RNF43 p.G659fs Leads to Natural Killer Cell Dysfunction in MSI-high Colorectal Cancer Through PI3K/AKT/mTOR Signaling and HLA-E Upregulation

ABSTRACT: The RNF43 p.G659fs (RNF43659mut) mutation occurs in 8% of colorectal cancers (CRCs) and is enriched in microsatellite instability-high (MSI-H) tumors. While RNF43659mut promotes tumor growth through PI3K/AKT/mTOR activation independent of WNT signaling, its immunologic effects are poorly defined. We show that RNF43659mut shapes an immunosuppressive NK cell landscape in MSI-H CRC. Single-cell RNA sequencing and multiplex immunohistochemistry revealed increased NK cell infiltration in RNF43659mut tumors, yet these cells displayed inhibitory phenotypes. Bulk RNA-seq and flow cytometry of NK cells co-cultured with RNF43659mut isogenic lines and MSI-H patient-derived organoids demonstrated reduced functional NK subsets, decreased activation markers, increased inhibitory receptors, and impaired cytotoxicity. Mechanistically, RNF43659mut-mediated PI3K/AKT activation induced HLA-E expression, suppressing NK cell function. Pharmacological or siRNA-mediated PI3K/AKT inhibition restored NK cell activity and enhanced tumor cell killing. Spatial analysis of MSI-H patient tumors revealed close proximity between NKG2A⁺NK cells and HLA-E⁺ tumor cells, which were themselves adjacent to PI3K/AKT-activated tumor cells, highlighting a localized immunosuppressive niche. These findings uncover an immune evasion mechanism in MSI-H CRC, implicating the PI3K/AKT-HLA-E/NKG2A axis as a promising therapeutic target to overcome immunotherapy resistance.

ORGANISM(S): Homo sapiens

PROVIDER: GSE342684 | GEO | 2026/09/21

REPOSITORIES: GEO