Systemic and local immunity following adoptive transfer of NY-ESO-1 SPEAR T cells in synovial sarcoma

Abstract

Background: Gene-modified autologous T cells expressing NY-ESO-1c259, an affinity-enhanced T-cell receptor (TCR) reactive against the NY-ESO-1-specific HLA-A*02-restricted peptide SLLMWITQC (NY-ESO-1 SPEAR T-cells; GSK 794), have demonstrated clinical activity in patients with advanced synovial sarcoma (SS). The factors contributing to gene-modified T-cell expansion and the changes within the tumor microenvironment (TME) following T-cell infusion remain unclear. These studies address the immunological mechanisms of response and resistance in patients with SS treated with NY-ESO-1 SPEAR T-cells.

Methods: Four cohorts were included to evaluate antigen expression and preconditioning on efficacy. Clinical responses were assessed by RECIST v1.1. Engineered T-cell persistence was determined by qPCR. Serum cytokines were evaluated by immunoassay. Transcriptomic analyses and immunohistochemistry were performed on tumor biopsies from patients before and after T-cell infusion. Gene-modified T-cells were detected within the TME via an RNAish assay.

Results: Responses across cohorts were affected by preconditioning and intra-tumoral NY-ESO-1 expression. Of the 42 patients reported (data cut-off 4June2018), 1 patient had a complete response, 14 patients had partial responses, 24 patients had stable disease, and 3 patients had progressive disease. The magnitude of gene-modified T-cell expansion shortly after infusion was associated with response in patients with high intra-tumoral NY-ESO-1 expression. Patients receiving a fludarabine-containing conditioning regimen experienced increases in serum IL-7 and IL-15. Prior to infusion, the TME exhibited minimal leukocyte infiltration; CD163+ tumor-associated macrophages (TAMs) were the dominant population. Modest increases in intra-tumoral leukocytes (≤5%) were observed in a subset of subjects at approximately 8 weeks. Beyond 8 weeks post infusion, the TME was minimally infiltrated with a TAM-dominant leukocyte infiltrate. Tumor-associated antigens and antigen presentation did not significantly change within the tumor post-T-cell infusion. Finally, NY-ESO-1 SPEAR T cells trafficked to the TME and maintained cytotoxicity in a subset of patients.

Conclusions: Our studies elucidate some factors that underpin response and resistance to NY-ESO-1 SPEAR T-cell therapy. From these data, we conclude that a lymphodepletion regimen containing high doses of fludarabine and cyclophosphamide is necessary for SPEAR T-cell persistence and efficacy. Furthermore, these data demonstrate that non-T-cell inflamed tumors, which are resistant to PD-1/PD-L1 inhibitors, can be treated with adoptive T-cell based immunotherapy.

Trial registration: ClinicalTrials.gov, NCT01343043 , Registered 27 April 2011.

Keywords: Adoptive immunotherapy; Antigen loss; Checkpoint therapy; Cyclophosphamide; Cytokine; Engineered cell therapy; Fludarabine; IL-15; NY-ESO-1; Synovial sarcoma; T cell; TCR.

Conflict of interest statement

IR, DEL, RDM, RW, SF, DN, GB, NB, AJT, LM, JMN, MI, TT, EVW, KC, RA, GKB, and SB: employees of Adaptimmune and have stock or other ownership interests in Adaptimmune.

JG: None

CLM: Consulting for Adaptimmune, GlaxoSmithKline, Allogene, Nektar, Vor, PACT, Unum, Bryologyx, Apricity, Roche, Lyell. Equity in Allogene, Vor, PACT, Unum, Lyell. Research Funding from: Obsidian.

SPD: Consulting for Amgen, EMD Serono, Nektar, travel support from Adaptimmune

DMA: None

WAC: Speaker’s bureau and research funding from Novartis, data safety monitoring board for Advenchen

GDD: None

BAVT: Basic science grant funding from Pfizer, Tracon, and Merck; consulting fees from Epizyme, Lilly, CytRX, Janssen, Immune Design, Daiichi Sankyo, Plexxicon and Adaptimmune; speaking fees from Caris, Janseen, and Lilly

MD: Consulting and speaker’s bureau for Eisai and Lilly

SG: Research and/or clinical trial support from Novartis, Servier, Adaptimmune, and Kite. Consulting, study steering committees, or scientific advisory boards: Novartis, Cellectis, Adaptimmune, Eureka, TCR2, Juno, GlaxoSmithKline, Vertex, Cure Genetics, Humanigen, and Roche.

ARAR: Consulting for Lilly, Merck, Boehringer Ingelheim, research funding from CASI Pharmaceuticals, Boehringer Ingelheim

BW: Research support from Merck, Pfizer, Agenus, and consulting for Lilly and Immune Design

Figures

Fig. 1

Clinical outcome in SS patients following NY-ESO-1 SPEAR T-cell infusion. Comparison of maximal tumor regression curves (waterfall plot) in 42 patients treated with NY-ESO-1 SPEAR T cells across four cohorts: a cohort 1, b cohort 2, c cohort 3, d cohort 4. Spider plots of tumor burden changes following NY-ESO-1 SPEAR T-cell infusion in 42 patients across four cohorts: e cohort 1, f cohort 2, g cohort 3, h cohort 4

Fig. 2

Pre-conditioning lymphodepletion regimen influences NY-ESO-1 SPEAR T-cell engraftment. a Peak expansion of transduced T cells in non-responders versus responders across all four cohorts was determined by measuring peak vector copies/μg of DNA in 42 patients treated with NY-ESO-1 SPEAR T cells. b IL-7 and c IL-15 levels in serum samples from 40 patients across all four cohorts were evaluated prior to (Pre-) and following (Post-) administration of pre-conditioning therapy, but prior to T-cell infusion. Box plots depict median, first and third quartiles. Dotted lines connect Pre- and Post- samples from the same patient. p-values between pre- and post-lymphodepletion in paired specimen in each cohort were calculated by the Wilcoxon matched-pairs signed-rank test

Fig. 3

SPEAR T-cell therapy alters cellular infiltrate in tumor microenvironment. a Markers associated with immune cells and their function were evaluated at pre-infusion (red), and post- infusion at week 8 (blue) or beyond week 8 (grey) by IHC and plotted as a percentage of marker area within tumor area. Statistical significance in marker positivity between time points was determined by a two-way ANOVA test. b Immune marker expression in a representative region of pre- and post- infusion biopsies in one patient with increased leukocyte infiltration at week 8, and in another patient with minimal changes at >week 8 time point. Scale bar = 50 μm

Fig. 4

SPEAR T-cell therapy does not affect antigen expression or presentation. a Representative IHC images of NY-ESO-1 expression at each of the time points evaluated. Scale bar = 100 μm. b NY-ESO-1 protein expression H-scores as determined by IHC in pre- and post-infusion biopsies from all patients where a minimum of one post-infusion biopsy was evaluable (N = 15). Where > 1 biopsy per timepoint was evaluated, average H-score is shown. Mann-Whitney statistical test was used to evaluate changes between pre- and post-infusion time points. Tumor-associated antigen (c) and antigen-processing machinery (d). RNA expression shown as normalized counts as determined by the NanoString assay performed on pre- and post-infusion biopsies. Where more than one biopsy was collected and tested separately, points show the mean. Box-plots depict the median, along with first and third quartiles

Fig. 5

Adoptively transferred NY-ESO-1 SPEAR T cells maintain functionality long after infusion. a Representative fields for detection of negative control RNA (DapB), positive control RNA (PPIB, POLR2A), and CD3 or NY-ESO-1c259TCR RNA by RNAish in one patient’s tumor collected over 2 years post-infusion. b A375 target killing shown as green object count as determined by the Incucyte killing assay performed on flow sorted CD3+CD8+dextramer+ T cells (red line) and CD3+CD8+dextramer− T cells (grey line) from a patient’s PBMCs collected 12 months post-infusion and on A375 alone (blue line)