Telomerase activation by genomic rearrangements in high-risk neuroblastoma

Abstract

Neuroblastoma is a malignant paediatric tumour of the sympathetic nervous system1. Roughly half of these tumours regress spontaneously or are cured by limited therapy. By contrast, high-risk neuroblastomas have an unfavourable clinical course despite intensive multimodal treatment, and their molecular basis has remained largely elusive2–4. Here we have performed whole-genome sequencing of 56 neuroblastomas (high-risk, n = 39; low-risk, n = 17) and discovered recurrent genomic rearrangements affecting a chromosomal region at 5p15.33 proximal of the telomerase reverse transcriptase gene (TERT). These rearrangements occurred only in high-risk neuroblastomas (12/39, 31%) in a mutually exclusive fashion with MYCN amplifications and ATRX mutations, which are known genetic events in this tumour type1,2,5. In an extended case series (n = 217), TERT rearrangements defined a subgroup of high-risk tumours with particularly poor outcome. Despite a large structural diversity of these rearrangements, they all induced massive transcriptional upregulation of TERT. In the remaining high-risk tumours, TERT expression was also elevated in MYCN-amplified tumours, whereas alternative lengthening of telomeres was present in neuroblastomas without TERT or MYCN alterations, suggesting that telomere lengthening represents a central mechanism defining this subtype. The 5p15.33 rearrangements juxtapose the TERT coding sequence to strong enhancer elements, resulting in massive chromatin remodelling and DNA methylation of the affected region. Supporting a functional role of TERT, neuroblastoma cell lines bearing rearrangements or amplified MYCN exhibited both upregulated TERT expression and enzymatic telomerase activity. In summary, our findings show that remodelling of the genomic context abrogates transcriptional silencing of TERT in high-risk neuroblastoma and places telomerase activation in the centre of transformation in a large fraction of these tumours.

Impact of Disseminated Neuroblastoma Cells on the Identification of the Relapse-Seeding Clone

“…Seventy percent of these alterations, which are exclusively present in patients !18 months with non-MNA tumors, were found in the form of deletions within this gene (6,(9)(10)(11)(12). This aberration is proposed to define a subgroup of high-risk neuroblastomas resulting in elongation of telomeres by alternative lengthening of telomeres, ALT (10,12). In line with these reports, we found intragenic ATRX deletions in 13.6% of stage 4 patients, exclusively older than 18 months without MNA.…”

“…Somatic alterations of the ATRX gene were reported to occur in 10% to 22% of stage 4 neuroblastoma tumors. Seventy percent of these alterations, which are exclusively present in patients !18 months with non-MNA tumors, were found in the form of deletions within this gene (6,(9)(10)(11)(12). This aberration is proposed to define a subgroup of high-risk neuroblastomas resulting in elongation of telomeres by alternative lengthening of telomeres, ALT (10,12).…”

“…Overall, low-risk neuroblastomas mostly have whole chromosomal gains without structural aberrations. High-risk neuroblastomas, for example, mostly stage 4, on the contrary, present with different structural aberrations in the form of gains or losses of large chromosomal segments, referred to as segmental chromosomal aberrations (SCAs), MYCN amplification (MNA), and/or mutations as well as copy-number alterations affecting certain genes or parts thereof (5)(6)(7)(8)(9)(10)(11)(12)(13). Whether genetic markers might help to identify the relapse-seeding clone and to categorize stage 4 patients into different prognostic subgroups is still a matter of debate.…”

A Phase I Study of the CDK4/6 Inhibitor Ribociclib (LEE011) in Pediatric Patients with Malignant Rhabdoid Tumors, Neuroblastoma, and Other Solid Tumors

“…It has also recently been shown that high-risk neuroblastoma may be defined by activation of telomere maintenance mechanisms caused by MYCN amplification, TERT rearrangements, or ATRX mutations (26), and relapsed neuroblastomas are frequently associated with RAS/mitogen-activated protein kinase (MAPK) pathway mutations that could also influence ribociclib sensitivity (27). In MRT, disruption of the SMARCB1 transcriptional regulator can alter the expression of multiple genes upstream and downstream of CDK4/6 (28,29).…”

The proto-oncogene Myc drives expression of the NK cell-activating NKp30 ligand B7-H6 in tumor cells

“…ChIP-seq and deep mRNA-sequencing (mRNA-seq) ChIP-seq methodology and mRNA-seq in N-Myc-modulated cell lines SH-SY5Y-MYCN and IMR5-75-shMYCN were as previously described 43,44 . B7-H6 and N-Myc expression profiles in primary neuroblastoma were derived from global RNA-seq analyses of 498 neuroblastoma patients.…”