Figure 5. Integrative analysis of snRNA-seq and Visium data identifies ligand-receptor (LR) interactions associated with schizophrenia (SCZ).

(A) The LR interaction between membrane-bound ligand ephrin A5 (EFNA5) and ephrin type-A receptor 5 (EPHA5) is a consensus target identified in both data-driven (Table S3) and clinical risk-driven LR (Table S4) analyses. Notably, this interaction also requires an intracellular interaction between EFNA5 and protein tyrosine kinase (FYN), which was also identified among clinical risk targets. (B) Cell-cell communication analysis predicts the sender/receiver cross-talk pattern of EFNA5-EPHA5 between layer-level cell types visualized in a circular plot. (C-D) Downstream analysis of snRNA-seq data characterizes FYN-EFNA5-EPHA5 signaling pathway, showing these genes are highly enriched (C) and co-expressed (D) in excitatory neuron populations. (E) Across all 30 tissue sections, EFNA5 and EPHA5 are co-expressed in a higher proportion of spots in Sp₉D₇ compared to other Sp₉Ds. (F) Spotplot of EFNA5 and EPHA5 co-expression in Br8667_mid. (G) Spotplot with spot-level pie charts for Br8667_mid showing the top 3 dominant cell types in each Visium spot predicted by Cell2location (c2l). (H) Visium spots co-expressing EFNA5 and EPHA5 have higher proportions of predicted Excit_L5/6 neurons (p=1.8e-12) and Excit_L6 (p=3.9e-4) compared to non-coexpressing spots, consistent with snRNA-seq specificity analyses (Fig S40). Few other cell types show this relationship (Fig S41). Complementary analyses of EFNA5 and FYN co-expression are shown in Fig S40. (I) Spatial network analysis of all 30 tissue sections, using top 3 dominant c2l cell types in each spot (exemplified in G with Br8667_mid), confirms EFNA5 and EPHA5 co-expression occurs frequently in spots containing Excit_L6 neurons. Complementary analyses using top 6 dominant c2l cell types as well as Tangram predictions are reported in Fig S40. (J) Schematic of a Visium spot depicting EFNA5-EPHA5 interactions between Excit_L5/6 neurons and Excit_L6. The high colocalization score in the spatial network analysis in (I) suggests oligodendrocytes also likely co-exist with Excit_L6 neurons.