While representing only a small portion of T cell population, Gamma delta (γδ) T cells have unique contributions to both innate and adaptive immunity. Compared to αβ T, γδ T cells have a more diverse TCR repertoire, allowing them to recognize a broader range of tumor antigens. Recent breakthrough discoveries indicate that the antitumor efficacy of γδ T cells can be potentiated or rescued through targeted therapeutic approaches. Despite their functional and translational significance, a comprehensive understanding of the γδ T cell repertoire within tumor tissues has yet to be fully achieved.In this work, we generated a pan-cancer γδ T cell repertoire Atlas through reanalyzing RNA-seq data from more than 11,000 tumors in TCGA utilizing TRUST4, an advanced computational method for reconstruction of TCR repertoires. This allowed us to offer the most accurate and comprehensive examination of the γδ TCR landscape spanning 33 cancer types, marking it the largest collection of γδ clones on human cancer to date. We processed 660 billion RNAseq reads, identified ~3 million CDR3 reads, applied a series of stringent filtering criteria to remove biologically implausible, ambiguous sequences, and out-of-frame TCRs, which resulted in 22,205 unique γδ TCR clones from 6,751 tumors. TCR gene enrichment scores were calculated to represent overall expression of γδ in each tumor. The γδ enrichment is highly variable between and within cancer types. As expected, tumors traditionally classified as immune-cold (UVM and GBM) show the lowest scores. Cancers intrinsically related to lymphatic system (LAML, THYM and DLBC), exhibit the highest scores. Beyond THYM, the top five solid-tumor cancers carrying the highest enrichment are PRAD, KIRC, TGCT, LUAD and KICH. We further profiled the clone counts, spectrum of clone sizes, CDR3 length, V-J pair usage, and clonality in 33 cancers. Overall, a dominant presence of large clone segment is not observed in most cancers. The most prevalent V-J pairs are TRGV10/9/2-TRGJ1 for γ, and TRDV1-TRDJ1 for δ chain. Cancers including LAML, KIRC, LUAD, SKCM, CESC, LUSC, STAD, display a relatively higher proportion of intermediate to larger clones. THYM exists the highest γδ diversity, with the lowest clonality and most diverse V-J pairs. In addition, we evaluated the prognostics value of γδ genes by multivariate Cox regression, adjusting for age, sex, stage, and tumor purity, and identified 38 γδ genes associated with patient survival with p<0.05 in 25 cancer types. Finally, within HNSC, we observed higher γδ gene enrichment (p=1.6e-9) and clone diversity (p=0.014) in HPV+ vs. HPV- tumors. The γδ gene enrichment is also found associated with patients’ survival (p=0.002) in HPV+, but not in HPV- HNSC. Similarly, COAD tumors with high Microsatellite Instability (MSI) shows higher γδ gene enrichment and clone diversity compared to MSI low COAD. Collectively, our findings serve as a foundational resource for γδ T cell research in oncology.


Citation Format: Xiaoqing Yu, Song Li, Ling Cen, Xuefeng Wang. A pancancer gamma delta T cell repertoire atlas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3557.