Dataset Information

The histone demethylase KDM5C functions as a tumor suppressor in AML by repression of bivalently marked immature genes (ChIP-seq)

ABSTRACT: Epigenetic regulators are frequently mutated in acute myeloid leukemia (AML). However, epigenetic dysregulation in AML extends beyond recurrently mutated factors and only little is known about the potential drivers in this context. Identification and characterization of novel epigenetic drivers impacting on AML biology will not only improve our basic understanding of AML but may also uncover novel options for therapeutic intervention. To uncover novel epigenetic regulators in AML, we performed an in vivo short hairpin RNA (shRNA) screen in the context of CEBPA mutant AML. We identified the H3K4me2/3 demethylase KDM5C as a novel tumor suppressor in AML. We found that lower Kdm5c/KDM5C expression levels are associated with accelerated growth of human and murine AML cell lines. In a CEBPA mutant AML mouse model, Kdm5c knockdown resulted in a more aggressive, immature and short-latency phenotype. Mechanistically, we show that knockdown of Kdm5c increased H3K4me3-levels globally. This translated into the up-regulation of a group of bivalently marked immature genes resulting in a de-differentiation phenotype which could be reversed by modulating levels of pro-differentiating factors. Finally, we could demonstrate that low levels of KDM5C was associated with a decrease in long-term disease-free survival, specifically in female patients. This emphasizes the clinical relevance of our findings and identifies KDM5C as a novel sex-specific tumor suppressor in AML.

ORGANISM(S): Mus musculus

PROVIDER: GSE153821 | GEO | 2023/01/11

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:The clinical impact of aberrant CEBPA promoter methylation (PM) in AML is controversial discussed. The aim of this study was to clarify the significance of aberrant CEBPA PM with regard to clinical features in a cohort of 572 de novo AML with wildtype CEBPA and normal karyotype. The distal promoter was methylated in 54/572 cases (9.41%) whereas proximal PM was never detected. Methylation of the core promoter was detected in only 8 of 326 cases (2.45%) and thus seems to be a rare event in AML. There was no correlation between CEBPA distal PM, age, sex, white blood cell (WBC) count or Hb levels at diagnosis. We also were not able to detect a significant correlation between the presence of CEBPA distal PM and molecular mutations such as FLT3-ITD, NPM1, AML1, MLL-PTD and IDH1. Solely the frequency of IDH2R140 mutations was significantly reduced in CEBPA distal PM positive compared to CEBPA distal PM negative cases (p=0.01). Furthermore, analysis of CEBPA mRNA expression level revealed no difference between CEBPA distal PM positive and CEBPA distal PM negative cases, suggesting that CEBPA distal PM has no influence on CEBPA expression. CEBPA distal PM did not show impact on overall survival (OS), event free survival (EFS) or incidence of relapse. Also when other mutations were taken into regard no prognostic impact of CEBPA distal PM could be shown. In contrast, a distinct expression profile of CEBPA distal PM positive cases compared to CEBPA mutated and CEBPA distal PM negative cases was observed. In addition, a significantly higher frequency of CEBPA distal PM was detected in RUNX1-RUNX1T1 positive AML compared to the CEBPA witdtype cases. We conclude that the presence of aberrant CEBPA PM has no clinical relevance and is therefore a negligible prognostic marker in de novo AML with normal karyotype. To detect underlying common differences in their gene expression profiles, we investigated 9 CEBPA methylated (unmutated), 8 CEBPA single-mutated, 10 CEBPA double-mutated, and 10 non-methylated/non-mutated cases (Affymetrix HG-U133 Plus 2.0 microarrays; Santa Clara, CA). The microarray sample preparation assay was performed as previously reported. Gene expression raw data were processed according to the manufacturer’s recommendations.

Dataset Information

The histone demethylase KDM5C functions as a tumor suppressor in AML by repression of bivalently marked immature genes (ChIP-seq)

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets