The characteristic of epithelial-specific phenotypes and immunosuppressive microenvironment in the context of tumour budding in colorectal cancer

Hatthakarnkul, P.; Fisher, N.; SchubertSantana, L.; Leslie, H.; Legrini, A.; Ammar, A.; Matly, A.; Pennel, K.; Powley, I.; Bull, C.; Alexander, P.; Sztanko, J.; Quinn, J.; Hay, J.; Morgan, H.; KennedyDietrich, C.; Doncheva, Y.; Lynch, G.; Maka, N.; Roxburgh, C.; Wyk, H. V.; Fu, X.; McMillan, D.; Dunne, P.; Jamieson, N.; Thuwajit, C.; Edwards, J.

doi:10.1101/2025.03.05.641608

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bioRxiv · 10.1101/2025.03.05.641608

The characteristic of epithelial-specific phenotypes and immunosuppressive microenvironment in the context of tumour budding in colorectal cancer

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Abstract

BackgroundTumour budding (TB), defined as a small cluster of up to four cells at the invasive front of the tumour, is a well-established independent and robust prognostic biomarker in colorectal cancer (CRC). This is strongly associated with adverse clinicopathological features and poor survival outcomes. Despite its clinical relevance, the precise underlying mechanism responsible for TB phenomenon remains unclear. MethodsMulti-omic approaches from bulk, regional GeoMx and Spatial Molecular Imager (SMI) RNA were used to identify the underlying mechanism of TB and its possible correlation with tumour microenvironment (TME) in CRC tissue. The results were validated using immunohistochemistry (IHC) and multiplex immunofluorescence (mIF) staining. ResultsPatients with high TB experience worse outcomes and associate with adverse clinical factors across two independent CRC cohorts. Bulk and regional RNA expression analyses reveal that tumours with high TB are significantly enriched for TNF- and TGF-{beta} signatures in both cohorts. Single cell CosMx SMI analysis confirmed TB cells exhibit higher expression of these signatures than adjacent invasive edge tumour cells. Elevated cyclinD1 expression was also observed within TB, and high cyclinD1 levels tend to experience poorer CRC prognosis. Furthermore, regional bulk RNA expression within the non-tumour (PanCK-) invasive edge areas demonstrated that tumours exhibiting high TB revealed the significantly differential expressions of immune-related genes (e.g. CD3, NKG7, IL6, CXCR6, CD47, IFNAR1 and VSIR). Single cell CosMx SMI analysis revealed that cancer-associated fibroblasts (CAFs) were physically the closest cells to TB cells. This spatial proximity was confirmed at the protein level using mIF, where the distance from TB to CD68+ macrophages predicted significantly poorer CRC outcomes. ConclusionThis multi-omic study confirms the prognostic significance of TB in CRC patients across two independent cohorts. Our findings highlight that TNF- and TGF-{beta} signalling play a crucial role in budding cells development by regulating cyclinD1. Furthermore, the transcriptomic analysis reveals an immunosuppressive niche characterised by reduced immune activity and close spatial interactions with CAFs and macrophages Ultimately, this study provides valuable insight into TBs underlying mechanism and its complex interactions within the TME. This could provide a foundation for developing targeted therapeutic strategies in CRC.

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Hatthakarnkul, P., Fisher, N., SchubertSantana, L., Leslie, H., Legrini, A., Ammar, A., Matly, A., Pennel, K., Powley, I., Bull, C., Alexander, P., Sztanko, J., Quinn, J., Hay, J., Morgan, H., KennedyDietrich, C., Doncheva, Y., Lynch, G., Maka, N., Roxburgh, C., Wyk, H. V., Fu, X., McMillan, D., Dunne, P., Jamieson, N., Thuwajit, C., Edwards, J.. 2025-03-07. The characteristic of epithelial-specific phenotypes and immunosuppressive microenvironment in the context of tumour budding in colorectal cancer. https://doi.org/10.1101/2025.03.05.641608

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