Influence of patient characteristics on chimeric antigen receptor T cell therapy in B-cell acute lymphoblastic leukemia

Abstract

CD19-specific chimeric antigen receptor T cell (CD19 CAR T) therapy has shown high remission rates in patients with refractory/relapsed B-cell acute lymphoblastic leukemia (r/r B-ALL). However, the long-term outcome and the factors that influence the efficacy need further exploration. Here we report the outcome of 51 r/r B-ALL patients from a non-randomized, Phase II clinical trial (ClinicalTrials.gov number: NCT02735291). The primary outcome shows that the overall remission rate (complete remission with or without incomplete hematologic recovery) is 80.9%. The secondary outcome reveals that the overall survival (OS) and relapse-free survival (RFS) rates at 1 year are 53.0 and 45.0%, respectively. The incidence of grade 4 adverse reactions is 6.4%. The trial meets pre-specified endpoints. Further analysis shows that patients with extramedullary diseases (EMDs) other than central nervous system (CNS) involvement have the lowest remission rate (28.6%). The OS and RFS in patients with any subtype of EMDs, higher Tregs, or high-risk genetic factors are all significantly lower than that in their corresponding control cohorts. EMDs and higher Tregs are independent high-risk factors respectively for poor OS and RFS. Thus, these patient characteristics may hinder the efficacy of CAR T therapy.

Fig. 1. Consort diagram.

A total of 72 patients with r/r B-ALL were screened, 51 who met the inclusion criteria and did not meet the exclusion criteria were enrolled; 4 patients did not have Sino 19 cell infusion due to production failure. Ultimately, 47 patients received Sino 19 cell infusion; 9 of them had no remission. 38 patients achieved CR/CRi; 10 of them were bridged to allo-HSCT; 19 out of the remaining 28 patients who were not bridged to allo-HSCT relapsed, out of which 16 died. Twelve patients remained in follow-up at the time of data cut off, which included 3 relapsed patients and 9 with sustained remission. Source data is provided as a Source Data file or available at 10.6084/m9.figshare.13136078.v1.

Fig. 2. Overall survival (OS) and subgroup analysis.

a The OS in all patients who received Sino 19 infusion, the median OS was 415.0 days (95% CI: 15.5–814.5). The rate of OS at 1 year was 53.0% (95% CI: 37.2–68.8). b The OS between pediatric and adult cohort showed no significant difference (p = 0.329). c The OS in patients with EMDs (CNS involvement only or EMDs other than CNS) was lower than that in patients without EMDs (p = 0.021 and 0.003), respectively, but no significant difference was observed between the two EMDs subgroups (p = 0.905). d The OS in patients with or without higher Tregs, 1-year OS rate was 29.3% vs. 64.2% (p = 0.011). e The OS in patients with or without high-risk cytogenetic factors, 1-year OS rate was 34.3% vs. 66.7% (p = 0.047). Patients who were bridged to allo-HSCT were excluded when we analyzed the influence of patient characteristics on OS (c–e). b–e were performed by the Kaplan–Meier approach and used a two-sided log-rank test. Source data is provided as a Source Data file or available at 10.6084/m9.figshare.13136078.v1.

Fig. 3. Relapse-free survival (RFS) and subgroup analysis.

a The RFS in all patients who received infusion, the median RFS was 319.0 days (95% CI: 182.6–455.4). The rate of RFS at 1 year was 45.0% (95% CI: 26.8–63.2). b The RFS between pediatric and adult cohort, no significant difference observed (p = 0.168). c The RFS in patients with the 2 subtypes of EMDs (CNS involvement only or EMDs other than CNS) were lower than that in patients without EMDs (p = 0.015 and 0.003), respectively, but no significant difference existed between the subtypes (p = 0.961). d The RFS in patients with or without higher Tregs before infusion, 1-year RFS rate was 11.9% vs. 56.7% (p = 0.002). e The RFS in patients with or without high-risk cytogenetic factors, 1-year RFS rate was 24.2% vs. 67.7% (p = 0.034). Patients who were bridged to allo-HSCT were excluded when we analyzed the influence of patient characteristics on RFS (c–e). b–e were performed by the Kaplan-Meier approach and used a two-sided log-rank test. Source data is provided as a Source Data file or available at 10.6084/m9.figshare.13136078.v1.

Fig. 4. Persistence of Sino 19 cell and B-cell aplasia.

a Panel shows the results of Sino 19 cells detected by qRT-PCR in peripheral blood samples. The first negative was defined as the time of first negative measurement by qRT-PCR. The median persistence time of Sino 19 cells for all patients who attained CR/CRi was 85 days (range 44–498 days), excluding 10 patients that were bridged to allo-HSCT. 15 (78.9%) patients relapsed after the Sino 19 cell loss or at the same time; another 4 (21.1%) relapsed under the state of Sino 19 cell persistence (Nos. 1, 3, 27, and 38). Nine patients (Nos. 2, 4, 7, 13, 16, 26, 28, 33, and 34) failed to achieve CR/CRi (indicated by NR), however, Sino 19 cell was detected in their blood from day 1 to day 60 after the infusion. Two patients (Nos. 8 and 18) who did not bridge to allo-HSCT maintained continue remission and survived for more than 1 year after the Sino 19 cell loss. b The panel shows the detection of B cell in a patient before and after the infusion of Sino 19 cells; B-cell aplasia was defined as CD45 strong and CD19-positive (CD19⁺CD45⁺⁺) B cells <2% in lymphocyte gate; recovery was defined as ≥2%. c The panel shows that the persistence time of Sino 19 cells positively well correlated with the duration of B cell aplasia in patients who achieved CR/CRi without bridging to allo-HSCT (p = 1.08e−7, R = 0.884, by using two-sided Pearson correlation coefficient). Source data of (a) and (c) are provided as a Source Data file or available at 10.6084/m9.figshare.13136078.v1.

Fig. 5. Correlations between Tregs and EMDs.

The circulating Tregs in patients with CNS involvement (10.43 ± 5.41, n = 6) or EMDs other than CNS (12.88 ± 5.79, n = 7) all higher than that in patients without EMDs (6.11 ± 2.70, n = 33) (p = 0.011 and 6.42e−5) respectively, but no significant difference observed between the two subtypes (p = 0.237). Tregs levels were all measured by flow cytometry during post-conditioning chemotherapy and before Sino 19 cells infusion. Error bars represent mean ± SD; * represents p < 0.05; *** represents p < 0.001; ns represents no significance; mean between groups were compared by one-way ANOVA and multiple comparisons were compared using LSD tests (two-sided). p < 0.017 was considered statistically significant after Bonferroni correction (α = 0.05/3 = 0.017). Source data is provided as a Source Data file or available at 10.6084/m9.figshare.13136078.v1.

Fig. 6. Diagnosis and therapeutic evaluation of EMDs before and after Sino 19 cell infusion.

B-ALL presented as a large breast mass in a patient with EMDs. a Computed tomography shows a large mass in the right breast (red arrow). b Flow cytometry on a breast mass sample acquired by puncture biopsy: shows CD19 and CD10 positive B lymphoblasts. c Cell morphology (Wright–Giemsa staining) shows lymphoblasts. At least three smears from this aspirated mass tissue were produced and stained, then three pathologists independently performed morphological view and evaluation, the final diagnosis was established when they had the consistent findings. Scale bar: 50 μM. d Computed tomography shows disappeared large mass at Day 50 following Sino 19 cell infusion (red arrow).