Clinical Characteristics and Prognostic Significance of Co-Mutated SETBP1/GATA2 Myeloid Neoplasms
Authors: Jabban Yazan , He Rong , Bessonen Kurt , Greipp Patricia , Jevremovic Dragan , Foran James M. , Arana Yi Cecilia Y. , Saliba Antoine N. , Hefazi Mehrdad , Matin Aasiya , Hogan William J. , Mangaonkar Abhishek A. , Patnaik Mrinal M. , Shah Mithun V , Alkhateeb Hassan B , Al-Kali Aref 
Published: December 2024

Background: SETBP1 gene, located on 18q12.3, is a major oncogene in myeloid neoplasms. GATA2 gene, located on 3q21, is one of the six GATA transcription factors regulating gene expression via two conserved zinc finger domains (ZF). Previous data suggested that in patients with germline GATA2 mutation (m), acquisition of a somatic SETBP1 mutation (m) was associated with leukemic transformation among patients with excess blast MDS and CMML.
Aim: To study the characteristics of patients with somatic SETBP1-GATA2 mutated myeloid neoplasms.
Methods: This study is a retrospective study at Mayo Clinic. After obtaining IRB approval, we retrospectively reviewed the charts of patients who had myeloid NGS panel results between 2016-2023. All data were recorded at time of first NGS. Cohort 1 was defined as patients with SETBP1m and GATA2m, cohort 2; patients with SETBP1m and GATA2wt, and cohort 3; patients with SETBP1wt and GATA2m. Germline work-up was not performed in the majority of GATA2 cases. We stratified risk based on the European LeukemiaNet 2022 guidelines for AML, IPSS-M for MDS and MDS/MPN, and CPSS-M for CMML. Overall survival (OS) was calculated from date of NGS to date of last follow-up based on Kaplan-Meier estimates and Cox regression analysis. For statistical analysis, we used BlueSky Statistics V10.3.1.
Results:
General characteristics: 114 patients had SETBP1m (median VAF= 39%), and 63 patients had GATA2m (median VAF= 35%). Nine patients had co-occurring SETBP1m/GATA2m mutations (cohort 1). 4/9 patients in cohort 1 had MDS/MPN (44.4%), while only 13/105 in cohort 2 (12.4%) had MDS/MPN (P=0.02). AML was seen in 2 patients in cohort 1 (22.2%) compared to18 in cohort 2 (17.1%) (p=0.6). The median WBC count was 22.9 x 109 cells/L among cohort 1 compared to 9 x 109 cells/L among cohort 2 cases (p=0.09). BM blasts were higher in cohort 3 (7%) compared to cohort 1 (5%) and cohort 2 (3%) (p=0.09), while peripheral blasts tended to be lower in cohort 2 (1%) in comparison to cohort 1 (6%) and cohort 3 (4%) (p=0.48).
Genetic characteristics: In cohort 1,7 GATA2m clustered in zinc finger 2 (ZF2) (77.8%), while the other two mutations were outside the ZF domains (22.2%). This was higher than the ZF2 mutated cases in cohort 3 (46.3%, p=0.1). Abnormal cytogenetics were seen in 66.7% of cohort 1 patients and 45% of cohort 2 (p= 0.3). Two cases with trisomy 8 were seen among patients in cohort 1 (22.2%), compared to only 4.9% in cohort 2 (p=0.09). Two incidences of isochromosome 17q [i(17q)] were seen in cohort 1 (22.2%), versus 5 cases in cohort 2 (4.8%) and 1 case in cohort 3 (1.9%) (p= 0.068).
Co-mutations: The median number of co-mutationswas 3 in both cohort 1 and cohort 2 (p= 0.6). In cohort 1, ASXL1 and SRSF2 mutations were the most common (7/9, 77.8%) followed by NRAS (22.2%) and TET2 (22.2%). 77.8% of cohort 1 patients had SRSF2 co-mutation, compared to 44.8% in cohort 2 (p=0.08), and 27.8% in cohort 3 (p= 0.006). No isolated SETBP1m/GATA2m cases were found.
Survival: Patients in cohort 1 had a numerically higher median OS compared to those in cohort 2 (19.4 vs 15.4 months, p= 0.3). When comparing with the cohort 3, patients in cohort 1 tended to have better outcomes (median OS= 19.4 vs 13.8 months, p=0.8). Among cohort 1, SRSF2 co-mutation was associated with worse survival outcomes compared to patients with SRSF2wt (median OS= 5.3 vs 19.4 months, p= 0.02); this association was not found in cohort 2 (12.5 vs 18.4 months, p= 0.3) and cohort 3 (13.2 vs 17.1 months, p= 0.4). Allogeneic hematopoietic cell transplantation was associated with favorable survival outcomes in all cohorts (cohort 1: 22.6 vs 7.8 months, p= 0.1; cohort 2: 20.9 vs 12.5 months, p= 0.04; cohort 3: 25.6 vs 13.1 months, p= 0.03).
Conclusion: SETBP1m/GATA2m myeloid neoplasms included a significantly higher proportion of MDS/MPN overlap cases in comparison with the SETBP1m/GATA2wt group. The SETBP1m/GATA2m group had a higher proportion of ZF2 GATA2m and SRSF2 co-mutation compared to patients with SETBP1wt/GATA2m. Survival of SETBP1m/GATA2m patients was not worse compared to SETBP1wt/GATA2m or SETBP1m/GATA2wt.