Tumor microenvironments (TMEs) influence cancer progression but are complex and often differ between patients. Considering that microenvironment variations may reveal rules governing intratumoral cellular programs and disease outcome, we focused on tumor-to-tumor variation to examine 52 head and neck squamous cell carcinomas. We found that macrophage polarity—defined by CXCL9 and SPP1 (CS) expression but not by conventional M1 and M2 markers—had a noticeably strong prognostic association. CS macrophage polarity also identified a highly coordinated network of either pro- or antitumor variables, which involved each tumor-associated cell type and was spatially organized. We extended these findings to other cancer indications. Overall, these results suggest that, despite their complexity, TMEs coordinate coherent responses that control human cancers and for which CS macrophage polarity is a relevant yet simple variable.

Tissues are organized in niches where cell types interact to implement specific functions. Spatial -omics technologies allow to decode the molecular features and spatial interactions that determine such niches. However, computational approaches to process and interpret spatial molecular profiles are challenged by the scale and diversity of this data. Here, we present CellCharter, an algorithmic framework for the identification, characterization, and comparison of cellular niches from heterogeneous spatial transcriptomics and proteomics datasets comprising multiple samples. CellCharter outperformed existing methods, identified biologically meaningful cellular niches in different contexts, and discovered spatial cancer cell states, characterized by cell-intrinsic features and spatial interactions between tumor and immune cells. In non-small cell lung cancer, CellCharter revealed a cellular niche composed of neutrophils and tumor cells expressing markers of hypoxia and cell migration. Expression of these markers determined a spatial gradient associated with cancer cell state transition and neutrophil infiltration. Moreover, CellCharter showed that similar compositions of immune cell types can exhibit remarkably different spatial organizations in different tumors, highlighting the need for exploring spatial cell interactions to decipher intratumor heterogeneity. Overall, CellCharter is a flexible and scalable framework to explore and compare the spatial organization of normal and malignant tissues.