Fig. 3: Distinct oncogenic drivers’ activation impact HCC immune landscape.

a Myeloid and lymphoid cell contents relative to total CD45⁺ leukocytes in end-stage HCC and age-matched control livers Control-4-weeks n = 5, Myc^OE/Trp53^KO n = 6, Myc^OE/Pten^KO n = 5, Nras^G12D/Pten^KO n = 4, Control-15-weeks n = 5, and Nras^G12V/Pten^KO n = 4). b Quantification of circulating myeloid cells relative to total CD45⁺ leukocytes at the indicated timepoints for each of the HCC models (Control n = 10, Myc^OE/Trp53^KO n = 20, Myc^OE/Pten^KO n = 18, Nras^G12D/Pten^KO n = 30, Nras^G12V/Pten^KO n = 16). Arrows indicate timepoints when tumors were detectable. Statistical significance: final analyzed blood samples of tumor-bearing mice versus aged-matched controls. c Percentage of the immune cell populations relative to total CD45⁺ leukocytes in control and HCCs at intermediate and end-stage (Control-4-weeks n = 5, Myc^OE/Trp53^KO intermediate n = 4 and end-stage n = 5, Myc^OE/Pten^KO intermediate n = 5 and end-stage n = 5, Control-15-weeks n = 5, Nras^G12D/Pten^KO intermediate n = 7 and end-stage n = 7 (for CD8T and CD4T n = 6); and Nras^G12V/Pten^KO intermediate n = 4 and end-stage n = 5). Statistical analyses of each model are performed comparing each tumor stage to its relative control group (Control 4-weeks for Myc^OE/Trp53^KO and Myc^OE/Pten^KO; and Control-15-weeks for Nras^G12D/Pten^KO and Nras^G12V/Pten^KO). d Quantification of CD11B, CD15, CD204 and S100A9 positive cells by immunohistochemistry in paraffin-embedded HCC patient samples from the Wu et al. dataset⁶⁹ segregated according to p-ERK1/2 (positive n = 99, negative n = 369 for CD11B, CD15 and CD204; positive n = 98, negative n = 367 for S100A9) and MYC (positive n = 78, negative n = 389 for CD11B, CD15 and CD204; positive n = 77, negative n = 386 for S100A9) expression in cancer cells. e Unsupervised hierarchical clustering of the transcriptome of CD45⁺ cells isolated from genetically-distinct HCCs (n = 3 for all genotypes) and their classification according to the human HCC immune subtypes clustering⁷⁵. f Unsupervised hierarchical clustering of the ssGSEA enrichment scores per control liver and HCC models (end-stage) using immune-related pathways presented in the Biocarta database. The color scale represents the z-score normalized enrichment per pathway (row) between HCC models (Control n = 5, Myc^OE/Trp53^KO n = 3, Myc^OE/Pten^KO n = 3, Nras^G12D/Pten^KO n = 4, Nras^G12V/Pten^KO n = 5). Graphs show mean ± SEM (a, c, d), +SEM (b). Statistical significance was determined by unpaired two-sided Student’s t-test (a–c), two-sided Mann-Whitney U test (d), one-sided Fisher’s test using Bonferroni multiple testing correction (e). See Supplementary Fig. 9j, k for gating strategy (a–c). Source data are provided as a Source Data file.