Impact of myelodysplasia-related gene mutations and residual mutations at remission in venetoclax/azacitidine for AML

Abstract

Venetoclax plus azacitidine (VEN + AZA) is widely used in acute myeloid leukemia (AML). This study explored the role of static and dynamic profiles of mutational clonal burden to predict outcomes by analyzing marrow samples from 228 VEN + AZA treated AML cases at "Pre-treatment" (n = 228), "Best-response" (n = 105), and "Relapse" (n = 27) phases using targeted-capture sequencing. In a multivariate model, older age, prior AZA, TP53 mutation with variant allele frequency ≥0.10, and RAS-pathway mutations predicted shorter overall survival (OS), while BCORL1 mutation predicted longer OS. Notably, myelodysplasia-related gene mutations, which constitute adverse factors in ELN 2022, predicted favorable survival. Achieving composite complete remission (CRc) significantly predicted longer OS (P < 0.001) but showed residual mutations in 76.2% of the cases. Among CRc cases, relapse-free survival was stratified by molecular clearance of mutations other than DNMT3A, ASXL1, and TET2 (P = 0.04). In addition, 37% of relapsed cases showed a change of major clones, with 40% having potential targets of molecular-targeting treatment. This study revealed the novel prognostic role of myelodysplasia-related gene mutations and established the importance of molecular response assessment in CRc phase.

Fig. 1. Clinical, genomic features, risk classification and OS analysis in AML patients treated with VEN + AZA.

A Frequency of genetic alterations in pre-treatment samples. Bar plots show the frequency of genetic alterations in more than 5% of cases (n = 228). B ELN 2022 risk classification (left) and VIALE-A risk classification (right) of pre-treatment samples. Stacked bar plot showing the proportion of patients across different risk categories per the ELN 2022 classification (n = 197). The adverse risk group is divided into subcategories based on MR-gene mutations alone and other adverse factors. C Kaplan–Meier curve showing overall survival (OS) for all AML patients included in the study (n = 228) undergoing VEN + AZA treatment. D Kaplan–Meier curves for OS by ELN 2022 classification. OS curves stratified by ELN 2022 risk categories (n = 197). Groups include favorable, intermediate, and adverse risk, with adverse risk further detailed in (E). E Kaplan–Meier curves for OS according to ELN 2022 adverse subgroups. The adverse risk group is divided into two subcategories: patients classified as adverse due to the presence of myelodysplasia-related gene (MR-gene) mutations alone (MR-gene-alone) versus those with other adverse risk factors. CNA, copy number alterations; ITD/PTD, internal tandem duplication/partial tandem duplication; MR-gene, myelodysplasia-related gene (including mutations of ASXL1, BCOR, EZH2, RUNX1, SF3B1, SRSF2, STAG2, U2AF1, ZRSR2); MR-gene-alone, patients classified as adverse-risk due to MR-gene mutations alone.

Fig. 2. Mutational profile in CRc status and its effect on survival.

Kaplan–Meier curves showing OS (A) or RFS (B) stratified by hematological response to VEN + AZA treatment. P values are calculated by log-rank test. C Box plots showing the number of genetic alterations per case (left: SNV, middle: CNA, right: SV) for the 89 cases that achieved CRc and had both Pre-treatment and Best-response samples analyzed. P values are calculated with paired-t test. D Bar charts showing the ratio of genetic alterations that were shared between Pre-treatment and Best-response samples. E Stacked bar charts showing the frequency of the cases having non-DTA mutations (red), DTA-mutations alone (purple), or no mutations (blue). The x-axis shows the hematological responses. The 121 patients who had any mutations in either Pre-treatment or Best-response were included in the analysis. P values were calculated using Fisher’s exact test to compare the ratio of cases with non-DTA mutations between response categories. F Stacked bar charts showing the difference of residual mutation status in CRc status for 80 cases who received VEN + AZA and 80 cases who received intensive chemotherapy. P values were calculated using Fisher’s exact test to compare the ratio of cases with non-DTA-mutations between treatment groups. G Kaplan–Meier curves showing RFS stratified by the residual mutations (red: residual non-DTA-mutations, blue: no residual mutations or DTA-mutations alone) in CRc status. P-values are calculated by log-rank test. H Cumulative incidence curves showing relapse (straight lines) or non-relapse mortality (dotted lines) for the same cohort as (G). OS overall survival, RFS relapse-free survival, SNV single nucleotide variants, CNA copy number alterations, SV structural variants, CRc composite complete remission, DTA, DNMT3A, TET2, and ASXL1.