Molecular Characterization of Relapsed Core-Binding Factor (CBF) Acute Myeloid Leukemia (AML)

Background: CBF-AML is defined by recurrent genetic abnormalities which encompass t(8;21)(q22;q22), inv(16)(p13.1q22) or less frequently t(16;16)(p13.1;q22). Most frequent secondary chromosome aberrations in t(8;21) AML are del(9q) or loss of a sex chromosome, and in inv(16)/t(16;16) AML trisomy 22 or trisomy 8. At the molecular level mutations involving KIT, FLT3, or NRAS were identified as recurrent lesions in CBF-AML. However, the underlying genetic alterations which might trigger relapse in CBF-AML are not well delineated. Thus, the aim of our study was to characterize the clonal architecture of relapsed CBF-AML.

Methods: We performed mutational profiling (KIT, FLT3-ITD, FLT3-TKD, NRAS, ASXL1) in paired samples obtained at diagnosis and at relapse from 66 adults with CBF-AML [inv(16), n=43; t(8;21), n=23] who all were treated within the AMLSG studies.

Results: In inv(16) AML, the following mutation pattern was identified at diagnosis: KIT 13/40 (33%; exon 8, n=6; exon 17, n=5; exon 8+17, n=1; exon 11, n=1; missing data, n=3), NRAS 18/43 (42%), FLT3-TKD 4/43 (9%); none of the pts harboured FLT3-ITD or ASXL1 mutations. At the time of relapse, there was a shift in the mutation pattern in 26 pts (60%): KIT mutations (exon 8, n=5; exon 17, n=2; exon 8+17, n=1) were lost in 8 pts and 1 pt acquired an exon 17 KIT mutation; similarly, 15 pts lost and 1 pt gained NRAS mutation, respectively. Of note, all FLT3-TKD mutations were lost at the time of relapse, and only one pt gained a FLT3-ITD mutation. Based on these findings we calculated the stability in inv(16) AML for KIT, NRAS and FLT3-TKD mutations as 38%, 17%, and 0%, respectively.

AML with t(8;21) presented a different diagnostic mutation profile: KIT 9/23 (39%; exon 17, n=8; exon 11, n=1), FLT3 -ITD 3/23 (13%), NRAS 2/23 (9%), and ASXL1 1/23 (4%); there were no FLT3-TKD mutations. At the time of relapse, the mutation pattern changed in 9 pts (39%); KIT mutations were lost in 4 pts (exon 17, n=3; exon 11, n=1), but acquired in 2 pts with both of them located in exon 17; only 1 pt lost the NRAS mutation. FLT3-ITD was lost in 2 and gained in 3 pts. There was no change in the ASXL1 mutation status. Thus, the stability for KIT, NRAS, FLT3-ITD and ASXL1 mutations in t(8;21) AML was calculated as 56%, 50%, 33% and 100%, respectively.

Of note, mutations affecting the KIT and NRAS gene were almost mutually exclusive; there were only 3 pts with concurrent KIT and NRAS mutations at diagnosis [inv(16), n=2; t(8;21), n=1].

Conclusion: CBF-AML cases display a high degree of molecular heterogeneity with shift of the mutation pattern at relapse in both CBF-AML subtypes. The frequent loss of KIT and NRAS mutations at relapse suggests that there might be other important secondary lesions driving relapse. Ongoing high-resolution genome-wide profiling will further unravel the clonal hierarchy and genomic landscape in CBF-AML.