A Lymphoid-Enriched Spatial Immune Niche Defines an Immunotherapy-Responsive State in Hepatocellular Carcinoma
Abstract
Background: Atezolizumab plus bevacizumab is a first-line therapy for advanced hepatocellular carcinoma (HCC), yet only a subset of patients achieve durable benefit. The spatial organization of the tumour microenvironment (TME) and its relationship to immunotherapy response remain incompletely understood. Methods: We integrated single-cell transcriptomics, spatial transcriptomics, spatial proteomics, and bulk RNA-sequencing cohorts to characterize spatially organized immune ecosystems associated with immunotherapy response in HCC. Single-cell RNA sequencing from 100 HCC samples was used to construct a cellular reference, which was integrated with spatial transcriptomics from 12 sections to identify nine consensus spatial niches. Results: Niche 9 represented a lymphoid-enriched immune state characterized by B cells, plasma cells, natural killer cells, T-cell subsets, macrophages, and tertiary lymphoid structure-associated transcriptional features. Independent validation in a pretreatment, response-annotated Visium cohort showed enrichment of Niche 9-associated transcriptional activity in immunotherapy responders, while spatially co-registered 51-plex CODEX profiling provided orthogonal protein-level support for its lymphoid and immune-enriched phenotype. Multi-omics characterization further revealed coordinated immune-cell localization, ligand–receptor-associated patterns, and distinct metabolic programmes, with MEI1-positive plasma cells displaying enhanced secretory and stress-adaptation states. A nine-gene transcriptional signature derived from Niche 9 was associated with atezolizumab-plus-bevacizumab response, enhanced lymphoid immune features, lower Tumour Immune Dysfunction and Exclusion scores, and favourable clinical outcomes in independent cohorts. Conclusions: These multi-cohort and multi-omics analyses define a spatially derived lymphoid-enriched immune programme and link its molecular features to immunotherapy sensitivity in HCC.