Early in vivo expressed antigens and their role in virulence, immune response, and vaccines for coccidioidomycosis

Project Summary/Abstract (Research Project 1) Emerging and endemic mycoses have a growing impact on human health on a global scale and little is known about virulence mechanisms for most emerging fungal pathogens. Coccidioides immitis and C. posadasii cause coccidioidomycosis (aka Valley Fever), which is of specific concern due to recent rapid increases in US disease incidence with a more than a 10-fold increase of reports over the last 20 years. The Centers for Dis- ease Control and Prevention (CDC) report that the average cost for treating Valley fever is $50,000 per patient, including extensive hospital stays and treatment regimes. Advanced genomic and genetic analyses of these fungal pathogens can help improve our understanding of mechanisms of pathogenicity, support the identifica- tion of new biomarker targets, and represent the foundational framework that is necessary for development of diagnostic tools, treatment strategies and prevention of disease via vaccination.

Currently, few specific viru- lence mechanisms have been investigated in Coccidioides. Complicating these investigations is the lack of in vivo data, as the biology and gene expression analysis of in vitro cultures does not replicate the infective se- quence. We have remedied this gap by detailed transcriptional analysis of both Coccidioides species in mouse lungs five days after infection. Based on our transcriptional analyses and existing genomic data, plus in silico functional predictions, we have identified 26 putative antigens/virulence factors.

These Coccidioides spp. tran- scripts are highly expressed under in vivo conditions and are predicted to be small secreted proteins. Our working hypothesis is that these proteins will be antigenic and potentially virulence factors. We will test this hy- pothesis by creating CRISPR-Cas9 gene deletion strains. These strains will be tested for virulence in two ani- mal models in collaboration with the Animal Core.

We will further investigate these genes’ functions in both Coccidioides species, specifically the effects on development of the parasitic structure (spherule), virulence, and host and pathogen response in vivo using nanoString. RNAseq analysis of gene deletion strains compared to parent strain will be used to compare transcriptional networks. Analysis of these data will provide new in- sights into gene functions and effectively double the number of gene deletion strains investigated for this path- ogen, which will increase our understanding of fungal pathogenesis mechanisms. These data will be used by the other two Research Projects to identify T cell epitopes and the cognate T cell receptors for understanding the host immune response and possible advanced diagnostic tests, as well as to identify targets for nucleic acid vaccines.

Programming the immune response toward early infection virulence factors has the great poten- tial to provide protective immunity to Valley Fever. In total, this proposal represents a unique pairing of ad- vanced genomic data analysis and functional assessments in an important, yet understudied, fungal pathogen.

Grant Number: 5U19AI166058-04
NIH Institute/Center: NIH
Principal Investigator: Bridget Barker