The genetic landscape of gliomas arising after therapeutic radiation

Giselle Y. López, Jessica Van Ziffle, Courtney Onodera, James P. Grenert, Iwei Yeh, Boris C. Bastian, Jennifer Clarke, Nancy Ann Oberheim Bush, Jennie Taylor, Susan Chang, Nicholas Butowski, Anuradha Banerjee, Sabine Mueller, Cassie Kline, Joseph Torkildson, David Samuel, Aleli Siongco, Corey Raffel, Nalin Gupta, Sandeep Kunwar, Praveen Mummaneni, Manish Aghi, Philip Theodosopoulos, Mitchel Berger, Joanna J. Phillips, Melike Pekmezci, Tarik Tihan, Andrew W. Bollen, Arie Perry, David A. Solomon

Radiotherapy improves survival for common childhood cancers such as medulloblastoma, leukemia, and germ cell tumors. Unfortunately, long-term survivors suffer sequelae that can include secondary neoplasia. Gliomas are common secondary neoplasms after cranial or craniospinal radiation, most often manifesting as high-grade astrocytomas with poor clinical outcomes. Here, we performed genetic profiling on a cohort of 12 gliomas arising after therapeutic radiation to determine their molecular pathogenesis and assess for differences in genomic signature compared to their spontaneous counterparts. We identified a high frequency of TP53 mutations, CDK4 amplification or CDKN2A homozygous deletion, and amplifications or rearrangements involving receptor tyrosine kinase and Ras-Raf-MAP kinase pathway genes including PDGFRA, MET, BRAF, and RRAS2. Notably, all tumors lacked alterations in IDH1, IDH2, H3F3A, HIST1H3B, HIST1H3C, TERT (including promoter region), and PTEN, which genetically define the major subtypes of diffuse gliomas in children and adults. All gliomas in this cohort had very low somatic mutation burden (less than three somatic single nucleotide variants or small indels per Mb). The ten high-grade gliomas demonstrated markedly aneuploid genomes, with significantly increased quantity of intrachromosomal copy number breakpoints and focal amplifications/homozygous deletions compared to spontaneous high-grade gliomas, likely as a result of DNA double-strand breaks induced by gamma radiation. Together, these findings demonstrate a distinct molecular pathogenesis of secondary gliomas arising after radiation therapy and identify a genomic signature that may aid in differentiating these tumors from their spontaneous counterparts.