Analysis of Molecular Minimal Residual Disease in Patients with Acute Leukemia during Complete Remission

Introduction: Acute leukemia is a group of clonal heterogeneous diseases with high recurrence rate. The monitoring of minimal residual disease (MRD) after treatment mainly relies on flow cytometric immunophenotyping. Genetic abnormalities as the basis of the development of leukemia, the prognosis value of gene mutations in complete remission (CR) has yet to be established except for NPM1 and FLT3-ITD mutations. Recent studies have reported that persistent mutations in non-DNMT3A, TET2, and ASXL1 (DTA) mutations during CR had significant independent prognostic value with respect to relapse and survival rates, but the detection of persistent DTA mutations did not have such prognostic value (Jongen-Lavrencic M et al., N Eng J Med 2018). In this study, we analyzed the molecular MRD of mutations in 58 genes during CR in patients with acute leukemia and explored its impact on prognosis.

Methods: Amplicon-targeted, next-generation sequencing (IonTorrent PGM platform, Thermo Fisher Scientific) of 58 genes that are frequently mutated in hematological malignancies was performed retrospectively on 202 patients of acute leukemia, including 117 cases of AML (median age, 23 years; rang, 1-65 years), 66 cases of B-ALL (median age, 13.5 years; rang, 1-45 years) and 19 cases of T-ALL (median age, 11 years; rang, 1-42 years). The average sequencing depth was 1000x. A minimum coverage of 100x and a variant allele frequency >5% were used as thresholds for calling variants.

Results: Mutations presented in 8.5% (10/17) of AML patients during CR and the variant allele frequency (VAF) ranged from 5.0% to 25.5% (median VAF, 12%), of which 80% (8/10) were epigenetic regulator gene mutations (DNMT3A, TET2, and IDH1/2). DNMT3A mutation (R882 locus) were detected in five cases, IDH2 mutation (R140Q) were detected in two cases, IDH1 (R132C), TET2 (C1211Y), KIT (D816H), NPM1 (W288Cfs*12), and U2AF1 (S34F) mutation were each presented in one case. There were four cases with DTA and non-DTA mutations respectively and two cases concomitant with DTA and non-DTA mutations (one with DNMT3A and IDH1 mutations and another one with DNMT3A and NPM1 mutations). The median age of four patients with DTA mutations was 45 years (rang, 22-54 years), and the median follow-up time was 15 months (rang, 10-19 months). Among them, three cases were relapsed, two of the three patients who underwent allogeneic hematopoietic stem cell transplantation (allo-HSCT) were relapsed. The median age of four patients with non-DTA mutations was 24.5 years (rang, 12-64 years), and the median follow-up time was 25.5 months (rang, 12-35 months). All the patients with non-DTA mutations underwent allo-HSCT and were in continuous CR. One of the two patients who concomitant with DTA and non-DTA mutations (mutation in DNMT3A and IDH1) relapsed after allo-HSCT.

Mutations presented in two cases of B-ALL patients during CR, of which PTPN11 (H520Y, VAF 5.9%) mutation was identified in one case who achieved MRD-negative after one course of induction and three courses of consolidation chemotherapy and in a state of sustained remission for two years after allo-HSCT at the time of reporting. KRAS (G12S, VAF 6.3%) mutation was identified in another case whose MRD persists positively after multiple courses of chemotherapy and relapsed in the third years after chemotherapy. At the time of reporting, the bone marrow is in a state of sustained remission for eight months after allo-HSCT. No mutations were detected in all T-ALL patient during CR.

Conclusion: Mutations in the epigenetic regulators DNMT3A, TET2, and IDH1/2 are most common in patients with AML during complete remission and the majority of mutations in genes related to the RTK/RAS pathway were cleared. DTA mutations are more common in older patients. The recurrence rate after allo-HSCT is higher in patients with DTA mutation than that of patients with non-DTA mutation and which need to be further verified in the expanded cohort due to the limited number of cases in this study. In contrast to AML, mutations detected in B-ALL during complete remission were mainly RAS pathway and its prognostic significance needs to be further studied.