Deciphering the interactive network of the DLK1-DIO3 locus in hematopoiesis and pediatric acute megakaryoblastic leukemia

Non-coding RNAs (ncRNAs) recently emerged as central regulators of chromatin and gene expression, posing a novel window for targeted therapies in pediatric acute megakaryoblastic leukemia (AMKL). We established a lncRNA expression atlas for the hematopoietic system including 46 pediatric acute myeloid leukemia samples, and discovered a ncRNA cluster within the DLK1-DIO3 locus that was highly expressed in hematopoietic stem cells (HSCs), megakaryocytes (MKs) and AMKL. ChIP-Seq performed for human CD34+ hematopoietic stem and progenitor cells (HSPCs), MKs and monocytes showed cell type specific activating (H3K3me3) and repressing (H3K27me3) histone marks. Bisulphite sequencing revealed a significant correlation between MEG3 expression and the methylation status of a CpG island downstream of the first exon of MEG3. Lentiviral expression of several highly expressed miRNAs of the cluster in CD34+ HSPCs resulted in accelerated MK maturation in vitro. CRISPR-Cas9-mediated deletion of MEG3 impaired proliferation of AMKL cell lines. Our study establishes the DLK1-DIO3 locus as an important regulator of megakaryopoiesis with different members controlling this process.