Colorectal cancer patients-derived immunity-organoid platform unveils cancer-specific tissue markers associated with immunotherapy resistance

Colorectal Cancer (CRC) is a devastating disease, ranking second in cancer-related deaths. Immune checkpoint inhibitors (ICIs) have reshaped the prognosis of many cancers, including Microstatellite Instable (MSI) CRC. However, a significant proportion of MSI patients do not benefit from immunotherapy, prompting the selection of patients based on factors beyond microsatellite status. Moreover, the overall lack of response of Microsatellite Stable (MSS) CRC may be due to an unselected approach for patient enrollment. To address these challenges and to enable more accurate and personalized testing of ICIs efficacy, we have developed interaction platforms between CRC organoids and autologous immune system. Using these platforms, we can assess ICIs resistance in CRC models, identifying new cancer-specific tissue markers (CST) associated with response to immunotherapy that go beyond microsatellite stability status. We assessed mutational profiles of 123 patients generating clinically relevant CRC organoids and immune system autologous interaction platforms to test the CRC patients ICI resistance. Transcriptomic analysis identified cancer-specific response markers to ICI, regardless microsatellite stability status, which were subsequently validated in an independent cohort of tissues using multiplex immunofluorescence (IF) technique. We observed that that organoids with reduced expression of CST markers exhibit increased susceptibility to T-cells engagement and demonstrate an ex vivo response to immunotherapy regardless of microsatellite stability status. We confirmed in an independent cohort of CRC patients treated with chemo-immunotherapy regimen the association of CST markers with an increased immune infiltration and T-cells activation by multiplex IF analysis. These findings will pave the way to improve immunotherapeutic strategies for CRC patients selection, regardless of their microsatellite stability status. This approach not only has the potential to identify MSI patients who will not benefit of ICIs avoiding adverse events, but also opens new scenarios for MSS patients, expanding the pool of individuals who could potentially benefit from immunotherapeutic treatments.