Histological subtypes of hepatocellular carcinoma are related to gene mutations and molecular tumour classification

•CTNNB1 and TP53 mutations define two distinct tumour phenotypes. •Histological subtypes of HCC are associated with clinical and molecular features. •The novel macrotrabecular-massive subtype has clinical and biological relevance. •Relationships between HCC phenotype and biology has translational implications. Background & Aims Our increasing understanding of hepatocellular carcinoma (HCC) biology holds promise for personalized care, however its translation into clinical practice requires a precise knowledge of its relationship to tumour phenotype. Methods We aimed at investigating molecular-phenotypic correlations in a large series of HCC. To this purpose, 343 surgically resected HCC samples were investigated by pathological review, immunohistochemistry, gene expression profiling and sequencing. Results CTNNB1 (40%) and TP53 (21%) mutations were mutually exclusive and defined two major groups of HCC characterized by distinct phenotypes. CTNNB1 mutated tumours were large (p = 0.002), well-differentiated (p <0.001), cholestatic (p <0.001), with microtrabecular (p <0.001) and pseudoglandular (p <0.001) patterns and without inflammatory infiltrates (p <0.001). TP53 mutated tumours were poorly differentiated (p <0.001) with a compact pattern (p = 0.02), multinucleated (p = 0.01) and pleomorphic (p = 0.02) cells and frequent vascular invasion (p = 0.02). World Health Organization (WHO) classification of histological subtypes were also strongly related to molecular features. The scirrhous subtype was associated with TSC1/TSC2 mutations (p = 0.005), epithelial-to-mesenchymal transition and a progenitor expression profile. The steatohepatitic subtype showed frequent IL-6/JAK/STAT activation without CTNNB1, TERT and TP53 pathway alterations (p = 0.01). Pathological review identified a novel subtype, designated as “macrotrabecular-massive” associated with poor survival (p <0.001), high alpha-fetoprotein serum level (p = 0.02), vascular invasion (p <0.001), TP53 mutations (p <0.001) and FGF19 amplifications (p = 0.02), features also validated in The Cancer Genome Atlas (TCGA) data. Finally, integration of HCC pathological characteristics with its transcriptomic classification showed phenotypically distinct tumour subclasses closely related to G1-G6 subgroups. Conclusion HCC phenotypes are tightly associated with gene mutations and transcriptomic classification. These findings may help in translating our knowledge of HCC biology into clinical practice. Lay summary: HCC is a very heterogenous tumour, both at the pathological and molecular levels. We show here that HCC phenotype is tightly associated to its molecular alterations and underlying oncogenic pathways. Our increasing understanding of hepatocellular carcinoma (HCC) biology holds promise for personalized care, however its translation into clinical practice requires a precise knowledge of its relationship to tumour phenotype. We aimed at investigating molecular-phenotypic correlations in a large series of HCC. To this purpose, 343 surgically resected HCC samples were investigated by pathological review, immunohistochemistry, gene expression profiling and sequencing. CTNNB1 (40%) and TP53 (21%) mutations were mutually exclusive and defined two major groups of HCC characterized by distinct phenotypes. CTNNB1 mutated tumours were large (p = 0.002), well-differentiated (p <0.001), cholestatic (p <0.001), with microtrabecular (p <0.001) and pseudoglandular (p <0.001) patterns and without inflammatory infiltrates (p <0.001). TP53 mutated tumours were poorly differentiated (p <0.001) with a compact pattern (p = 0.02), multinucleated (p = 0.01) and pleomorphic (p = 0.02) cells and frequent vascular invasion (p = 0.02). World Health Organization (WHO) classification of histological subtypes were also strongly related to molecular features. The scirrhous subtype was associated with TSC1/TSC2 mutations (p = 0.005), epithelial-to-mesenchymal transition and a progenitor expression profile. The steatohepatitic subtype showed frequent IL-6/JAK/STAT activation without CTNNB1, TERT and TP53 pathway alterations (p = 0.01). Pathological review identified a novel subtype, designated as “macrotrabecular-massive” associated with poor survival (p <0.001), high alpha-fetoprotein serum level (p = 0.02), vascular invasion (p <0.001), TP53 mutations (p <0.001) and FGF19 amplifications (p = 0.02), features also validated in The Cancer Genome Atlas (TCGA) data. Finally, integration of HCC pathological characteristics with its transcriptomic classification showed phenotypically distinct tumour subclasses closely related to G1-G6 subgroups. HCC phenotypes are tightly associated with gene mutations and transcriptomic classification. These findings may help in translating our knowledge of HCC biology into clinical practice.