Identification of long non-coding RNAs involved in leukemogenesis and venetoclax response in acute myeloid leukemia through functional CRISPR-dCas9 interference screens

Acute myeloid leukemia (AML) is a malignant hematologic disease with poor prognosis, and improved understanding of its biology is critical for patient outcomes. While protein-coding genes in AML are well characterized, the role of long non-coding RNAs (lncRNAs) remains largely unexplored. Here, we investigated how lncRNAs contribute to AML biology and treatment resistance. Three high-throughput lncRNA-CRISPR-interference (CRISPRi) screens were performed in the AML cell line MOLM-13, targeting 7996 lncRNAs expressed in hematopoietic cells, with knockdowns directed to transcription start sites defined through cap analysis of gene expression (CAGE) sequencing. Effects on proliferation, differentiation, and response to the Bcl-2 inhibitor venetoclax were assessed. In total, 58, 4, and 23 lncRNAs were found to affect proliferation, differentiation, and venetoclax sensitivity, respectively. Three proliferation-associated lncRNAs (MIR17HG, CATG00000106133.1, and CATG00000056792.1) and one venetoclax-associated lncRNA (AC009299.3) were further investigated. CATG00000106133.1 was enriched in de novo and cytogenetically normal AML and correlated with NPM1 and IDH2 mutations. Gene Ontology and Reactome analyses of RNA-seq from CATG00000106133.1 knockout cells revealed roles in cytokine signaling and immune pathways. AC009299.3, linked to venetoclax response, was associated with poor outcome, adverse risk, and increased age in AML patients. Collectively, this study identifies four lncRNAs implicated in key leukemogenic processes, highlighting their potential for understanding AML biology, prognosis, and therapeutic response.