Transcriptomic and lipidomic analysis of the cryptococcal lung granuloma reveals macrophage boundary programs and sphingolipid remodeling

Cryptococcosis is a life-threatening fungal disease caused by Cryptococcus neoformans. The immunocompetent response results in the formation of a lung granuloma, which contains the fungal cells. We have previously developed a mouse model of the cryptococcal granuloma that is histologically similar to the human lung granuloma. In this study, we characterize the lung granuloma in mice using transcriptomics and lipidomics, elucidating the immune cell types present and the transcriptional landscape of macrophages at the granuloma border. Macrophage subtypes are identified, which form a characteristic boundary of the lung granuloma and were observed to have differentially expressed genes involved in the control of the infection. Lipidomic studies revealed that several sphingolipid-associated genes and their products involved in the regulation of phagocytosis were found to be upregulated and in vivo validation studies confirmed their key role in granuloma formation. Lastly, as the granuloma structure develops, the fungal replication inside the granuloma decreases concomitantly to the decrease of the macrophage activation. These studies identified important immune mechanisms of host protection at the granuloma site. Our results provide mechanistic insight into cryptococcal granuloma maturation and refine current models of host-pathogen interaction, which may open avenues for future immunomodulatory strategies.