Spatial Transcriptomic Profiling of the Host-Microbiome Interactome in Oronasal Mucosal Melanoma (PhD Studentship, Reference Number 2026-27-006)

This PhD studentship at the University of Edinburgh offers an exciting opportunity to investigate the spatial transcriptomic profiling of the host-microbiome interactome in oronasal mucosal melanoma (OMM), a devastating tumour affecting both humans and dogs. OMM is biologically equivalent in both species, sharing histopathological and immunological features, but while rare in humans, it is the most common oral tumour in dogs, making canine tissue a powerful comparative model for translational cancer research. The project aims to address the currently unexplored role of microbial communities in OMM initiation and progression. Preliminary work has revealed significant microbial differences across species and between tumour and normal tissues, suggesting that the microbiome may influence tumour behaviour and outcomes. This research will integrate advanced spatial transcriptomics, functional in vitro models, and longitudinal patient sampling to build a comprehensive understanding of how microbes shape mucosal melanoma biology. Aim 1: Using cutting-edge platforms such as Stereo-seq and Nanostring, the project will generate high-resolution spatial maps of host and microbial transcriptomes within OMM tissues. These maps will help identify microbial niches and their associations with host gene expression, immune infiltration, and tumour behaviour, comparing tumour centres, invasive margins, and adjacent non-neoplastic mucosa. Aim 2: Functional interrogation will involve establishing patient-derived OMM organoids from both dogs and humans, co-cultured with microbial species identified in Aim 1. Phenotypic changes in proliferation, invasion, and signalling pathways will be assessed, uncovering mechanistic links between microbial colonisation and tumour progression. The dog model will serve as an initial discovery platform, with findings translated to human OMM. Aim 3: Clinical validation will be conducted in collaboration with UK clinical centres, collecting longitudinal oronasal swabs from OMM patients (human and canine). Microbiome profiles will be correlated with clinical outcomes such as recurrence and treatment response. Industry partnerships may support the development of predictive tools and at-home microbiome testing kits. Significance: This project will establish the first detailed spatial and functional atlas of the host-microbiome interactome in OMM, accelerating discovery pipelines for this rare human cancer by leveraging the abundant dog model. Comparative insights will illuminate conserved microbial drivers of tumour initiation and progression, informing new diagnostic biomarkers and therapeutic strategies at the intersection of infection and oncology. Funding: The studentship provides a monthly stipend at the UKRI minimum level for 42 months, along with a research budget for costs, training, and conference attendance. Both UK and international students are eligible for on-campus study. Eligibility: Applicants should have a first or upper second class undergraduate degree (or equivalent) in a relevant biological or medical science discipline. Experience in molecular biology, microbiology, or cancer research is desirable. International students must meet University of Edinburgh English language requirements. A strong interest in translational research and comparative oncology is preferred. Application: Download the application form from the website and submit it to [email protected] by noon (GMT) on 13th February 2026, including the reference code “2026-27-006” in the subject line. If applying for multiple studentships, submit a separate application for each. References: Recent publications relevant to the project include Blacklock et al. (J. Pathol.), Saarenpää et al. (Nat Biotechnol), and Lötstedt et al. (Nat Biotechnol).