A pan-cancer single cell landscape reveals heterogeneity and functional diversity of double-negative T cells.

[BACKGROUND] Double-Negative T (DNT) cells, lacking both CD4 and CD8 expression, play critical roles in cancer immunology, and have garnered increasing attention in cancer research. However, their heterogeneity and functional diversity within the tumor microenvironment (TME) remain underexplored.

[METHODS] In-house and publicly available single-cell RNA sequencing (scRNA-seq) data for different cancer types were integrated after quality control and batch effect correction, followed by DNT cells separation from CD3 T cells subtypes. Functional characteristics, intercellular communication, differentiation trajectories, regulatory networks, and clinical relevance were analyzed among different DNT subsets. Key findings were validated using multiplex immunofluorescence and spatial transcriptomics to investigate the spatial localization of DNT subsets and their interactions within the TME. Impact of γδ T cells on immunotherapy response was also assessed using MC38-based murine tumor model.

[RESULTS] By integrating scRNA-seq data from 2,369 samples across 23 cancer types, we established a comprehensive single-cell atlas of 157,025 high-quality DNT cells. Fourteen distinct DNT subsets (6 αβ DNT and 8 γδ T cell subsets) were identified, demonstrating tumor both type-specific and shared distribution patterns, as well as unique cell-cell interaction network within the TME. These subsets displayed specialized functional profiles, including cytotoxicity, antigen presentation, and immune modulation, indicating that the functional diversity of DNT cells is largely subset-specific rather than a manifestation of multifunctionality within a single population. We also delineated divergent trajectories for αβ DNT and γδ T cell subsets, including the functional plasticity of gut-resident γδ T cells transitioning between cytotoxic and immunosuppressive states. Notably, several DNT subsets were significantly associated with favorable clinical treatment outcomes, including improved responses to cancer immunotherapy. Consistently, depletion of γδ T cells in the murine tumor model significantly decreased the efficacy of PD-1 blockade, underscoring their critical role in therapeutic response.

[CONCLUSIONS] Our study uncovers the previously underappreciated heterogeneity and functional diversity of DNT cells in the TME and demonstrates their profound impact on tumor progression and immunotherapy outcomes.