PT  - JOURNAL ARTICLE
AU  - Elisabeth R. Wilson
AU  - Nichole M. Helton
AU  - Sharon E. Heath
AU  - Robert S. Fulton
AU  - Jacqueline E. Payton
AU  - John S. Welch
AU  - Matthew J. Walter
AU  - Peter Westervelt
AU  - John F. DiPersio
AU  - Daniel C. Link
AU  - Christopher A. Miller
AU  - Timothy J. Ley
AU  - David H. Spencer
TI  - Genome-wide analysis of focal DNA hypermethylation in <em>IDH</em>-mutant AML samples
AID  - 10.1101/2021.03.03.433799
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.03.03.433799
4099  - http://biorxiv.org/content/early/2021/05/26/2021.03.03.433799.short
4100  - http://biorxiv.org/content/early/2021/05/26/2021.03.03.433799.full
AB  - Recurrent mutations in IDH1 or IDH2 in acute myeloid leukemia (AML) are associated with increased DNA methylation, but the genome-wide patterns of this hypermethylation phenotype have not been comprehensively studied in AML samples. We analyzed whole-genome bisulfite sequencing data from 15 primary AML samples with IDH1 or IDH2 mutations, which identified ~4,000 focal regions that were uniquely hypermethylated vs. normal CD34+ cells. These regions had modest, but significant, hypermethylation in AMLs with biallelic TET2 mutations, and 5-hydroxymethylation levels that were dependent on functional TET2, indicating that hypermethylation in these regions is caused by inhibition of TET-mediated demethylation. Focal hypermethylation in IDHmut AMLs occurred in regions with low methylation in normal CD34+ cells, implying that DNA methylation and demethylation are active at these loci. AML samples containing IDH and DNMT3AR882 mutations were significantly less hypermethylated, suggesting that methylation in these regions is mediated by DNMT3A. IDHmut-specific hypermethylation was highly enriched for enhancers that form direct interactions with genes involved in normal hematopoiesis and AML, including MYC and ETV6. These results suggest that focal hypermethylation in IDH-mutant AML occurs by altering the balance between DNA methylation and demethylation, and that disruption of these pathways at enhancers may contribute to AML pathogenesis.Competing Interest StatementThe authors have declared no competing interest.