Novel microenvironment-based classification of intrahepatic cholangiocarcinoma with therapeutic implications

Objective The diversity of the tumour microenvironment (TME) of intrahepatic cholangiocarcinoma (iCCA) has not been comprehensively assessed. We aimed to generate a novel molecular iCCA classifier that incorporates elements of the stroma, tumour and immune microenvironment ('STIM' classification). Design We applied virtual deconvolution to transcriptomic data from similar to 900 iCCAs, enabling us to devise a novel classification by selecting for the most relevant TME components. Murine models were generated through hydrodynamic tail vein injection and compared with the human disease. Results iCCA is composed of five robust STIM classes encompassing both inflamed (35%) and non-inflamed profiles (65%). The inflamed classes, named immune classical (similar to 10%) and inflammatory stroma (similar to 25%), differ in oncogenic pathways and extent of desmoplasia, with the inflammatory stroma showing T cell exhaustion, abundant stroma and KRAS mutations (p<0.001). Analysis of cell-cell interactions highlights cancer-associated fibroblast subtypes as potential mediators of immune evasion. Among the non-inflamed classes, the desert-like class (similar to 20%) harbours the lowest immune infiltration with abundant regulatory T cells (p<0.001), whereas the hepatic stem-like class (similar to 35%) is enriched in 'M2-like' macrophages, mutations in IDH1/2 and BAP1, and FGFR2 fusions. The remaining class (tumour classical: similar to 10%) is defined by cell cycle pathways and poor prognosis. Comparative analysis unveils high similarity between a KRAS/p19 murine model and the inflammatory stroma class (p=0.02). The KRAS-SOS inhibitor, BI3406, sensitises a KRAS-mutant iCCA murine model to anti-PD1 therapy. Conclusions We describe a comprehensive TME-based stratification of iCCA. Cross-species analysis establishes murine models that align closely to human iCCA for the preclinical testing of combination strategies.

Automated summary

We present a comprehensive stratification of iCCA based on the tumor microenvironment (TME). The tumor is divided into five stable STIM classes, including 35% inflamed and 65% non-inflamed profiles. The inflamed classes, immune classical and inflammatory stroma, differ in oncogenic pathways and extent of desmoplasia. Analysis of cell-cell interactions highlights cancer-associated fibroblast subtypes as potential mediators of immune evasion. Among the non-inflamed classes, the desert-like class has the lowest immune infiltration with abundant regulatory T cells, while the hepatic stem-like class is enriched in 'M2-like' macrophages and specific mutations. Comparative analysis reveals high similarity between a KRAS/p19 murine model and the inflammatory stroma class. The KRAS-SOS inhibitor sensitizes a KRAS-mutant iCCA murine model to anti-PD1 therapy. Our findings provide valuable insights into the TME of iCCA and offer potential therapeutic targets for future research.