Co-Occurring Mutations in ASXL1 and SRSF2 Define a Unique, Prognostically Relevant Chromatin-Spliceosome Gene Signature in De Novo acute Myeloid Leukemia

Background: Prior studies with extensive acute myeloid leukemia (AML) molecular profiling identified various subgroups wherein co-mutations in genes related to chromatin regulation and RNA splicing showed no survivors, irrespective of age or treatment. Within the chromatin-spliceosome family, co-mutations of ASXL1 and SRSF2 are linked to poor outcomes. However, the representation of this co-mutational pair in de novo, secondary, and therapy-associated AML is not well described. Also, there is no evidence to demonstrate if HSCT would alter poor prognostic outcomes in this unique molecular subgroup of AML. We sought to assess the clinicogenomic characteristics of ASXL1/SRSF2 co-mutation and its outcomes in a large, well-annotated, sequenced cohort of real-world AML patients.

Methods: We conducted a retrospective analysis of adult AML patients with ASXL1^MT/SRSF2^MT by screening well-annotated public databases, cBioPortal (Cerami et al., 2012) and AACR GENIE (v 13.1), and expanded with a published metanalytic cohort of various sub-studies from Cleveland Clinic Foundation from 2012-2021 (Awada et al., Blood 2021, Kewan et al., Nature Communications, 2023). We analyzed the NGS data in the context of baseline clinical parameters, coexisting mutations, variant allele frequencies, karyotype, and AML subtypes. The primary endpoint was overall survival (OS), and secondary outcomes included survival based on AML subtype, karyotype, and hematopoietic stem cell transplant treatment (HSCT). The chi-square test was used to study various described parameters, and Kaplan-Meir curves were used for survival analyses.

Results: We screened a total of 15,742 adult patients with AML, and 2,471 eligible patients were separated into 3 cohorts: 280 (11.3%) patients with ASXL^MT/SRSF2^MT, 1,025 (41.5%) patients with ASXL^MT/SRSF2^WT and 1,166 (47.2%) patients with ASXL^WT/SRSF2^MT. In addition, three AML subtypes were established: de novo AML (dnAML), secondary AML (sAML), and therapy-associated AML (tAML).

The median age of the co-mutated cohort was 70.1 ys. [range 42-100 ys.], compared to the ASXL1^MT [17-100 ys., p=0.0046] and SRSF2^MT cohorts [25-99 ys., p=0.5]. Females were more prominently represented in the ASXL1^MT cohort compared to the SRSF2^MT cohort [47% vs 30%, p<0.0001]. All three cohorts were predominantly enriched by dnAML (69%, 70%, and 67%), the ASXL1^MT cohort had the most tAML (2.2%), and sAML enriched the SRSF2^MT cohort (31%). Abnormal karyotype enriched the ASXL1^MT/SRSF2^WT cohort compared to SRSF2^MT [50% vs 39%, p=0.0001] and equivalent in ASXL1^MT cohorts (50% vs 51%, p=0.06].

Median OS was driven in part by the ASXL1^MT clone and lowest for the co-mutated compared to the ASXL1^MT [12.0 vs 12.5 mo., p=0.0055] and SRSF2^MT cohorts [12.0 vs 17.5 mo., p =<0.0001]. When divided by AML-subtype, dnAML had the lowest median OS in the co-mutated, compared to the ASXL1^MT [12 vs 15 mo., p =0.03] and the SRSF2^MT cohorts [12 vs 17 mo., p =0.02]. sAML had nearly equivalent survival across all cohorts (10.0 vs 9.3 vs 9.4 mo.), and although tAML offered numerically better survival (NE vs 8.7 vs 17.5 mo.), it was not significant. Normal karyotype offered a numerical survival advantage (NE vs 14.39 vs 16.85 mo.).

The median number of mutations in the co-mutated cohort was 4 (range 3 - 7), Fig 1(A). The most common co-occurring mutations in this cohort were RUNX1 (78%), TET2 (48%), IDH2 (43%), NRAS (16%), and CEBPA (15%). 21 patients were transplant-eligible from the co-mutated cohort, with median OS after HSCT being 33 vs 12 mo. without HCT (p =0.0010), Fig 1 (B).

Conclusions: ASXL1/SRSF2 co-mutated patients represent a unique chromatin-spliceosome signature, most prominently in de novo AML, associated with a significantly lower OS. Therefore, it must be identified at diagnosis for improved prognostic assessment and potential therapeutic implications. HSCT can provide longer-term survival in these patients. This represents the largest reported cohort of patients with ASXL1/SRSF2 co-mutated AML. Further studies are warranted to validate the chromatin-spliceosome signature and prognosis.