AUTHORS
Anushka Walia, MD, Arun Nalla, Ph.D2, Todd A. Alonzo, PhD3, Jim Wang4, Rhonda E. Ries, MA5, Helen Tian6, Yanling Liu7, Jeevitha D'Souza, Postdoctoral fellow8, Aishwarya Ballapuram9, Alexa Rane Batingana10, Alan S. Gamis, MD11, Richard Aplenc I, MD, PhD12, Xiaotu Ma, PhD13, Lisa Eidenschink Brodersen, PhD14, Bettina Burnworth, Ph.D15, Dongbin Xu, Ph.D16, Michael Loken, PhD17, Katherine Tarlock I, MD18, Soheil Meshinchi, MD, PhD19, Benjamin J. Huang, MD20
AFFILIATIONS
1 Brigham and Women's Hospital, Boston, United States
2 Hematologics, Inc., Seattle, Washington, United States
3 University of Southern California, Los Angeles, California, United States
4 Children's Oncology Group, Arcadia, United States
5 Fred Hutchinson Cancer Center, Seattle, Washington, United States
6 University of California San Francisco, San Francisco, California, United States
7 St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
8 University of California San Francisco, San Francisco, California, United States
9 University of California San Francisco, San Francisco, California, United States
10 University of California San Francisco, San Francisco, California, United States
11 Children's Mercy Hospitals and Clinics, Kansas City, Missouri, United States
12 University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States
13 St. Jude Children’s Research Hospital, Memphis, Tennessee, United States
14 Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
15 Hematologics, Inc., Seattle, Washington, United States
16 Hematologics, Inc., Seattle, Washington, United States
17 Hematologics, Inc., Seattle, Washington, United States
18 Fred Hutchinson Cancer Center, Seattle, Washington, United States
19 Fred Hutchinson Cancer Center, Seattle, Washington, United States
20 University of California San Francisco, San Francisco, California, United States
ABSTRACT
Introduction
A key prognostic marker in acute myeloid leukemia (AML) is the detection of measurable residual disease (MRD) during and following therapy. Currently, multidimensional flow cytometry (MFC) is the gold standard for MRD detection in pediatric AML due its broad applicability across disease subtypes. Molecular assays detecting leukemic fusion transcripts have emerged as highly specific and sensitive methods for MRD detection, however their utility in various pediatric AML subgroups remains unclear. In this study, we assess the prognostic value of quantitative polymerase chain reaction (RT-qPCR) MRD in pediatric CBF and KMT2A-rearranged AML.
Methods
We performed RT-qPCR targeting RUNX1::RUNX1T1, CBFB::MYH11, and KMT2Ar partners MLLT3, MLLT10, ELL, MLLT1, and SEPT6 on bone marrow aspirates collected with informed consent from patients diagnosed with AML and enrolled on Children’s Oncology Group (COG) trials AAML03P1, AAML0531, and AAML1031. For CBF AML patients, sequencing was performed at the time of enrollment and end of induction 1 (EOInd1, N = 56) or end of induction 2 (EOInd2, N = 75). For KMT2Ar AML patients, sequencing was performed at the time of enrollment and EOInd1 (N = 80). MRD status thresholds were determined based on receiver operating curve analysis and the resultant area under the curve. Disease free survival (DFS) and overall survival (OS) analysis was performed using Kaplan-Meier estimates. Relapse rates were reported as cumulative incidence of relapse (CIR).
Results
Within the CBF AML cohort, 75% (N = 42) were RT-qPCR negative at EOInd1 while 25% (N=14) were positive. At EOInd2, 60% (N = 45) were RT-qPCR negative and 40% (N = 30) were positive. Negative RT-qPCR MRD at EOInd1 and EOInd2 was associated with superior outcomes. Specifically, patients with negative RT-qPCR MRD at EOInd1 had a 5-year OS of 80.2% from EOInd1 compared to 57.1% for those who had positive MRD (p = 0.088), DFS of 64.1% compared to 35.7% (p = 0.039), and CIR of 28.8% compared to 50% (p = 0.133). Similarly, patients with negative RT-qPCR MRD at EOInd2 had a 5-year OS of 93.3% from EOInd2 compared to 75.4% for those who had positive MRD (p = 0.048), DFS of 82.2% compared to 56.7% (p = 0.020), and CIR of 13.4% compared to 40.0% (p = 0.009).
Within the KMT2Ar AML cohort, negative RT-qPCR MRD at EOInd1 was also associated with superior outcomes. Patients with negative RT-qPCR MRD at EOInd1 (N=61) had a 5-year OS of 73.3% from EOInd1 compared to 28.4% for those who had positive MRD (N=19) (p < 0.001), DFS of 56.5% compared to 21.1% (p = 0.010), and CIR of 43.5% compared to 73.7% (p = 0.039). In multivariable analysis, negative RT-qPCR MRD maintained its association with improved OS, DFS, and CIR.
Given that MFC is the mainstay of evaluating MRD for AML, we compared MRD measurements based on MFC and RT-qPCR for patients with KMT2Ar AML. We found that 10 of 63 (15.9%) of patients had positive MRD based on both MFC and RT-qPCR (“double positive”) at EOInd1. Notably, patients with “double positive” MRD had particularly adverse outcomes. Patients with positive MFC and RT-qPCR MRD at EOInd1 had a 5-year OS of 0.0% from EOInd1 compared to 71.2% for those who had either negative MFC MRD or negative RT-qPCR MRD (p < 0.001) and DFS of 0.0% compared to 52.6% (p = 0.001).
Conclusions
The prognostic role of molecular MRD in AML is expanding. As the majority of pediatric leukemias are fusion-driven, molecular detection of fusion transcripts has the potential to be broadly applicable to disease monitoring in pediatric AML. We show for the first time that RT-qPCR MRD is prognostic in pediatric CBF and KMT2Ar AML. While MFC MRD will likely continue to play a role in AML risk stratification, molecular MRD may further refine risk assessment and guide decisions regarding consolidative and novel targeted approaches. Additional prospective studies are required to determine optimal time points for MRD assessment and to tailor post-remission therapies based on MRD status. We anticipate that future assays with a superior limit of detection will improve upon RT-qPCR, enabling more sensitive assessment of MRD in pediatric AML.
DISCLOSURES
Anushka Walia, MD: No relevant conflicts of interest to declare.