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Tobiasson M, Abdulkadir H, Lennartsson A, Katayama S, Marabita F, De Paepe A, Karimi M, Krjutskov K, Einarsdottir E, Grövdal M, Jansson M, Ben Azenkoud A, Corddedu L, Lehmann S, Ekwall K, Kere J, Hellström-Lindberg E, Ungerstedt J. Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease. Oncotarget 2018; 8:28812-28825. [PMID: 28427179 PMCID: PMC5438694 DOI: 10.18632/oncotarget.15807] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/01/2017] [Indexed: 02/07/2023] Open
Abstract
Azacitidine (Aza) is first-line treatment for patients with high-risk myelodysplastic syndromes (MDS), although its precise mechanism of action is unknown. We performed the first study to globally evaluate the epigenetic effects of Aza on MDS bone marrow progenitor cells assessing gene expression (RNA seq), DNA methylation (Illumina 450k) and the histone modifications H3K18ac and H3K9me3 (ChIP seq). Aza induced a general increase in gene expression with 924 significantly upregulated genes but this increase showed no correlation with changes in DNA methylation or H3K18ac, and only a weak association with changes in H3K9me3. Interestingly, we observed activation of transcripts containing 15 endogenous retroviruses (ERVs) confirming previous cell line studies. DNA methylation decreased moderately in 99% of all genes, with a median β-value reduction of 0.018; the most pronounced effects seen in heterochromatin. Aza-induced hypomethylation correlated significantly with change in H3K9me3. The pattern of H3K18ac and H3K9me3 displayed large differences between patients and healthy controls without any consistent pattern induced by Aza. We conclude that the marked induction of gene expression only partly could be explained by epigenetic changes, and propose that activation of ERVs may contribute to the clinical effects of Aza in MDS.
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Affiliation(s)
- Magnus Tobiasson
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Division of Hematology Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Hani Abdulkadir
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Division of Hematology Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm County, Sweden
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm County, Sweden
| | - Francesco Marabita
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden.,National Bioinformatics Infrastructure Sweden, Stockholm, Sweden
| | - Ayla De Paepe
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Division of Hematology Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Mohsen Karimi
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Division of Hematology Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Kaarel Krjutskov
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm County, Sweden.,Molecular Neurology Research Program, University of Helsinki, and Folkhälsan Institute of Genetics, Helsinki, Finland.,Competence Centre on Health Technologies, Tartu, Estonia
| | - Elisabet Einarsdottir
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm County, Sweden.,Molecular Neurology Research Program, University of Helsinki, and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Michael Grövdal
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Division of Hematology Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Monika Jansson
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Division of Hematology Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Asmaa Ben Azenkoud
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Division of Hematology Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Lina Corddedu
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm County, Sweden
| | - Sören Lehmann
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Division of Hematology Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden.,Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm County, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm County, Sweden.,Molecular Neurology Research Program, University of Helsinki, and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Eva Hellström-Lindberg
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Division of Hematology Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Johanna Ungerstedt
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Division of Hematology Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden
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