Extended Data Fig. 4: RNA sequencing comparison to other recurrent glioblastoma samples.
We combined our RNA sequencing dataset to that of GSE79671 (an RNA sequencing 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 cell cycle/cancer proliferation signatures (GSVA score ≥ 0.2). The proportion of positive enrichment of cell cycle/cancer proliferation signatures in our dataset as a whole is similar to GSE79671 (14 out of 29 (48%) versus 11 out of 20 (55%)). The number of samples with positive enrichment in the TCGA GBM is lower, at 41%. We observed that the neoadjuvant PD-1 monoclonal antibody therapy group is associated with a lower fraction of tumors with cell cycle signatures. Only 3 out of 14 tumors in the neoadjuvant group demonstrated positive enrichment, with 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.
