Profiling of somatic mutations in acute myeloid leukemia with FLT3-ITD at diagnosis and relapse

Acute myeloid leukemia (AML) with a FLT3 internal tandem duplication ( FLT3 - ITD ) mutation is an aggressive hematologic malignancy with a grave prognosis. To identify mutational spectrum associated with relapse, whole exome sequencing was performed on 13 matched diagnosis, relapse and remission trios followed by targeted sequencing of 299 genes in 67 FLT3 - ITD patients. FLT3 - ITD genome has an average of 13 mutations per sample, similar to other AML subtypes, which is a low mutation rate compared to solid tumors. Recurrent mutations occur in genes related to DNA-methylation, chromatin, histone-methylation, myeloid transcription factors, signaling, adhesion, cohesin-complex and spliceosome-complex. Their pattern of mutual exclusivity and cooperation among mutated genes suggests that these genes have a strong biologic relationship. In addition, we identify mutations in previously unappreciated genes such as MLL3 , NSD1 , FAT1 , FAT4 , and IDH3B . Mutations in nine genes are observed in the relapse specific phase. DNMT3A mutations are the most stable mutations and this DNMT3A transformed clone can be present even in morphological complete remissions. Of note, all matched trios AML samples share at least one genomic alteration at diagnosis and relapse, suggesting common ancestral clones. Two types of clonal evolution occur at relapse either: (a) the founder clone recurs or (b) a subclone of the founder clone escapes from the induction chemotherapy and expands at relapse by acquiring new mutations. Relapse-specific mutations display increase in transversions. Functional assays demonstrate both MLL3 and FAT1 exert tumor-suppressor activity in the FLT3 - ITD subtype. An inhibitor of XPO1 synergized with standard AML induction chemotherapy to inhibit FLT3 - ITD growth. This study clearly shows that FLT3 - ITD AML requires additional driver genetic alterations in addition to FLT3 - ITD alone.