The Presence of SETBP1, RUNX1 or EZH2 Mutation in MDS/MPN Is Associated with Absence of Response to Hypo-Methylating Agents
Authors: Karantanos Theodoros , Tsai Hua-Ling , Levis Mark , Varadhan Ravi , Jones Richard J. , Jain Tania 
Published: November 2021

Abstract
INTRODUCTION: The management of myelodysplastic syndrome/myeloproliferative overlap neoplasms (MDS/MPN) remains challenging due to their molecular complexity. Hypo-methylating agents (HMA) have been used for cytoreduction and preparation of patients for allogeneic blood or marrow transplantation (BMT). However, less than 50% patients have a meaningful response to HMA and predictive factors for response remain unknown. The aim of our study is to examine molecular predictors of response to HMA in patients with MDS/MPN.
PATIENTS AND METHODS: We performed a retrospective analysis of 150 patients evaluated at our center for chronic myelomonocytic leukemia (CMML), atypical chronic myeloid leukemia (aCML) and unclassifiable MDS/MPN (MDS/MPN-U) between 1/1/2010 and 12/31/2020. Forty-three individuals who were treated with HMA during chronic phase and had next generation sequencing (NGS) using the established 63-genes panel were identified. Complete and partial remission (CR and PR), and marrow response (MR) were assessed based on the MDS/MPN International Working Group response criteria. Univariate logistic regression analysis was used to associate the number of somatic mutations or high-risk (HR) mutations (NRAS, SETBP1, RUNX1, EZH2, TP53, ASXL1, STAG2), and other disease specific factors at the time of the initiation of HMA with response categories. Multivariable analysis for modeling response were conducted via Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression approach, where the predictors were selected based on 5-fold cross validation with turning parameter selected to minimize deviance of logistic regression model. Kaplan-Meier was used to assess the overall survival based on the CR/PR status at 6 months from the initiation of HMA in landmark analysis. Cox-regression analysis considering the occurrence of CR/PR as a time-varying covariate was used to assess the impact of CR/PR on overall survival.
RESULTS: Fifteen women and 28 men with a median age 67 years (range: 45 - 85 years) and a median follow up of 1.5 years (range: 91 days - 5.2 years) were included. Twenty five (58.1%) had CMML, 15 (34.9%) had MDS/MPN-U and 3 (7%) had aCML. Thirty-four patients (79.1%) received azacitidine (median number of cycles: 4.5, range: 1 - 65) and 9 patients (20.9%) received decitabine (median number of cycles: 4, range: 3 - 21). Seventeen patients (39.5%) underwent BMT following HMA therapy. The incidence of AML transformation was 16%. No patients had CR while 56% achieved a PR and 42% had an MR. Univariate analysis showed that ≥2 HR mutations (OR 0.19, 95% CI 0.05-0.67), SETBP1 mutation (OR 0.16, 95% CI 0.02-0.76), RUNX1 mutation (OR 0.1, 95% CI 0.01-0.48) and a mutation in at least one out of the SETBP1, RUNX1 and EZH2 genes (OR 0.05, 95% CI 0.01-0.21) were associated with absence of PR. ≥2 HR mutations (OR 0.23, 95% CI 0.05-0.9), and the presence of a mutation in one out of the SETBP1, RUNX1 and EZH2 genes (OR 0.16, 95% CI 0.03-0.62) were associated with absence of MR on univariate analysis. Finally, older age as a continuous variable was associated with PR (OR 1.09, 95% CI 1.01-1.19) and MR (OR 1.12, 95% CI 1.03-1.24). Presence of a mutation in one of the SETBP1, RUNX1 and EZH2 genes with age adjusted was selected from LASSO approach and significantly predicted the absence of PR (OR 0.05, 95% CI 0.01-0.27), and MR (OR 0.19, 95% CI 0.04-0.91) (Table 1). Using the landmark of 6 months after the initiation of treatment, Kaplan-Meier analysis showed that PR at 6 months was associated with superior overall survival (P=0.010) compared to patients with no response (Figure 1). Similarly, Cox-regression analysis revealed that the occurrence of PR following the initiation of treatment was associated with better overall survival (HR 0.26, 95% CI 0.9-0.13, P=0.010).
CONCLUSIONS: Mutations in SETBP1, RUNX1 or EZH2 genes predicted absence of response to HMA among patients with MDS/MPN independent of other factors including karyotype, blast percentage and R-IPSS. These findings suggest that the molecular profile of MDS/MPN patients can potentially identify patients with HMA-refractory phenotype. Multi-institutional studies of larger cohorts are required to verify these results and develop novel treatment strategies especially for patients with high-risk mutations in MDS/MPN.
Figure 1. Kaplan-Meier estimates of OS by PR status at 6 months in landmark analysis. P-value was based on log-rank test.
Figure 1 Figure 1.

Disclosures
Levis: BMS: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Jazz: Consultancy, Honoraria; Amgen, Astellas Pharma, Daiichi-Sankyo, FujiFilm, and Menarini: Honoraria; AbbVie: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Astellas and FujiFilm: Research Funding; Pfizer: Consultancy, Honoraria; Takeda: Honoraria. Jain: Syneos Health: Research Funding; CTI Biopharma: Research Funding; CareDx: Other: for advisory board participation; Bristol Myers Squibb: Other: for advisory board participation; Targeted Healthcare Communications: Consultancy.