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: Rafal Pacholczyk, Sarthak Satpathy, Zuzana Berrong, Franklin Chien, Chenbin Huang, Ramses F. Sadek, Beena E. Thomas, Christopher Smith, Tobey J. MacDonald, Eugene Paul Kennedy, Theodore S. Johnson, Manoj K. Bhasin, David H. Munn
Journal: Journal of Clinical Oncology (2024)

2566 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 &lt;1% to &gt;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.