A multi-organ map of the human immune system across age, sex and ethnicity

Abstract

The presence of immune cells in non-lymphoid tissues throughout the body is vital in the fight against infections and cancer. Yet, a detailed map of immune cell distribution and interactions throughout the body is lacking. To address this gap, we harmonised and annotated 29 million cells across 12,981 single-cell RNA sequencing samples covering 45 anatomical sites to create a comprehensive compositional and communication map of the healthy immune system. This resource represents a 30-fold increase in cell count and a 10-fold increase in tissue coverage compared to the existing state-of-the-art. We used this resource to model compositional changes in the immune system with age and diversity across demographic groups and to investigate the impact of different technologies using a novel multilevel Bayesian model. Our analysis revealed patterns of progressive tissue-specific inflammation, loss of plasticity with age, and significant differences between ethnicities. This study represents a comprehensive healthy reference for precision medicine, immunology, infectious disease, and cancer.