Abstract

The Nature, Nietzsche and Nurture of 500 macrophages: Triggering an Existential Crisis to Study Single-cell Gene-environment Interactions

Quin Wills, Research Fellow, Wellcome Trust Centre for Human Genetics and Weatherall Institute of Molecular Medicine. University of Oxford

Improvements in single-cell perturbation, imaging and single-cell sequencing are enabling the detailed dissection of heterogeneous cell states and gene function. Combining all three modalities with a microfluidics platform, we individually cultured, live-cell imaged and RNA sequenced over 500 macrophages. Half of the cells were knocked out for the HIV-1 inhibitor (‘restriction factor’) SAMHD1 before stimulation with various inflammatory and macrophage signaling microenvironments. We describe striking phenotypic plasticity, in addition to altered SOD1 behaviour in knockouts that is amplified by inter-macrophage signaling. Interestingly, SOD1 differential co-expression across the cells significantly enriches for proteasome genes involved in inflammatory regulation and APOBEC3G degradation, another well described HIV-1 restriction factor. This integration of high throughput single-cell methods and reverse genetics to study gene-environment interactions and gene co-regulation promises to provide new insights into the modifiers of host-pathogen relationships.