A characteristic gene expression profile regulated by ACIN1::NUTM1 fusion in a newly identified infant leukaemic cell line and an ACIN1::NUTM1-inducible model.

Abstract

NUTM1-rearranged (NUTM1-R) infant acute lymphoblastic leukaemia (ALL) is a newly identified subgroup of non-KMT2A-R infant ALL, with ACIN1::NUTM1 the most frequent fusion. KMT2A-R and NUTM1-R infant ALL are characterized by fewer copy number alterations. Moreover, the gene expression profile in NUTM1-R infant ALL characteristically reveals upregulation of the genes that are involved in KMT2A-R infant ALL development, including HOXA9 and HOXA10. However, the direct association of NUTM1-fusion with this gene expression remains unexplored. Clinically, in sharp contrast to KMT2A-R infant ALL, the prognosis of NUTM1-R infant ALL is excellent, although its drug sensitivity profile remains unclear. Here, we newly identified an ACIN1::NUTM1-positive ALL cell line, KOPN32, which was previously established from a relapsed infant-ALL case, as the only cell line with NUTM1-fusion. KOPN32 had fewer copy number alterations, like KMT2A-R ALL cell lines. Both KOPN32 and an ACIN1::NUTM1-inducible ALL model, which was established using the ACIN1::NUTM1 fusion cDNA subcloned from KOPN32, revealed upregulation of HOXA9, HOXA10, SKIDA1 and BMI1, indicating direct involvement of ACIN1::NUTM1 fusion in the upregulation of these genes. In the drug sensitivity to eight standard agents, KOPN32 showed high sensitivity to both daunorubicin and vincristine; both are crucial agents in the induction therapy for infant ALL.