Project 1

Project 1: Inferring cell-cell interactions from visium

Background

Tumor cells form complex ecosystems with other stromal cells. These ecosystems influence tumor initiation and progression as well as response to treatment. Single-cell and spatial transcriptomics data allows to investigate the interactions between cell types by leveraging information about receptor and ligand gene expression.

In the context of the lungNENomics project, we have performed spatial transcriptomics (VISIUM) on 4 "supra-carcinoid" samples, the most aggressive molecular subtype of lung neuroendocrine tumors. Bulk sequencing analyses suggest that supra-carcinoids experience a very specific microenvironmental niche, with many tumor cells. The project consists in investigating the cellular interactions between tumor and stromal cells.

Data

• Processed VISIUM data (R object) for 4 samples

Requirements

Scripting in R, data exploration, statistics

Steps

1. Install cell-cell interaction software
2. Load the data
3. Run the method
4. Visualise and interpret the results
5. Discuss limitations/biases in the study

Expected difficulties

• Conceptual understanding of the subject (reading the papers to understand the method is essential)
• R scripting

Resources

• Cell-cell interaction method