Effect of indoximod-based chemo-immunotherapy in patients with pediatric brain tumors on activation and clonal proliferation of a circulating population of early non-exhausted stem-like CD8+ T cells whose on-treatment expansion is predictive of long-term outcome.
Authors: Pacholczyk Rafal , Satpathy Sarthak , Berrong Zuzana , Chien Franklin , Huang Chenbin , Sadek Ramses F. , Thomas Beena E. , Smith Christopher , MacDonald Tobey J. , Kennedy Eugene Paul , Johnson Theodore S. , Bhasin Manoj K. , Munn David H. 
Published: June 2024

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Background: Combination chemo-immunotherapy is a promising strategy, but it is difficult to determine whether clinical responses are associated with on-target immune activation or just due to chemotherapy. The field lacks well-accepted readouts of on-treatment T cell activation/expansion to answer this question. Methods: We analyzed longitudinal blood samples from 30 patients with pediatric brain tumors treated with the IDO-inhibitor drug indoximod combined with either chemotherapy (n=27, NCT02502708, NCT04049669) or chemotherapy plus ibrutinib (n=3, NCT05106296). Patients in this “Training Set” were selected to include multiple trials, various histologies/molecular risk factors, and a range of outcomes (overall survival (OS) range 6-55 months). Longitudinal blood samples (2-11 samples/patient) were obtained over 4-36 months, depending on duration of treatment, and analyzed by single-cell RNA and TCR sequencing (scRNAseq/TCRseq). TCR clonotypes of interest were defined as having at least 2-fold expansion (or appearance de novo) during treatment compared to baseline. To calculate a “Clonal Expansion Index” (CEI), the total number of T cells belonging to treatment-expanded clonotypes was summed for each sample and expressed as a percentage of total T cells. The peak CEI value for each patient was used to stratify subjects into “Immune Responders” vs “Non-responders”, based on an optimized cutoff established by Receiver Operating Characteristic (ROC) analysis with Youden’s J statistic. Results: In these patients, CEI ranged from <1% to >60% of all circulating T cells. The optimized cut-point was found to be a CEI of 8.6%, producing a sensitivity of 91% and specificity of 77% for this dataset. Kaplan-Meier analysis showed a highly significant 3-fold difference in median OS for the CEI-High patients (26.5 months) compared to CEI-Low (8.9 months, p=0.0003). The CEI metric was far superior as a predictor of long-term outcome than radiographic response by RANO, RAPNO or iRANO criteria, which were not predictive. UMAP clustering and Monocle trajectory analysis of the treatment-expanded T cells revealed that the majority arose from a population of early stem-like cells (TCF7+ LEF1+ FOXP1+), progressing through a more activated stem-like population (HOBIT/ZNF683+) to attain proliferation and effector maturation states. Throughout this sequence, the T cells showed minimal markers of exhaustion (PDCD1, HAVCR2, TOX) and acquired a lytic effector phenotype. Conclusions: We hypothesize that clonal expansion of this population of non-exhausted stem-like T cells, as quantitated by the CEI assay, provides a mechanistically based pharmacodynamic readout of T cell response to indoximod-based (and perhaps other) chemo-immunotherapy.