Multiplex analysis of colorectal cancer tissue describes the composition, cell biology and spatial effects of cell-in-cell events and identifies a T cell-dependent prognostic signature.

Cell-in-cell (CIC) structures, in which one cell is entirely engulfed by another, have been associated with poor outcomes in cancers. However, the mechanisms underlying this association remain poorly understood. We performed multiplex imaging of 56 cell identity, cell 'state' and cancer 'hallmark' proteins to characterise CICs, map their spatial interactions, and assess clinical associations across 444 tumour cores from 148 colorectal cancer patients, which contained over one million spatially resolved cells. We found that tumour regions containing CICs were associated with lower levels of cytotoxic T cells. We identified upregulated glucose metabolism as a consistent metabolic hallmark of CICs independent of cell type. Spatial analyses revealed that T cells adjacent to CICs underwent selective remodeling with distinct apoptotic and metabolic signatures. Finally, the presence of T cells within CIC neighbourhoods identified a subset of patients with improved survival. Our findings suggest that CICs may be a feature of metabolically competitive niches and a potential factor contributing to T-cell exclusion in tumours.