Next-Generation Sequencing-Based T-Cell Receptor (TR) Measurable Residual Disease Monitoring Does Not Predict Relapse in T-Lineage Acute Lymphoblastic Leukemia
Authors: Madero-Marroquin Rafael , Askari Adnan , Moreno Yenny Vanegas , Anderson Clare E , Badar Talha , Guru Murthy Guru Subramanian , Lin Chenyu , Coltoff Alexander , Duvall Adam S. , Larson Richard A. , Odenike Olatoyosi , Stock Wendy , Patel Anand Ashwin , Saygin Caner 
Published: December 2024

Introduction:
The development of increasingly sensitive tests for the detection of measurable residual disease (MRD), such as multiparameter flow cytometry (MFC) and next-generation sequencing (NGS) assays, has changed clinical practice in acute lymphoblastic leukemia (ALL). IGH V(D)J-based NGS MRD is the most sensitive assay to predict relapse in patients (pts) with B-ALL (Short, Blood Adv 2022). However, data regarding the use of T-cell receptor (TR) NGS MRD in T-ALL are limited and recent reports from pediatric cohorts suggest that persistent TR MRD may not predict relapse in T-ALL (Roy, ASH 2023, abstract 2976). With limited options for the treatment of relapsed/refractory T-ALL, accurate prediction of high relapse risk may provide an opportunity for early intervention. In this study, we evaluated the prognostic utility of TRB/TRG NGS MRD and its correlation with MFC MRD in adult patients with T-ALL.
Methods:
We retrospectively evaluated the MRD data and clinical outcomes of precursor T (pre-T) and early T precursor (ETP) ALL patients treated at four academic centers in the US. MRD was evaluated using MFC in CLIA-certified labs at individual sites with a sensitivity of 10-4, and the clonoSEQ (Adaptive Technologies, lnc) NGS assay, with a sensitivity of 10-6. Pts were included if they had a trackable TR clone and NGS MRD remission assessment in at least one time point. The correlation between the percentage of MRD by MFC vs NGS was calculated with the Pearson correlation coefficient, using every available MRD assessment for T-ALL pts in complete remission. Relapse-free survival was stratified based on NGS MRD level at the time of post-induction and post-consolidation assays, and comparisons were made with the log-rank test. The positive predictive value (PPV) for relapse of NGS MRD was calculated for pts with MRD &gt; 10-6 at the post-induction and post-consolidation period.
Results:
A total of 19 pts who met our inclusion criteria, with a median age of 30 years (range, 18-65). 9 pts (47%) had ETP-ALL, 10 pts had pre-T ALL. Pts had a trackable TRB/TRG clone in 76% of cases, with 66% having a trackable TRG clone and 38% having a trackable TRB clone. 10 pts (53%) were treated with a modified AALL0434 regimen as first line therapy, 6 pts (32%) were treated with CALGB10403, 1 pt (5%) was treated with hyperCVAD, 1 pt (5%) was treated with a BFM regimen, and 1 pt (5%) was treated with CALGB9511.
Out of 11 T-ALL pts with MRD data available post-induction, 6 pts (55%) had detectable MRD by NGS and no detectable MRD by MFC. Out of 13 pts with available post-consolidation MRD data, 2 pts (15%) had undetectable MRD by both NGS and MFC and 9 pts (69%) had detectable MRD by NGS only. There were no pts with detectable MRD by MFC and undetectable MRD by NGS at either timepoint. A total of 64 MRD data points from 19 pts were available to evaluate MRD correlation by MFC vs NGS, for which the Pearson correlation coefficient showed a statistically significant linear correlation (p &lt; 0.01).
At post-induction, 9 pts had NGS MRD &gt; 10-4 and 2 pts had NGS MRD &lt; 10-4. With a median follow-up time of 19.8 months, pts with NGS MRD &gt; 10-4 had a median RFS of 19.8 months and pts with NGS MRD &lt; 10-4 had a median RFS of 14.8 months. The log-rank test comparing RFS between these two groups was not statistically significant (p= 0.18). Persistent NGS MRD at post-induction had a PPV for relapse of only 18%.
At post-consolidation, 7 pts had NGS MRD &gt; 10-4, 4 pts had NGS MRD &lt; 10-4, and 2 pts had undetectable MRD by NGS. With a median follow-up time of 17.3 months, pts with NGS MRD &gt; 10-4 had a median RFS of 15.3 months and pts with NGS MRD &lt; 10-4 or undetectable had a median RFS of 20.6 months. The log-rank test comparing RFS between these two groups was not statistically significant (p= 0.6). Persistent NGS MRD at post-consolidation had a PPV for relapse of only 27%.
Conclusion:
Despite statistically significant linear correlation between MFC and NGS MRD testing, there were no RFS differences between pts with NGS MRD &gt; 10-4 vs NGS MRD &lt; 10-4. All patients had persistent NGS MRD post-induction, which is markedly lower than the reported 20-25% NGS undetectable MRD rate in B-ALL post-induction. Persistent NGS MRD has low PPV for relapse in T-ALL, which limits its utility in clinical decision making for this population.