Genomic and Global Gene Expression Profiling in Pediatric and Young Adult Acute Leukemia with PICALM::MLLT10 Fusion

Abstract PICALM::MLLT10 fusion is a rare but recurrent genetic driver in acute leukemias. To better understand the genomic landscape of PICALM::MLLT10 (PM) positive acute leukemia, we performed genomic profiling and gene expression profiling in twenty PM-positive patients, including AML (n = 10), T-ALL/LLy (n = 8), Mixed-phenotype acute leukemia (MPAL), T/B (n=1) and acute undifferentiated leukemia (AUL) (n=1). Besides confirming the known activation of HOXA, our study suggested PHF6 disruption as a key cooperating event in PICALM::MLLT10-positive leukemias. In addition, we demonstrated differences in gene expression profiles as well as remarkably different spectra of co-occurring mutations between PM-AML and PM-ALL (including T-ALL/LLy and MPAL, T/B). Alterations affecting TP53 and NF1 are hallmarks of PM-AML and are strongly associated with disease progression and relapse, whereas EZH2 alterations are highly enriched in PM-ALL. This comprehensive genomic and transcriptomic profiling provides insights into the pathogenesis and development of PICALM::MLLT10 positive acute leukemia. The dramatic differences in the landscapes of co-occurring mutations for these related acute leukemia subtypes highlight the value of performing real-time genomic profiling of acute leukemia for molecular diagnostics.