Gene expression profiling of 50 glioblastoma multiforme tissue samples

Hypothetically the intratumor genomic heterogeneity has the potential to foster the tumor-infiltrating lymphocytes (TILs) diversity or activity, but no one has directly connected them by simultaneously investigating somatic mutations, TILs diversity and immune response activity. We have performed whole-exome sequencing, immune repertoire sequencing and gene expression profiling analysis simultaneously on ten spatially separated tumor samples obtained from two tumor bulks (the primary tumor and its metastatic offspring) of a glioblastoma multiforme (GBM) patient as well as his peripheral blood. We found that although the multi-region samples from one tumor shared more common mutations than those from different ones, the TIL populations did not. The TILs repertoire diversity was not significantly correlated with and the number of nonsynonymous mutations (Spearman's rank correlation, p = 0.4614), but it was highly related to the local immune status as it showed a significant positive correlation both with the local immune cytolytic activity and its down regulating factors. Furthermore, the tumor region having the highest TILs repertoire diversity was founded to show simultaneous local immune activation and suppression. A 20-gene signature was found to represent such contradictory local immune status. 50 GBM patients were stratified by the expression pattern of this signature in their tumors. Survival analysis suggested most of GBM patients (~80%) might be suffered from the simultaneous local immune activation and suppression status, which was unfavorable to patients’ prognoses (log-rank test, p = 0.012). This finding was validated when the similar analysis applied to the existing TCGA GBM dataset (log-rank test, p = 0.005). Through integration analysis of multi-omics data, we provided new insight into the complex relationship among the characteristics of TILs repertoire, somatic mutation pattern, and immune status. 50 GBM samples, corresponding to the microscopic sections containing > 50% tumor cells, obtained from patients operated between September 2005 and June 2009, were used for the expression profiling analysis part of the study.