Deciphering the genetically interactive network of the DLK1-DIO3 ncRNA locus in the hematopoietic system and in infant leukemias

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Numerous studies have established the dysregulation of non-coding RNAs (ncRNAs) – in particular of microRNAs (miRNAs) – as a causative factor in leukemogenesis. These studies have largely examined the functions of individual miRNAs or long non-coding RNAs (lncRNAs). However, since 42% of miRNA genes are organized in polycistronic transcripts, studying their interaction is crucial for understanding how miRNAs or miRNA networks control essential cellular functions and cell-fate decisions. In our ncRNA expression atlas of the human hematopoietic system, we uncovered specific and coordinated expression of the DLK1-DIO3 locus – which contains the largest miRNA cluster of the human genome (54 miRNAs; called a miRNA megacluster), numerous box C/D snoRNAs and lncRNAs – in megakaryocytes and megakaryoblastic leukemias. The latter leukemia type occurs most frequently in infants and thus has strong developmental ties. As a part of this ongoing DFG-funded project, we laid a foundation for interrogating the DLK1-DIO3 locus in megakaryopoiesis and acute megakaryoblastic leukemia (AMKL) pathogenesis. We first elucidated an upstream regulatory mechanism in megakaryocytes and megakaryoblasts, allowing us to interfere with expression from the locus. We also identified miRNAs within the locus that drive megakaryocytic differentiation, as well as a novel cis-regulatory long intergenic ncRNA (lincRNA; LINC02285) that affects megakaryopoiesis and controls expression of the locus. Further, we established an LNP packaging and delivery platform in anticipation of the preclinical testing of RNA-centered therapy concepts. In this proposed follow-up project for the Research Unit, we will continue our efforts to dissect the DLK1-DIO3 locus and the ncRNAs within it. We intend to move forward with (1) delineating the network of interactions within the miRNA megacluster – including co-expressed lncRNAs – during normal hematopoiesis and AMKL, (2) resolving the features and mechanisms of individual players, and (3) pre-clinical testing of therapeutic interventions involving these ncRNAs. Overall, this project aims to elucidate how complex organ systems are regulated by interactive genetic networks and how dysregulation of these networks impacts oncogenesis.