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Hu Z, Tang X, Chen F, Li T, Liu Y, Zhou G, Liu S, Wang Y, Liu S, Mai H, Wang L. Molecular genetics profiling of core-binding factor acute myeloid leukemia in pediatrics. Ther Adv Hematol 2025; 16:20406207251330064. [PMID: 40290757 PMCID: PMC12033452 DOI: 10.1177/20406207251330064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Accepted: 03/07/2025] [Indexed: 04/30/2025] Open
Abstract
Core-binding factor acute myeloid leukemia (CBF-AML) is a subtype of AML characterized by specific genetic rearrangements, including t(8;21) and inv(16), which are associated with a relatively favorable prognosis with relapse rates around 30%. The mutational profiling of CBF-AML is highly heterogeneous in pediatrics, with mutations in the tyrosine kinase pathway (including KIT, FLT3, and N/KRAS), epigenetic regulators, cohesin, and additional cytogenetic abnormalities. The identification of high-risk mutations, such as those in KIT and FLT3, underscores the need for targeted therapies and highlights the importance of high-throughput sequencing technologies, providing critical insights into the prognosis and informing treatment strategies. Integrating targeted agents with existing treatment protocols has the potential to enhance treatment efficacy and significantly improve patient outcomes. However, CBF-AML presents significant heterogeneity in both pathophysiology and clinical characteristics, with cooperating cytogenetic mutations, leading to difficulties and uncertainties in the prognosis and treatment of CBF-AML in pediatrics. Given the relapse rates and the significant impact of specific mutations on prognosis, there is a critical need for improved risk stratification and personalized treatment approaches in pediatric CBF-AML. Ongoing research and clinical trials focusing on the molecular and genetic profiling of pediatric CBF-AML will be essential for developing more effective and targeted therapies, ultimately improving patient outcomes. This review summarizes the molecular genetics profiling in CBF-AML among pediatrics, targeting its effect and interactions on prognosis and treatment to provide an overview for further research based on mutations among CBF-AML in pediatrics.
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Affiliation(s)
- Zhilin Hu
- Shantou University Medical College, Shantou, Guangdong, China
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Xue Tang
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Fen Chen
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Tonghui Li
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Yi Liu
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Guichi Zhou
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Shilin Liu
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Ying Wang
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Sixi Liu
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Huirong Mai
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Lulu Wang
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong 518026, China
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston 02215, MA, USA
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Dao B, Trinh VN, Nguyen HV, Nguyen HL, Le TD, Luu PL. Crosstalk between genomic variants and DNA methylation in FLT3 mutant acute myeloid leukemia. Brief Funct Genomics 2025; 24:elae028. [PMID: 38944027 PMCID: PMC11735749 DOI: 10.1093/bfgp/elae028] [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: 01/10/2024] [Revised: 05/31/2024] [Accepted: 06/20/2024] [Indexed: 07/01/2024] Open
Abstract
Acute myeloid leukemia (AML) is a type of blood cancer with diverse genetic variations and DNA methylation alterations. By studying the interaction of gene mutations, expression, and DNA methylation, we aimed to gain valuable insights into the processes that lead to block differentiation in AML. We analyzed TCGA-LAML data (173 samples) with RNA sequencing and DNA methylation arrays, comparing FLT3 mutant (48) and wild-type (125) cases. We conducted differential gene expression analysis using cBioPortal, identified DNA methylation differences with ChAMP tool, and correlated them with gene expression changes. Gene set enrichment analysis (g:Profiler) revealed significant biological processes and pathways. ShinyGo and GeneCards were used to find potential transcription factors and their binding sites among significant genes. We found significant differentially expressed genes (DEGs) negatively correlated with their most significant methylation probes (Pearson correlation coefficient of -0.49, P-value <0.001) between FLT3 mutant and wild-type groups. Moreover, our exploration of 450 k CpG sites uncovered a global hypo-methylated status in 168 DEGs. Notably, these methylation changes were enriched in the promoter regions of Homebox superfamily gene, which are crucial in transcriptional-regulating pathways in blood cancer. Furthermore, in FLT3 mutant AML patient samples, we observed overexpress of WT1, a transcription factor known to bind homeobox gene family. This finding suggests a potential mechanism by which WT1 recruits TET2 to demethylate specific genomic regions. Integrating gene expression and DNA methylation analyses shed light on the impact of FLT3 mutations on cancer cell development and differentiation, supporting a two-hit model in AML. This research advances understanding of AML and fosters targeted therapeutic strategy development.
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Affiliation(s)
- Bac Dao
- Hanoi Medical University, Hanoi, Vietnam
- School of Biomedical Sciences, The University of Western Australia, Perth, Australia
| | - Van Ngu Trinh
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Huy V Nguyen
- Health Innovation and Transformation Centre, Federation University, Victoria, Australia
| | - Hoa L Nguyen
- Department of Population and Quantitative Health Sciences, UMass Chan Medical School
| | - Thuc Duy Le
- University of South Australia, Adelaide, Australia
| | - Phuc Loi Luu
- Data Science Division, Tam Anh Research Institute (TamRI), 2B Pho Quang Street, Ward 2, Tan Binh District, Ho Chi Minh City 700000, Vietnam
- Mathematics Department, Faculty of Fundamental Sciences, University of Medicine and Pharmacy at Ho Chi Minh City (UMP), 217 Hong Bang street, Ward 11, District 5, Ho Chi Minh City 700000, Vietnam
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Van Camp L, Depreter B, De Wilde J, Hofmans M, Van der Linden M, Terras E, Chantrain C, Dedeken L, Van Damme A, Uyttebroeck A, Lammens T, De Moerloose B. Acute myeloid leukemia stem cell signature gene EMP1 is not an eligible therapeutic target. Pediatr Res 2025; 97:160-168. [PMID: 38879624 DOI: 10.1038/s41390-024-03341-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/17/2024] [Accepted: 06/04/2024] [Indexed: 02/07/2025]
Abstract
BACKGROUND Relapse in pediatric acute myeloid leukemia (pedAML) patients is known to be associated with residual leukemic stem cells (LSC). We have previously shown that epithelial membrane protein 1 (EMP1) is significantly overexpressed in LSC compared to hematological stem cell fractions. EMP1 was also documented as part of the 17-gene stemness score and a 6-membrane protein gene score, both correlating high EMP1 expression with worse overall survival. However, its potential as a therapeutic target in pedAML is still unexplored. METHODS Association analyses of EMP1 expression with clinical and molecular AML characteristics were performed. Expression of EMP1 was evaluated in pedAML and cord blood samples. Expression in normal blood cells and tissues was evaluated by flow cytometry and immunohistochemistry, respectively. RESULTS In silico analyses showed variable mRNA expression of EMP1 in multiple pedAML datasets, and a significant correlation between high EMP1 transcript levels and the presence of inv(16). Flow cytometry showed overexpression of EMP1 in pedAML samples, as well as expression in normal blood subsets. Importantly, immunohistochemistry revealed EMP1 expression in multiple normal tissues. CONCLUSION Although EMP1 presents as an interesting membrane-associated target in pedAML, its abundant expression in normal blood cells and tissues will impede it from further exploration as a therapeutic target. IMPACT EMP1 is highly expressed in multiple cancer types, but expression in acute myeloid leukemia (AML) and normal tissues is unexplored. As EMP1 is investigated in other cancer types, expression in normal tissues and blood cells is relevant in predicting the success of EMP1-targeted therapies. In this study, we showed expression of EMP1 in multiple tissues, predicting high on-target off-tumor toxicity, which will warn other researchers of possible toxicities when generating EMP1-targeted therapy. Finally, we showed that high EMP1 expression is associated with better overall survival of pediatric AML patients, reducing the need for EMP1-targeted therapy.
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Affiliation(s)
- Laurens Van Camp
- Ghent University, Department of Internal Medicine and Pediatrics, Ghent, Belgium
- Ghent University Hospital, Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent, Belgium
| | - Barbara Depreter
- AZ Delta General Hospital, Department of Laboratory Medicine, Roeselare, Belgium
- Vrije Universiteit Brussel (VUB), Department Pharmaceutical Sciences (FARM), Brussels, Belgium
| | - Jilke De Wilde
- Ghent University Hospital, Department of Pathology, Ghent, Belgium
- Ghent University, Department of Biomolecular Medicine, Ghent, Belgium
| | - Mattias Hofmans
- Ghent University Hospital, Laboratory of Hematology, Ghent, Belgium
- Ghent University, Department of Diagnostic Sciences, Ghent, Belgium
| | - Malaïka Van der Linden
- Ghent University Hospital, Department of Pathology, Ghent, Belgium
- Ghent University, Department of Biomolecular Medicine, Ghent, Belgium
| | - Eva Terras
- Ghent University Hospital, Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent, Belgium
| | - Christophe Chantrain
- Centre Hospitalier Chrétien (CHC), MontLégia, Division of Pediatric Hematology-Oncology, Liège, Belgium
| | - Laurence Dedeken
- Queen Fabiola Children's University Hospital, Department of Pediatric Hematology-Oncology, Brussels, Belgium
| | - An Van Damme
- University Hospital Saint-Luc, Department of Pediatric Hematology Oncology, Brussels, Belgium
| | - Anne Uyttebroeck
- University Hospital Gasthuisberg, Department of Pediatrics, Leuven, Belgium
| | - Tim Lammens
- Ghent University, Department of Internal Medicine and Pediatrics, Ghent, Belgium.
- Ghent University Hospital, Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent, Belgium.
| | - Barbara De Moerloose
- Ghent University, Department of Internal Medicine and Pediatrics, Ghent, Belgium
- Ghent University Hospital, Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent, Belgium
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Schittenhelm MM, Kaiser M, Győrffy B, Kampa-Schittenhelm KM. Evaluation of apoptosis stimulating protein of TP53-1 (ASPP1/PPP1R13B) to predict therapy resistance and overall survival in acute myeloid leukemia (AML). Cell Death Dis 2024; 15:25. [PMID: 38195541 PMCID: PMC10776670 DOI: 10.1038/s41419-023-06372-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/26/2023] [Accepted: 12/05/2023] [Indexed: 01/11/2024]
Abstract
ASPP1 (PPP1R13B) belongs to a family of p53-binding proteins and enhances apoptosis by stimulation of p53-transactivation of selected proapoptotic target genes. It is preferentially expressed in hematopoietic stem cells (HSC) and together with p53 preserves the genomic integrity of the HSC pool. Consequently, dysfunction of ASPP1 has been associated with malignant transformation and development of acute lymphoblastic leukemias and lymphomas - whereas methylation of the promoter region is linked to reduced transcription and ultimately attenuated expression of ASPP1. The role of ASPP1 in AML is not known. We now show that impaired regulation of PPP1R13B contributes to the biology of leukemogenesis and primary therapy resistance in AML. PPP1R13B mRNA expression patterns thereby define a distinct prognostic profile - which is not reflected by the European leukemia net (ELN) risk score. These findings have direct therapeutic implications and we provide a strategy to restore ASPP1 protein levels using hypomethylating agents to sensitize cells towards proapoptotic drugs. Prospective clinical trials are warranted to investigate the role of ASPP1 (PPP1R13B) as a biomarker for risk stratification and as a potential therapeutic target to restore susceptibility to chemotherapy.
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Affiliation(s)
- Marcus M Schittenhelm
- Medical research center (MFZ) and Clinic of Medical Oncology and Hematology, Cantonal Hospital St. Gallen (KSSG), St. Gallen, Switzerland
| | - Max Kaiser
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen (UKT), Tübingen, Germany
| | - Balázs Győrffy
- Semmelweis University Dept. of Bioinformatics and Dept. of Pediatrics, Budapest, H-1094, Hungary
- TTK Cancer Biomarker Research Group, Institute of Enzymology, Budapest, H-1117, Hungary
| | - Kerstin M Kampa-Schittenhelm
- Medical research center (MFZ) and Clinic of Medical Oncology and Hematology, Cantonal Hospital St. Gallen (KSSG), St. Gallen, Switzerland.
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen (UKT), Tübingen, Germany.
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Chianese U, Papulino C, Megchelenbrink W, Tambaro FP, Ciardiello F, Benedetti R, Altucci L. Epigenomic machinery regulating pediatric AML: clonal expansion mechanisms, therapies, and future perspectives. Semin Cancer Biol 2023; 92:84-101. [PMID: 37003397 DOI: 10.1016/j.semcancer.2023.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/07/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease with a genetic, epigenetic, and transcriptional etiology mainly presenting somatic and germline abnormalities. AML incidence rises with age but can also occur during childhood. Pediatric AML (pAML) accounts for 15-20% of all pediatric leukemias and differs considerably from adult AML. Next-generation sequencing technologies have enabled the research community to "paint" the genomic and epigenomic landscape in order to identify pathology-associated mutations and other prognostic biomarkers in pAML. Although current treatments have improved the prognosis for pAML, chemoresistance, recurrence, and refractory disease remain major challenges. In particular, pAML relapse is commonly caused by leukemia stem cells that resist therapy. Marked patient-to-patient heterogeneity is likely the primary reason why the same treatment is successful for some patients but, at best, only partially effective for others. Accumulating evidence indicates that patient-specific clonal composition impinges significantly on cellular processes, such as gene regulation and metabolism. Although our understanding of metabolism in pAML is still in its infancy, greater insights into these processes and their (epigenetic) modulation may pave the way toward novel treatment options. In this review, we summarize current knowledge on the function of genetic and epigenetic (mis)regulation in pAML, including metabolic features observed in the disease. Specifically, we describe how (epi)genetic machinery can affect chromatin status during hematopoiesis, leading to an altered metabolic profile, and focus on the potential value of targeting epigenetic abnormalities in precision and combination therapy for pAML. We also discuss the possibility of using alternative epidrug-based therapeutic approaches that are already in clinical practice, either alone as adjuvant treatments and/or in combination with other drugs.
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Affiliation(s)
- Ugo Chianese
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Chiara Papulino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Wout Megchelenbrink
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy; Princess Máxima Center, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands.
| | - Francesco Paolo Tambaro
- Bone Marrow Transplant Unit, Pediatric Oncology Department AORN Santobono Pausilipon, 80129, Naples Italy.
| | - Fortunato Ciardiello
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Rosaria Benedetti
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy; Biogem Institute of Molecular and Genetic Biology, 83031 Ariano Irpino, Italy; IEOS, Institute for Endocrinology and Oncology "Gaetano Salvatore" (IEOS), 80131 Naples, Italy.
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6
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Identification of the Thyrotropin-Releasing Hormone (TRH) as a Novel Biomarker in the Prognosis for Acute Myeloid Leukemia. Biomolecules 2022; 12:biom12101359. [PMID: 36291567 PMCID: PMC9599642 DOI: 10.3390/biom12101359] [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: 08/30/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
Acute myeloid leukemia (AML) is a biologically and genetically heterogeneous hematological malignance with an unsatisfactory risk stratification system. Recently, through the novel single-cell RNA sequencing technology, we revealed heterogeneous leukemia myeloblasts in RUNX1-RUNX1T1 AML. Thyrotropin-releasing hormone (TRH), as biomarkers of CD34+CD117bri myeloblasts, were found to be prognostic in RUNX1-RUNX1T1 AML. However, the clinical and genetic features of TRH in AML patients are poorly understood. Here, with data from TCGA AML, TRH was found to be downregulated in patients older than 60 years old, with DNMT3A and NPM1 mutations, while overexpressed in patients with KIT mutations. This was further validated in three other cohorts of primary AML including Beat AML (n = 223), GSE6891 (n = 461), and GSE17855 (n = 237). Furthermore, we demonstrated that the expression of TRH in AML could be used to improve the ELN 2017 risk stratification system. In conclusion, our preliminary analysis revealed that TRH, a novel biomarker for AML patients, could be used to evaluate the survival of AML.
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Matsumoto A, Yoshida T, Shima T, Yamasaki K, Tadagaki K, Kondo N, Kuwahara Y, Zhang DE, Okuda T. C11ORF21, a novel RUNX1 target gene, is down-regulated by RUNX1-ETO. BBA ADVANCES 2022; 2:100047. [PMID: 37082605 PMCID: PMC10074976 DOI: 10.1016/j.bbadva.2022.100047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 10/19/2022] Open
Abstract
The fusion protein RUNX1-ETO is an oncogenic transcription factor generated by t(8;21) chromosome translocation, which is found in FAB-M2-type acute myeloid leukemia (AML). RUNX1-ETO is known to dysregulate the normal RUNX1 transcriptional network, which should involve essential factors for the onset of AML with t(8;21). In this study, we screened for possible transcriptional targets of RUNX1 by reanalysis of public data in silico, and identified C11orf21 as a novel RUNX1 target gene because its expression was down-regulated in the presence of RUNX1-ETO. The expression level of C11orf21 was low in AML patient samples with t(8;21) and in Kasumi-1 cells, which carry RUNX1-ETO. Knockdown of RUNX1-ETO in Kasumi-1 cells restored C11orf21 expression, whereas overexpression of RUNX1 up-regulated C11orf21 expression. In addition, knockdown of RUNX1 in other human leukemia cells without RUNX-ETO, such as K562, led to a decrease in C11orf21 expression. Of note, the C11orf21 promoter sequence contains a consensus sequence for RUNX1 binding and it was activated by exogenously expressed RUNX1 based on our luciferase reporter assay. This luciferase signal was trans-dominantly suppressed by RUNX1-ETO and site-directed mutagenesis of the consensus site abrogated the reporter activity. This study demonstrated that C11orf21 is a novel transcriptional target of RUNX1 and RUNX1-ETO suppressed C11orf21 transcription in t(8;21) AML. Thus, through this in silico approach, we identified a novel transcriptional target of RUNX1, and the depletion of C11orf21, the target gene, may be associated with the onset of t(8;21) AML.
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Li X, Dai Y, Chen B, Huang J, Chen S, Jiang L. Clinical significance of CD34 +CD117 dim/CD34 +CD117 bri myeloblast-associated gene expression in t(8;21) acute myeloid leukemia. Front Med 2021; 15:608-620. [PMID: 33754282 DOI: 10.1007/s11684-021-0836-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/09/2020] [Indexed: 01/22/2023]
Abstract
t(8;21)(q22;q22) acute myeloid leukemia (AML) is a highly heterogeneous hematological malignancy with a high relapse rate in China. Two leukemic myeloblast populations (CD34+CD117dim and CD34+CD117bri) were previously identified in t(8;21) AML, and CD34+CD117dim cell proportion was determined as an independent factor for this disease outcome. Here, we examined the impact of CD34+CD117dim/CD34+CD117bri myeloblast-associated gene expression on t(8;21) AML clinical prognosis. In this study, 85 patients with t(8;21) AML were enrolled. The mRNA expression levels of CD34+CD117dim-associated genes (LGALS1, EMP3, and CRIP1) and CD34+CD117bri-associated genes (TRH, PLAC8, and IGLL1) were measured using quantitative reverse transcription PCR. Associations between gene expression and clinical outcomes were determined using Cox regression models. Results showed that patients with high LGALS1, EMP3, or CRIP1 expression had significantly inferior overall survival (OS), whereas those with high TRH or PLAC8 expression showed relatively favorable prognosis. Univariate analysis revealed that CD19, CD34+CD117dim proportion, KIT mutation, minimal residual disease (MRD), and expression levels of LGALS1, EMP3, CRIP1, TRH and PLAC8 were associated with OS. Multivariate analysis indicated that KIT mutation, MRD and CRIP1 and TRH expression levels were independent prognostic variables for OS. Identifying the clinical relevance of CD34+CD117dim/CD34+CD117bri myeloblast-associated gene expression may provide new clinically prognostic markers for t(8;21) AML.
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Affiliation(s)
- Xueping Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yuting Dai
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bing Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jinyan Huang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Saijuan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lu Jiang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Beghini A. Core Binding Factor Leukemia: Chromatin Remodeling Moves Towards Oncogenic Transcription. Cancers (Basel) 2019; 11:E1973. [PMID: 31817911 PMCID: PMC6966602 DOI: 10.3390/cancers11121973] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 11/25/2022] Open
Abstract
Acute myeloid leukemia (AML), the most common acute leukemia in adults, is a heterogeneous malignant clonal disorder arising from multipotent hematopoietic progenitor cells characterized by genetic and concerted epigenetic aberrations. Core binding factor-Leukemia (CBFL) is characterized by the recurrent reciprocal translocations t(8;21)(q22;q22) or inv(16)(p13;q22) that, expressing the distinctive RUNX1-RUNX1T1 (also known as Acute myeloid leukemia1-eight twenty-one, AML1-ETO or RUNX1/ETO) or CBFB-MYH11 (also known as CBFβ-ΣMMHX) translocation product respectively, disrupt the essential hematopoietic function of the CBF. In the past decade, remarkable progress has been achieved in understanding the structure, three-dimensional (3D) chromosomal topology, and disease-inducing genetic and epigenetic abnormalities of the fusion proteins that arise from disruption of the CBF subunit alpha and beta genes. Although CBFLs have a relatively good prognosis compared to other leukemia subtypes, 40-50% of patients still relapse, requiring intensive chemotherapy and allogenic hematopoietic cell transplantation (alloHCT). To provide a rationale for the CBFL-associated altered hematopoietic development, in this review, we summarize the current understanding on the various molecular mechanisms, including dysregulation of Wnt/β-catenin signaling as an early event that triggers the translocations, playing a pivotal role in the pathophysiology of CBFL. Translation of these findings into the clinical setting is just beginning by improvement in risk stratification, MRD assessment, and development of targeted therapies.
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Not Only Mutations Matter: Molecular Picture of Acute Myeloid Leukemia Emerging from Transcriptome Studies. JOURNAL OF ONCOLOGY 2019; 2019:7239206. [PMID: 31467542 PMCID: PMC6699387 DOI: 10.1155/2019/7239206] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/12/2019] [Indexed: 01/08/2023]
Abstract
The last two decades of genome-scale research revealed a complex molecular picture of acute myeloid leukemia (AML). On the one hand, a number of mutations were discovered and associated with AML diagnosis and prognosis; some of them were introduced into diagnostic tests. On the other hand, transcriptome studies, which preceded AML exome and genome sequencing, remained poorly translated into clinics. Nevertheless, gene expression studies significantly contributed to the elucidation of AML pathogenesis and indicated potential therapeutic directions. The power of transcriptomic approach lies in its comprehensiveness; we can observe how genome manifests its function in a particular type of cells and follow many genes in one test. Moreover, gene expression measurement can be combined with mutation detection, as high-impact mutations are often present in transcripts. This review sums up 20 years of transcriptome research devoted to AML. Gene expression profiling (GEP) revealed signatures distinctive for selected AML subtypes and uncovered the additional within-subtype heterogeneity. The results were particularly valuable in the case of AML with normal karyotype which concerns up to 50% of AML cases. With the use of GEP, new classes of the disease were identified and prognostic predictors were proposed. A plenty of genes were detected as overexpressed in AML when compared to healthy control, including KIT, BAALC, ERG, MN1, CDX2, WT1, PRAME, and HOX genes. High expression of these genes constitutes usually an unfavorable prognostic factor. Upregulation of FLT3 and NPM1 genes, independent on their mutation status, was also reported in AML and correlated with poor outcome. However, transcriptome is not limited to the protein-coding genes; other types of RNA molecules exist in a cell and regulate genome function. It was shown that microRNA (miRNA) profiles differentiated AML groups and predicted outcome not worse than protein-coding gene profiles. For example, upregulation of miR-10a, miR-10b, and miR-196b and downregulation of miR-192 were found as typical of AML with NPM1 mutation whereas overexpression of miR-155 was associated with FLT3-internal tandem duplication (FLT3-ITD). Development of high-throughput technologies and microarray replacement by next generation sequencing (RNA-seq) enabled uncovering a real variety of leukemic cell transcriptomes, reflected by gene fusions, chimeric RNAs, alternatively spliced transcripts, miRNAs, piRNAs, long noncoding RNAs (lncRNAs), and their special type, circular RNAs. Many of them can be considered as AML biomarkers and potential therapeutic targets. The relations between particular RNA puzzles and other components of leukemic cells and their microenvironment, such as exosomes, are now under investigation. Hopefully, the results of this research will shed the light on these aspects of AML pathogenesis which are still not completely understood.
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Milan T, Canaj H, Villeneuve C, Ghosh A, Barabé F, Cellot S, Wilhelm BT. Pediatric leukemia: Moving toward more accurate models. Exp Hematol 2019; 74:1-12. [PMID: 31154068 DOI: 10.1016/j.exphem.2019.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/19/2019] [Accepted: 05/22/2019] [Indexed: 02/07/2023]
Abstract
Leukemia is a complex genetic disease caused by errors in differentiation, growth, and apoptosis of hematopoietic cells in either lymphoid or myeloid lineages. Large-scale genomic characterization of thousands of leukemia patients has produced a tremendous amount of data that have enabled a better understanding of the differences between adult and pediatric patients. For instance, although phenotypically similar, pediatric and adult myeloid leukemia patients differ in their mutational profiles, typically involving either chromosomal translocations or recurrent single-base-pair mutations, respectively. To elucidate the molecular mechanisms underlying the biology of this cancer, continual efforts have been made to develop more contextually and biologically relevant experimental models. Leukemic cell lines, for example, provide an inexpensive and tractable model but often fail to recapitulate critical aspects of tumor biology. Likewise, murine leukemia models of leukemia have been highly informative but also do not entirely reproduce the human disease. More recent advances in the development of patient-derived xenografts (PDXs) or human models of leukemias are poised to provide a more comprehensive, and biologically relevant, approach to directly assess the impact of the in vivo environment on human samples. In this review, the advantages and limitations of the various current models used to functionally define the genetic requirements of leukemogenesis are discussed.
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MESH Headings
- Adolescent
- Animals
- Cell Differentiation
- Child
- Child, Preschool
- Female
- Heterografts
- Humans
- Infant
- Infant, Newborn
- Leukemia, Myeloid/genetics
- Leukemia, Myeloid/pathology
- Leukemia, Myeloid/therapy
- Male
- Mice
- Neoplasm Transplantation
- Neoplasms, Experimental/genetics
- Neoplasms, Experimental/metabolism
- Neoplasms, Experimental/pathology
- Neoplasms, Experimental/therapy
- Translocation, Genetic
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Affiliation(s)
- Thomas Milan
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC, Canada
| | - Hera Canaj
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC, Canada
| | - Chloe Villeneuve
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC, Canada
| | - Aditi Ghosh
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC, Canada
| | - Frédéric Barabé
- Centre de recherche en infectiologie du CHUL, Centre de recherche du CHU de Québec, Quebec City, QC, Canada; CHU de Québec Hôpital Enfant-Jésus, Quebec City, QC, Canada; Department of Medicine, Université Laval, Quebec City, QC, Canada
| | - Sonia Cellot
- Division of Hematology, Department of Pediatrics, Ste-Justine Hospital, Montréal, Université de Montréal, Montréal, QC, Canada
| | - Brian T Wilhelm
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC, Canada; Department of Medicine, Université de Montréal, Montréal, QC, Canada.
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12
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Gal O, Auslander N, Fan Y, Meerzaman D. Predicting Complete Remission of Acute Myeloid Leukemia: Machine Learning Applied to Gene Expression. Cancer Inform 2019; 18:1176935119835544. [PMID: 30911218 PMCID: PMC6423478 DOI: 10.1177/1176935119835544] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 01/29/2019] [Indexed: 11/17/2022] Open
Abstract
Machine learning (ML) is a useful tool for advancing our understanding of the patterns and significance of biomedical data. Given the growing trend on the application of ML techniques in precision medicine, here we present an ML technique which predicts the likelihood of complete remission (CR) in patients diagnosed with acute myeloid leukemia (AML). In this study, we explored the question of whether ML algorithms designed to analyze gene-expression patterns obtained through RNA sequencing (RNA-seq) can be used to accurately predict the likelihood of CR in pediatric AML patients who have received induction therapy. We employed tests of statistical significance to determine which genes were differentially expressed in the samples derived from patients who achieved CR after 2 courses of treatment and the samples taken from patients who did not benefit. We tuned classifier hyperparameters to optimize performance and used multiple methods to guide our feature selection as well as our assessment of algorithm performance. To identify the model which performed best within the context of this study, we plotted receiver operating characteristic (ROC) curves. Using the top 75 genes from the k-nearest neighbors algorithm (K-NN) model (K = 27) yielded the best area-under-the-curve (AUC) score that we obtained: 0.84. When we finally tested the previously unseen test data set, the top 50 genes yielded the best AUC = 0.81. Pathway enrichment analysis for these 50 genes showed that the guanosine diphosphate fucose (GDP-fucose) biosynthesis pathway is the most significant with an adjusted P value = .0092, which may suggest the vital role of N-glycosylation in AML.
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Affiliation(s)
- Ophir Gal
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Noam Auslander
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.,Center for Bioinformatics and Computational Biology, Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Yu Fan
- Center for Biomedical Informatics & Information Technology, National Cancer Institute, Rockville, MD, USA
| | - Daoud Meerzaman
- Center for Biomedical Informatics & Information Technology, National Cancer Institute, Rockville, MD, USA
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13
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Prognostic impact of t(16;21)(p11;q22) and t(16;21)(q24;q22) in pediatric AML: a retrospective study by the I-BFM Study Group. Blood 2018; 132:1584-1592. [PMID: 30150206 DOI: 10.1182/blood-2018-05-849059] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/14/2018] [Indexed: 12/30/2022] Open
Abstract
To study the prognostic relevance of rare genetic aberrations in acute myeloid leukemia (AML), such as t(16;21), international collaboration is required. Two different types of t(16;21) translocations can be distinguished: t(16;21)(p11;q22), resulting in the FUS-ERG fusion gene; and t(16;21)(q24;q22), resulting in RUNX1-core binding factor (CBFA2T3). We collected data on clinical and biological characteristics of 54 pediatric AML cases with t(16;21) rearrangements from 14 international collaborative study groups participating in the international Berlin-Frankfurt-Münster (I-BFM) AML study group. The AML-BFM cohort diagnosed between 1997 and 2013 was used as a reference cohort. RUNX1-CBFA2T3 (n = 23) had significantly lower median white blood cell count (12.5 × 109/L, P = .03) compared with the reference cohort. FUS-ERG rearranged AML (n = 31) had no predominant French-American-British (FAB) type, whereas 76% of RUNX1-CBFA2T3 had an M1/M2 FAB type (M1, M2), significantly different from the reference cohort (P = .004). Four-year event-free survival (EFS) of patients with FUS-ERG was 7% (standard error [SE] = 5%), significantly lower compared with the reference cohort (51%, SE = 1%, P < .001). Four-year EFS of RUNX1-CBFA2T3 was 77% (SE = 8%, P = .06), significantly higher compared with the reference cohort. Cumulative incidence of relapse was 74% (SE = 8%) in FUS-ERG, 0% (SE = 0%) in RUNX1-CBFA2T3, compared with 32% (SE = 1%) in the reference cohort (P < .001). Multivariate analysis identified both FUS-ERG and RUNX1-CBFA2T3 as independent risk factors with hazard ratios of 1.9 (P < .0001) and 0.3 (P = .025), respectively. These results describe 2 clinically relevant distinct subtypes of pediatric AML. Similarly to other core-binding factor AMLs, patients with RUNX1-CBFA2T3 rearranged AML may benefit from stratification in the standard risk treatment, whereas patients with FUS-ERG rearranged AML should be considered high-risk.
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14
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NKL homeobox gene activities in hematopoietic stem cells, T-cell development and T-cell leukemia. PLoS One 2017; 12:e0171164. [PMID: 28151996 PMCID: PMC5289504 DOI: 10.1371/journal.pone.0171164] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/16/2017] [Indexed: 12/18/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) cells represent developmentally arrested T-cell progenitors, subsets of which aberrantly express homeobox genes of the NKL subclass, including TLX1, TLX3, NKX2-1, NKX2-5, NKX3-1 and MSX1. Here, we analyzed the transcriptional landscape of all 48 members of the NKL homeobox gene subclass in CD34+ hematopoietic stem and progenitor cells (HSPCs) and during lymphopoiesis, identifying activities of nine particular genes. Four of these were expressed in HSPCs (HHEX, HLX1, NKX2-3 and NKX3-1) and three in common lymphoid progenitors (HHEX, HLX1 and MSX1). Interestingly, our data indicated downregulation of NKL homeobox gene transcripts in late progenitors and mature T-cells, a phenomenon which might explain the oncogenic impact of this group of genes in T-ALL. Using MSX1-expressing T-ALL cell lines as models, we showed that HHEX activates while HLX1, NKX2-3 and NKX3-1 repress MSX1 transcription, demonstrating the mutual regulation and differential activities of these homeobox genes. Analysis of a public T-ALL expression profiling data set comprising 117 patient samples identified 20 aberrantly activated members of the NKL subclass, extending the number of known NKL homeobox oncogene candidates. While 7/20 genes were also active during hematopoiesis, the remaining 13 showed ectopic expression. Finally, comparative analyses of T-ALL patient and cell line profiling data of NKL-positive and NKL-negative samples indicated absence of shared target genes but instead highlighted deregulation of apoptosis as common oncogenic effect. Taken together, we present a comprehensive survey of NKL homeobox genes in early hematopoiesis, T-cell development and T-ALL, showing that these genes generate an NKL-code for the diverse stages of lymphoid development which might be fundamental for regular differentiation.
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15
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Duployez N, Marceau-Renaut A, Boissel N, Petit A, Bucci M, Geffroy S, Lapillonne H, Renneville A, Ragu C, Figeac M, Celli-Lebras K, Lacombe C, Micol JB, Abdel-Wahab O, Cornillet P, Ifrah N, Dombret H, Leverger G, Jourdan E, Preudhomme C. Comprehensive mutational profiling of core binding factor acute myeloid leukemia. Blood 2016; 127:2451-9. [PMID: 26980726 PMCID: PMC5457131 DOI: 10.1182/blood-2015-12-688705] [Citation(s) in RCA: 192] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/08/2016] [Indexed: 12/26/2022] Open
Abstract
Acute myeloid leukemia (AML) with t(8;21) or inv(16) have been recognized as unique entities within AML and are usually reported together as core binding factor AML (CBF-AML). However, there is considerable clinical and biological heterogeneity within this group of diseases, and relapse incidence reaches up to 40%. Moreover, translocations involving CBFs are not sufficient to induce AML on its own and the full spectrum of mutations coexisting with CBF translocations has not been elucidated. To address these issues, we performed extensive mutational analysis by high-throughput sequencing in 215 patients with CBF-AML enrolled in the Phase 3 Trial of Systematic Versus Response-adapted Timed-Sequential Induction in Patients With Core Binding Factor Acute Myeloid Leukemia and Treating Patients with Childhood Acute Myeloid Leukemia with Interleukin-2 trials (age, 1-60 years). Mutations in genes activating tyrosine kinase signaling (including KIT, N/KRAS, and FLT3) were frequent in both subtypes of CBF-AML. In contrast, mutations in genes that regulate chromatin conformation or encode members of the cohesin complex were observed with high frequencies in t(8;21) AML (42% and 18%, respectively), whereas they were nearly absent in inv(16) AML. High KIT mutant allele ratios defined a group of t(8;21) AML patients with poor prognosis, whereas high N/KRAS mutant allele ratios were associated with the lack of KIT or FLT3 mutations and a favorable outcome. In addition, mutations in epigenetic modifying or cohesin genes were associated with a poor prognosis in patients with tyrosine kinase pathway mutations, suggesting synergic cooperation between these events. These data suggest that diverse cooperating mutations may influence CBF-AML pathophysiology as well as clinical behavior and point to potential unique pathogenesis of t(8;21) vs inv(16) AML.
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MESH Headings
- Adolescent
- Adult
- Alleles
- Cell Cycle Proteins/genetics
- Child
- Child, Preschool
- Chromatin/genetics
- Chromatin/ultrastructure
- Chromosomal Proteins, Non-Histone/genetics
- Chromosome Inversion
- Chromosomes, Human, Pair 16/genetics
- Chromosomes, Human, Pair 21/genetics
- Chromosomes, Human, Pair 8/genetics
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factors/genetics
- DNA Mutational Analysis
- DNA, Neoplasm/genetics
- Female
- Genetic Association Studies
- High-Throughput Nucleotide Sequencing
- Humans
- Infant
- Leukemia, Myeloid, Acute/genetics
- Male
- Middle Aged
- Mutation
- Oncogene Proteins, Fusion/genetics
- Prognosis
- RUNX1 Translocation Partner 1 Protein
- Translocation, Genetic
- Young Adult
- Cohesins
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Affiliation(s)
- Nicolas Duployez
- Biology and Pathology Center, Laboratory of Hematology, Centre Hospitalier Universitaire (CHU) Lille, Lille, France; Cancer Research Institute, INSERM Unité Mixte de Recherche (UMR)-S 1172, Lille, France
| | - Alice Marceau-Renaut
- Biology and Pathology Center, Laboratory of Hematology, Centre Hospitalier Universitaire (CHU) Lille, Lille, France; Cancer Research Institute, INSERM Unité Mixte de Recherche (UMR)-S 1172, Lille, France
| | - Nicolas Boissel
- Department of Hematology, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Arnaud Petit
- Department of Pediatric Hematology and Oncology, Trousseau Hospital, AP-HP, Paris, France
| | - Maxime Bucci
- Biology and Pathology Center, Laboratory of Hematology, Centre Hospitalier Universitaire (CHU) Lille, Lille, France
| | - Sandrine Geffroy
- Biology and Pathology Center, Laboratory of Hematology, Centre Hospitalier Universitaire (CHU) Lille, Lille, France; Cancer Research Institute, INSERM Unité Mixte de Recherche (UMR)-S 1172, Lille, France
| | | | - Aline Renneville
- Biology and Pathology Center, Laboratory of Hematology, Centre Hospitalier Universitaire (CHU) Lille, Lille, France; Cancer Research Institute, INSERM Unité Mixte de Recherche (UMR)-S 1172, Lille, France
| | - Christine Ragu
- Department of Pediatric Hematology and Oncology, Trousseau Hospital, AP-HP, Paris, France
| | - Martin Figeac
- Functional and Structural Genomic Platform, Lille University, Lille, France
| | - Karine Celli-Lebras
- Department of Hematology, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | | | - Jean-Baptiste Micol
- Department of Hematology, Gustave Roussy Institute, INSERM UMR 1170, Villejuif, France; Human Oncology and Pathogenesis Program and Leukemia Service, Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program and Leukemia Service, Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | | | - Norbert Ifrah
- Department of Hematology, CHU Angers, Angers, France; and
| | - Hervé Dombret
- Department of Hematology, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Guy Leverger
- Department of Pediatric Hematology and Oncology, Trousseau Hospital, AP-HP, Paris, France
| | - Eric Jourdan
- Department of Hematology, CHU Nîmes, Nîmes, France
| | - Claude Preudhomme
- Biology and Pathology Center, Laboratory of Hematology, Centre Hospitalier Universitaire (CHU) Lille, Lille, France; Cancer Research Institute, INSERM Unité Mixte de Recherche (UMR)-S 1172, Lille, France
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16
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RNA-sequencing analysis of core binding factor AML identifies recurrent ZBTB7A mutations and defines RUNX1-CBFA2T3 fusion signature. Blood 2016; 127:2498-501. [PMID: 26968532 DOI: 10.1182/blood-2016-03-703868] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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