Factors associated with durable EFS in adult B-cell ALL patients achieving MRD-negative CR after CD19 CAR T-cell therapy

Abstract

Autologous T cells engineered to express a CD19-specific chimeric antigen receptor (CAR) have produced impressive minimal residual disease-negative (MRD-negative) complete remission (CR) rates in patients with relapsed/refractory B-cell acute lymphoblastic leukemia (B-ALL). However, the factors associated with durable remissions after CAR T-cell therapy have not been fully elucidated. We studied patients with relapsed/refractory B-ALL enrolled in a phase 1/2 clinical trial evaluating lymphodepletion chemotherapy followed by CD19 CAR T-cell therapy at our institution. Forty-five (85%) of 53 patients who received CD19 CAR T-cell therapy and were evaluable for response achieved MRD-negative CR by high-resolution flow cytometry. With a median follow-up of 30.9 months, event-free survival (EFS) and overall survival (OS) were significantly better in the patients who achieved MRD-negative CR compared with those who did not (median EFS, 7.6 vs 0.8 months; P < .0001; median OS, 20.0 vs 5.0 months; P = .014). In patients who achieved MRD-negative CR by flow cytometry, absence of the index malignant clone by IGH deep sequencing was associated with better EFS (P = .034). Stepwise multivariable modeling in patients achieving MRD-negative CR showed that lower prelymphodepletion lactate dehydrogenase concentration (hazard ratio [HR], 1.38 per 100 U/L increment increase), higher prelymphodepletion platelet count (HR, 0.74 per 50 000/μL increment increase), incorporation of fludarabine into the lymphodepletion regimen (HR, 0.25), and allogeneic hematopoietic cell transplantation (HCT) after CAR T-cell therapy (HR, 0.39) were associated with better EFS. These data allow identification of patients at higher risk of relapse after CAR T-cell immunotherapy who might benefit from consolidation strategies such as allogeneic HCT. This trial was registered at www.clinicaltrials.gov as #NCT01865617.

Conflict of interest statement

Conflict-of-interest disclosure: K.A.H. has served on ad hoc advisory boards for Celgene. D.L. is an employee of and has equity interests in Juno Therapeutics (a Celgene company). B.G.T. received research funding from Mustang Biopharma and has patents licensed to Mustang Biopharma. H.-P.K. served as a consultant for Rocket Pharmaceuticals, Homology Medicine, and Magenta. J.D.R. is an employee of and has equity ownership in Seattle Genetics. M.S. received research funding from Acerta Pharma, Beigene, Celgene, Genentech, Gilead Sciences, Mustang Biopharma, Pharmacyclics, and TG Therapeutics and served as a consultant for Qilu Puget Sound Biotherapeutics, AbbVie, Genentech, Verastem, and AstraZeneca. R.D.C. received research funding from Amgen, Incyte, Kite (a Gilead Company), Merck, Pfizer, and Seattle Genetics and served as a consultant for Adaptive Biotechnologies, Pfizer, Amgen, and Jazz Pharmaceuticals. U.H.A. received research funding from Juno Therapeutics. S.R.R. served as an advisor and has equity interests in Juno Therapeutics, Adaptive Biotechnologies, and Nohla Therapeutics. D.G.M. received research funding from GlaxoSmithKline and Juno Therapeutics. C.J.T. received research funding from Juno Therapeutics and Nektar Therapeutics, has patents licensed to Juno Therapeutics, serves on scientific advisory boards, has equity ownership in Caribou Biosciences, Eureka Therapeutics, and Precision Biosciences, and has served on ad hoc advisory boards for Aptevo, Juno Therapeutics, Kite, Nektar Therapeutics, and Novartis. The remaining authors declare no competing financial interests.

© 2019 by The American Society of Hematology.

Figures

Graphical abstract

Figure 1.

EFS and OS in B-cell ALL patients after CD19 CAR T-cell therapy. (A-B) Kaplan-Meier analyses demonstrating better EFS and OS in patients who achieve MRD-negative CR by high-resolution flow cytometry on restaging (black line, n = 45) compared with patients who do not respond (red line, n = 8; P < .0001 and P = .014, respectively; log-rank test). (C-D) In the MRD-negative CR patients who had a leukemic clone detected by HTS (n = 28) before CD19 CAR T cells, absence of the leukemic clone (black line, n = 20) after CAR T cells was associated with significantly better EFS (P = .036) and a trend toward better OS (log-rank test P = .14) compared with those with a persistent leukemic clone (red line, n = 8).

Figure 2.

Impact of CAR T-cell in vivo expansion kinetics on achievement of MRD-negative CR. (A) CAR T-cell counts in the blood over the first 90 days after CAR T-cell infusion for patients who achieved MRD-negative CR (blue lines) compared with patients who did not respond (red lines). Each thin line represents a single patient; bold lines represent LOESS (local polynomial regression) curve fitting data approximation with the standard error shown in gray; data were censored at the time of a subsequent CAR T-cell infusion. The dashed horizontal line indicates the limit of quantitation of the qPCR assay. Patients who achieved MRD-negative CR (blue) had a higher mean peak (P = .0002 [B]) and AUC from day 0 to day 28 (AUC28; P < .0001 [C]) of CAR T cells compared with those who did not respond (red). CAR T-cell counts in the blood were measured by qPCR for FlapEF1α transgene copies per μg of DNA in all patients (n = 53).

Figure 3.

Effect of factors associated with better EFS in multivariable model. (A-B) Log relative hazard effect relationship with the prelymphodepletion serum LDH concentration and platelet count, demonstrating increasing relative hazard with higher LDH or lower platelet count, respectively. The standard error is shown in pink; dashed line indicates the upper limit of normal of LDH concentration and lower limit of normal of platelet count. (C-D) Kaplan-Meier analyses demonstrate better EFS and OS in patients with low-risk characteristics (receiving fludarabine-containing lymphodepletion with a prelymphodepletion LDH concentration in the normal range, and platelet count >100 000/μL) identified by stepwise multivariable modeling (blue line) compared with those with high-risk characteristics (red line).

Figure 4.

Relapse after treatment with CD19 CAR T cells. (A) Cumulative incidence of CD19+ (red line) and CD19– (blue line) relapse after CD19 CAR T-cell therapy. (B-C) Patients who subsequently developed CD19+ relapse had a lower peak (4.34 vs 5.18 log10 transgene copies per μg of DNA; P = .034) and AUC from day 28 to day 90 (AUC28-90; 5.47 vs 6.60 log10 transgene copies per μg of DNA; P = .0042) of CAR T cells in the blood compared with those who developed CD19– relapse. (B) Each thin line represents a single patient; the bold lines represent the averaged data using LOESS curve fitting approximation with the standard error shown in pink and light blue. (D) Swimmer plots demonstrating CAR T-cell counts in the blood from day 0 to day 600 in patients who either did not relapse (left) or who relapsed with CD19+ (center) or CD19– (right) disease. The timing of B-cell recovery (Ο), relapse (+), allogeneic HCT (⋄), and death (Δ) are shown. Patients 17, 27, 29, and 34 died on days 608, 818, 1079, and 1174, respectively. All patients who developed CD19– relapse (right panel) had detectable levels of CAR T cells in the blood at the last time point before relapse and ongoing B-cell aplasia. CAR T-cell counts in the blood were measured by qPCR to detect FlapEF1α and are reported as transgene copies per μg of DNA in the color-coded legend. Patients 24, 25, 26, 28, 30, 32, 33, 34, 35, and 36 received a second infusion of CAR T cells after relapse.

Figure 5.

Outcomes after allogeneic HCT after CD19 CAR T-cell therapy. (A-B) Kaplan-Meier analyses demonstrating EFS and OS in patients who received allogeneic HCT while in MRD-negative CR after CD19 CAR T-cell therapy (n = 18). Two-year Kaplan-Meier point estimates of EFS and OS were 61% and 72%, respectively. (C) Cumulative incidence of relapse (blue line) and NRM (green line), with 2-year estimates of 17% and 23%, respectively. Day 0 was defined as the date of allogeneic HCT.