Mass cytometry data integration methods reveal rural-urban gradient of immune profiles across geography

The human immune system strongly varies across populations and is impacted by a range of host and environmental factors. As such, a rural compared to urban lifestyle has previously been associated with baseline differences in immune profiles and reduced vaccine responsiveness. Here, using three mass cytometry datasets, we studied shared and population-specific immune characteristics of healthy rural- or urban-living Indonesian, Senegalese and Tanzanian adults and urban-living Europeans. After harmonized preprocessing and quality control, 75.4 million cells were integrated using in total four data-integration methods. CytoNorm with in silico references performed best, revealing shared differences in the differentiation state within the lymphocyte compartment distinguishing rural from urban. Differentiated CD4 ⁺ T cells exhibited high levels of immune checkpoint receptors, including CTLA-4, PD-1 and ICOS. Additionally, CD4 ⁺ T cells in rural-living individuals showed high expression of CD161 along with CRTH2 and GATA3 in varying combinations. In contrast, CD161 ⁺ CD8 ⁺ T cell clusters were decreased in rural-living individuals. Within the innate compartment, we found increased frequencies of mature NK cell clusters in rural-compared to urban-living individuals. Using a harmonized pipeline and various machine learning tools, this study serves as an example on the integration and analysis of large mass cytometry datasets. Despite population-specific environmental influences, shared immunological hallmarks identified in low-responding populations may serve as targets for future vaccine studies.