Wellcome Sanger Institute

Microenvironment of kidney cancer

The renal tumour microenvironment refers to the cellular composition of kidney cancer which has been characterised through the use of single cell RNA sequencing, spatial transcriptomics, and whole exome sequencing.

These studies are fundamental to better understand cancer biology as tumour behaviour is intricately dependent both on the oncogenic properties of cancer cells and their multi-cellular interactions.

Here we provide an overview of the data visualisation and links to download for over 270,000 single cell transcriptomes and spatial transcripomic data from this project.

A comprehensive single cell atlas of kidney cancer

Over 270,000 single cell transcriptomes have been carefully annotated from 12 patients with kidney tumours.  Cells were sampled from multiple regions within the tumour and the wider tumour microenvironment, including peripheral blood, the normal adjacent kidney, the tumour-normal interface, the adrenal gland, and any associated metastatic disease.

For the ~100,000 T cells captured, we have performed TCR sequencing, providing detailed insights into clonotypic evolution and expansion.

The data can be visualised via an interactive web-browser here.

The raw and processed data is available for download here (h5ad).

Spatial transcriptomic analysis at the tumour-normal interface

Kidney tumours are commonly enveloped with fibrous connective tissue that is the pseudocapsule or tumour-normal interface. It appears as though this layer constrains tumour growth and pseudocapsule invasion is correlated with tumour stage and grade. As part of this study, we compared the cellular make up of this interface with the tumour core.

Several notable differences are seen, including important interactions that are clinical targetable.

The data can be visualised via an interactive web-browser here.

Data can be downloaded from here (h5ad).

Sanger people

Photo of Mr Thomas Mitchell

Mr Thomas Mitchell

Clinician Scientist Fellow

External Contributors

Photo of Urological Malignancies Programme, Cancer Research UK Cambridge Centre

Urological Malignancies Programme, Cancer Research UK Cambridge Centre

External partners and funders