Glioblastomas exhibit highly branched, treatment-specific clonal evolution patterns.
Major finding: Glioblastomas exhibit highly branched, treatment-specific clonal evolution patterns.
Approach: WES and transcriptome analysis was performed on initial and recurrent tumors from 114 patients.
Impact: Elucidation of clonal evolutionary and mutation patterns can identify potential therapeutic targets.
Glioblastoma multiforme (GBM) tumors are highly malignant brain tumors that almost inevitably recur after standard therapy, which is a combination of surgery, radiation, and the oral alkylating agent temozolomide (TMZ). To identify the genetic determinants driving recurrence and characterize the clonal evolutionary patterns of GBMs under therapy, Wang and colleagues performed whole-exome sequencing (WES) of untreated tumors, recurrent tumors, and matched normal tissues from 93 patients, and transcriptome profiling of untreated and recurrent tumors from 65 patients, for a total of 114 patients with GBM. Whole-exome analysis showed that GBM clonal evolution is highly branched, and that branched evolution of the untreated and recurrent tumors is an early event that occurs prediagnosis. Evaluation of genetic alterations that exhibited a gain or loss revealed that a mutated gene harbored by the initial tumor was replaced by a differently mutated version of the same gene in the recurrent tumor. Further, these mutational switching events occurred more frequently in known GBM driver genes than in known nondriver genes, suggesting that genes that undergo mutational switching are drivers. Patients treated with TMZ exhibited hypermutation in TMZ-treated, but not untreated, tumors, most frequently associated with mutations of the mismatch repair gene mutS homolog 6 (MSH6). Primary GBMs, especially hypermutated primary GBMs, exhibited transcriptional subtype switching between the initial diagnosis and relapse. Several genes were found to be mutated much more frequently in recurrent GBM, including latent transforming growth factor beta binding protein 4 (LTBP4), an activator of TGFβ signaling. Elevated LTBP4 expression was correlated with poor prognosis in patients with wild-type IDH GBM, and depletion of LTBP4 resulted in decreased TGFβ signaling and proliferation in vitro. Taken together, these findings show that treated GBMs exhibit a highly branched clonal evolutionary pattern associated with specific genetic alterations, and provide evidence supporting the TGFβ signaling pathway as a potential therapeutic target for recurrent GBMs.