Altered Peptide Ligands Impact the Diversity of Polyfunctional Phenotypes in T Cell Receptor Gene-Modified T Cells

Abstract

The use of T cell receptor (TCR) gene-modified T cells in adoptive cell transfer has had promising clinical success, but often, simple preclinical evaluation does not necessarily accurately predict treatment efficacy or safety. Preclinical studies generally evaluate one or a limited number of type 1 cytokines to assess antigen recognition. However, recent studies have implicated other "typed" T cells in effective anti-tumor/viral immunity, and limited functional evaluations may underestimate cross-reactivity. In this study, we use an altered peptide ligand (APL) model and multi-dimensional flow cytometry to evaluate polyfunctionality of TCR gene-modified T cells. Evaluating six cytokines and the lytic marker CD107a on a per cell basis revealed remarkably diverse polyfunctional phenotypes within a single T cell culture and among peripheral blood lymphocyte (PBL) donors. This polyfunctional assessment identified unexpected phenotypes, including cells producing both type 1 and type 2 cytokines, and highlighted interferon γ^neg (IFNγ^neg) antigen-reactive populations overlooked in our previous studies. Additionally, APLs skewed functional phenotypes to be less polyfunctional, which was not necessarily related to changes in TCR-peptide-major histocompatibility complex (pMHC) affinity. A better understanding of gene-modified T cell functional diversity may help identify optimal therapeutic phenotypes, predict clinical responses, anticipate off-target recognition, and improve the design and delivery of TCR gene-modified T cells.

Keywords: T cell; T cell receptor; adoptive cell therapy; affinity; altered peptide ligand; gene-modified T cells; multi-dimensional flow cytometry; polyfunctionality.

Figure 1

Polyfunctional Phenotypes of HCV1406 TCR-Transduced T Cells Are Remarkably Heterogeneous within Individual Cultures and among PBL Donors HCV1406 TCR-transduced T cells derived from PBL of three healthy donors were co-cultured for 5 hr with T2 cells loaded with 10 μg/mL NS3:1406-1415 or tyrosinase:368-376 peptide. T cells were evaluated for surface lineage markers, CD107a, and intracellular IFNγ, TNFα, IL-2, IL-4, IL-17A, and IL-22. (A and B) Boolean gating seven functional markers for TCR-transduced (A) CD8⁺ and (B) CD4⁺ T cells generated functional categories producing no (gray; non-reactive), 1 (red), two (green), 3 (yellow), 4 (blue), 5 (orange), 6 (purple), or 7 (pink) simultaneous functions. Three donors from a representative experiment are shown. (C and D) Of the 128 possible phenotypes of 7-dimensional analysis, frequency of individual populations >1% in at least one donor are shown for (C) CD8⁺ and (D) CD4⁺ TCR-transduced T cells. A representative experiment is shown comparing donor 1 (blue bars), donor 2 (red bars), and donor 3 (green bars). Each column represents an individual phenotype, the presence of a functional marker indicated by a shaded box. Black asterisks denote shared phenotypes among more than one donor referenced in the text. Blue, red, or green asterisks represent donor-specific phenotypes referenced in the text. Black arrows indicate antigen-reactive populations lacking IFNγ. Red arrows indicate populations producing both type 1 and type 2 cytokines.

Figure 2

Altered TCR-pMHC Interactions Induce Fewer Polyfunctional Phenotypes (A and B) Boolean gating seven functional markers for TCR-transduced (A) CD8⁺ and (B) CD4⁺ T cells generated functional categories with same color scheme as Figure 1. Frequencies are background subtracted (irrelevant tyrosinase:368-376 peptide stimulation) to show specific reactivity for each donor. (C and D) Relative fold-change of altered ligand compared to WT for each functional category is shown for (C) CD8⁺ and (D) CD4⁺ TCR-transduced T cells. The category of 7 functions was removed from fold change analysis because frequencies were 1%. A linear regression model was used to determine if there was a trend in fold change for each peptide relative to WT. Each model included fold change as the outcome, main effects of the number of functions (continuous), and donor (categorical). p values reported represent the evidence of linear trend between number of functions and fold change (*p < 0.05, **p < 0.01, ***p < 0.0001). Previously reported TCR-pMHC affinity values (K_D, μM) are displayed below each peptide ligand for reference.

Figure 3

Changes in pMHC Ligand and Ligand Density Skew Individual Polyfunctional Phenotypes Software packages Pestle/SPICE were used to generate cool plots based on FlowJo Boolean gating of 7 functional markers. Cool plot is condensed to show relevant populations based on the frequency gradation scale. Data reflect (A) T2-stimulated CD8⁺ T cells, (B) T2-stimulated CD4⁺ T cells, (C) HCV⁺ HepG2-stimulated CD8⁺ T cells, and (D) HCV⁺ HepG2-stimulated CD4⁺ T cells of donor 2 from Figure 2, but uncondensed cool plots for all donors can be found in Figure S3. The presence of a cytokine or CD107a is indicated by a shaded/colored box, and individual phenotypes are listed as columns along the x axis. Phenotypes are also color coordinated to easily show the number of functions similar to Figures 1 and 2. For a given pMHC ligand, elicited phenotypes are read across the x axis. Frequency of cells positive for a given phenotype corresponds to the blue shaded scale. Changes in frequencies of an individual phenotype across various ligand stimulations can be read in the y-direction. TCR-pMHC interactions are ranked from bottom to top by decreasing affinity. Black arrows indicate functional phenotypes with fluctuating frequencies not associated with TCR-pMHC affinity. Red arrows indicate low-affinity APL-reactive populations lacking IFNγ discussed in the text.

Figure 4

Frequency and Number of Polyfunctional Phenotypes Is Not Necessarily Dictated by TCR-pMHC Affinity Hierarchical clustering analysis of Boolean-gated functional phenotypes and altered pMHC ligands was performed using hierarchical clustering based on the correlation matrix. Data reflect (A) T2-stimulated CD8⁺ T cells, (B) T2-stimulated CD4⁺ T cells, and (C) HCV⁺ HepG2-stimulated CD8⁺ T cells of donor 2. Relatedness of ligand-stimulated responses is shown in dendograms. Clustering diagrams are shown cut off to positive phenotypes. Complete clustering analyses can be found in Figure S5.

Figure 5

Key Peptide Variations Occur in MHC-Buried Peptide Residues (A) Amino acids V1408 and I1412 are not direct TCR contact residues, but instead are buried in the base of the HLA-A2 binding groove. (B) The molecular environments around V1408 and I1412 are tightly packed, such that changes here are likely to alter peptide conformation, potentially altering how the TCR engages the peptide-MHC complex, contributing to alterations in signaling outcomes.