Comprehensive Genomic Profiling Reveals Molecular Subsets of ASXL1-Mutated Myeloid Neoplasms

Abstract ASXL1 is a dynamic epigenetic regulator frequently mutated in myeloid neoplasia. However, a large-scale analysis of patients with ASXL1-mutated myeloid disease has not been performed to date. We retrospectively analyzed comprehensive genomic profiling results from clinical samples from 6,043 adult patients to characterize the spectrum of ASXL1 mutation sites, co-mutation patterns, and to investigate for clinicopathologic differences between ASXL1-wild type patients. ASXL1 mutations occurred in 1,414 patients (23%). Patients with the hotspot c.1934dupG mutation had phenotypic and co-mutational distinctions from those with other ASXL1 mutations. Notably, TP53 (p < 0.01) and SETBP1 (p = 0.04) mutations more often occurred with non-c.1934dupG mutations in acute myeloid leukemia (AML). ASXL1 cohesin-binding motif (CBM) mutations were generally, but not mutually exclusive with cohesin mutations. Co-mutation patterns further suggested that non-cohesin driver mutations may be selectively favored when the CBM is compromised. Overall, ASXL1-mutated and ASXL1-wild type patients had significant differences in age, sex, ancestry, and co-mutation burden (p < 0.01). Mutation co-occurrence and mutual exclusivity testing revealed strong co-occurrence (q < 0.01) between mutations in ASXL1 and nine genes (SRSF2, U2AF1, RUNX1, SETBP1, EZH2, STAG2, CUX1, CSF3R, CBL), and we further analyzed patients with these co-mutations. We found that in spliceosome co-mutated patients, mutational characteristics suggested that ASXL1/SF3B1 co-mutation may be distinct from ASXL1/non-SF3B1 spliceosome co-mutation. In ASXL1/SRSF2 co-mutated AML, STAG2 (42%) and SETBP1 (16%) mutations were common and dependent on the presence of both ASXL1 and SRSF2 mutations (p < 0.05). STAG2 and SETBP1 mutations were mutually exclusive in ASXL1/SRSF2 co-mutated patients and were associated with divergent phenotypes in chronic myeloid neoplasms. Our findings in a large cohort support that ASXL1 mutation site and certain ASXL1 multi-mutant genotypes may be biologically relevant in patients with myeloid neoplasia, and further study is warranted to assess for therapeutic or prognostic impacts in these molecular subsets.