Erdoğan Pekcan Erkan, Emmi Hämäläinen, Julia Kolikova, Tiia Nikupaavola, Karishma Sajnani, Kornelia Kuc, Kalle Ojala, Meiju Kukkonen, Ismaïl Hermelo, Antti Kurttila, Selja Koskensalo, Timo Tarvainen, Alli Leppä, Ilona Keränen, Carola Haapamäki, Essi Karjalainen, Monika Carpelan-Holmström, Laura Renkonen‐Sinisalo, Laura Koskenvuo, Pauli Puolakkainen, Jukka‐Pekka Mecklin, Juha P. Väyrynen, Elina Virolainen, iCAN, Matti Nykter, Lauri A. Aaltonen, Alfonso Urbanucci, Anna Lepisto, Ari Ristimäki, Toni T. Seppälä
Abstract Although chemotherapy in colorectal cancer (CRC) primarily targets epithelial tumor cells, the epithelial cell-intrinsic mechanisms underlying heterogeneous treatment responses remain poorly understood. We integrated the genomic, transcriptomic, and in vitro drug response profiles of CRC patient-derived tumor organoids (PDTOs) with functional assays to identify epithelial cell-intrinsic determinants of chemotherapy response. An epithelial interferon-stimulated gene (ISG) program, reflecting JAK-STAT pathway activity, was associated with reduced chemosensitivity in PDTOs. Single-cell RNA sequencing data of CRC tumors before and after neoadjuvant chemotherapy showed persistent epithelial ISG expression, with EPSTI1 notably enriched in tumors with incomplete pathological responses. Functional studies demonstrated that EPSTI1 knockdown reduced CRC cell viability and enhanced chemosensitivity. Pharmacologic JAK-STAT inhibition with ruxolitinib suppressed ISG expression and attenuated chemotherapy-induced ISG upregulation. These findings highlight the utility of PDTOs for studying tumor-intrinsic mechanisms of treatment response and identify EPSTI1 as an epithelial modulator of chemosensitivity.