Xenium at MDC: A Case Study for Hypoxia in Head and Neck Cancer

Challenge: What does hypoxia look like inside a tumour, cell by cell?

At Medicines Discovery Catapult, we can map single-cell spatial transcriptomics for up to 5,000 targets in standard FFPE tissue.

Below is a head and neck tumour core from a larger study with the Manchester Cancer Research Centre exploring the effect of hypoxia on the tumour microenvironment. Using the 10x Genomics Xenium platform, we mapped key genes driving the hypoxic response at single-cell resolution across the tissue.

These genes corresponded to different tumour cell subtypes within the same tumour, and we confirmed hypoxia in these regions using CA9 immunofluorescence staining on the same slide.

One tissue core, every cell accounted for

From raw tissue to cell-by-cell identity

Cells are clustered by identity, visualised on a UMAP plot, then mapped straight back onto the tissue.

Our Approach: The same tissue, checked two ways

Using the Xenium platform, we mapped the genes driving the hypoxic response at single-cell resolution, then confirmed hypoxia in the same regions by CA9 immunofluorescence staining on the same slide.

Uncover the signatures that drive disease

These genes corresponded to different subtypes of tumour cells within the same tumour, mapped to their exact position, cell by cell.

Hypoxia in head and neck cancer is just one question this technology can answer. Others we are helping teams work through:

• Identifying new drug targets in complex tissue
• Mapping how prevalent a target is across patient samples
• Understanding why some patients respond to treatment, and others don’t
• Characterising immune infiltration in the tumour microenvironment

The Xenium platform can provide insights across immunology, neuroscience, and other oncology programmes too, and has joined the ranks of our spatial biology platforms at MDC. If any of this sounds like your project, get in touch