Description

This is the repository for the scripts used in the study "Divergent therapeutic and prognostic impacts of immunogenic features in undifferentiated pleomorphic sarcoma and myxofibrosarcoma", Cancer Immunol Immunother (2025), https://doi.org/10.1007/s00262-025-04123-y

This repository has the following structure:

1. input_files - .tsv & .RData files containing the necessary input to perform the analysis e.g. annotation files and processed data files.
2. RNAseq - scripts used for analysing the RNA sequencing data & generating the figures. See GEO link below for raw data of USTS and myxofibrosarcomas.
3. IMC - scripts used for analysing the imaging mass cytometry data & generating the figures. See BioStudies link for raw data.
4. IF - scripts used for analysing the multispectral immunofluorescence & double immunohistochemical data, as well as generating the figures (including a QuPath script).
5. Survival - scripts used for analysing survival data & generating the figures. Actual survival data can be requested.

Authors

S. van Oost, D.M. Meijer, Z.B. Erdem, M.E. IJsselsteijn, J. Roelands, S. Lam, M.S. Boejharat, B.E.W.M. van den Akker, R. van der Breggen, I.H. Briaire-de Bruijn, L.J.A.C. Hawinkels, A.A. Kruiswijk, M. van der Ploeg, P.M. Wijers-Koster, R.L. Haas, M.A.J. van den Sande, N.F.C.C. de Miranda, J.V.M.G. Bovee

Data availability

RNAseq data (GEO): https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE285944;

Imaging mass cytometry data (BioStudies): https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1555