes remains obscure. Here, “multi-layered” genome-wide analyses and validation were performed on a total of 124 de novo cases of infant B-cell acute lymphoblastic leukemia uniformly diagnosed and treated according to the Interfant 99/06 protocol. These patients showed the most silent mutational landscape reported so far for any sequenced pediatric cancer. Recurrent mutations were exclusively found in K-RAS and N-RAS, were subclonal and were frequently lost at relapse, despite a larger number of non-recurrent/non-silent mutations. Unlike non-MLL-rearranged B-cell acute lymphoblastic leukemias, B-cell receptor repertoire analysis revealed minor, non-expanded B-cell clones in t(4;11)+ infant B-cell acute lymphoblastic leukemia, and RNA-sequencing showed transcriptomic similarities between t(4;11)+ infant B-cell acute lymphoblastic leukemias and the most immature human fetal liver hematopoietic stem and progenitor cells, confirming a “pre-VDJ” fetal cellular origin for both t(4;11) and RASmut. The reciprocal fusion AF4-MLL was expressed in only 45% (19/43) of the t(4;11)+ patients, and HOXA cluster genes are exclusively expressed in AF4-MLL-expressing patients. Importantly, AF4-MLL/HOXA-expressing patients had a significantly better 4-year event-free survival (62.4% vs. 11.7%, P=0.001), and overall survival (73.7 vs. 25.2%, P=0.016). AF4-MLL expression retained its prognostic significance when analyzed in a Cox model adjusting for risk stratification according to the Interfant-06 protocol based on age at diagnosis, white blood cell count and response to prednisone. This study has clinical implications for disease outcome and diagnostic risk-stratification of t(4;11)+ infant B-cell acute lymphoblastic leukemia.
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Affiliation(s)
- Antonio Agraz-Doblas
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain.,Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Spain
| | | | - Anindita Roy
- Department of Paediatrics, University of Oxford, UK
| | - Pauline Schneider
- Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Michela Bardini
- Centro Ricerca Tettamanti, Department of Pediatrics, University of Milano Bicocca, Fondazione MBBM, Monza, Italy
| | | | - Gianni Cazzaniga
- Centro Ricerca Tettamanti, Department of Pediatrics, University of Milano Bicocca, Fondazione MBBM, Monza, Italy
| | - Thaidy Moreno
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Carlos Revilla
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Marta Gut
- CNAG-CRG, Center for Genomic Regulation, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Maria G Valsecchi
- Interfant Trial Data Center, University of Milano-Bicocca, Monza, Italy
| | - Irene Roberts
- Department of Paediatrics, University of Oxford, UK.,MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Rob Pieters
- Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Paola De Lorenzo
- Interfant Trial Data Center, University of Milano-Bicocca, Monza, Italy
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Spain .,Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), ISCIII, Barcelona, Spain
| | - Ronald W Stam
- Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands
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16
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Somers K, Wen VW, Middlemiss SMC, Osborne B, Forgham H, Jung M, Karsa M, Clifton M, Bongers A, Gao J, Mayoh C, Raoufi-Rad N, Kusnadi EP, Hannan KM, Scott DA, Kwek A, Liu B, Flemming C, Chudakova DA, Pandher R, Failes TW, Lim J, Angeli A, Osterman AL, Imamura T, Kees UR, Supuran CT, Pearson RB, Hannan RD, Davis TP, McCarroll J, Kavallaris M, Turner N, Gudkov AV, Haber M, Norris MD, Henderson MJ. A novel small molecule that kills a subset of MLL-rearranged leukemia cells by inducing mitochondrial dysfunction. Oncogene 2019; 38:3824-3842. [PMID: 30670779 PMCID: PMC6756102 DOI: 10.1038/s41388-018-0666-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 08/21/2018] [Accepted: 12/11/2018] [Indexed: 12/27/2022]
Abstract
Survival rates for pediatric patients suffering from mixed lineage leukemia (MLL)-rearranged leukemia remain below 50% and more targeted, less toxic therapies are urgently needed. A screening method optimized to discover cytotoxic compounds selective for MLL-rearranged leukemia identified CCI-006 as a novel inhibitor of MLL-rearranged and CALM-AF10 translocated leukemias that share common leukemogenic pathways. CCI-006 inhibited mitochondrial respiration and induced mitochondrial membrane depolarization and apoptosis in a subset (7/11, 64%) of MLL-rearranged leukemia cell lines within a few hours of treatment. The unresponsive MLL-rearranged leukemia cells did not undergo mitochondrial membrane depolarization or apoptosis despite a similar attenuation of mitochondrial respiration by the compound. In comparison to the sensitive cells, the unresponsive MLL-rearranged leukemia cells were characterized by a more glycolytic metabolic phenotype, exemplified by a more pronounced sensitivity to glycolysis inhibitors and elevated HIF1α expression. Silencing of HIF1α expression sensitized an intrinsically unresponsive MLL-rearranged leukemia cell to CCI-006, indicating that this pathway plays a role in determining sensitivity to the compound. In addition, unresponsive MLL-rearranged leukemia cells expressed increased levels of MEIS1, an important leukemogenic MLL target gene that plays a role in regulating metabolic phenotype through HIF1α. MEIS1 expression was also variable in a pediatric MLL-rearranged ALL patient dataset, highlighting the existence of a previously undescribed metabolic variability in MLL-rearranged leukemia that may contribute to the heterogeneity of the disease. This study thus identified a novel small molecule that rapidly kills MLL-rearranged leukemia cells by targeting a metabolic vulnerability in a subset of low HIF1α/low MEIS1-expressing MLL-rearranged leukemia cells.
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Affiliation(s)
- Klaartje Somers
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia
| | - Victoria W Wen
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia
| | - Shiloh M C Middlemiss
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia
| | - Brenna Osborne
- Mitochondrial Bioenergetics Laboratory, School of Medical Sciences, UNSW, Randwick, NSW, Australia
| | - Helen Forgham
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Australian Centre for NanoMedicine, UNSW Australia, Sydney, NSW, Australia
| | - MoonSun Jung
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia
| | - Mawar Karsa
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia
| | - Molly Clifton
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia
| | - Angelika Bongers
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia
| | - Jixuan Gao
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia
| | - Newsha Raoufi-Rad
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia
| | - Eric P Kusnadi
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Kate M Hannan
- The John Curtin School of Medical Research, The Australian National University, Canberra City, ACT, Australia
| | - David A Scott
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Alan Kwek
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia
| | - Bing Liu
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia
| | - Claudia Flemming
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia
| | - Daria A Chudakova
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia
| | - Ruby Pandher
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia
| | - Tim W Failes
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia.,ACRF Drug Discovery Centre, Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, New South Wales, Australia
| | - James Lim
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia
| | - Andrea Angeli
- Neurofarba Department, University of Florence, Florence, Italy
| | - Andrei L Osterman
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Toshihiko Imamura
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ursula R Kees
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | | | | | - Ross D Hannan
- The John Curtin School of Medical Research, The Australian National University, Canberra City, ACT, Australia
| | - Thomas P Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology Monash Institute of Pharmaceutical Sciences, Monash University, Clayton, VIC, Australia.,Department of Chemistry, University of Warrick, Coventry, UK
| | - Joshua McCarroll
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Australian Centre for NanoMedicine, UNSW Australia, Sydney, NSW, Australia
| | - Maria Kavallaris
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Australian Centre for NanoMedicine, UNSW Australia, Sydney, NSW, Australia
| | - Nigel Turner
- Mitochondrial Bioenergetics Laboratory, School of Medical Sciences, UNSW, Randwick, NSW, Australia
| | - Andrei V Gudkov
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA.,Oncotartis, Inc., Buffalo, NY, USA
| | - Michelle Haber
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia
| | - Murray D Norris
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia.,UNSW Centre for Childhood Cancer Research, Sydney, NSW, Australia
| | - Michelle J Henderson
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick, NSW, Australia.
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17
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Zhang P, Liu N, Xu X, Wang Z, Cheng Y, Jin W, Wang X, Yang H, Liu H, Zhang Y, Tu Y. Clinical significance of Iroquois Homeobox Gene - IRX1 in human glioma. Mol Med Rep 2018; 17:4651-4656. [PMID: 29328446 DOI: 10.3892/mmr.2018.8404] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 01/02/2018] [Indexed: 11/05/2022] Open
Abstract
The present study aimed to investigate the location, expression and clinical significance of Iroquois homeobox gene (IRX1) in human glioma. The expression of IRX1 gene in glioma cell lines (U87, U373, LN229 and T98G) and normal brain tissue was detected via reverse transcription-polymerase chain reaction. The IRX1 protein in fresh glioma specimens, with the adjacent normal brain tissue, was quantified through western blotting. The archived glioma only specimens from the present hospital and glioma specimens with adjacent normal brain tissue, from Alenabio biotechnology, were subjected to immunohistochemistry and tissue microarray analysis, respectively. The Kaplan-Meier method was employed to assess the correlation between the IRX1 level and the overall survival time of the patients. IRX1 gene was demonstrated to be expressed at varying levels in U373, LN229 and T98G cells, however not in U87 cells and normal brain tissue. Western blotting revealed increased IRX1 expression in glioma tissue compared with adjacent normal brain tissue. Furthermore, a direct correlation was observed between the IRX1 expression and the clinical glioma grade, with a significant difference in the gene expression between high grade and low grade glioma (P<0.05). Notably, IRX1 was identified to be localized to the cytoplasm in the adjacent normal brain and World Health Organization grade I glioma, whereas was identified to be present in the nucleus in higher grade glioma. In addition to being established as a significant prognostic variable, IRX1 expression was positively correlated with the overall survival of glioma patients. IRX1 gene may therefore exhibit an oncogenic role in glioma condition, and thus may be of clinical importance as a future therapeutic target.
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Affiliation(s)
- Pengxing Zhang
- Department of Experimental Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Nan Liu
- Department of Experimental Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Xiaoshan Xu
- Department of Experimental Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Zhen Wang
- Department of Experimental Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Yingduan Cheng
- Department of Experimental Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Weilin Jin
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, Key Laboratory for Thin Film and Microfabrication Technology of Ministry of Education, School of Electronic Information and Electronic Engineering, Shanghai Jiao Tong University, Shanghai 200240, P.R China
| | - Xin Wang
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Hongwei Yang
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Hui Liu
- Department of Experimental Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Yongsheng Zhang
- Department of Experimental Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Yanyang Tu
- Department of Experimental Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, P.R. China
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Steinhilber D, Marschalek R. How to effectively treat acute leukemia patients bearing MLL-rearrangements ? Biochem Pharmacol 2017; 147:183-190. [PMID: 28943239 DOI: 10.1016/j.bcp.2017.09.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 09/19/2017] [Indexed: 10/18/2022]
Abstract
Chromosomal translocations - leading to the expression of fusion genes - are well-studied genetic abberrations associated with the development of leukemias. Most of them represent altered transcription factors that affect transcription or epigenetics, while others - like BCR-ABL - are enhancing signaling. BCR-ABL has become the prototype for rational drug design, and drugs like Imatinib and subsequently improved drugs have a great impact on cancer treatments. By contrast, MLL-translocations in acute leukemia patients are hard to treat, display a high relapse rate and the overall survival rate is still very poor. Therefore, new treatment modalities are urgently needed. Based on the molecular insights of the most frequent MLL rearrangements, BET-, DOT1L-, SET- and MEN1/LEDGF-inhibitors have been developed and first clinical studies were initiated. Not all results of these studies have are yet available, however, a first paper reports a failure in the DOT1L-inhibitor study although it was the most promising drug based on literature data. One possible explanation is that all of the above mentioned drugs also target the cognate wildtype proteins. Here, we want to strengthen the fact that efforts should be made to develop drugs or strategies to selectively inhibit only the fusion proteins. Some examples will be given that follow exactly this guideline, and proof-of-concept experiments have already demonstrated their feasibility and effectiveness. Some of the mentioned approaches were using drugs that are already on the market, indicating that there are existing opportunities for the future which should be implemented in future therapy strategies.
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Affiliation(s)
- Dieter Steinhilber
- Institute of Pharm. Chemistry, Goethe-University, Frankfurt/Main, Germany
| | - Rolf Marschalek
- Institute of Pharm. Biology/DCAL, Goethe-University, Frankfurt/Main, Germany.
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Deciphering KRAS and NRAS mutated clone dynamics in MLL-AF4 paediatric leukaemia by ultra deep sequencing analysis. Sci Rep 2016; 6:34449. [PMID: 27698462 PMCID: PMC5048141 DOI: 10.1038/srep34449] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/09/2016] [Indexed: 12/28/2022] Open
Abstract
To induce and sustain the leukaemogenic process, MLL-AF4+ leukaemia seems to require very few genetic alterations in addition to the fusion gene itself. Studies of infant and paediatric patients with MLL-AF4+ B cell precursor acute lymphoblastic leukaemia (BCP-ALL) have reported mutations in KRAS and NRAS with incidences ranging from 25 to 50%. Whereas previous studies employed Sanger sequencing, here we used next generation amplicon deep sequencing for in depth evaluation of RAS mutations in 36 paediatric patients at diagnosis of MLL-AF4+ leukaemia. RAS mutations including those in small sub-clones were detected in 63.9% of patients. Furthermore, the mutational analysis of 17 paired samples at diagnosis and relapse revealed complex RAS clone dynamics and showed that the mutated clones present at relapse were almost all originated from clones that were already detectable at diagnosis and survived to the initial therapy. Finally, we showed that mutated patients were indeed characterized by a RAS related signature at both transcriptional and protein levels and that the targeting of the RAS pathway could be of beneficial for treatment of MLL-AF4+ BCP-ALL clones carrying somatic RAS mutations.
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