Fig. 1: scRNA-seq uncovers cell types and the space-, time- and sex-dependent organization of gene expression in the mouse liver.
A t-SNE plots show a main cluster of hepatocytes with antizonated Cyp2e1 and Cdh1 expression, and clusters of non-parenchymal cells identified with marker genes including Rgs5, Pecam1 and Cd74 (n = 12). B Pearson correlations are conserved between the selected portally and centrally biased genes independently of time and sex in hepatocytes (n = 12). C Immunofluorescence demonstrates that spatial patterns of canonical zonation markers E-CAD, CYP2E1 and GS are indistinguishable in males and females (n = 2). D Spatial reconstructions of lobular mRNA profiles combined with a model selection identified genes differentially affected by time (T), sex (S) and space (Z). The × denotes interacting effects (non-additive in log), resulting in changes of the shape of the spatial profile in function of time or sex. A subset of zonated genes (Z) also change their mean expression with sex or time, but not the shape of zonation (in log). These can be subdivided into genes whose expression is > 50% higher in one sex (Z + S), at one time (Z + T), in function of both sex and time (Z + S + T), or constant across conditions (Zc). Most zonated genes have a pericentral bias. E Reconstructed spatial profiles of gene expression in 12 layers, 1 corresponding to the most pericentral layer. Counts are normalized to the total counts of cytoplasmic unique molecular identifiers and represented as counts per million (CPM; n = 11; n = 2-3, per condition). Examples include a non-zonated gene (Fgl1) and zonated genes, with the slope either not affected by time or sex (Hsd17b13), or with different effects of time and sex on the spatial profile in Ces3a, Cyp2c29, Por and Nr1i3. F Sexual dimorphism and temporal changes of zonated genes, represented by the average slope (negative slopes characterize central profiles) across all conditions vs. the ZT22 to ZT10 (left panel) or female to male expression ratio (right panel). Genes in the corners are highly zonated and strongly regulated by time or highly zonated and sexually dimorphic, including Vldlr.
