Engineering A Potent Cancer Vaccine Using Immunoproteasome-Expressing Mesenchymal Stromal Cells

Raw RNA-seq counts from reads aligned to the mouse genome (mm10 assembly) were generated with Htseq-count (PMID: 25260700). Differentially expressed genes between IPr and Ctl MSCs were calculated by DESeq2 (PMID: 25516281). Pre-ranked gene set enrichment was performed as recommended for RNA-seq data (PMID: 16199517). Custom R scripts were used to filter highly redundant biological processes. A false discovery rate of 0.05 was considered as an acceptable threshold for further investigation. All analyses were conducted in R (v3.6) or Python (v3.7) programming language. The ggplot2, ClusterProfiler and dplyr packages were used for data visualization. Student’s t-test was performed for normally distributed data to compute the p-value and the Benjamini-Hochberg procedure was used for adjusting the statistical inference of multiple comparisons. We report in this study the effect of IPr subunit expression on the antigen cross-presenting abilities of MSCs.