Breakpoint Features of Genomic Rearrangements in Neuroblastoma with Unbalanced Translocations and Chromothripsis

Abstract

Neuroblastoma is a pediatric cancer of the peripheral nervous system in which structural chromosome aberrations are emblematic of aggressive tumors. In this study, we performed an in-depth analysis of somatic rearrangements in two neuroblastoma cell lines and two primary tumors using paired-end sequencing of mate-pair libraries and RNA-seq. The cell lines presented with typical genetic alterations of neuroblastoma and the two tumors belong to the group of neuroblastoma exhibiting a profile of chromothripsis. Inter and intra-chromosomal rearrangements were identified in the four samples, allowing in particular characterization of unbalanced translocations at high resolution. Using complementary experiments, we further characterized 51 rearrangements at the base pair resolution that revealed 59 DNA junctions. In a subset of cases, complex rearrangements were observed with templated insertion of fragments of nearby sequences. Although we did not identify known particular motifs in the local environment of the breakpoints, we documented frequent microhomologies at the junctions in both chromothripsis and non-chromothripsis associated breakpoints. RNA-seq experiments confirmed expression of several predicted chimeric genes and genes with disrupted exon structure including ALK, NBAS, FHIT, PTPRD and ODZ4. Our study therefore indicates that both non-homologous end joining-mediated repair and replicative processes may account for genomic rearrangements in neuroblastoma. RNA-seq analysis allows the identification of the subset of abnormal transcripts expressed from genomic rearrangements that may be involved in neuroblastoma oncogenesis.

Chromothripsis: potential origin in gametogenesis and preimplantation cell divisions. A review

“…The discovery of such a pattern of complex interchromosomal rearrangements, including joining deletions, duplications, and inversions, was made by combining single nucleotide polymorphism (SNP) assays and next-generation paired-end sequencing. Similar cataclysmic phenomenons have been documented in various cancers such as medulloblastoma, neuroblastoma, myeloma, melanoma, colorectal cancers, prostatic cancers, and hematologic malignancies (13)(14)(15)(16)(17)(18). Recently, a survey of 4,934 cancers indicated that chromothripsis was found in 5% of all samples, with incidences ranging from 0 in head carcinoma to 16% in glioblastoma (19).…”

Human Structural Variation: Mechanisms of Chromosome Rearrangements

“…The breakpoints on chromosome 9 are not the same, but this raises the possibility that the PTPRD locus is a chromothripsis hotspot. Deletions and duplications within PTPRD are among the most common SVs in chromothriptic neuroblastoma genomes [94,95]. …”

Recent insights into the biology of neuroblastoma

“…Indeed, recurrent structural alterations of the ODZ3 , PTPRD and CSMD1 genes were observed, which play a role in neuronal growth cone stabilization. Structural rearrangements were also shown to occur within NBAS in the vicinity of MYCN …”

“…Although in a subsequent study some cases also presented a high number of chromosome breakpoints, the many complex copy‐number states and retention of heterozygosity in lower copy‐number regions were not believed to suggest a chromothripsis‐linked origin of these alterations. Further evidence of the genomic structure of rearrangements, including those observed in association with chromothripsis, has been provided by whole‐genome sequencing of two cell lines and two NBs, the latter with a genomic chromothripsis profile . Analysis of 59 breakpoint junctions of both chromothripsis‐associated and ‐nonassociated rearrangements at a single base resolution revealed frequent microhomologies (40/59) at the junction, as well as complex rearrangements with templated insertions of fragments of nearby sequences in 4/59 cases.…”