Guohe Song

Supplementary Table S7. Patient information.

Supplementary Table S2. Differential ASEs, primers and sequences information.

Supplementary Table S1. Samples and transcriptomics information.

Supplementary Table S6. GO term and KEGG pathway information in Gzmb+ Cd8+ T cells.

Supplementary Table S5. Top 200 genes for each T cell cluster obtained by wilcox test with the rank_genes_groups function in Scanpy.

Supplementary Table S3. Signature and marker information.

Supplementary Table S4. Neutrophil-related information.

Supplementary Figure S1. Determination of AS index in iCCA. Supplementary Figure S2. Validation of distinct immune features in iCCA. Supplementary Figure S3. Detection of KRAS mutation associated indicators. Supplementary Figure S4. Exploration of the molecular mechanisms of IL1RN201/203 in iCCA. Supplementary Figure S5. Comparison between KRAS mutant (YAK) or KRASWT (YA) iCCA mice and functional validation of IL1RN-201/203. Supplementary Figure S6. Definition, validation and functional exploration of neutrophil clusters. Supplementary Figure S7. Effects of T cells, especially GZMB+ CD8+ T cells, on IL1RN-201/203 efficacy. Supplementary Figure S8. The roles of anti-PD1 Ab in KRASWT iCCA mice and anti-PD1 Ab plus anakinra in KRAS mutant iCCA mice. Supplementary Figure S9. Immunologic features of cancer patients with or without KRAS mutation.

Dissecting the spatial heterogeneity of cancer-associated fibroblasts (CAFs) is vital for understanding tumor biology and therapeutic design. By combining pathological image analysis with spatial proteomics, we revealed two stromal archetypes in hepatocellular carcinoma (HCC) with different biological functions and extracellular matrix compositions. Using paired single-cell RNA and epigenomic sequencing with Stereo-seq, we revealed two fibroblast subsets CAF-FAP and CAF-C7, whose spatial enrichment strongly correlated with the two stromal archetypes and opposing patient prognosis. We discovered two functional units, one is the intratumor inflammatory hub featured by CAF-FAP plus CD8_PDCD1 proximity and the other is the marginal wound-healing hub with CAF-C7 plus Macrophage_SPP1 co-localization. Inhibiting CAF-FAP combined with anti-PD-1 in orthotopic HCC models led to improved tumor regression than either monotherapy. Collectively, our findings suggest stroma-targeted strategies for HCC based on defined stromal archetypes, raising the concept that CAFs change their transcriptional program and intercellular crosstalk according to the spatial context.

Supplementary Table S2. Differential ASEs, primers and sequences information.