Molecular Measurable Residual Disease Testing of Blood During AML Cytotoxic Therapy for Early Prediction of Clinical Response

Abstract

Measurable residual disease (MRD) testing after initial chemotherapy treatment can predict relapse and survival in acute myeloid leukemia (AML). However, it has not been established if repeat molecular or genetic testing during chemotherapy can offer information regarding the chemotherapy sensitivity of the leukemic clone. Blood from 45 adult AML patients at day 1 and 4 of induction (n = 35) or salvage (n = 10) cytotoxic chemotherapy was collected for both quantitative real-time PCR (qPCR) assessment (WT1) and next generation sequencing (>500 × depth) of 49 gene regions recurrently mutated in MDS/AML. The median age of subjects was 62 (23–78); 42% achieved a complete response. WT1 was overexpressed in most patients tested but was uninformative for very early MRD assessment. A median of 4 non-synonymous variants (range 0–7) were detected by DNA sequencing of blood on day 1 of therapy [median variant allele frequency (VAF): 29%]. Only two patients had no variants detectable. All mutations remained detectable in blood on day 4 of intensive chemotherapy and remarkably the ratio of mutated to wild-type sequence was often maintained. This phenomenon was not limited to variants in DNMT3A, TET2, and ASXL1. The kinetics of NPM1 and TP53 variant burden early during chemotherapy appeared to be exceptions and exhibited consistent trends in this cohort. In summary, molecular testing of blood on day 4 of chemotherapy is not predictive of clinical response to cytotoxic induction therapy in AML. The observed stability in variant allele frequency suggests that cytotoxic therapy may have a limited therapeutic index for clones circulating in blood containing these mutations. Further validation is required to confirm the utility of monitoring NPM1 and TP53 kinetics in blood during cytotoxic therapy.

Timed Sequential Salvage Chemotherapy for Relapsed or Refractory Acute Myeloid Leukemia

“…Assessment of early MRD prior to the standard response assessment time points needs to be further explored. However, very early molecular response measurement by NGS at day 4 of chemotherapy in our analysis did not correlate with the clinical outcome [15].…”

“…The early assessment of MRD identified NGS-trackable variants in 70% of the patients (n = 7). All variants present in the peripheral blood at day 1 of EMA remained detectable at day 4, with consistent variant allele frequencies, and were not contributors to the clinical response prediction [15].…”

“…All patients provided written informed consent and were treated on National Heart, Lung, and Blood Institute (NHLBI) IRB-approved protocol (NCT00001397) with co-enrollment on laboratory protocol PEARL15 (NCT02527447) [15] at the of the National Institutes of Health (NIH) Clinical Center. Patients with non-APL AML, no prior hematopoietic cell transplant and ECOG performance status ≤ 2 were included.…”

“…The CR and complete remission with incomplete hematological recovery (CRi) were defined according to the ELN 2017 guidelines [1]. In addition, early assessment of molecular measurable residual disease (MRD) was performed on days 1 and 4 of EMA for nine of the ten patients using an NGS assay as previously described [15].…”

Next‐generation sequencing for measurable residual disease detection in acute myeloid leukaemia

“…Recent studies utilizing NGS for the detection of MRD in AML vary greatly in their design and technical aspects. Cohorts studied have included AML patients undergoing allogeneic haematopoietic cell transplantation (alloHCT) (Getta et al , ; Kim et al , ; Thol et al , ; Zhou et al , ; Press et al , ), receiving standard induction chemotherapy (Klco et al , ; Gaksch et al , ; Jongen‐Lavrencic et al , ; Morita et al , ; Onecha et al , ; Rothenberg‐Thurley et al , ; Thol et al , ; Wong et al , ), receiving novel therapies in clinical trials (Levis et al , ), or having only specific mutations (Thol et al , ; Kohlmann et al , ; Salipante et al , ; Levis et al , ; Patkar et al , ; Zhou et al , ; Patel et al , ). Also, since most studies to date have had access to diagnostic samples, de novo leukaemia‐associated mutation discovery using remission samples alone remains an important unmet challenge.…”