Abstract
BACKGROUND: Immunotherapy for liver cancer is used to rejuvenate tumor-infiltrating lymphocytes by modulating the immune microenvironment. Thus, early protective functions of T cell subtypes with tissue-specific residency have been studied in the tumor microenvironment (TME). We identified tumor-associated tissue-resident memory T (TA-T(RM)) cells in hepatocellular carcinoma (HCC) and characterized their molecular signatures. METHODS: We obtained single-cell RNA and single-cell TCR sequencing data from five patients with HCC. The heterogeneous characteristics of T(RM) cell subsets within the TME were then investigated and validated. Risk scores were calculated for survival analysis using significant core marker genes based on data from The Cancer Genome Atlas and the International Cancer Genome Consortium. The signaling pathways, trajectories, and clonal diversity of TA-T(RM) cells were investigated. RESULTS: We characterized two T(RM) clusters (CD69(+) and CD103(+)) that expressed unique signature genes and validated their similar molecular patterns in an independent dataset. Risk scores based on core gene expression in TA-T(RM) cells were associated with survival in both datasets. Trajectory analysis revealed that the two lineages followed different trajectory paths with distinct marker gene expression across pseudo-time. CD103(+) TA-T(RM) cells showed diverse clonotypes and shared clonotypes with other cell groups. Lower clonal diversity and distinct signaling interactions were observed in the recurrent than in the non-recurrent samples. The CXCL13-CXCR3 interaction between CD103(+) TA-T(RM) and regulatory T cells was observed only in the recurrent samples. CONCLUSIONS: We identified two subtypes of TA-T(RM) cells in HCC and demonstrated their unique molecular signatures, relevance to survival, and distinct signaling networks according to recurrence. The study findings provide a better understanding of the molecular characteristics of TA-T(RM) cells in HCC and potential immunotherapeutic strategies.