Transcriptome analysis reveals tumor microenvironment changes in glioblastoma

A better understanding of transcriptional evolution of IDH-wild-type glioblastoma may be crucial for treatment optimization. Here, we perform RNA sequencing (RNA-seq) (n = 322 test, n = 245 validation) on paired primary-recurrent glioblastoma resections of patients treated with the current standard of care. Transcriptional subtypes form an interconnected continuum in a two-dimensional space. Recur-rent tumors show preferential mesenchymal progression. Over time, hallmark glioblastoma genes are not significantly altered. Instead, tumor purity decreases over time and is accompanied by co -in-creases in neuron and oligodendrocyte marker genes and, independently, tumor-associated macro-phages. A decrease is observed in endothelial marker genes. These composition changes are confirmed by single-cell RNA-seq and immunohistochemistry. An extracellular matrix-associated gene set increases at recurrence and bulk, single-cell RNA, and immunohistochemistry indicate it is expressed mainly by pericytes. This signature is associated with significantly worse survival at recur-rence. Our data demonstrate that glioblastomas evolve mainly by microenvironment (re-)organization rather than molecular evolution of tumor cells.

Automated summary

A better understanding of the transcriptional evolution of IDH-wild-type glioblastoma is crucial for optimizing treatment. Through RNA sequencing, this study demonstrates that glioblastomas mainly evolve through microenvironmental reorganization rather than molecular evolution of tumor cells. The changes in tumor composition over time, including alterations in neuron and oligodendrocyte marker genes and an increase in tumor-associated macrophages, are confirmed by single-cell RNA-seq and immunohistochemistry.