A Spatial Transcriptomics Atlas of the Malaria-infected Liver Indicates a Crucial Role for Lipid Metabolism and Hotspots of Inflammatory Cell Infiltration

During liver infection, the malaria parasite undergoes massive replication whilst remaining clinically silent. Spatial coordination of immune response regulation and metabolic zonation during malaria infection in the true tissue context remains unexplored. We perform spatial transcriptomics combined with snRNA-seq over multiple time points to delineate transcriptional programs of host-pathogen interactions across P. berghei-infected liver tissues. Our data suggest changes in gene expression related to lipid metabolism adjacent to infected hepatocytes, particularly modulation of the expression of genes involved in peroxisome proliferator-activated receptor pathway signaling. The data further indicates the presence of inflammatory hotspots with differential inflammation programs along the lobular axis in infected tissues. Additionally, upregulation of genes involved in inflammation is observed, but considerably delayed, in livers of control mice injected with mosquito salivary gland components. Our study establishes a benchmark for investigating host-parasite interactions, and can easily be implemented to validate de novo malaria drug and vaccine efforts. For this study mice were infected with 400.000 sporozoites of P.berghei ANKA and their livers were collected after 12, 24 or 38h post-infection. Control mice were challenged with salivary gland lysate of the same number of mosquitos collected for P. berghei ANKA challenges and their livers were also collected after 12, 24 or 38h post-injection. Nuclei were isolated from the snap frozen liver tissues, and two biological replicates of each condition were pooled. Thus, the full single-nuclei RNA sequencing protocol, including sequencing and computational analysis, was performed for a total of 6 liver samples, of which 3 were infected with Plasmodium berghei parasites and 3 challenged with mosquito salivary gland lysate.