Naïve T-cell Deficits at Diagnosis and after Chemotherapy Impair Cell Therapy Potential in Pediatric Cancers

Abstract

Translational data on chimeric antigen receptor (CAR) T-cell trials indicate that the presence of naïve T cells in the premanufacture product is important to clinical response and persistence. In anticipation of developing CAR trials for other tumors, we investigated the T-cell distribution from children with solid tumors and lymphomas at diagnosis and after every cycle of chemotherapy. We found that patients with T cells enriched for naïve and stem central memory cells expanded well in vitro, but the majority of tumor types showed chemotherapy-related depletion of early lineage cells with a corresponding decline in successful ex vivo stimulation response. Unexpectedly, many pediatric patients with solid tumors had low numbers of naïve T cells prior to any therapy. These data indicate the ex vivo manufacture of CAR T cells may need to be customized based on the nature of T cells available in each disease type. SIGNIFICANCE: Cumulative chemotherapy cycles deplete naïve T cells in many pediatric cancer regimens, reducing expansion potential associated with successful adoptive cellular therapies. Naïve T-cell deficits can be seen at diagnosis as well, implying immune deficits that exist prior to chemotherapy, which may also affect the development of immune-based therapies.See related commentary by Leick and Maus, p. 466.This article is highlighted in the In This Issue feature, p. 453.

Figure 1.

Percentage of peripheral blood samples that demonstrated >5-fold in vitro expansion. A, Samples from patients with solid tumors (Wilms tumor, neuroblastoma, osteosarcoma, Ewing sarcoma, rhabdomyosarcoma) display low pass rates with CD3/CD28 stimulation, and this declines over time (X axis is cycle of chemotherapy, with 0 = diagnosis). B, Samples from patients with lymphoblastic or myeloid leukemia show high pass rates but also decline over time with each chemotherapy cycle. C, Line graph showing data from A/B with pass and indeterminate added together. D, Each individual disease type with pass rates over time. Asterisk indicates a significant decline over time (increasing number of chemotherapy cycles) by regression analysis (P < 0.05). N for each disease group is as in Table 1. See Supplementary Table S1 for summary of statistics for each disease compared with SR ALL.

Figure 2.

T-cell phenotypes of cells harvested from the peripheral blood of patients undergoing chemotherapy. Each disease from Fig. 1 is represented with percentages of each of the five subsets of T cells described. The X axis represents each cycle of chemotherapy (0 is prechemotherapy). Error bars, SD of each subset. The pattern of naïve T-cell percentage largely tracks with expansion potential. SR ALL, AML, Wilms tumor, and osteosarcoma are notable for the stable percentage of naïve T cells compared with other diseases. The definitions of the T-cell phenotypes are described in the Methods. See Supplementary Table S2 for statistical summary of significant trends.

Figure 3.

Effect of naïve or SCM percentage and cytokines on expansion potential. A, There is a significant difference in expansion potential when using 25% naïve T cells (P = 0.028) or 25% naïve plus SCM (P = 0.0053) as a cutoff. The green line represents 5-fold expansion. Samples are from time point 0 (diagnosis). B, Addition of IL7 and IL15 to the expansion procedure results in a higher percentage of patient samples surpassing 5-fold expansion in all tumor types (n = 79 patients in total). C, Prechemotherapy/diagnostic samples were separated into three groups based on initial pass rate and response to the addition of IL7 and IL15. Supplementary cytokines did not rescue some samples (fail to improve), rescued others (improve), and always increased the cell number in samples that passed initially without them (already pass). D, Diagnostic/prechemotherapy samples after bead expansion demonstrate a majority of CM T cells in most disease types, with a possible inverse relationship between SCM and effector memory (EM) cells that is not statistically significant. Please see the Methods for the phenotypic definitions of each subset.