Fusion Gene KMT2A::SEPTIN6 in Acute Myeloid Leukemia Cell Line KOPM-88

(1) Background: KMT2A (alias MLL) is located at chromosome 11q23 and encodes histone methyltransferase 2A which activates target genes via chromatin methylation of histone H3 lysine K4. Mutations of KMT2A, including partial tandem duplication (PTD) and fusion with partner genes, are present in both lymphoid and myeloid acute leukemia. More than 100 various KMT2A fusion genes have been described, with only a minority represented by cell line models. (2) Methods: Cytogenetic and genomic copy number analyses, PCR, Western blot and RNA-sequencing were performed to characterize aberrations in acute myeloid leukemia (AML) cell line KOPM-88. Bioinformatic analysis of public AML patient data revealed differentially expressed genes. Functional analyses were performed by siRNA-mediated knockdown and live-cell imaging. (3) Results: The AML cell line KOPM-88 is derived from a boy at relapse and has been reported to carry t(X;11)(q24;q23), albeit with uncharacterized breakpoints. In KOPM-88 we identified fusion gene KMT2A::SEPTIN6 generated by this translocation, but excluded KMT2A-PTD. KMT2A::SEPTIN6 activated bone morphogenetic protein (BMP)-signalling and inhibited expression of HOXA7 and HOXA9. BMP signalling in turn activated cell proliferation and inhibited CDKN2B expression. (4) Conclusions: KOPM-88 contains fusion gene KMT2A::SEPTIN6, representing the only cell line model for this rare type of KMT2A rearrangement. KOPM-88 may serve to advance novel therapeutic treatments for KMT2A::SEPTIN6-positive AML.