Abstract 2281: Molecular profiling of the RUNX1 RUNT domain in myeloid disorders

Abstract Background: AML with RUNX1 mutation is a provisional entity in the WHO classification. RUNX1 variants generally consist of truncating mutations throughout the gene, as well as SNVs, insertions, and deletions in the RUNT domain. In the germline setting, these mutations may lead to familial platelet disorders and have profound implications in donor selection for allogeneic stem cell transplant. Approximately half of mutations in RUNX1 are classified as variants of unknown clinical significance (VOUS), underscoring the unmet needs of this patient population. Methods: Bone marrow, peripheral blood, or FFPE tissue samples from 10,118 patients with suspected myeloid disease were sequenced using a 303 gene myeloid NGS panel. A total of 1209 RUNX1-mutated patients formed the cohort for this study. While pair-matched samples were not available and germline status not established, these patients were likely to be in the 40-60% variant allele frequency (VAF) range. Statistics were performed using Fishers exact test. Results: Among RUNX1-mutated patients, 277 (22.9%) had a RUNX1 variant at a subclonal VAF (<20%), 505 (41.7%), 352 (29.1%), & 75 (6.2%) had variants at VAFs of 20-39%, 40-60%, & >60%, respectively. While all truncating mutations were classified as pathogenic, 84.3% of non-truncating RUNT domain mutations were classified as VOUS. RUNT domain mutations included 272 non-truncating and 220 truncating mutations. There were 599 (49.5%) truncating mutations throughout the entire gene. Non-truncating RUNT domain-mutated patients most frequently harbored mutations in ASXL1 (31.6%), SRSF2 (31.3%), TET2 (29.4%), STAG2 (19.1%), RAS (18.3%), and BCOR/BCORL1 (17.3%). The frequency of RUNT domain co-mutations in the ASXL1 (36.8% [35] vs. 10.4% [5]; p=0.0007) and RAS families (28.4% [26] vs. 10.4% [5]; p=0.03) were significantly higher in the 40-60% VAF group compared to subclonal populations, while BCOR/BCORL1 mutations (10.5% [10] vs. 29.1% [14]; p=0.008) were significantly lower. These results were recapitulated in a cohort of VOUS-only RUNT domain patients with a VAF of 40-60% compared to subclonal populations: ASXL1 (36.8% [21] vs. 22.2% [10]), RAS family (24.5% [14] vs. 10.9% [5]), and BCOR/BCORL1 (8.8% [5] vs. 31.1% [14]; p=0.005). Among patients with truncating mutations in RUNX1, mutations in ASXL1 (34.4% [44] vs 20.3% [42]; p=0.0047) and RAS family members (25.8% [33] vs. 10.1% [21]; p=0.0002) were more frequent in patients with VAFs of 40-60% when compared to subclonal populations, and mutations in BCOR/BCORL1 were similar (28.1% [36] vs. 20.7% [42]). Conclusions: The majority of RUNX1 mutations clustered in the RUNT domain are VOUS. This study demonstrates that both truncations and RUNT domain mutations harbor molecular signatures that reflect similar oncogenic mechanisms. These molecular signatures are also present when filtering exclusively by VOUS in the RUNT domain. Citation Format: Frank J. Scarpa, Madhuri Paul, Rachel Daringer, Sally Agersborg, Vincent A. Funari, Forrest J. Blocker. Molecular profiling of the RUNX1 RUNT domain in myeloid disorders [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2281.