Impact of myelodysplasia‐related mutations on 2022 European <scp>LeukemiaNet</scp> genetic risk classification in de novo acute myeloid leukemia with normal karyotype
Authors: Srija Shanker, Robert P. Hasserjian, Yazan Madanat, Olga K. Weinberg, Miguel D. Cantu
Journal: American Journal of Hematology (2024)

De novo normal karyotype AML 2017ELN and 2022ELN Genetic Risk Category Changes and Overall Survival in Induction Treated Patients. Acute myeloid leukemia (AML) is a genetically diverse neoplasm that can arise de novo or secondarily from myeloid neoplasms, broadly referred to as "secondary AML."1, 2 Cytogenetic abnormalities are frequent, however, approximately 50% lack cytogenetic abnormalities, referred to as "normal karyotype" AML. The European LeukemiaNet (ELN) classification system is widely used to evaluate prognosis at the time of AML diagnosis in adults with major updates in 2017 and 2022 that include cytogenetic aberrations and gene mutations associated with outcome in intensively treated patients.3 The only myelodysplasia-related gene mutations (MDRM) recognized in the 2017ELN genetic risk stratification guidelines were RUNX1 and ASXL1. The 2022ELN risk classification includes additional MDRM (BCOR, EZH2, SF3B1, SRSF2, STAG2, U2AF1, ZRSR2) as adverse-risk in the absence of concurrent favorable-risk genetic abnormalities. The 2022ELN recommendation to retain AML with concomitant MDRM and favorable-risk genetic lesions in the favorable-risk category is due to limited data to support higher risk.3 Few studies have evaluated the updated 2022ELN genetic risk classification in AML. Cohorts have largely consisted of patients with genetically diverse AML, including de novo AML, secondary AML, and AML with cytogenetic aberrations.4-6 Data on these classification updates in patients with normal karyotype de novo AML (NK-dn-AML) is sparse.5 Given the frequent occurrence of NK-dn-AML, genetic risk largely hinges on the presence of somatic mutations when cytogenetic aberrations are absent. In this study we evaluated disease characteristics and patient outcomes using the 2017ELN and 2022ELN genetic risk guidelines in a large cohort of adult patients with NK-dn-AML. Patient medical records and diagnostic pathology material of adult patients were reviewed from the time of AML diagnosis from four academic medical institutions between 2015 and 2022.1, 2 Patient consent and approval from the institutional review boards of participating institutions was obtained. Clinicopathologic characteristics were examined, including peripheral blood and bone marrow parameters as well as therapy type administered for AML including intensive induction chemotherapy (e.g., cytarabine, daunorubicin, 7 + 3, CPX-351), hypomethylating agents (e.g., azacitidine, decitabine with/without venetoclax), low-intensity chemotherapy (low-dose or other cytotoxic drugs not otherwise specified), and supportive therapy. Allogeneic stem-cell transplant (SCT) and achievement of remission were documented. To limit the analysis to de novo AML, patients with prior exposure to radiation/cytotoxic therapy for treatment of unrelated disease (i.e., "therapy-related" AML), or prior MDS/MPN ("secondary AML") were excluded. To limit the analysis to NK-dn-AML, patients with any cytogenetic aberrations, including MDS-defining aberrations1, 2 detected by conventional cytogenetic and/or FISH studies were excluded. Overall survival (OS) was measured from the time of AML diagnosis to the date of death or last follow-up. Relapse-free survival (RFS) was estimated from the time of AML diagnosis to the date of relapse/death, or the date of last follow-up for living, relapse-free patients. Mutation analysis by massively parallel sequencing (45 genes evaluated across participating institutions) was performed in accordance with institutional protocols as part of routine diagnostic work-up. 2017ELN and 2022ELN genetic risk categories (favorable, intermediate, or adverse) were assigned to subjects, defined by the previously described pathogenic variants.3 Favorable-risk genetic lesions (e.g., NPM1 mutation) that co-occurred with MDRM were retained in the favorable-risk category rather than the adverse-risk category.3 Fisher's exact and Mann–Whitney tests were performed on categorical and continuous variables, respectively. p-Values were unadjusted, two-tailed, and considered significant if values were <.05. Kaplan–Meier method estimated OS and RFS. Groups were compared using log-rank test. We identified 226 NK-dn-AML (Table 1A). The median age was 63 years (range, 19–88 years). Most patients received intensive induction chemotherapy (83%) and 56% received allogeneic SCT. Massively parallel sequencing detected myeloid malignancy associated pathogenic variants in 100% of patients. Following the 2017ELN criteria, 47% were considered favorable, 28% intermediate, 25% adverse. NPM1 was the most frequently mutated gene in the favorable category (91%, N = 98). FLT3-ITD (25%, N = 16) and RUNX1 mutations (71%, N = 40) were most frequent in the intermediate and adverse groups, respectively. Following the 2022ELN criteria, 44% were classified as favorable, 25% as intermediate, and 31% as adverse. NPM1 remained the most frequently mutated gene in the favorable category (89%, N = 89). FLT3-ITD (41%, N = 23) and RUNX1 (57%, N = 40) mutations were again most frequent in the intermediate and adverse groups, respectively. Most reclassified patients were upgraded in the 2022ELN system (Figure S1). Nine patients (4%) were upgraded from favorable to intermediate-risk. Fourteen patients (6%) were upgraded from intermediate to adverse-risk. Only two patients (<1%) were downgraded from intermediate to favorable-risk due to monoallelic basic leucine zipper (bZIP) domain mutations in CEBPA that were not recognized as favorable in the 2017ELN. Patients upgraded from favorable to intermediate-risk were largely due to NPM1 and FLT3-ITD (low allelic ratio) co-mutation, considered intermediate-risk in the 2022ELN. Upgrades from the 2017ELN intermediate-risk group to the 2022ELN adverse-risk group were predominantly due to newly incorporated MDRM. Aside from SRSF2 pathogenic variants, other spliceosome mutations (e.g., SF3B1, U2AF1, ZRSR2) were infrequent. The impact of MDRM with concurrent favorable NPM1 mutations was further assessed (Table 1B). There was co-occurrence in 7% (N = 15) of total cases, representing 14% of cases with NPM1 mutation and 17% of cases with MDRM. The most common MDRM to co-occur with NPM1 mutation was SRSF2 (47%, N = 7) and STAG2 (20%, N = 3). These patients were largely retained in the favorable-risk category in both ELN classifications. Only three cases were upgraded from 2017ELN favorable-risk to 2022ELN intermediate-risk due to concurrent FLT3-ITD (low allelic ratio). Patients treated with induction therapy were included in the survival analysis and evaluated across 2017 and 2022 ELN genetic risk categories (Figure S2). In both ELN systems, favorable risk groups showed significant differences in OS compared to the adverse-risk groups (2017: 44.5 mo vs. 20.3 mo; p = .0029, 2022: 55.2 mo vs. 21.7 mo; p = .0058). There was no significant difference in OS when comparing the 2017ELN favorable and intermediate groups (median OS: 44.5 mo vs. 36.38 mo; p = .3346) or between intermediate and adverse groups (median OS: 36.38 mo vs. 20.3 mo; p = .0819). The 2022ELN favorable and intermediate-risk groups showed no significant difference in OS (median: 55.2 mo vs. 31.4 mo; p = .0501) and no significant difference in OS between the intermediate and adverse groups (median: 31.4 mo vs. 21.7 mo; p = .5502). There was no significant difference in RFS based on the 2017/2022ELN genetic risk categories, presence of MDRM, or presence of multiple MDRM (Table S1). No significant difference in RFS was observed comparing patients with MDRM and without MDRM (median: 16 mo vs. 56.8 mo; p = .055). Induction-treated patients with NPM1 mutation and MDRM compared to patients with NPM1 mutation without MDRM showed no significant difference in OS (median, 31.6 mo vs. 44.5 mo; p = .4747). Similarly, the 2022ELN favorable category, which largely consisted of NPM1-mutated AML (89%), showed no significant difference in OS among patients with MDRM and patients without MDRM (median, 42.4 vs. 55.2; p = .7830). There was no significant difference in RFS between patients harboring NPM1 mutation with MDRM and patients with NPM1 mutation lacking MDRM (median, 16.3 vs. 32.3; p = .434). Studies applying the 2022ELN genetic risk system in NK-dn-AML are limited and have largely focused on its application across genetically diverse cohorts of AML.4-6 Currently, 2022ELN recommends that MDRM not be considered adverse prognostic markers if they co-occur with favorable-risk AML (e.g., NPM1 mutation) due to limited data.3 Our study compared the impact of the 2017 and 2022ELN genetic risk classifications in adult patients with NK-dn-AML, including NPM1-mutated AML with MDRM. Updates in the 2022ELN classification that impact NK-dn-AML include the additional MDRM, recognition of CEBPA in-frame bZIP domain mutations as favorable-risk regardless of the presence of biallelic CEPBA mutations, and redesignation of FLT3-ITD as intermediate-risk irrespective of allelic ratio or co-occurrence with NPM1 mutation.3 In our study, most patients with NK-dn-AML received induction chemotherapy (83%) and met criteria for favorable-risk in both ELN classifications. Most patients with favorable-risk were due to NPM1 mutations. A larger proportion of patients were upgraded to adverse-risk due to the presence of newly incorporated MDRM. However, a subset (7%) harbored NPM1 mutation with MDRM, accounting for 14% of NPM1-mutated NK-dn-AML and 17% of NK-dn-AML with MDRM. Though MDRM are typically associated with adverse outcomes, some studies have shown that this is not always consistent.4, 6 In our study, MDRM showed no significant difference in survival when comparing 2022ELN intermediate/adverse groups. This suggests that, at least in the setting of NK-dn-AML, MDRM may be better classified as intermediate-risk as others have suggested.6 It is possible that adverse cytogenetic aberrations in AML with MDRM may play a more significant role in prognosis compared to NK-dn-AML with MDRM that lack defined cytogenetic aberrations with established prognostic significance. Given that secondary AML frequently harbors high-risk cytogenetic and molecular lesions, inclusion may allow for better 2022ELN risk stratification among genetically heterogenous AML. Our study further supports the rationale for retaining NPM1-mutated AML with MDRM in the favorable-risk category as these patients did not demonstrate significant differences in OS or RFS compared to favorable-risk patients with NPM1-mutated AML without MDRM.5 Our findings suggest the 2022ELN continues to distinguish adverse from favorable-risk but does not clearly segregate intermediate from favorable/adverse-risk in NK-dn-AML, despite 2022ELN adverse-risk including more cases previously categorized as 2017ELN intermediate-risk. Karyotype risk may impact the adverse vs. intermediate distinction more than MDRM. The authors declare no conflict of interest. The data that supports the findings of this study are available in the supplementary material of this article. Figure S1: 2017 ELN and 2022 ELN genetic risk group category changes. Figure S2: Overall survival of NK-dn-AML comparing 2017 ELN and 2022 ELN genetic risk categories. Table S1: Relapse free survival (RFS). 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