Single-cell T-cell receptor repertoire profiling in dogs

Spontaneous cancers in companion dogs are robust models of human disease. Tracking tumor-specific immune responses in these models requires reagents to perform species-specific single cell T cell receptor sequencing (scTCRseq). scTCRseq and integration with scRNA data have not been demonstrated on companion dogs with cancer. Here, five healthy dogs, two dogs with T cell lymphoma and four dogs with melanoma are selected to demonstrate applicability of scTCRseq in a cancer immunotherapy setting. Single-cell suspensions of PBMCs or lymph node aspirates are profiled using scRNA and dog-specific scTCRseq primers. In total, 77,809 V(D)J-expressing cells are detected, with an average of 3498 (348–5,971) unique clonotypes identified per sample. In total, 29/34, 40/40, 22/22 and 9/9 known functional TRAV, TRAJ, TRBV and TRBJ gene segments are observed respectively. Pseudogene or otherwise defective gene segments are also detected supporting re-annotation of several as functional. Healthy dogs exhibit highly diverse repertoires, T cell lymphomas exhibit clonal repertoires, and vaccine-treated melanoma dogs are dominated by a small number of highly abundant clonotypes. scRNA libraries define large clusters of V(D)J-expressing CD8+ and CD4+ T cells. Dominant clonotypes observed in melanoma PBMCs are predominantly CD8+ T cells, with activated phenotypes, suggesting possible anti-tumor T cell populations.

My H. Hoang, Zachary L. Skidmore, Hans Rindt, Shirley Chu, Bryan Fisk, Jennifer A. Foltz, Catrina Fronick, Robert Fulton, Mingyi Zhou, Nathan J. Bivens, Carol N. Reinero, Todd A. Fehniger, Malachi Griffith, Jeffrey N. Bryan, Obi L. Griffith