Abstract LB200: Indoximod or ibrutinib/indoximod based clinical chemo-immunotherapy drives conversion of extra-tumoral circulating stem-like precursor CD8+ T cells into clonally expanded, rejuvenated effector cells
Authors: Johnson Theodore S. , Pacholczyk Rafal , Berrong Zuzana , Huang Chenbin , Kennedy Eugene P. , Ring Eric , Sadek Ramses F. , Satpathy Sarthak , Thomas Beena E. , MacDonald Tobey J. , Bhasin Manoj , Munn David H. 
Published: April 2023

Abstract
Increasing evidence suggests that many of the effector CD8+ T cells reactivated (‘rejuvenated”) by immunotherapy come from outside the tumor, derived from a circulating pool of “stem-like” memory or “precursor-exhausted” (TPEX) cells. These cells have been characterized in mice, but, despite their importance, circulating counterparts in humans have not yet been identified for study. We hypothesized that immunotherapy designed to enhance immunogenic antigen-presentation during chemotherapy might produce extensive reactivation of these precursor T cells. While the antigen-presentation step occurs in tissues, homing of the rejuvenated T cells to the tumor is via the circulation; thus, we hypothesized that they would be visible in blood. Informative patients were selected from two ongoing clinical trials of children with brain tumors treated with the IDO-inhibitor drug indoximod: a Phase 2 trial (NCT04049669) of indoximod plus chemotherapy; and a Phase 1 trial (NCT05106296) of indoximod, chemotherapy and the BTK-inhibitor ibrutinib, which synergistically destabilizes IDO (Immunity 54:2354-2371, 2021). Patient selection criteria included either (i) massive clonal expansion of activated CD8+ T cells on therapy (expanded clones reaching 16-25% of total CD8+ T cells); or (ii) complete radiographic tumor response (CR) on treatment; or (iii) both. Longitudinal blood samples (4-10 samples per patient) were obtained over a period of 6-24 months and analyzed by single-cell RNA-sequencing (scRNA-seq) with paired single-cell T cell receptor sequencing (scTCR-seq). TCR clonotypes of interest were identified based on robust clonal expansion on-treatment; then each clonotype was traced back through earlier samples to the pre-treatment baseline, or the earliest sample in which that clone could be detected. Clones were pooled, subjected to UMAP clustering, and differential gene-expression and trajectory analysis performed. At earliest appearance, each clonotype was enriched for a phenotype dominated by early transcription factors TCF7 and IKZF2 (Helios). These cells expressed little PDCD1 (PD-1) but showed a “hybrid” combination of genes associated with immaturity/arrest (BACH2, DUSP2, LTB, IL7R, CD160) and effector/memory (NKG7, GZMK, GZMA). Within each responding clone, this “precursor” phenotype could be observed to progressively transition into a mature cytotoxic/effector phenotype (PRF1, GZMB, GZMH, FGFBP2, KLRB1, IFNG). Trajectory analysis of this maturation sequence allowed us to analyze key gene-regulatory networks and transcription factor profiles at each stage. To our knowledge, this is the first study in humans to identify this key stem-like precursor population in circulation, allowing us to sequentially follow the molecular changes in these cells during rejuvenation.
Citation Format: Theodore S. Johnson, Rafal Pacholczyk, Zuzana Berrong, Chenbin Huang, Eugene P. Kennedy, Eric Ring, Ramses F. Sadek, Sarthak Satpathy, Beena E. Thomas, Tobey J. MacDonald, Manoj Bhasin, David H. Munn. Indoximod or ibrutinib/indoximod based clinical chemo-immunotherapy drives conversion of extra-tumoral circulating stem-like precursor CD8+ T cells into clonally expanded, rejuvenated effector cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB200.