Pre-print: Spatial analysis of ligand-receptor interactions

12 Sep 2020

Full title

Spatial analysis of ligand-receptor interactions in skin cancer at genome-wide and single-cell resolution.

M Tran, S Yoon, M Teoh, S Andersen, PY Lam, P Purdue, A Raghubar, SJ Hanson, K Devitt, K Jones, S Walters, ZK Tuong, A Kulasinghe, J Monkman, HP Soyer, I Frazer, Q Nguyen.


The ability to study cancer-immune cell communication across the whole tumor section without tissue dissociation is important to understand molecular mechanisms of cancer immunotherapy and drug targets. Current experimental methods such as immunohistochemistry allow researchers to investigate a small number of cells or a limited number of ligand-receptor pairs at tissue scale with limited cellular resolution. In this work, we developed a powerful experimental and analytical pipeline that allows for the genome-wide discovery and targeted validation of cellular communication. By profiling thousands of genes, spatial transcriptomic and single-cell RNA sequencing data show genes that are possibly involved in interactions. The expression of the candidate genes could be visualized by single-molecule in situ hybridization and droplet digital PCR. We developed a computational pipeline called STRISH that enables us to quantitatively model cell-cell interactions by automatically scanning for local expression of RNAscope data to recapitulate an interaction landscape across the whole tissue. Furthermore, we showed the strong correlation of microscopic RNAscope imaging data analyzed by STRISH with the gene expression values measured by droplet digital PCR. We validated the unique ability of this approach to discover new cell-cell interactions in situ through analysis of two types of cancer, basal cell carcinoma and squamous cell carcinoma. We expect that the approach described here will help to discover and validate ligand receptor interactions in different biological contexts such as immune-cancer cell interactions within a tumor.

GIH contribution

Dr Sohye Yoon
Dr Sohye Yoon

As one of the sucessful outcomes from the GIH funded collaborative project "Spatial genomics technologies to study cancer and genetic diseases in tissue contexts", GIH team member Dr Sohye Yoon, as the first co-author of the paper, conducted RNAscope Hiplex and droplet digital PCR assays. 

Sohye also contributed to drafting the manuscript including the work-flow illustration. 


Stacey Andersen
Stacey Andersen

Contributing author and team member of both GIH and the IMB Sequencing Facilty, Stacey Andersen, performed the NextSeq sequencing with the ST libraries.

Stacey also contributed to sample preparation and performed droplet digital PCR experiments.


Dr Brooke Purdue
Dr Brooke Purdue

Contributing author and team member Dr Brooke Purdue assisted with initial microscopy and imaging optimisations.