Introduction: Intra-tumoral heterogeneity is a prominent characteristic of hepatocellular carcinoma (HCC). However, it remains unexplored whether intra-tumoral transcriptomic differences can capture crucial information regarding HCC evolution and be utilized to derive a predictive signature for patient’s clinical trajectories.Methods: We quantified transcriptomic heterogeneity using four multiregional HCC cohorts comprising 172 samples from 37 patients, and validated transcriptomic heterogeneity and spatial dynamics using multiregional single-cell transcriptomic profiling of 110,817 cells from 34 liver specimens. The HCC evolutionary signature (HCCEvoSig) was developed and assessed across six cross-platform HCC cohorts.Results: Genes exhibiting high intra- and inter-tumor expression variation were significantly enriched in a gene set associated with HCC prognosis, from which we developed and validated a reproducible and robust transcriptomic signature, HCCEvoSig. Multiregional single-cell data confirmed the high intra- and inter-tumoral heterogeneity of HCCEvoSig genes across different cell types, and importantly, demonstrated that the dysregulation of HCCEvoSig genes exhibited a geospatially gradual transition from the non-tumor region to the tumor border and tumor core, as well as from non-malignant to malignant epithelial cells. HCCEvoSig showed significant positive associations with adverse features of HCC, and a high HCCEvoSig risk score predicted increased risks of disease progression and mortality, independent of established clinicopathological indices. Furthermore, HCCEvoSig outperformed 15 published signatures in discriminative ability and prognostic accuracy, particularly regarding 1-year survival rates. Notably, HCCEvoSig demonstrated predictive utility for responses to immunotherapy and trans-arterial chemoembolization. Additionally, we established a well-calibrated predictive nomogram that integrates HCCEvoSig and TNM stage to generate an individualized numerical probability of mortality.Conclusion: Our study reveals that regional transcriptional heterogeneity within tumors is substantial enough to capture survival signals, and the constructed and validated HCCEvoSig provides reliable prognostic information for HCC patients.

Background Tissue-resident memory T cells (Trm) are crucial local sentinels in cancer immunity; yet, their functional diversity and the role in non-small cell lung cancer (NSCLC) immune checkpoint blockade (ICB) therapy remain incompletely understood. Methods In this study, we conducted an integrated multidimensional analysis, incorporating single-cell RNA and TCR sequencing, as well as large-scale omics data to elucidate the functions of CD8⁺ Trm subsets in NSCLC patients receiving anti-PD-1/PD-L1 therapy. Results The Trm subsets, Trm-CD103, Trm-ZNF683, and Trm-NR4A1, expressed high levels of tissue-residency markers ITGAE (CD103) and ITGA1 (CD49a), alongside their respective key transcriptional regulators ZNF683 (Hobit) or NR4A1 (Nur77), respectively, while sharing core functional features of cytotoxicity and tissue residency. Importantly, CD103⁺ Trm cells were significantly enriched in anti-PD-1/PD-L1 therapy responders and their abundance correlated with improved survival after treatment. Repertoire analysis revealed clonal expansion and TCR overlap between Trm and effector/memory CD8⁺ T-cell subsets, underscoring their differentiation origins and integrated role in the antitumor immune response. We further developed a core gene signature associated with Trm-CD103 cells that can predict anti-PD-1/PD-L1 therapy response and patient prognosis and found it to be associated with an immunologically active tumor microenvironment. Mechanistically, we identified the transcription factor RBPJ as a key driver of Trm proliferation through integrated single-cell analyses and cross-referencing of a previous knockout mouse experiment dataset, linking its expression to enhanced ICB efficacy. Conclusions Together, our findings elucidate the multifaceted functions of Trm cells in NSCLC patients, establishing them as critical mediators of antitumor immunity and promising biomarkers and therapeutic targets for immunotherapy.