Single-nucleus transcriptomic atlas of the goat lung characterizes cell types associated with Pasteurella multocida...

Pasteurella multocida (P. multocida) infection can induce severe pulmonary lesions in goats. However, little is known about the cellular changes in goat lungs caused by P. multocida. This exploratory study employs single-nucleus RNA sequencing (snRNA-seq) to systematically map the dynamic cellular landscape of caprine lung tissue during P. multocida infection. We analyzed 37,847 high-quality nuclei from control and seven days post-infection groups, and systematically annotated 12 major cell types. Immune cells (B cells, T cells and Macrophages) and serous cells underwent further reclustering. Compared to the control group, there was an increase in the relative proportions of pulmonary alveolar type II cells and serous cells after P. multocida infection, whereas ciliated, basal, airway goblet, pulmonary alveolar type I and immune cells showed a decrease in their relative proportions. Potential marker genes for each cell type were analyzed in the goat lung tissue. The macrophage marker CD163 showed a significant decrease, and the T cell marker CD3G showed a decreasing trend by RNA fluorescence in situ hybridization, which supported that the macrophages and T cells decreased after the P. multocida infection. Additionally, to mitigate single-sample limitations, we compared the differentially expressed genes obtained using snRNA-seq and bulk RNA-seq. A total of 312 genes were differentially expressed and showed consistent trends in both sets of data. Trajectory analysis revealed that B cells, macrophages, and alveolar cells exhibited 1, 2, and 1 differentiation lineages, respectively. These differentiation trajectories were consistent with the biological context. GO and KEGG analysis indicated the involvement of the humoral immune response and secretory IgA complexes at seven days post-infection, and the transcriptional pathways associated with the ability of B cells to present antigens and macrophages to kill bacteria were downregulated. Intercellular communication analysis predicted that the communication changes of serous cells were the most obvious after infection. Our findings provide a classification landscape of lung cells and offer dynamic cell immune responses in goat lung tissue to P. multocida infection, which provides novel insights into goat host reactions to P. multocida infection.