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Jaiswal, Abhinav; Verma, Akanksha; Dannenfelser, Ruth; Melssen, Marit; Tirosh, Itay; Izar, Benjamin; Kim, Tae-Gyun; Nirschl, Christopher J.; Devi, K. Sanjana P.; Olson, Walter C.; Slingluff, Craig L.; Engelhard, Victor H.; Garraway, Levi; Regev, Aviv; Minkis, Kira; Yoon, Charles H.; Troyanskaya, Olga; Elemento, Olivier; Suárez-Fariñas, Mayte; Anandasabapathy, Niroshana
Cancer cell, 05/2022, Volume: 40, Issue: 5Journal Article
There is a need for better classification and understanding of tumor-infiltrating lymphocytes (TILs). Here, we applied advanced functional genomics to interrogate 9,000 human tumors and multiple single-cell sequencing sets using benchmarked T cell states, comprehensive T cell differentiation trajectories, human and mouse vaccine responses, and other human TILs. Compared with other T cell states, enrichment of T memory/resident memory programs was observed across solid tumors. Trajectory analysis of single-cell melanoma CD8+ TILs also identified a high fraction of memory/resident memory-scoring TILs in anti-PD-1 responders, which expanded post therapy. In contrast, TILs scoring highly for early T cell activation, but not exhaustion, associated with non-response. Late/persistent, but not early activation signatures, prognosticate melanoma survival, and co-express with dendritic cell and IFN-γ response programs. These data identify an activation-like state associated to poor response and suggest successful memory conversion, above resuscitation of exhaustion, is an under-appreciated aspect of successful anti-tumoral immunity. Display omitted •Improved global TIL classification methods are required to deconvolve cell states•αPD-1 non-responder TILs and dysfunctional TILs score for T activation, not exhaustion•αPD-1 response and patient survival associates with late T cell memory/TRM scoring•Persistent programs co-express with DC maturation and IFN-γ response programs Jaiswal et al. highlight the need for improved tumor-infiltrating lymphocyte (TIL) classification by showing that current transcriptome assignments may misclassify early activated/effector TILs as exhausted. The study surveys 9,000 solid tumors, multiple single-cell RNA sequencing sets, mouse and human models, and scoring methods to reclassify TILs and associate melanoma survival to T cell memory/resident memory.
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