Neuroblastoma (NB) is a malignant pediatric tumor of the sympathetic nervous system with a low mutation frequency.
We searched for new structural rearrangements in a series of 350 NBs of all stages using high density SNP microarrays. Exome sequencing was also performed on 15 tumor/constitutional DNA pairs and 25 additional tumors, mainly high-risk NBs, using paired-end sequencing on Illumina instrument.
Recurrent rearrangements as well as gain of TERT gene were observed in 15 of 350 neuroblastomas analyzed by SNP array. 12 out of these 15 tumors with TERT rearrangement belong to 11q-deletion subgroup of NB patients marking tumors with a poor prognosis. This remodeling of the genomic context abrogates transcriptional silencing of TERT in high-risk neuroblastoma and places telomerase activation in the centre of transformation. These rearrangements occurred in high-risk NBs in an almost mutually exclusive fashion with MYCN amplifications. Furthermore, by exome sequencing, we detect extensive structural rearrangements and amplification of chromosome 2, 5 and 7 leading to amplification of MYCN, TERT and CDK6 respectively in one tumor.
Exome sequencing approach detected at average 14 somatic protein-changing alterations per tumor. Combining structural and mutational data shows recurrent alterations in ATRX gene in four non MYCN-amplified tumors: two focal deletions, one nonsense mutation and one deleterious missense mutation. ATRX inactivation results in alternative lengthening of telomeres (ALT). This means that high-risk neuroblastomas cancer cells can preserve their telomeres by ALT or by activation of telomerase reverse transcriptase (encoded by TERT). Alterations in TERT and ATRX were mutually exclusive, which is in agreement with the independent activation by these genes of telomere lengthening. Moreover three cases had chromothripsis of chromosome 5 with rearrangements affecting the TERT.
This study identifies recurrent TERT and ATRX rearrangements and telomere lengthening as an important mechanism characterizing high-risk tumors and supports the pharmacological inhibition of these targets.