Functional relevance of circRNA aberrant expression in pediatric acute leukemia with KMT2A::AFF1 fusion

Abstract

Circular RNAs (circRNAs) are emerging molecular players in leukemogenesis and promising therapeutic targets. In KMT2A::AFF1 (MLL::AF4) rearranged leukemia, an aggressive disease compared to other pediatric B-cell precursor (BCP) acute lymphoblastic leukemia (ALL), data about circRNAs are limited. Here we disclose the circRNA landscape of KMT2A::AFF1 translocated BCP-ALL infant patients, showing dysregulated, mostly ectopically expressed, circRNAs in leukemia cells. Most of these circRNAs, apart from circHIPK3 and circZNF609 previously associated with oncogenic behavior in ALL, are still uncharacterized. A loss-of-function screening in vitro identified an oncogenic role of circFKBP5, circKLHL2, circNR3C1 and circPAN3 in KMT2A::AFF1 ALL, whose silencing impacted cell proliferation and apoptosis. Further study in an extended cohort disclosed a significantly correlated expression of these oncogenic circRNAs and their putative involvement in common regulatory networks. Moreover, it showed that circAFF1 upregulation occurs in a subset of cases with HOXA KMT2A::AFF1 ALL. Collectively, functional analyses and patient data reveal oncogenic circRNA upregulation as a relevant mechanism that sustains the malignant cell phenotype in KMT2A::AFF1 ALL.-