Integrating histopathology and transcriptomics for spatial tumor microenvironment profiling in a melanoma case study

This repository holds the code for all analyses related to

Lapuente-Santana, Ó., Kant, J. & Eduati, F. Integrating histopathology and transcriptomics for spatial tumor microenvironment profiling in a melanoma case study. npj Precis. Onc. 8, 254 (2024). https://doi.org/10.1038/s41698-024-00749-w

Our pipeline (SPoTLIghT) to derive spatial graph-based interpretable features from H&E tissue slides is packaged as a docker container, which is available here: https://github.com/SysBioOncology/SPoTLIghT.

Spatial features for used cohorts

Spatial features for the TCGA and CPTAC melanoma cohorts are provided here:

• data/spatial_features_matrix_TCGA.csv: TCGA-SKCM spatial features
• data/spatial_features_matrix_CPTAC.csv: CPTAC-CM spatial features

Notebook to reproduce the figures from the manuscript

Required .xlsx files

Download the following files and place them in the data directory:

• bagaev_file: bagaev microenvironment subtypes for TCGA patients (available from Bagaev et al. 2021, Table S6, sheet 1)
• tcga_survival_file: survival data for TCGA patients (available from Liu et al. 2018, Table S1, sheet 1).

# First, activate conda environment

conda env create -f spatial_features.yml
conda activate spatial_features

Enter R and install the following packages prior to rendering the notebook.

# These packages aren't included in the conda environment

install.packages("pak")
pak::pkg_install(c("tidyverse", "GaitiLab/GaitiLabUtils", "patchwork", "Seurat", "patchwork", "ggplot2", "data.table", "glue", "stringr", "rstatix", "prabhakarlab/Banksy", "satijalab/seurat-wrappers", "ggrastr", "gridExtra" ) )

Alternatively, these packages are also loaded through pacman::p_load so if package is missing it will automatically be installed.

After installation you can render a notebook as follows in the terminal or using a bash script.

Rscript -e "rmarkdown::render('analysis/analysis/Fig1de_SuppFig3c_spatial_validation_maps_xenium_skin_panel_w_add_on.Rmd')"

# If you want to run all notebooks, you can run: 
Rscript -e "analysis/run_notebooks.R"