Prognostic relevance of mutational profile in secondary Acute Myeloid Leukemia patients treated with CPX-351.

Abstract Introduction and aims Acute Myeloid Leukemia (AML) is a heterogeneous disease, driven by the serial acquisition of somatic mutations. Recent evidence has demonstrated that mutations in ASXL1, BCOR, EZH2, RUNX1, SF3B1, SRSF2, STAG2, U2AF1, and ZRSR2 are independently associated with a worse prognosis and, as a consequence, 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 and in this view 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. The impact of these high-risk mutations and others common mutation on treatment response to CPX-351 remains underexplored. The primary objective of this study was to evaluate the molecular profile in a cohort of s-AML patients treated with CPX-351, aiming to identify specific molecular patterns related to treatment response or failure. Methods and Materials 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. The classification proposed by Lindsley et al (Blood, 2015) was adopted for the definition of the biological effect of mutations. Mutations were also categorized as MPN-like (MPL, CALR, JAK2, cKIT, CSF3R) or CMML-like (K/NRAS, PTPN11). Due to high incidence of comutations, patients were assigned hierarchically: TP53 -> MPN-likeorCMML-like ->SPLICING ->CHROMATIN ORGANIZATION or SIGNALING ->DNA METHILATION ->COHESION GENES. 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 According to ELN 2022 risk stratification, 8 patients (10%) were classified as favourable, 5 (6%) as intermediate, and 68 (84%) as adverse. The cohort showed a median of 7 mutations (range 2-14), with 36% of patients showing a high mutational burden, defined as having more than 8 mutations. A substantial proportion of patients harboured high-risk ELN 2022 mutations (88%). Key high-risk mutations included ASXL1 (36%), RUNX1 (35%), TP53 (26%), SRSF2 (23%). After cycle 1, 66/81 patients (81%) achieved CR, with MFC-MRD negativity in 40/66 CR patients (61%). Notably, the presence of ELN 2022 high-risk mutations, or of any other single gene mutation, did not a significant influence on CR and MRD negativity rates. However, a subsequent investigation into the functional categorization of mutations demonstrated a significant association between mutations related to DNA methylation and higher CR rates (p<0.05). 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%. Mutations in ASXL1, CEBPA, KMT2A, ANKRD26, BCORL1, BCOR, DDX41 had single-mutation impact on survival, however the impact was not conserved in the COX regression, mainly due to the high number of co-existing mutations. No co-mutation pattern emerged as prognostic significant. Thereafter, we created a genetic model that's based on the biological effect of the mutation. Survival was longer for patients with MPN-like mutations or splicing mutations in the absence of TP53 (p<0.05). Landmark analysis showed that patients achieving CR and subsequently undergoing hematopoietic stem cell transplantation (HSCT; n=24) had superior outcomes compared to those who did not receive HSCT (n=41; p<0.05). Among HSCT patients, mutational status did not impact survival. Interestingly, among patients not undergoing HSCT, mutations in cohesion genes were associated with worse outcome (p<0.05), whereas mutations in DNA methylation genes correlated with longer survival (p<0.05). Conclusions CPX-351 is able to induce MRD negative CR in a significant proportion of s-AML patients, regardless of mutational patterns. It is noteworthy that mutations in DNA methylation genes or a MPN-CMML like profile appear to confer a survival advantage, while cohesin gene mutations suggest poor prognosis in patients not undergoing HSCT.