Fig. 2
Transcriptional signatures of the tumor microenvironment of DC-LAMPHi versus DC-LAMPLo HGSCs. a Hierarchical clustering of genes significantly upregulated in 9 DC-LAMPHi versus 9 DC-LAMPLo HGSCs, as determined by RNA-Seq. Highly expressed genes are in red, and lowly expressed genes are in green. b Relative abundance of T cells, CD8+ T cells, cytotoxic lymphocytes and NK cells across DC-LAMPHi and DC-LAMPLo HGSCs, as determined by MCP-counter on RNA-Seq data. Box plots: lower quartile, median, upper quartile; whiskers, minimum, maximum. c Relative expression levels of genes linked to T cells, CD8 cytotoxicity, TH1 polarization, TH2 polarization, T cell activation, T cell phenotype, NK cells, B cells and plasma cells in 9 DC-LAMPHi versus 9 DC-LAMPLo HGSCs, as determined by RNA-Seq and IHC. Benjamin-Hochberg correction was used for RNA-Seq data. Highly expressed genes are in red, and lowly expressed genes are in green. d qRT-PCR-assisted quantification of CCL5, CCR4, CD3, CD4, CD40, CD40L, CD8A, CTLA4, GZMA, GZMB, IL18 and PRF1 expression levels in 23 DC-LAMPHi and 23 DC-LAMPLo HGSCs patients who did not receive neoadjuvant chemotherapy. Box plots: lower quartile, median, upper quartile; whiskers, minimum, maximum. Ct values were normalized using the global normalization method (n = 46 samples). qRT-PCR data were analyzed by unpaired Student’s t tests using GenEx software (MultiD Analysis). All values are presented as mean ± SD