CRISPRi Screen Identifies a Novel Growth Suppressor lncRNA, INSTAR, in Human Monocytes

Abstract

Acute myeloid leukemia (AML) is a heterogeneous disease that arises from dysregulated myeloid proliferation. We performed a high-throughput CRISPR interference (CRISPRi) screen in the THP-1 monocytic cancer cell line to identify long noncoding RNAs (lncRNAs) that play a role in contributing to cell proliferation. Our screen identified INSTAR (Intergenic Nuclear Suppressor lncRNA Targeting Adjacent Regulator SFMBT2) as a top candidate. RNA-seq on INSTAR deficient THP-1 cells revealed transcriptional changes in genes involved in cell proliferation as well as other cellular processes. Loss of INSTAR selectively reduced expression of its neighboring gene, SFMBT2. Functional assays confirmed that both genes suppress cell growth, revealing a cis-regulatory mechanism in which INSTAR regulates SFMBT2 expression to control monocyte proliferation. Here, we leverage high-throughput screening to rapidly pinpoint functional lncRNAs providing novel insights into a key regulatory locus consisting of INSTAR and SFMBT2 which could be critical for better understanding dysregulation contributing to acute myeloid leukemia.