Analysis of T cell receptor clonotypes in tumor microenvironment identifies shared cancer-type-specific signatures

Abstract

Despite the conventional view that a truly random V(D)J recombination process should generate a highly diverse immune repertoire, emerging reports suggest that there is a certain bias toward the generation of shared/public immune receptor chains. These studies were performed in viral diseases where public T cell receptors (TCR) appear to confer better protective responses. Selective pressures generating common TCR clonotypes are currently not well understood, but it is believed that they confer a growth advantage. As very little is known about public TCR clonotypes in cancer, here we set out to determine the extent of shared TCR clonotypes in the intra-tumor microenvironments of virus- and non-virus-driven head and neck cancers using TCR sequencing. We report that tumor-infiltrating T cell clonotypes were indeed shared across individuals with the same cancer type, where the majority of shared sequences were specific to the cancer type (i.e., viral versus non-viral). These shared clonotypes were not particularly enriched in EBV-associated nasopharynx cancer but, in both cancers, exhibited distinct characteristics, namely shorter CDR3 lengths, restricted V- and J-gene usages, and also demonstrated convergent V(D)J recombination. Many of these shared TCRs were expressed in patients with a shared HLA background. Pattern recognition of CDR3 amino acid sequences revealed strong convergence to specific pattern motifs, and these motifs were uniquely found to each cancer type. This suggests that they may be enriched for specificity to common antigens found in the tumor microenvironment of different cancers. The identification of shared TCRs in infiltrating tumor T cells not only adds to our understanding of the tumor-adaptive immune recognition but could also serve as disease-specific biomarkers and guide the development of future immunotherapies.

Keywords: Immune repertoire sequencing; Public TCR; T cell receptor; TCR sharing; Tumor-infiltrating T cells.

Fig. 1

Sharing of TCR clonotypes is common across patients in two different cancers. a Jaccard similarity matrix of TCR clonal overlap between samples. Boxes shaded in gray are similarities between self. b Number of shared TCR clonotypes found between number of patients. x-axis: Log2(counts + 1) of shared TCRs found in any number of patients (y-axis). c Baseline frequency of shared TCR clonotypes (found in each cancer type or in both cancer types) over total number of unique clonotypes per sample. d Frequency of shared TCR clonotypes per patient. Colors represent the number of patients that share the same TCR clonotype within the cancer cohort. Shapes represent TCR clonotypes found uniquely within a single cancer type, in both cancers or found in an independent cohort of healthy individuals. e Proportion of shared TCRs that are found in healthy donors, single cancer type or both cancer types. f Frequency of high-frequency clonally expanded TCRs per patient. Legend same as 1D. g Proportion of private, less shared, shared TCR clonotypes in the high-frequency clonally expanded TCRs. h CDR3 length distribution of private (green), less shared (red) and shared (blue) TCRs. i V- and J-gene usage heatmap of shared TCR clonotypes. Fold-change in V + J use between shared and private TCRs. j Number of nucleotides coding for each shared TCR clonotype. Each dot represents a single shared TCR. X-axis: number of patients each shared TCR found in. y-axis: number of nucleotides found in each cohort that codes for same shared TCR

Fig. 2

Public TCR clonotypes converge on motif signatures that are unique to cancers. a Number of shared TCRs in patients expressing same HLA alleles. X-axis: percentage of patients with same HLA = Patients with same HLA type and expressing same shared TCR/total number of patients expressing same shared TCR. Y-axis: number of shared TCRs. Color represents cancer cohort. b Inset diagram of shared TCRs that are shared in more than 75% of patients with the same HLA-types. c Representative convergent motifs found in shared TCR clonotypes that are specific to each cancer type. Black box: HNN Red box: NPC. Blue number on top left of box reveals total number of patients who have convergent TCRs. Red number on bottom right of box shows total number of different TCRs that contain that motif. d Heatmap of motif convergence to TCR sequences from public databases. Y-axis is individual motif patterns. X-axis is source of database. Red denotes convergence, while blue denotes non-convergence