CRISPR/Cas9-based screens identify an essential long noncoding RNA locus in pediatric acute myeloid leukemia cells

Long noncoding RNAs (lncRNAs) have emerged as important players in numerous biological processes, yet the vast majority lack functional characterization. To address this in the context of pediatric AML, we screened 619 lncRNA genes from 9 stem cell-AML and subgroup-specific signatures via a CRISPRi-based dropout approach. One candidate was essential for 6 of the 8 tested cell lines – LNC666, a low-abundance nuclear transcript. On chr15, it is flanked by 2 coding genes, which both appear dispensable for AML cells. In contrast, LNC666 repression and excision both reduce proliferation. Ectopic expression and shRNA-mediated knockdown did not yield notable growth effects, implying a cis mode of action. Indeed, CRISPRi tiling of the locus distinguished 3 key regions, including the LNC666 promoter, all of which enhance transcription from a minimal promoter. Saturating mutagenesis further refined these regions to short stretches where intact sequence is vital. Our data directly implicate the deregulation of lncRNA loci in pediatric AML, and suggest LNC666 as a new player in its pathophysiology. We also highlight the power of CRISPR/Cas9 approaches for interrogating complex genomic loci.

Publication History

Article published online:
13 May 2020