Colorectal cancer organoids drive patient-specific inflammation, cytotoxicity and tissue-residency programs in NK cells

Natural killer (NK) cells represent a promising strategy for cellular cancer immunotherapy, but it remains unclear which patients benefit by such therapies. Using co-cultures of primary human allogenic NK cells and patient-derived colon cancer organoids (PDOs), we could stratify PDOs into NK cell “highly susceptible” and “rather resistant” groups reflected by differential expression of NKG2D-ligands, MHC class I and CEACAM. RNA-seq unveiled that hypoxia- and TGF-ß-related gene signatures were induced in NK cells after PDO co-culture. Deletion of hypoxia inducible factor (HIF)-2a in primary NK cells or blocking of TGF-ß-R1 empowered NK cell-mediated PDO killing. We further demonstrate that upon PDO killing, NK cells adopted an activation/inflammationhigh, cytotoxicitylow, tissue-residencyhigh program as evidenced by CXCR6 and CD49a expression coinciding with a “hot” cytokine/chemokine-rich microenvironment. Since PDO-exposed NK cells largely resemble features of NK cells from CRC patient tissues, our NK cell/PDO platform could be highly relevant for the optimization of NK cell products for personalized medicine. Overall design: RNA seq. profiling of NK cells only and NK cells after 4-day exposure to PDO7 and PDO22