Tumour evolution and microenvironment interactions in 2D and 3D space

Overview

This is the repo for the manuscript "Spatial clonal evolution and clone-specific microenvironment interactions within three-dimensional tumor structures"

Repo structure

• Figure 1. Spatial microregions across cancers
• Figure 2. Focal clonal evolution in microregions
• Figure 3. Genetic changes drive tumour disparities & Cellular pathways at tumour core and edge
• Figure 4. Clonal-specific Tumor-TME interaction
• Figure 5 & 6. 3D tumour structure and TME interactions

Data Access

Data file for each data type can be accessed using ID listed in the file "Data_access/Sample_ID_Lookup_table_v1.xlsx"

• CPTAC: CPTAC snRNA-seq data can be accessed through NIH GDC Data Portal using the CPTAC Case ID: https://portal.gdc.cancer.gov/cases/

• HTAN: HTAN data can be accessed with HTAN Biospecimen and HTAN Participant ID on HTAN DCC, WUSTL Atlas: https://humantumoratlas.org/explore?selectedFilters=%5B%7B%22group%22%3A%22AtlasName%22%2C%22value%22%3A%22HTAN+WUSTL%22%7D%5D&tab=file

Manuscript:

DOI https://doi.org/10.1038/s41586-024-08087-4

Cite this article

Mo, CK., Liu, J., Chen, S. et al. Tumour evolution and microenvironment interactions in 2D and 3D space. Nature 634, 1178–1186 (2024). https://doi.org/10.1038/s41586-024-08087-4