Novel microenvironment-based classification of intrahepatic cholangiocarcinoma with therapeutic implications.

Abstract

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). We applied virtual deconvolution to transcriptomic data from ~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. iCCA is composed of five robust STIM classes encompassing both inflamed (35%) and non-inflamed profiles (65%). The inflamed classes, named <i>immune classical</i> (~10%) and <i>inflammatory stroma</i> (~25%), differ in oncogenic pathways and extent of desmoplasia, with the <i>inflammatory stroma</i> showing T cell exhaustion, abundant stroma and <i>KRAS</i> 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 <i>desert-like class</i> (~20%) harbours the lowest immune infiltration with abundant regulatory T cells (p<0.001), whereas the <i>hepatic stem-like</i> class (~35%) is enriched in 'M2-like' macrophages, mutations in <i>IDH1/2</i> and <i>BAP1,</i> and <i>FGFR2</i> fusions. The remaining class (<i>tumour classical</i>: ~10%) is defined by cell cycle pathways and poor prognosis. Comparative analysis unveils high similarity between a <i>KRAS/p19</i> murine model and the <i>inflammatory stroma</i> class (p=0.02). The KRAS-SOS inhibitor, BI3406, sensitises a <i>KRAS</i>-mutant iCCA murine model to anti-PD1 therapy. 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.