Oropharyngeal candidiasis (OPC) is still a common disease among HIV-infected people, despite the availability of antiretroviral therapy. The long-term goal of this work is to develop new treatments for oral fungal disease in HIV-infected patients. Treatments must be effective against Candida albicans, the most-common cause of OPC, as well as other pathogenic fungal species. Adhesion of fungal cells to the oral mucosa is required for development of OPC. Therefore, interfering with fungal adhesion is a rational strategy to reduce disease incidence. The availability of genome sequence data has advanced the study of fungal adhesion. However, genes encoding adhesins are often large, belong to families that have many highly similar loci, and encode long stretches of repeated DNA that are difficult to assemble especially from short-read sequence data. These circumstances are a barrier to a thorough understanding of fungal adhesins and their relatedness across the OPC pathogens. This project will leverage a foundation of new genome sequences for the OPC-causing fungi that were assembled from a combination of short- (Illumina MiSeq) and long-read (Oxford Nanopore MinION) sequences. These genome assemblies proved useful for characterizing the agglutinin-like sequence (ALS) family across the OPC pathogens and will now be used to characterize the adhesinome, which is defined as the genes encoding proteins with the potential for adhesive function. The project will also resolve persistent issues with fragmented genome assemblies for some OPC-causing fungal species. Despite the use of leading-edge methods for DNA sequencing and assembly, some genomes still have far more contigs than chromosomes. Physical mapping techniques will be used to arrange contigs on specific chromosomes. Long PCR and Sanger sequencing will be used to close gaps and produce a complete assembly. The adhesinome catalog and finalized genome assemblies will contribute valuable information to public databases. Consistent with the goals of the AREA program, undergraduate students from Millikin University and the University of Illinois will conduct much of the proposed work. Students will learn computer-based analysis of genome data and gain valuable molecular biology laboratory skills. The project will enhance the research environment of both institutions and overcome critical barriers to progress in the development of anti-adhesion therapies.
AIDS patients commonly suffer from oral fungal disease. Fungi need to stick (adhere) to oral surfaces in order to cause disease. The long-term goal of this work is to understand how fungi adhere to the oral cavity and use that information to develop therapies that inhibit fungal adhesion, thereby reducing the incidence of disease in this patient population.
