Fig. 4. RNAseq comparison to other recurrent glioblastoma samples.

We combined our RNAseq dataset with that of GSE79671 (an RNAseq dataset of recurrent glioblastoma pre- and post- bevacizumab treatment; only pre-treatment (Pre-Tx) samples were used) and The Cancer Genome Atlas (TCGA) glioblastoma samples. We applied appropriate batch correction on log transformed, normalized mRNA expression values using the removeBatchEffect function in the R package limma to estimate the fraction of glioblastoma patients with positive enrichment of the cell cycle/cancer proliferation signatures (GSVA score ≤ 0.2). The proportion of positive enrichment of the cell cycle/cancer proliferation signatures in our dataset as a whole is similar to GSE79671 (14 out of 29 (48%) vs. 11 out of 20 (55%)). The number of samples with positive enrichment in the TCGA GBM is lower at 41%. We observed that neoadjuvant PD-1 monoclonal antibody therapy group is associated with lower fraction of tumors with the cell cycle signatures. There were only 3 out of 14 tumors in the neoadjuvant group demonstrating positive enrichment while there were 11 of 15 tumors in the adjuvant group and 11 of 20 tumors in the GSE79671 set (one-sided Fisher exact test P = 0.01 and P = 0.05, respectively). GSVA: gene set variation analysis.