Identification of intratumoral and peripheral T-cell receptor (TCR) repertoire features associated with acquired (Ar) and primary (Pr) resistance to immune checkpoint inhibitors (ICI).
Authors: Genta Sofia , Soleimani Shirin , Li Xuan , Pedersen Stephanie , Nguyen Alisa , Abdul Razak Albiruni Ryan , Saibil Samuel , Butler Marcus O. , Bedard Philippe L. , Zhang Tong , Tsao Ming Sound , Wang Ben X , Singaravelan Nittusha , Covelli Andrea , de Almeida John R. , Hansen Aaron Richard , Eng Lawson , Pugh Trevor J. , Siu Lillian L. , Spreafico Anna 
Published: August 2023

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Background: Our understanding of the mechanisms of Pr vs Ar to ICI is limited. T-cells are the main driver of ICI response. Therefore, interrogation of intratumoral and peripheral TCR repertoire could expand our comprehension of T-cell mediated factors underlying Pr and Ar to ICI. Methods: The Immune Resistance Interrogation Study (NCT04243720) is a prospective study to comprehensively characterize cancers with Pr vs Ar to ICI (Genta et. al., ASCO 2021). We conducted TCRβ capture and sequencing (CapTCR-seq) on paired tumors and blood samples collected from solid tumor patients (pts) at the time of progression on ICI. Tumor and peripheral TCR diversities were calculated for each pt. Grouping Lymphocyte Interactions by Paratope Hotspots (GLIPHII) was used to investigate the potential antigen specificities of intratumoral T-cells. Pt-derived TCRs were pooled with TCRs from a public database with known antigen specificities (TCRdb). GLIPHII grouped pt-derived and external TCRs with similar CDR3s (hypervariable TCR domains) in clusters. The clusters were then converted into a network model representing unique TCRs as nodes. The number of connections between each pt-derived TCR and similar TCRs from TCRdb was defined as node degree. Comparisons between groups were done using Mann Whitney U Test. Results: As of February 2023, 75 pts (45 Pr/30 Ar) were enrolled. CapTCR-Seq in blood and tumor samples was completed in 13 pts (7Pr/6Ar) with the following characteristics: median age 57 years (26-77), 8 male (62%), 8 melanoma (62%), 4 HNSCC (31%), and 1 GE-junction (7%). 5 pts received PD-1/PD-L1 inhibitor monotherapy (38%), 8 pts ICl-based combinations (62%). No significant differences in intratumoral (10.3 [1.3-34.2] vs 15.2 [6.6-32.4] p=0.29) and peripheral (145.5 [65.3- 521.9] vs 136.0 [35.1-474.4] p=0.53) Shannon diversities were observed between Pr and Ar. Twelve of 13 (92%) pts had at least 1 intratumoral TCR clustered with TCRdb derived TCRs. A higher median of node degree was observed in non-melanoma tumors (5.5 [2-12] vs 2.0 [1-4] p=0.03). A trend towards a higher median of node degree was reported in Ar vs Pr (5.5 [1-12] vs 2.0 [1-4] p=0 .07 ). Some of the GLIPHll-identified clusters contained TCRs derived from multiple Ar pts. Conclusions: lntratumoral TCRs from non-melanoma and Ar pts had a higher node degree, indicating similarity with a larger number of external TCRs. The difference between Pr and Ar was not significant, potentially due to the small sample size. Similar TCRs belonging to the same GLIPHll-identified clusters were shared among multiple Ar pts. If confirmed in a larger dataset, these findings might suggest the existence of a set of intratumoral exhausted T-cells shared by multiple pts contributing to Ar but not to Pr. Pt accrual, sample collection and analysis are ongoing. Additional data will be presented.