Spatial TCR clonality and clonal expansion in the in situ microenvironment of non-small cell lung cancer

T-cell activation and clonal expansion are essential to effective immunotherapy responses in non-small cell lung cancer (NSCLC). The distribution of T-cell clones may offer insights into immunogenic mechanisms and imply potential prognostic and predictive information.

We analyzed α/β T-cell receptor (TCR) clonality using RNA-sequencing of bulk frozen tumor tissue from 182 patients with NSCLC. The data was integrated with molecular and clinical characteristics, extensive in situ imaging, and spatial sequencing of the tumor immune microenvironment. TCR clonality was also determined in an independent cohort of nine patients with immune checkpoint-treated NSCLC.

TCR clonality (Gini index) patterns ranged from high T-cell clone diversity with high evenness (low Gini index) to clonal dominance with low evenness (high Gini index). Generally, TCR clonality in cancer was lower than in matched normal lung parenchyma distant from the tumor (p=0.021). The TCR clonality distribution between adenocarcinoma and squamous cell carcinoma was similar; however, smokers showed a higher Gini index. While in the operated patient with NSCLC cohort, TCR clonality was not prognostic, in an immune checkpoint inhibitor-treated cohort, high TCR clonality was associated with better therapy response (p=0.016) and prolonged survival (p=0.003, median survival 13.8 vs 2.9 months). On the genomic level, a higher Gini index correlated strongly with a lower frequency of epidermal growth factor receptor (EGFR) and adenomatous polypsis coli (APC) gene mutations, but a higher frequency of P53 mutations, and a higher tumor mutation burden. In-depth characterization of the tumor tissue revealed that high TCR clonality was associated with an activated, inflamed tumor phenotype (PRF1, GZMA, GZMB, INFG) with exhaustion signatures (LAG3, TIGIT, IDO1, PD-1, PD-L1). Correspondingly, PD-1+, CD3+, CD8A+, CD163+, and CD138+immune cells infiltrated cancer tissue with high TCR clonality. In situ sequencing recovered single dominant T-cell clones within the patient tumor tissue, which were predominantly of the CD8 subtype and localized closer to tumor cells.

Our robust analysis pipeline characterized diverse TCR repertoires linked to distinct genotypes and immunologic tumor phenotypes. The spatial clustering of expanded T-cell clones and their association with immunological activation underscores a functional, clinically relevant immune response, particularly in patients with NSCLC treated with checkpoint inhibitors.