Multi‐omics insights for deciphering prognosis‐related T cell subsets in hepatocellular carcinoma

Abstract Background Hepatocellular carcinoma (HCC) is one of the leading causes of tumour‐related death. T cells and cytokines play a critical role in tumour progression, but the T cell landscape correlated with HCC prognosis remains undepicted. Methods The prognostic significance of intra‐tumoural immune cells, chemokines and cytokines were analysed using mass cytometry, bulk RNA sequencing and scRNA‐seq data with survival information. The signature of CD4 + CD8 + double positive T (DPT) cells was constructed using scRNA‐seq and quantified by ssGSEA scores, whose association with the response to atezolizumab plus bevacizumab was evaluated. Cellular cross‐talk and spatial patterns were analysed by scRNA‐seq and spatial transcriptomics. Flow cytometry, gene knockdown, transwell migration, co‐culture assays, qPCR and wound healing assay were performed to further validate the DPT‐associated niche. Findings Higher intra‐tumoural levels of DPT cells, CD45RA + CD4 + conventional T cells, HBEGF and CX3CR1 were associated with unfavourable prognosis in HCC. In contrast, higher infiltration of CD161 + CD45RA − CD4 + conventional T cells and CD8 + T cells correlated with prolonged survival. CD45 + EpCAM + and CD45 + α‐SMA + cells were more frequent in short‐term survivors. DPT infiltration was identified across HCC multi‐cohorts and syngeneic mouse models. In patients receiving atezolizumab plus bevacizumab, responders exhibited higher DPT ssGSEA scores than non‐responders. Multi‐omics analyses indicated cross‐talk and spatial association of DPT cells with capillary‐associated endothelial cells, supporting a pro‐tumour niche. HBEGF was positively correlated with DPT cells and highly expressed in endothelial compartments. Endothelial‐derived HBEGF knockdown reduced DPT migration. Moreover, DPT co‐culture increased expression of signatures associated with immunosuppressive checkpoints, chemokine signalling, epithelial–mesenchymal transition and stemness in Hep3B cells and promoted their migration. Conclusion Our findings depicted the prognostic immune landscape of HCC by identifying distinct T cell populations and molecular interactions. DPT cells emerged as a critical biomarker for poor prognosis, and the endothelial‐derived HBEGF–DPT axis could represent a potential therapeutic target.