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Lysenkova Wiklander M, Arvidsson G, Bunikis I, Lundmark A, Raine A, Marincevic-Zuniga Y, Gezelius H, Bremer A, Feuk L, Ameur A, Nordlund J. A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing. Life Sci Alliance 2024; 7:e202302481. [PMID: 38777370 PMCID: PMC11111970 DOI: 10.26508/lsa.202302481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
The B-cell acute lymphoblastic leukemia (ALL) cell line REH, with the t(12;21) ETV6::RUNX1 translocation, is known to have a complex karyotype defined by a series of large-scale chromosomal rearrangements. Taken from a 15-yr-old at relapse, the cell line offers a practical model for the study of pediatric B-ALL. In recent years, short- and long-read DNA and RNA sequencing have emerged as a complement to karyotyping techniques in the resolution of structural variants in an oncological context. Here, we explore the integration of long-read PacBio and Oxford Nanopore whole-genome sequencing, IsoSeq RNA sequencing, and short-read Illumina sequencing to create a detailed genomic and transcriptomic characterization of the REH cell line. Whole-genome sequencing clarified the molecular traits of disrupted ALL-associated genes including CDKN2A, PAX5, BTG1, VPREB1, and TBL1XR1, as well as the glucocorticoid receptor NR3C1 Meanwhile, transcriptome sequencing identified seven fusion genes within the genomic breakpoints. Together, our extensive whole-genome investigation makes high-quality open-source data available to the leukemia genomics community.
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Affiliation(s)
- Mariya Lysenkova Wiklander
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Gustav Arvidsson
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Anders Lundmark
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Amanda Raine
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Yanara Marincevic-Zuniga
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Henrik Gezelius
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Anna Bremer
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/01apvbh93 Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Lars Feuk
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Adam Ameur
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
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2
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Fagnan A, Aid Z, Baille M, Drakul A, Robert E, Lopez CK, Thirant C, Lecluse Y, Rivière J, Ignacimouttou C, Salmoiraghi S, Anguita E, Naimo A, Marzac C, Pflumio F, Malinge S, Wichmann C, Huang Y, Lobry C, Chaumeil J, Soler E, Bourquin J, Nerlov C, Bernard OA, Schwaller J, Mercher T. The ETO2 transcriptional cofactor maintains acute leukemia by driving a MYB/EP300-dependent stemness program. Hemasphere 2024; 8:e90. [PMID: 38903535 PMCID: PMC11187848 DOI: 10.1002/hem3.90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/13/2024] [Accepted: 05/01/2024] [Indexed: 06/22/2024] Open
Abstract
Transcriptional cofactors of the ETO family are recurrent fusion partners in acute leukemia. We characterized the ETO2 regulome by integrating transcriptomic and chromatin binding analyses in human erythroleukemia xenografts and controlled ETO2 depletion models. We demonstrate that beyond its well-established repressive activity, ETO2 directly activates transcription of MYB, among other genes. The ETO2-activated signature is associated with a poorer prognosis in erythroleukemia but also in other acute myeloid and lymphoid leukemia subtypes. Mechanistically, ETO2 colocalizes with EP300 and MYB at enhancers supporting the existence of an ETO2/MYB feedforward transcription activation loop (e.g., on MYB itself). Both small-molecule and PROTAC-mediated inhibition of EP300 acetyltransferases strongly reduced ETO2 protein, chromatin binding, and ETO2-activated transcripts. Taken together, our data show that ETO2 positively enforces a leukemia maintenance program that is mediated in part by the MYB transcription factor and that relies on acetyltransferase cofactors to stabilize ETO2 scaffolding activity.
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Affiliation(s)
- Alexandre Fagnan
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Zakia Aid
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
| | - Marie Baille
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
| | - Aneta Drakul
- Division of Oncology and Children's Research CentreUniversity Children's Hospital ZurichZurichSwitzerland
| | - Elie Robert
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
| | - Cécile K. Lopez
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
| | - Cécile Thirant
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
| | - Yann Lecluse
- Gustave Roussy, Plateforme Imagerie et Cytométrie, Université Paris‐Saclay, UMS AMMICA, INSERM US23, CNRS UMS 3655VillejuifFrance
| | - Julie Rivière
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
| | - Cathy Ignacimouttou
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
| | - Silvia Salmoiraghi
- Department of Oncology and HematologyAzienda Socio Sanitaria Territoriale Papa Giovanni XXIII, FROM Research Foundation, Papa Giovanni XXIII HospitalBergamoItaly
| | - Eduardo Anguita
- Hematology Department, Hospital Clínico San Carlos (HCSC), IML, IdISSC, Department of MedicineUniversidad Complutense de Madrid (UCM)MadridSpain
| | - Audrey Naimo
- Gustave Roussy, Genomic PlatformUniversité Paris‐Saclay, UMS AMMICA, INSERM US23, CNRS UMS 3655VillejuifFrance
| | - Christophe Marzac
- Department of HematologyLeukemia Interception Program, Personalized Cancer Prevention Center, Gustave RoussyVillejuifFrance
| | - Françoise Pflumio
- Equipe Labellisée Ligue Contre le CancerParisFrance
- Unité de Recherche (UMR)‐E008 Stabilité Génétique, Cellules Souches et Radiations, Team Niche and Cancer in Hematopoiesis, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)Université de Paris‐Université Paris‐SaclayFontenay‐aux‐RosesFrance
- OPALE Carnot Institute, The Organization for Partnerships in LeukemiaParisFrance
| | - Sébastien Malinge
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- Telethon Kids Institute, Perth Children's HospitalNedlandsAustralia
| | - Christian Wichmann
- Department of Transfusion Medicine, Cell Therapeutics and HaemostasisLudwig‐Maximilians‐University of MunichMunichGermany
| | - Yun Huang
- Division of Oncology and Children's Research CentreUniversity Children's Hospital ZurichZurichSwitzerland
| | - Camille Lobry
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- INSERM U944, CNRS UMR7212Institut de Recherche Saint Louis and Université de ParisParisFrance
| | - Julie Chaumeil
- Université de Paris, Institut Cochin, INSERM, CNRSParisFrance
| | - Eric Soler
- IGMM, University of Montpellier, CNRS, Montpellier, France & Université de Paris, Laboratory of Excellence GR‐ExParisFrance
| | - Jean‐Pierre Bourquin
- Division of Oncology and Children's Research CentreUniversity Children's Hospital ZurichZurichSwitzerland
| | - Claus Nerlov
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe HospitalUniversity of OxfordOxfordUK
| | | | - Juerg Schwaller
- Department of BiomedicineUniversity Children's Hospital Beider Basel (UKBB), University of BaselBaselSwitzerland
| | - Thomas Mercher
- Gustave Roussy, INSERM U1170Université Paris‐SaclayVillejuifFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
- OPALE Carnot Institute, The Organization for Partnerships in LeukemiaParisFrance
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3
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Liu XS, Liu ZY, Zeng DB, Hu J, Chen XL, Gu JL, Gao Y, Pei ZJ. Functional enrichment analysis reveals the involvement of DARS2 in multiple biological pathways and its potential as a therapeutic target in esophageal carcinoma. Aging (Albany NY) 2024; 16:3934-3954. [PMID: 38382106 PMCID: PMC10929822 DOI: 10.18632/aging.205569] [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: 10/06/2023] [Accepted: 01/17/2024] [Indexed: 02/23/2024]
Abstract
OBJECTIVE The enzyme Aspartyl tRNA synthetase 2 (DARS2) is a crucial enzyme in the mitochondrial tRNA synthesis pathway, playing a critical role in maintaining normal mitochondrial function and protein synthesis. However, the role of DARS2 in ESCA is unclear. MATERIALS AND METHODS Transcriptional data of pan-cancer and ESCA were downloaded from UCSC XENA, TCGA, and GEO databases to analyze the differential expression of DARS2 between tumor samples and normal samples, and its correlation with clinicopathological features of ESCA patients. R was used for GO, KEGG, and GSEA functional enrichment analysis of DARS2 co-expression and to analyze the connection of DARS2 with glycolysis and m6A-related genes. In vitro experiments were performed to assess the effects of interfering with DARS2 expression on ESCA cells. TarBase v.8, mirDIP, miRTarBase, ENCORI, and miRNet databases were used to analyze and construct a ceRNA network containing DARS2. RESULTS DARS2 was overexpressed in various types of tumors. In vitro experiments confirmed that interfering with DARS2 expression significantly affected the proliferation, migration, apoptosis, cell cycle, and glycolysis of ESCA cells. DARS2 may be involved in multiple biological pathways related to tumor development. Furthermore, correlation and differential analysis revealed that DARS2 may regulate ESCA m6A modification through its interaction with METTL3 and YTHDF1. A ceRNA network containing DARS2, DLEU2/has-miR-30a-5p/DARS2, was successfully predicted and constructed. CONCLUSIONS Our findings reveal the upregulation of DARS2 in ESCA and its association with clinical features, glycolysis pathway, m6A modification, and ceRNA network. These discoveries provide valuable insights into the molecular mechanisms underlying ESCA.
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Affiliation(s)
- Xu-Sheng Liu
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Zi-Yue Liu
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Dao-Bing Zeng
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Jian Hu
- Department of Critical Care Medicine, Danjiangkou First Hospital, Danjiangkou 420381, Hubei, China
| | - Xuan-Long Chen
- Department of Medical Ultrasound, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Jiao-Long Gu
- Department of Obstetrics and Gynecology, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Yan Gao
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Zhi-Jun Pei
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
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4
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Leary JR, Bacher R. Interpretable trajectory inference with single-cell Linear Adaptive Negative-binomial Expression (scLANE) testing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572477. [PMID: 38187622 PMCID: PMC10769309 DOI: 10.1101/2023.12.19.572477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The rapid proliferation of trajectory inference methods for single-cell RNA-seq data has allowed researchers to investigate complex biological processes by examining underlying gene expression dynamics. After estimating a latent cell ordering, statistical models are used to determine which genes exhibit changes in expression that are significantly associated with progression through the biological trajectory. While a few techniques for performing trajectory differential expression exist, most rely on the flexibility of generalized additive models in order to account for the inherent nonlinearity of changes in gene expression. As such, the results can be difficult to interpret, and biological conclusions often rest on subjective visual inspections of the most dynamic genes. To address this challenge, we propose scLANE testing, which is built around an interpretable generalized linear model and handles nonlinearity with basis splines chosen empirically for each gene. In addition, extensions to estimating equations and mixed models allow for reliable trajectory testing under complex experimental designs. After validating the accuracy of scLANE under several different simulation scenarios, we apply it to a set of diverse biological datasets and display its ability to provide novel biological information when used downstream of both pseudotime and RNA velocity estimation methods.
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Affiliation(s)
- Jack R. Leary
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, USA
| | - Rhonda Bacher
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, USA
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5
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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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6
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Li Y, Liu Y, Gao X, Zhao W, Zhou F, Liu H, Wang W. Identification of novel PIEZO1::CBFA2T3 and INO80C::SETBP1 fusion genes in an acute myeloid leukemia patient by RNA-seq. Mol Biol Rep 2023; 50:1961-1966. [PMID: 36472727 DOI: 10.1007/s11033-022-08138-x] [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: 07/22/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Fusion genes are recurrent molecular aberrations in acute myeloid leukemia, with significant diagnostic and therapeutic value. The identification of novel fusion genes provides advanced biomarkers for diagnosis and facilitates the discovery of drug targets. METHODS Bone marrow sample was extracted from an acute myeloid leukemia patient and RNA-sequencing was performed. Several bioinformatic methods, including differential analysis and Gene Set Enrichment Analysis (GSEA) pathway analyses were conducted based on the expression data. RESULTS Two novel fusion genes, PIEZO1::CBFA2T3 and INO80C::SETBP1, were identified by RNA-seq. Differential analysis found that SETBP1 and CBFA2T3 were overexpressed, and GSEA analysis showed the activation of immune-related pathways. These findings indicate dysfunction of the fusion related- genes and possible pathogenic effect of the fusion genes. CONCLUSION We reported a male AML patient with presence of PIEZO1::CBFA2T3 and INO80C::SETBP1 fusion genes.
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Affiliation(s)
- Yanling Li
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yao Liu
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xinyu Gao
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Weiwei Zhao
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Fanghui Zhou
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hongxing Liu
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, 065201, China.
- Beijing Lu Daopei Institute of Hematology, Beijing, 100076, China.
- Division of Pathology & Laboratory Medicine, Beijing Lu Daopei Hospital, Beijing, 100076, China.
| | - Wei Wang
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.
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7
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RUNX1 and RUNX3 Genes Expression Level in Adult Acute Lymphoblastic Leukemia-A Case Control Study. Curr Issues Mol Biol 2022; 44:3455-3464. [PMID: 36005134 PMCID: PMC9406551 DOI: 10.3390/cimb44080238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022] Open
Abstract
The genetic factors of adult acute lymphoblastic leukemia (ALL) development are only partially understood. The Runt-Related Transcription Factor (RUNX) gene family play a crucial role in hematological malignancies, serving both a tumor suppressor and promoter function. The aim of this study was the assessment of relative RUNX1 and RUNX3 genes expression level among adult ALL cases and a geographically and ethnically matched control group. The relative RUNX1 and RUNX3 genes expression level was assessed by qPCR. The investigated group comprised 60 adult patients newly diagnosed with ALL. The obtained results were compared with a group of 40 healthy individuals, as well as clinical and hematological parameters of patients, and submitted for statistical analysis. ALL patients tend to have significantly higher RUNX1 gene expression level compared with controls. This observation is also true for risk group stratification where high-risk (HR) patients presented higher levels of RUNX1. A higher RUNX1 transcript level correlates with greater leukocytosis while RUNX3 expression is reduced in Philadelphia chromosome bearers. The conducted study sustains the hypothesis that both a reduction and increase in the transcript level of RUNX family genes may be involved in leukemia pathogenesis, although their interaction is complex. In this context, overexpression of the RUNX1 gene in adult ALL cases in particular seems interesting. Obtained results should be interpreted with caution. Further analysis in this research field is needed.
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Jakobczyk H, Jiang Y, Debaize L, Soubise B, Avner S, Sérandour AA, Rouger-Gaudichon J, Rio AG, Carroll JS, Raslova H, Gilot D, Liu Z, Demengeot J, Salbert G, Douet-Guilbert N, Corcos L, Galibert MD, Gandemer V, Troadec MB. ETV6-RUNX1 and RUNX1 directly regulate RAG1 expression: one more step in the understanding of childhood B-cell acute lymphoblastic leukemia leukemogenesis. Leukemia 2021; 36:549-554. [PMID: 34535762 PMCID: PMC8807389 DOI: 10.1038/s41375-021-01409-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 11/14/2022]
Abstract
ETV6-RUNX1 and RUNX1 directly promote RAG1 expression. ETV6-RUNX1 and RUNX1 preferentially bind to the −1200 bp enhancer of RAG1 and the −80 bp promoter of RAG1 gene respectively, and compete for these bindings. ETV6-RUNX1 and RUNX1 induce an excessive RAG recombinase activity. ETV6-RUNX1 participates directly in two events of the multi-hit ALL leukemogenesis: as an initiating event and as an activator of RAG1 expression.
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Affiliation(s)
- Hélène Jakobczyk
- Univ Rennes 1, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, Rennes, France
| | - Yan Jiang
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France.,Department of Hematology, The First Hospital of Jilin University, Changchun, China
| | - Lydie Debaize
- Univ Rennes 1, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, Rennes, France
| | | | - Stéphane Avner
- Univ Rennes 1, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, Rennes, France
| | | | | | - Anne-Gaëlle Rio
- Univ Rennes 1, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, Rennes, France
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Hana Raslova
- INSERM, UMR 1287, Gustave Roussy, Université Paris Saclay, Villejuif, France.,Equipe labellisée Ligue Nationale contre le Cancer, Villejuif, France
| | - David Gilot
- INSERM, Université Rennes, CLCC Eugène Marquis, UMR_S 1242, Rennes, France
| | - Ziling Liu
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Jocelyne Demengeot
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, Oeiras, Portugal
| | - Gilles Salbert
- Univ Rennes 1, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, Rennes, France
| | - Nathalie Douet-Guilbert
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France.,CHRU Brest, Service de génétique, laboratoire de génétique chromosomique, Brest, France
| | | | - Marie-Dominique Galibert
- Univ Rennes 1, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, Rennes, France.,Centre Hospitalier Universitaire de Rennes (CHU-Rennes), Service de Génétique et Génomique Moléculaire, Rennes, France
| | - Virginie Gandemer
- Univ Rennes 1, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, Rennes, France.,Centre Hospitalier Universitaire de Rennes (CHU-Rennes), Department of pediatric hemato-oncology, Rennes, France
| | - Marie-Bérengère Troadec
- Univ Rennes 1, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, Rennes, France. .,Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France. .,CHRU Brest, Service de génétique, laboratoire de génétique chromosomique, Brest, France.
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9
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Kasprzyk ME, Sura W, Dzikiewicz-Krawczyk A. Enhancing B-Cell Malignancies-On Repurposing Enhancer Activity towards Cancer. Cancers (Basel) 2021; 13:3270. [PMID: 34210001 PMCID: PMC8269369 DOI: 10.3390/cancers13133270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 01/19/2023] Open
Abstract
B-cell lymphomas and leukemias derive from B cells at various stages of maturation and are the 6th most common cancer-related cause of death. While the role of several oncogenes and tumor suppressors in the pathogenesis of B-cell neoplasms was established, recent research indicated the involvement of non-coding, regulatory sequences. Enhancers are DNA elements controlling gene expression in a cell type- and developmental stage-specific manner. They ensure proper differentiation and maturation of B cells, resulting in production of high affinity antibodies. However, the activity of enhancers can be redirected, setting B cells on the path towards cancer. In this review we discuss different mechanisms through which enhancers are exploited in malignant B cells, from the well-studied translocations juxtaposing oncogenes to immunoglobulin loci, through enhancer dysregulation by sequence variants and mutations, to enhancer hijacking by viruses. We also highlight the potential of therapeutic targeting of enhancers as a direction for future investigation.
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