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

Abstract

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.

Skin‐ny deeping: Uncovering immune cell behavior and function through imaging techniques*

“…Investigations on ligand‐receptor interactions within skin cancer tissue further revealed ongoing tumorigenic signalling of the IL‐34‐CSF1R axis within cancer nest areas, which could be linked to its role as a biomarker for malignancy. The study further uncovered the identification of infiltrating immune cell signature which is correlated with CD90 and the integrin ITGAM 173 . Collectively, these studies illustrate the utility of spatial transcriptomics to delineate heterogenous cell populations, as well as the possibility of integrating information from spatial and other single‐cell related data to provide an unbiased overview of the tissue section in order to drive biological discovery.…”

“…The study further uncovered the identification of infiltrating immune cell signature which is correlated with CD90 and the integrin ITGAM. 173 Collectively, these studies illustrate the utility of spatial transcriptomics to delineate heterogenous cell populations, as well as the possibility of integrating information from spatial and other single-cell related data to provide an unbiased overview of the tissue section in order to drive biological discovery.…”

Computational exploration of cellular communication in skin from emerging single-cell and spatial transcriptomic data

“…Incorporating spatial information will likely reduce false-positive inferred signaling links, because cells only communicate directly over a limited spatial distance. Computational methods that do not use spatial information may fail to detect certain expected ligand–receptor interactions [ 43 ]. Here, we discuss some emerging approaches that have been developed to infer cell–cell communication using spatial information [ 44 ].…”

“…Several exciting new directions still not covered by existing approaches include the spatially dependent interplay of signaling networks and gene regulatory networks, the correlation of cell–cell communication inferred from different molecular modalities in spatial multiomics, and the incorporation of 3D neighborhood information of cells. Further development is also needed to infer cell–cell communication to fully characterize cell function and spatial cellular organization across a whole tissue [ 43 ]. While the rapid development of spatial transcriptomics has provided new opportunities, it also brings additional exciting challenges.…”

High-Dimensional Single-Cell Transcriptomics in Melanoma and Cancer Immunotherapy

“…This technology also offered new insights into B cell functional states, suggesting that tertiary lymphoid structures are involved in immunotherapy response [102]. Likewise, the technology can be used to detect the interaction of ligand and receptor pairs in the TME, as the resolution of these analyses increases, the ability to locate individual cells and their ligand-receptor pairing could provide vital information to the rationalisation of novel immunogenic agents [138]. These spatial techniques have not been widely used in research and clinical assessments due to the high cost and throughput considerations.…”