Dynamic monitoring of circulating tumor DNA reveals outcomes and genomic alterations in patients with relapsed or refractory large B-cell lymphoma undergoing CAR T-cell therapy

Abstract

BackgroundOver 50% of patients with relapsed or refractory large B-cell lymphoma (r/r LBCL) receiving CD19-targeted chimeric antigen receptor (CAR19) T-cell therapy fail to achieve durable remission. Early identification of relapse or progression remains a significant challenge. In this study, we prospectively investigate the prognostic value of dynamic circulating tumor DNA (ctDNA) and track genetic evolution non-invasively, for the first time in an Asian population of r/r patients undergoing CAR19 T-cell therapy.MethodsLongitudinal plasma samples were prospectively collected both before lymphodepletion and at multiple timepoints after CAR19 T-cell infusion. ctDNA was detected using a capture-based next-generation sequencing which has been validated in untreated LBCL.ResultsThe study enrolled 23 patients with r/r LBCL and collected a total of 101 ctDNA samples. Higher pretreatment ctDNA levels were associated with inferior progression-free survival (PFS) (p=0.031) and overall survival (OS) (p=0.023). Patients with undetectable ctDNA negative (ctDNA–) at day 14 (D14) achieved an impressive 3-month complete response rate of 77.8% vs 22.2% (p=0.015) in patients with detectable ctDNA positive (ctDNA+), similar results observed for D28. CtDNA– at D28 predicted significantly longer 1-year PFS (90.9% vs 27.3%; p=0.004) and OS (90.9% vs 49.1%; p=0.003) compared with patients who remained ctDNA+. Notably, it is the first time to report that shorter ctDNA fragments (<170 base pairs) were significantly associated with poorer PFS (p=0.031 for D14; p=0.002 for D28) and OS (p=0.013 for D14; p=0.008 for D28) in patients with LBCL receiving CAR T-cell therapy. Multiple mutated genes exhibited an elevated prevalence among patients with progressive disease, includingTP53,IGLL5,PIM1,BTG1,CD79B,GNA13, andP2RY8. Notably, we observed a significant correlation betweenIGLL5mutation and inferior PFS (p=0.008) and OS (p=0.014).ConclusionsOur study highlights that dynamic ctDNA monitoring during CAR T-cell therapy can be a promising non-invasive method for early predicting treatment response and survival outcomes. Additionally, the ctDNA mutational profile provides novel insights into the mechanisms of tumor-intrinsic resistance to CAR19 T-cell therapy.

Circulating Tumor DNA as a Complementary Prognostic Biomarker during CAR-T Therapy in B-Cell Non-Hodgkin Lymphomas

“…ctDNA < 10 LG/mL or between 10 and 100 LG/mL had similar 1-year PFS of 78% and 77% and similar 1-year OS of 90% and 91%, respectively, whereas concentrations between 100 and 1000 and >1000 LG/mL both had median PFS of 3 months, while median OS was 19 months and 7.4 months, respectively [67]. Lastly, Zou et al reported that low pre-LD ctDNA (n = 11) predicted superior 1-year PFS (81.8 vs. 33.3%, p = 0.031) and OS (90 vs. 46.7%; p = 0.023) [68].…”

“…Zou et al identified baseline mutations associated with higher risk of disease progression after CAR-T therapy and resultant inferior PFS and OS including IGLL5, CD79B, P2RY8, ETV6, and KLH6. Interestingly, co-occurrence of TP53 and IGLL5 mutations was observed more frequently in patients with disease progression, suggesting a synergistic role in tumorigenesis and resistance to CAR-T therapy [68]. Lastly, Zhou et al reported mutations at the time of initial diagnosis in GNA13, SOCS1, TNFAIP3, and XPO1 were associated with R/R disease after CAR-T therapy [75].…”

“…Studies suggest achieving early MRD negativity at week 2 predicts improved outcomes after CAR-T therapy in LBCL. Zou et al demonstrated that undetectable ctDNA at day 14 predicted improved 3-month CR rates (77.8 vs. 22.2%, p = 0.015) [68]. An emerging study by Delfau-Larue et al showed that 93% (n = 13) of patients achieving radiographic CR at 3 months had undetectable ctDNA at day 14 (p = 0.009).…”

“…Persistence of MRD at 1 month predicts poor outcomes after CAR-T therapy in LBCL. Zou et al demonstrated that achieving ctDNA negativity at day 28 predicted superior 1-year PFS (90.9 vs. 27.3%, p = 0.004) and OS (90.9 vs. 49.1%, p = 0.003) [68]. Frank et al showed that the presence of MRD positivity, defined as any detectable ctDNA, at day 28 predicted shorter survival compared to MRD negativity with median PFS of 3.03 months versus NR (p < 0.0001) and median OS of 19.0 months versus NR (p = 0.0080) [67].…”