A mature tertiary lymphoid structure-associated spatial niche is inversely associated with ACC1-related lipid metabolism in neoadjuvant-treated hepatocellular carcinoma.

Tumor heterogeneity in hepatocellular carcinoma (HCC) is shaped by spatially organized immune and metabolic ecosystems that may influence therapeutic response. However, how mature tertiary lymphoid structure (TLS) niches relate to tumor metabolic heterogeneity remains poorly defined. We integrated seven 10x Visium sections from patients with locally advanced HCC treated with neoadjuvant cabozantinib plus nivolumab, a single-cell reference atlas, three independent bulk cohorts, and a pathological validation cohort of 69 HCC specimens. Reference-based deconvolution and neighborhood-composition clustering identified eleven recurrent multicellular niches, including a B-cell-, plasma-cell-, and T-cell-enriched mature TLS-associated niche (Niche5). Niche5 showed greater spatial aggregation in pathological responders, accompanied by stronger CCL21-CCR7, CXCL13-CXCR5, and CCL19-CCR7 signaling. Within Niche5, fatty-acid metabolism was inversely correlated with the TLS program (Spearman r=-0.35) and chemokine-ligand expression. A six-gene Niche5-derived signature selected using a machine-learning framework stratified overall survival across three independent cohorts. Among fatty-acid-metabolism enzymes, ACACA, encoding ACC1, showed the most reproducible negative association with TLS chemokines, antigen presentation, CD8-positive T-cell programs, and survival. Multiplex immunofluorescence and immunohistochemistry confirmed mature TLS architecture and demonstrated spatial separation between TLS and ACC1-, FABP5-, and PLIN2-enriched tumor compartments. In the validation cohort, TLS-positive tumors showed lower ACC1, FABP5, and PLIN2 expression but higher CCL21, CXCL13, and CCR7 expression, while high ACC1 expression was independently associated with reduced TLS positivity. Together, these findings provide exploratory evidence of immune-metabolic spatial heterogeneity in HCC and identify an inverse, associative relationship between mature TLS organization and ACC1-related lipid metabolism.