Molecular profile linked to resistance to hypomethilating agents plus venetoclax does not predict outcome in secondary Acute Myeloid Leukemia patients receiving CPX-351 induction.

Abstract Introduction Acute Myeloid Leukemia (AML) is a heterogeneous disease, driven by the serial acquisition of somatic mutations, that may be evolve (s-AML) from a previous myelodysplastic syndrome (MDS) or after cytotoxic chemotherapy for an unrelated neoplasm. Mutations in ASXL1, BCOR, EZH2, SF3B1, SRSF2, STAG2, U2AF1, or ZRSR2 have recently been shown to be highly associated with the diagnosis of s-AML and are therefore considered as secondary-type mutations. Consequently, these mutations are now recognized as defining secondary type mutations (STMs) and are considered as ontogeny markers into the updated International Consensus Classification (ICC) and World Health Organization (WHO) 2022 classification systems. In addition, the presence of any of those mutations constitutes adverse risk as per the European LeukemiaNet (ELN) 2022 risk classification, when conventional chemotherapy is administered. However, their prognostic impact may differ with the introduction of novel therapies, including hypomethylating agents plus Venetoclax (HMA+VEN), where a different molecular pattern including RUNX1, FLT3-ITD, N/KRAS, CBL, and KIT mutations proved to predict treatment failure. CPX-351 is currently approved for secondary AML (s-AML), a subset of AML which is frequently associated with a high prevalence of adverse-risk genetic mutations. Despite the recognized association of these high-risk mutations with s-AML, their specific impact on treatment response to CPX-351 remains underexplored. Elucidating the relationship between these mutational profiles and therapeutic outcomes is critical to optimizing treatment strategies and improving prognostic stratification in this high-risk patient population. The primary objective of this study was to assess the association between the presence of STMs or HMA-VEN resistance profiles and MRD clearance and overall survival (OS). Materials and Methods Eighty-one patients (median age 69; range 37-77) diagnosed with s-AML (n=55) or therapy-related AML (t-AML, n=26), according to WHO 2016 criteria, received CPX-351 at our Center. NGS was performed on bone marrow samples at diagnosis using the Myeloid Solution panel by SOPHiA Genetics, targeting 34 critical genes. Sequencing was conducted on the Illumina MiSeq platform and analyzed using SOPHiA DDM® Software. Minimal Residual Disease (MRD) analysis was conducted via multicolour flow-cytometry (MFC) in all patients achieving complete remission (CR), with a threshold of 0.1%. Results The median number of mutations at diagnosis was 7 (range 2-14), and 36% of patients had a high mutational burden, defined as having more than 8 mutations. Most patients showed STMs (68%), and 73% displayed molecular features linked to HMA-VEN resistance. According to ELN 2022 risk stratification, 8 patients (10%) were classified as favourable, 5 (6%) as intermediate, and 68 (84%) as adverse. After cycle 1, 66/81 patients (81%) achieved CR, with MFC-MRD negativity in 40/66 CR patients (61%). CR rate and MRD negative CR probability were not affected by ELN 2022 high-risk mutations, or STMs, HMA-VEN resistance profile. After a median follow up of 34 months (CI 95%; 23.2-64.8 months), the median OS was 15 months (CI 95%; 10.7-19.3), whereas 1-year OS was 52,7%. OS was not affected by any of the high-risk mutations, STMs, or HMA-VEN resistance profile. In order to evaluate the impact of hematopoietic stem cell transplantation (HSCT), we conducted a Landmark analysis, including only patients alive and in CR at day 90. The landmark model showed that patients undergoing hematopoietic stem cell transplantation (HSCT; n=24, median OS not reached) had superior outcomes compared to those who did not receive HSCT (n=41; median OS 12 months, p<0.05). Among HSCT patients, mutational status did not impact survival, whereas a negative MRD status showed a trend towards improved OS (median OS not reached vs 22 months in MRD negative or positive patients, respectively, p=0.060) . Among patients not undergoing HSCT, none of the analysed variables, including ELN 2022 high risk mutations, STMs and HMA-VEN resistance profile impacted OS. Conclusions The probability of response to CPX-351 is not affected by the presence of STMs and HMA-VEN resistance profile. Patients who achieve response to CPX and are able to proceed to HSCT have the best prognosis. CPX-351 may therefore be a reasonable choice in patients who are fit for HSCT and show molecular features predictive of HMA-VEN failure.