Comprehensive Transcriptome Profiling of Cryptic <i>CBFA2T3-GLIS2</i> Fusion-Positive AML Defines Novel Therapeutic Options: A COG and TARGET Pediatric AML Study.

Abstract

A cryptic inv(16)(p13.3q24.3) encoding the <i>CBFA2T3-GLIS2</i> fusion is associated with poor outcome in infants with acute megakaryocytic leukemia. We aimed to broaden our understanding of the pathogenesis of this fusion through transcriptome profiling. Available RNA from children and young adults with <i>de novo</i> acute myeloid leukemia (AML; <i>N</i> = 1,049) underwent transcriptome sequencing (mRNA and miRNA). Transcriptome profiles for those with the <i>CBFA2T3-GLIS2</i> fusion (<i>N</i> = 24) and without (<i>N</i> = 1,025) were contrasted to define fusion-specific miRNAs, genes, and pathways. Clinical annotations defined distinct fusion-associated disease characteristics and outcomes. The <i>CBFA2T3-GLIS2</i> fusion was restricted to infants <3 years old (<i>P</i> < 0.001), and the presence of this fusion was highly associated with adverse outcome (<i>P</i> < 0.001) across all morphologic classifications. Further, there was a striking paucity of recurrent cooperating mutations, and transduction of cord blood stem cells with this fusion was sufficient for malignant transformation. <i>CBFA2T3-GLIS2</i> positive cases displayed marked upregulation of genes with cell membrane/extracellular matrix localization potential, including <i>NCAM1</i> and <i>GABRE</i>. Additionally, miRNA profiling revealed significant overexpression of mature <i>miR-224</i> and <i>miR-452</i>, which are intronic miRNAs transcribed from the <i>GABRE</i> locus. Gene-set enrichment identified dysregulated Hippo, TGFβ, and hedgehog signaling, as well as <i>NCAM1</i> (CD56) interaction pathways. Therapeutic targeting of fusion-positive leukemic cells with CD56-directed antibody-drug conjugate caused significant cytotoxicity in leukemic blasts. The <i>CBFA2T3-GLIS2</i> fusion defines a highly refractory entity limited to infants that appears to be sufficient for malignant transformation. Transcriptome profiling elucidated several highly targetable genes and pathways, including the identification of CD56, providing a highly plausible target for therapeutic intervention.