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Discovering Novel Pathogenic Factors during the Evolution of Antifungal Resistance

Primary Supervisor: Dr Hung-Ji Tsai, School of Biosciences

Secondary supervisor: Rebecca Drummond

PhD project title: Secrete to Survive: Discovering Novel Pathogenic Factors during the Evolution of Antifungal Resistance

University of Registration: University of Birmingham

Project outline:

Background

Fungal infections have impacted our medical system, causing >1.5 million deaths every year. While only three classes of antifungals are available, the emergence of drug resistant fungal pathogens in the clinic poses a devastating problem. One common challenge fighting antifungal resistance is our limited understanding of the causal relationship between drug resistance and aneuploidy. Aneuploidy, an unbalanced genome with gain or loss of chromosomes, drives rapid adaptation to antifungals in clinical fungal pathogens [1]. While “aneuploidy” is a collective term of thousands of random chromosome stoichiometries, the indefinite genome types confer a wide range of phenotype variation and have prevented the development of strategies against drug resistance.

Recently, we discovered that aneuploid cells are under hypo-osmotic state due to proteome imbalance across aneuploid cells [2]. This common biophysical signature triggers an increased turgor pressure against the cell surface, altering the surface/extracellular protein compositions. While fungal surface and secretory factors can be recognized by the host immune system as the frontline of the host-pathogen interactions, this finding raises the possibility of developing diagnostic strategies against drug resistance during clinical interventions. This project aims to identify novel fungal factors associated with antifungal resistance in human fungal pathogen Candida albicans and understand their roles during the evolution of antifungal resistance.

Objective and Methods:

Objective 1: Decipher the surface proteome and secretome in aneuploid C. albicans.

To characterize the distinct extracellular protein compositions of aneuploid C. albicans, quantitative proteomics will be used to comprehensively identify cell surface proteome and secretome in aneuploid and euploid C. albicans. The results will represent the first comprehensive profiling of protein factors (or immunogens) affecting the host-pathogen interactions in the context of antifungal resistance.

Objective 2: Develop a molecular platform to discover novel antigens associated with antifungal resistance.

To address the need of diagnostic strategies against antifungal resistance, a proteo-genomics platform for novel antigen discovery will be developed in this project. This platform will enable the genome-wide expression of full-length proteins using Candida ORFeome collections, labelled with DNA barcodes. This protein library will be used to detect novel antigens through the incubations with serum antibodies directly from patient samples.

The identified proteins from above objectives will be correlated and verified in animal models of infections, including invertebrate and mouse models to understand their biological function in the host-pathogen interactions during the evolution of antifungal resistance.

This project will leverage both genomics, proteomics, biochemistry and cell biological approaches, combined with animal models of infections to understand the host-pathogen interactions during the evolution of antifungal resistance.

This project will leverage both genomics, proteomics, biochemistry and cell biological approaches, combined with animal models of infections to understand the host-pathogen interactions during the evolution of antifungal resistance.

References:

  1. Tsai, H.-J.; Nelliat, A. A Double-Edged Sword: Aneuploidy is a Prevalent Strategy in Fungal Adaptation. Genes 2019, 10, 787.
  2. Tsai, H.-J.; Nelliat, A.R.; Choudhury, M.I.; Kucharavy, A.; Bradford, W.D.; Cook, M.E.; Kim, J.; Mair, D.B.; Sun, S.X.; Schatz, M.C.; et al. Hypo-osmotic-like stress underlies general cellular defects of aneuploidy. Nature 2019, 570, 117–121.

BBSRC Strategic Research Priority: Understanding the Rules of Life: Microbiology

      Techniques that will be undertaken during the project:

      Molecular technologies: both basic and high-throughput lab techniques, including genome-wide cloning and strain manipulations in automation systems.

      Biochemistry: protein purifications, western blotting and immunoprecipitation assays.

      Cell biological methods: advanced quantitative microscopy, phagocytosis assays and related host-pathogen interactions assays.

      Basic animal model of infections.

      Genomics: genome-sequencing, barcode-sequencing.

      Proteomics: LC/MS-based quantitative proteomics.

      Contact: Dr Hung-Ji Tsai, University of Birmingham