Systematic infectome–phenome profiling reveals cryptococcal infection-associated proteins driving immune system remodeling and immunization potential

Invasive fungal infections are an escalating global health challenge driven by host immune status and antifungal resistance. Here, we present an integrated infectome-phenome platform that combines high-resolution proteomics with systematic phenotypic profiling to map host-pathogen interactions in Cryptococcus neoformans . This approach captures coordinated host immune suppression alongside complementary fungal virulence programs and enables the prioritization of infection-associated proteins. Phenome fingerprinting of targeted mutants resolves functional relevance and therapeutic potential, supported by in vitro assays and a murine model of cryptococcosis. We identify a conserved, previously uncharacterized protein, CipC, that alters extracellular vesicle composition and enhances antigenicity. Immunization with CipC-derived vesicles elicits a robust and diversified host immune response, highlighting a role for fungal vesicles in immune priming. Together, this work establishes a scalable framework to define functional drivers of fungal infection and accelerate discovery of therapeutic and immunological targets across pathogenic fungi.