Comprehensive T cell repertoire characterization of non-small cell lung cancer

Abstract

Immunotherapy targeting T cells is increasingly utilized to treat solid tumors including non-small cell lung cancer (NSCLC). This requires a better understanding of the T cells in the lungs of patients with NSCLC. Here, we report T cell repertoire analysis in a cohort of 236 early-stage NSCLC patients. T cell repertoire attributes are associated with clinicopathologic features, mutational and immune landscape. A considerable proportion of the most prevalent T cells in tumors are also prevalent in the uninvolved tumor-adjacent lungs and appear specific to shared background mutations or viral infections. Patients with higher T cell repertoire homology between the tumor and uninvolved tumor-adjacent lung, suggesting a less tumor-focused T cell response, exhibit inferior survival. These findings indicate that a concise understanding of antigens and T cells in NSCLC is needed to improve therapeutic efficacy and reduce toxicity with immunotherapy, particularly adoptive T cell therapy.

Fig. 1. TCR clonality is associated with CD8 T cell function.

Correlation between T cell clonality and (a) CD3 density (n = 135), (b) CD4 density (n = 135) and (c) CD8 density (n = 135) by IHC as well as (d) GzmB expression (n = 141), (e) IFN-γ expression (n = 141) by gene expression profiling.

Fig. 2. T cell density, richness and clonality are enriched in PD-1^hi tumors.

(a) T cell density (n = 135), (b) richness (n = 134) and (c) clonality (n = 135) in CD45RO^hi and CD45RO^lo tumors. (d) T cell density (n = 135), (e) richness (n = 134) and (f) clonality (n = 135) in PD-1^hi and PD-1^lo tumors. Bars represent median and quartiles.

Fig. 3. T cell clonality is lower in EGFR mutant tumors.

a Correlation between tumor mutational burden (n = 215) by whole exome sequencing and clonality. b Tumor mutational burden (n = 186), (c) T cell density (n = 186), (d) richness (n = 186) and (e) clonality (n = 186) in EGFR wildtype (white) and mutant (red) tumors. f Tumor mutational burden (n = 51), (g) T cell density (n = 43), (h) richness (n = 43) and (i) clonality (n = 43) in EGFR wildtype (white) and mutant (red) tumors when analyzing only tumors with a low (bottom tertile) TMB. Bars represent median and quartiles.

Fig. 4. The T cell repertoire is associated to clinicopathologic attributes.

a T cell density in adenocarcinomas (n = 135) and squamous cell carcinomas (n = 89). (b) T cell richness in adenocarcinomas (n = 134) and squamous cell carcinomas (n = 89). c Correlation between T cell density or (d) richness and tumor size (n = 225). e T cell clonality in current (n = 101), former (n = 107), and never smokers (n = 16). f T cell richness in relapsed (n = 70) versus non-relapsed (n = 64) adenocarcinoma patients. Bars represent median and quartiles.

Fig. 5. T cell clonality is increased in the tumor-adjacent lung.

a T cell density, (b) richness, and (c) clonality in the peripheral blood (green, n = 121), uninvolved tumor-adjacent lung (blue, n = 216) and tumor (red, n = 225). d T cell density (n = 253), (e) richness (n = 253), and f clonality (n = 253) in healthy (white), COPD (light blue), and tumor-adjacent uninvolved lungs (blue) from smokers and non-smokers. Bars represent median and quartiles.

Fig. 6. T cell repertoire overlap between adjacent uninvolved lung and tumor.

a Jaccard Index when comparing PBMC, uninvolved tumor-adjacent lung, and tumor T cell repertoires (n = 215). b Proportion of the top 100 T cells in the tumor shared with the uninvolved tumor-adjacent lung (n = 225). c Jaccard Index in the T cell repertoire when comparing the tumor-adjacent uninvolved lung to tumors, lung-enriched (e) T cell repertoire between the tumor-adjacent uninvolved lung and tumor, and different regions of the same tumor (ITH) (n = 215). Bars represent median and quartiles.

Fig. 7. Some mutations are shared between the tumor and adjacent uninvolved lung.

a Tumor mutational burden in patients with NSCLC (n = 96). b Mutational burden in the tumor-adjacent uninvolved lung (n = 96). c Number of mutations shared between the tumor and tumor-adjacent uninvolved lung (n = 96). d–e Proportion of mutations found exclusively in the tumor (red), in the tumor-adjacent uninvolved lung (blue), or shared (purple) (n = 96).

Fig. 8. Shared T cells may target shared mutations and viruses.

a Correlation between the proportion of shared mutations (NSEM) and shared top 100 T cells between the uninvolved tumor-adjacent lung and tumor (n = 92). b–c Fold difference between non-viral and viral T cell motifs found exclusively in the tumor-adjacent uninvolved lung (blue), tumor (red), or shared (n = 178). d Proportion of patients with viral (solid) or non-viral (white) motifs enriched in the uninvolved tumor-adjacent lung (blue), tumor (red), or shared T cells (purple) (n = 178). e Proportion of non-viral (n = 215) and (f) viral motifs (n = 215) in healthy, COPD, or tumor-adjacent uninvolved lungs. Bars represent median and quartiles.

Fig. 9. A more tumor-focused lung T cell repertoire is associated with improved overall survival (OS).

a Association between high (red) and low (blue) T cell density in PBMC and OS (n = 120). b Association between high (red) and low (blue) T cell density in the uninvolved tumor-adjacent lung and OS (n = 216). c Association between high (red) and low (blue) T cell clonality in the uninvolved tumor-adjacent lung (enriched compared to the tumor) and OS (n = 214). d Association between high (red) and low (blue) T cell density in PBMC and lung cancer-specific survival (n = 90). e Association between high (red) and low (blue) T cell density in the uninvolved tumor-adjacent lung and lung cancer-specific survival (n = 157). f Association between high (red) and low (blue) T cell clonality in the uninvolved tumor-adjacent lung (enriched compared to the tumor) and lung cancer-specific survival (n = 156). High, above median; Low, below median.