Modelling Sporothrix Skin Infection and Identifying Genetic Determinants of Pathogenicity

About the Project

Sporothrix species, particularly S. schenckii and S. brasiliensis, are thermally dimorphic fungi responsible for sporotrichosis; a chronic subcutaneous infection with zoonotic potential and rising antifungal resistance. Despite its clinical importance, the molecular mechanisms underlying skin colonisation, tissue invasion, and host-pathogen interactions remain poorly defined. This project will establish a next-generation skin-on-a-chip infection platform for Sporothrix, identify genetic pathways essential for skin tropism, and implement CRISPR-Cas9 genome editing to functionally validate novel antifungal targets.

Objective 1: Developing a Microfluidic Skin-on-a-Chip Model for Sporothrix Infection

The first objective will engineer a dynamic, multilayered human skin-on-a-chip system to study Sporothrix skin colonisation and host responses under physiologically relevant conditions. Unlike static skin models, the chip will integrate a microfluidic system to simulate perfusion, nutrient gradients, and immune cell recruitment, enabling real-time monitoring of infection dynamics.

The chip will incorporate a layered structure: primary human keratinocytes (epidermis), fibroblasts embedded in collagen (dermis), and optional endothelial cells to mimic microvascular interfaces. Infection progression will be tracked using live-cell microscopy, CFU quantification, histology and immunofluorescence for fungal structures and host markers. Cytokine release and barrier integrity (via TEER) will be monitored over time.

Training will include microfluidic chip assembly, cell co-culture techniques, live-cell infection imaging, and host response assays.

Objective 2: Identifying Genetic Determinants of Skin Colonisation and Pathogenicity in Sporothrix Species

This objective will define the fungal genetic programs activated during skin infection using the skin-on-a-chip model. S. schenckii and S. brasiliensis will be harvested at defined infection stages, and fungal RNA will be extracted for transcriptomic profiling. Particular focus will be given to genes involved in thermal dimorphism, adhesion, stress resistance, and secretion of virulence-associated proteins.

Comparative transcriptomics will highlight differentially expressed genes between the two species and between environmental and host-associated states. Genes highly induced during skin invasion. Bioinformatic pipelines will integrate transcriptomic data with orthology mapping to identify potential druggable targets. These will inform CRISPR-based functional studies in Objective 3.

Training will include dual RNA-seq, fungal transcriptomics during infection, and comparative genome analysis.

Objective 3: Establishing CRISPR-Cas9 Genome Editing in Sporothrix

The third objective will develop CRISPR-Cas9 genome editing for Sporothrix to functionally interrogate genes identified in Objective 2. Due to low transformation efficiency and dimorphism, Sporothrix remains genetically intractable. This project will adapt a ribonucleoprotein (RNP)-based CRISPR approach, utilising transient Cas9 delivery with species-optimised sgRNAs and homologous repair templates.We will first optimise transformation via electroporation or PEG-mediated protoplast fusion, testing selectable markers (hph, nat1) and homologous recombination rates. Mutant validation will involve PCR genotyping and phenotyping in both filamentous and yeast phases.

Knockout strains will be assessed in the skin-on-a-chip model for changes in colonisation, invasion depth, stress resistance, and immunogenicity. Mutants with attenuated virulence or hypersensitivity to antifungals will be screened for drug-target feasibility under host-relevant conditions.

Training will include sgRNA design, fungal transformation optimisation, and CRISPR-based functional screening in organotypic models.

Candidates are expected to hold (or be about to obtain) a minimum 2:1 Bachelors Degree with Honours (or equivalent) in a related subject. Candidates with experience in fungal biology or with an interest in infection biology are encouraged to apply.

Eligibility

Applicants must have obtained or be about to obtain a minimum Upper Second class UK honours degree, or the equivalent qualifications gained outside the UK, in a relevant discipline.

Before you Apply

Applicants must make direct contact with preferred supervisors before applying. It is your responsibility to make arrangements to meet with potential supervisors, prior to submitting a formal online application.

How to Apply

To be considered for this project you MUST submit a formal online application form – on the application form select PhD Molecular Biology Programme. Full details on how to apply can be found on the Website: How to apply for postgraduate research at The University of Manchester

If you have any queries regarding making an application please contact our admissions team FBMH.doctoralacademy.admissions@manchester.ac.uk

Equality, Diversity and Inclusion

Equality, diversity and inclusion is fundamental to the success of The University of Manchester, and is at the heart of all of our activities. The full Equality, diversity and inclusion statement can be found on the website: Equality, diversity and inclusion (EDI | Postgraduate Research | Biology, Medicine and Health | University of Manchester)

Funding Notes

Applications are invited from self-funded students. This project has a Band 3 (high) fee. Details of our different fee bands can be found on our website View Website