Early B-cell factor 3 (EBF3) is a novel tumor suppressor gene with promoter hypermethylation in pediatric acute myeloid leukemia

Abstract

BackgroundPediatric acute myeloid leukemia (AML) comprises up to 20% of all childhood leukemia. Recent research shows that aberrant DNA methylation patterning may play a role in leukemogenesis. The epigenetic silencing of the EBF3 locus is very frequent in glioblastoma. However, the expression profiles and molecular function of EBF3 in pediatric AML is still unclear.MethodsTwelve human acute leukemia cell lines, 105 pediatric AML samples and 30 normal bone marrow/idiopathic thrombocytopenic purpura (NBM/ITP) control samples were analyzed. Transcriptional level of EBF3 was evaluated by semi-quantitative and real-time PCR. EBF3 methylation status was determined by methylation specific PCR (MSP) and bisulfite genomic sequencing (BGS). The molecular mechanism of EBF3 was investigated by apoptosis assays and PCR array analysis.ResultsEBF3 promoter was hypermethylated in 10/12 leukemia cell lines. Aberrant EBF3 methylation was observed in 42.9% (45/105) of the pediatric AML samples using MSP analysis, and the BGS results confirmed promoter methylation. EBF3 expression was decreased in the AML samples compared with control. Methylated samples revealed similar survival outcomes by Kaplan-Meier survival analysis. EBF3 overexpression significantly inhibited cell proliferation and increased apoptosis. Real-time PCR array analysis revealed 93 dysregulated genes possibly implicated in the apoptosis of EBF3-induced AML cells.ConclusionIn this study, we firstly identified epigenetic inactivation of EBF3 in both AML cell lines and pediatric AML samples for the first time. Our findings also showed for the first time that transcriptional overexpression of EBF3 could inhibit proliferation and induce apoptosis in AML cells. We identified 93 dysregulated apoptosis-related genes in EBF3-overexpressing, including DCC, AIFM2 and DAPK1. Most of these genes have never been related with EBF3 over expression. These results may provide new insights into the molecular mechanism of EBF3-induced apoptosis; however, further research will be required to determine the underlying details.Our findings suggest that EBF3 may act as a putative tumor suppressor gene in pediatric AML.

The inhibitory effect of MEG3/miR-214/AIFM2 axis on the growth of T-cell lymphoblastic lymphoma

“…For example, activated AIFM2 enhanced apoptosis of human lung cancer cells undergoing toxicological stress (25). Down-regulated expression of AIFM2 was detected in various cancers, including in pediatric acute myeloid leukemia, indicating an anticancer effect (26,27).…”

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De novo variants in EBF3 are associated with hypotonia, developmental delay, intellectual disability, and autism

“…Mice and humans have four COE paralogs, EBF1-4 ( Daburon et al 2008 ), which may have complementary and redundant roles ( Dubois and Vincent 2001 ; Liberg et al 2002 ). Among the COE paralogs, EBF3 is highly expressed throughout the brain during development in mice and humans ( Zhao et al 2006 ; Tao et al 2015 ) and is required for the migration of Cajal–Retzius cells during corticogenesis and the terminal differentiation and maintenance of specialized neurons in the adult brain ( Dubois and Vincent 2001 ; Garcia-Dominguez et al 2003 ; Thuret et al 2004 ; Chiara et al 2012 ). EBF3 also acts as a putative tumor suppressor by activating cell cycle arrest and inducing apoptosis ( Zhao et al 2006 ).…”