RNA sequencing as an alternative tool for detecting measurable residual disease in core-binding factor acute myeloid leukemia

Abstract

DNA sequencing-based measurable residual disease (MRD) detection has shown to be clinically relevant in AML. However, the same methodology cannot be applied to fusion gene-driven subtypes of AML such as core-binding factor AML (CBF-AML). Here in this study, we evaluated the effectiveness of using DNA and RNA sequencing in MRD detection and in tracking clonal dynamics in CBF-AML. Using RNA-seq, we were able to quantify expression levels of RUNX1-RUNX1T1 and CBFB-MYH11 at diagnosis and their levels of reduction during remission (P < 6.3e−05 and P < 2.2e−13). The level of reduction of RUNX1-RUNX1T1 as measured by RNA-seq and qPCR were highly correlated (R2 = 0.74, P < 5.4e−05). A decision tree analysis, based on 3-log reduction of RUNX1-RUNX1T1 and cKIT-D816mut at diagnosis, stratified RUNX1-RUNX1T1 AML patients into three subgroups. These three subgroups had 2-year overall survival rates at 87%, 74%, and 33% (P < 0.08) and 2-year relapse incidence rates at 13%, 42%, and 67% (P < 0.05). On the other hand, although low residual allelic burden was common, it was not associated with long-term outcome, indicating that mutation clearance alone cannot be interpreted as MRD-negative. Overall, our study demonstrates that the clinical utility of RNA sequencing as a potential tool for MRD monitoring in fusion gene-driven AML such as RUNX1-RUNX1T1 AML.

The prognostic impact of reduced variant burden in elderly patients with acute myeloid leukemia treated with decitabine

“…MRD assessments are widely studied as prognostic factors after induction chemotherapy and after transplantation [ 13 , 14 , 23 ]. However, NGS-based MRD assessment in patients receiving low-intensity treatment has not been fully evaluated.…”

“…Most patients with AML have molecular mutations at diagnosis, and NGS analysis has been widely used to detect and trace gene mutations. Therefore, NGS-based measurable residu-al disease (MRD) monitoring has been used to predict relapse in patients who have undergone intensive treatment [13,14]. Recent studies have been conducted to detect MRD to predict relapse risk [13][14][15][16][17].…”

“…Therefore, NGS-based measurable residu-al disease (MRD) monitoring has been used to predict relapse in patients who have undergone intensive treatment [13,14]. Recent studies have been conducted to detect MRD to predict relapse risk [13][14][15][16][17]. However, the genetic mutations associated with prognosis among older HMA-treated AML patients have not been well delineated, and an appropriate MRD marker for elderly AML patients has yet to be established [18,19].…”

Molecular MRD Assessment in Acute Myeloid Leukemias

“…76 The utility of RNA sequencing has also been explored by Kim et al in cases of CBF-AML, where they demonstrated that the reduction in disease burden was comparable between RNA sequencing and RT-qPCR. 77 However, unlike DNA-based NGS MRD, the literature on RNA sequencing based MRD for follow-up of fusion transcripts is still sparse and requires further exploration.…”