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Haider Z, Larsson P, Landfors M, Köhn L, Schmiegelow K, Flaegstad T, Kanerva J, Heyman M, Hultdin M, Degerman S. An integrated transcriptome analysis in T-cell acute lymphoblastic leukemia links DNA methylation subgroups to dysregulated TAL1 and ANTP homeobox gene expression. Cancer Med 2018; 8:311-324. [PMID: 30575306 PMCID: PMC6346238 DOI: 10.1002/cam4.1917] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/12/2018] [Accepted: 11/19/2018] [Indexed: 01/01/2023] Open
Abstract
Classification of pediatric T‐cell acute lymphoblastic leukemia (T‐ALL) patients into CIMP (CpG Island Methylator Phenotype) subgroups has the potential to improve current risk stratification. To investigate the biology behind these CIMP subgroups, diagnostic samples from Nordic pediatric T‐ALL patients were characterized by genome‐wide methylation arrays, followed by targeted exome sequencing, telomere length measurement, and RNA sequencing. The CIMP subgroups did not correlate significantly with variations in epigenetic regulators. However, the CIMP+ subgroup, associated with better prognosis, showed indicators of longer replicative history, including shorter telomere length (P = 0.015) and older epigenetic (P < 0.001) and mitotic age (P < 0.001). Moreover, the CIMP+ subgroup had significantly higher expression of ANTP homeobox oncogenes, namely TLX3, HOXA9, HOXA10, and NKX2‐1, and novel genes in T‐ALL biology including PLCB4, PLXND1, and MYO18B. The CIMP− subgroup, with worse prognosis, was associated with higher expression of TAL1 along with frequent STIL‐TAL1 fusions (2/40 in CIMP+ vs 11/24 in CIMP−), as well as stronger expression of BEX1. Altogether, our findings suggest different routes for leukemogenic transformation in the T‐ALL CIMP subgroups, indicated by different replicative histories and distinct methylomic and transcriptomic profiles. These novel findings can lead to new therapeutic strategies.
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Affiliation(s)
- Zahra Haider
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Pär Larsson
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Mattias Landfors
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Linda Köhn
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
| | - Kjeld Schmiegelow
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Trond Flaegstad
- Department of Pediatrics, University of Tromsø and University Hospital of North Norway, Tromsø, Norway
| | - Jukka Kanerva
- Children's Hospital, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Mats Heyman
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Hultdin
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Sofie Degerman
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
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Larmonie NSD, Arentsen-Peters TCJM, Obulkasim A, Valerio D, Sonneveld E, Danen-van Oorschot AA, de Haas V, Reinhardt D, Zimmermann M, Trka J, Baruchel A, Pieters R, van den Heuvel-Eibrink MM, Zwaan CM, Fornerod M. MN1 overexpression is driven by loss of DNMT3B methylation activity in inv(16) pediatric AML. Oncogene 2018; 37:107-115. [PMID: 28892045 DOI: 10.1038/onc.2017.293] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 06/09/2017] [Accepted: 07/17/2017] [Indexed: 12/15/2022]
Abstract
In acute myeloid leukemia (AML), specific genomic aberrations induce aberrant methylation, thus directly influencing the transcriptional programing of leukemic cells. Therefore, therapies targeting epigenetic processes are advocated as a promising therapeutic tool for AML treatment. However, to develop new therapies, a comprehensive understanding of the mechanism(s) driving the epigenetic changes as a result of acquired genetic abnormalities is necessary. This understanding is still lacking. In this study, we performed genome-wide CpG-island methylation profiling on pediatric AML samples. Six differentially methylated genomic regions within two genes, discriminating inv(16)(p13;q22) from non-inv(16) pediatric AML samples, were identified. All six regions had a hypomethylated phenotype in inv(16) AML samples, and this was most prominent at the regions encompassing the meningioma (disrupted in balanced translocation) 1 (MN1) oncogene. MN1 expression primarily correlated with the methylation level of the 3' end of the MN1 exon-1 locus. Decitabine treatment of different cell lines showed that induced loss of methylation at the MN1 locus can result in an increase of MN1 expression, indicating that MN1 expression is coregulated by DNA methylation. To investigate this methylation-associated mechanism, we determined the expression of DNA methyltransferases in inv(16) AML. We found that DNMT3B expression was significantly lower in inv(16) samples. Furthermore, DNMT3B expression correlated negatively with MN1 expression in pediatric AML samples. Importantly, depletion of DNMT3B impaired remethylation efficiency of the MN1 exon-1 locus in AML cells after decitabine exposure. These findings identify DNMT3B as an important coregulator of MN1 methylation. Taken together, this study shows that the methylation level of the MN1 exon-1 locus regulates MN1 expression levels in inv(16) pediatric AML. This methylation level is dependent on DNMT3B, thus suggesting a role for DNMT3B in leukemogenesis in inv(16) AML, through MN1 methylation regulation.
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MESH Headings
- Adolescent
- Azacitidine/analogs & derivatives
- Azacitidine/pharmacology
- Carcinogenesis/genetics
- Cell Line, Tumor
- Child
- Child, Preschool
- CpG Islands/genetics
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation/drug effects
- DNA Methylation/genetics
- Decitabine
- Epigenesis, Genetic/genetics
- Exons/genetics
- Female
- Gene Expression Regulation, Leukemic
- Humans
- Infant
- Infant, Newborn
- Leukemia, Myeloid, Acute/blood
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Male
- Nucleic Acid Hybridization/methods
- Oligonucleotide Array Sequence Analysis/methods
- Oncogene Proteins, Fusion/genetics
- Promoter Regions, Genetic/genetics
- Trans-Activators
- Tumor Suppressor Proteins/genetics
- DNA Methyltransferase 3B
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Affiliation(s)
- N S D Larmonie
- Department of Pediatric Oncology/Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - T C J M Arentsen-Peters
- Department of Pediatric Oncology/Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - A Obulkasim
- Department of Pediatric Oncology/Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - D Valerio
- Department of Pediatric Oncology/Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - E Sonneveld
- Dutch Childhood Oncology Group (DCOG), The Hague, The Netherlands
| | - A A Danen-van Oorschot
- Department of Pediatric Oncology/Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - V de Haas
- Dutch Childhood Oncology Group (DCOG), The Hague, The Netherlands
| | - D Reinhardt
- Department of Pediatric Oncology/Hematology, Medical High School, Hannover, Germany
| | - M Zimmermann
- Department of Pediatric Oncology/Hematology, Medical High School, Hannover, Germany
| | - J Trka
- Pediatric Hematology/Oncology, 2nd Medical School, Charles University, Prague, Czech Republic
| | - A Baruchel
- CHU de Paris-Hôpital Robert Debré, Paris, France
| | - R Pieters
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - C M Zwaan
- Department of Pediatric Oncology/Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - M Fornerod
- Department of Pediatric Oncology/Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
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