Global proteomic analysis of <i>Cryptococcus neoformans</i> clinical strains reveals significant differences between latent and lethal infection

To predict the outcomes of disseminated fungal disease, a deeper understanding of host-pathogen interactions at the site of infection is needed to identify targets for clinical intervention and diagnostic development. <i>Cryptococcus neoformans</i> is the causative agent of cryptococcosis, the largest infectious killer of individuals living with HIV. Cryptococcal infection begins in the lungs, and loss of immunological control leads to disseminated central nervous system disease and death. Using advanced mass spectrometry-based proteomic techniques, <i>in vivo</i> infection models, and patient-derived clinical strains, we explored the proteomic profiles of <i>C. neoformans</i> infections related to differences in strain virulence. Our findings reveal that non-lethal latent infection produces a proteomic response that differs significantly from the response caused by lethal infections, and that the proteomic profiles of typical and hypervirulent infections are markedly similar despite differences in time-to-death. Overall, the mouse pulmonary proteomic response in latent infection is defined by enrichment of proteins and pathways involved in extracellular matrix organization, cell adhesion, and structural changes, while the lethal infection is dominated by host defense, translation, and metabolic processes. These results provide clinically relevant information on how infections caused by different <i>Cryptococcus</i> strains may produce significantly different outcomes. We also identified abundant fungal proteins that could be future drug targets in latent and lethal cryptococcal infection.IMPORTANCE<i>Cryptococcus neoformans</i> is a fungal pathogen that causes substantial morbidity and mortality in immunocompromised individuals. The initial infection begins in the lungs after exposure to inhaled spores, after which local immune cells respond by either killing or containing the fungal cells. Immunosuppression weakens the immune system and allows fungal cells in the lungs to escape through the circulatory system and invade the central nervous system and cause fatal disease. However, differences between fungal strains influence the severity of disease manifestation. Our group has previously described genetic differences that contribute to strain-specific disease manifestations. In this study, we expanded our analysis to investigate the proteomic differences between strains of <i>C. neoformans</i> to identify candidate proteins and pathways that contribute to disease manifestation. We found that latent infection differs significantly from lethal disease from both the host and pathogen proteomic perspectives and identified several fungal protein targets for future study.