Somatic structural variation targets neurodevelopmental genes and identifies SHANK2 as a tumor suppressor in neuroblastoma

• Published in: Genome research Vol. 30; no. 9; pp. 1228 - 1242
• Main Authors: Lopez, Gonzalo, Conkrite, Karina L, Doepner, Miriam, Rathi, Komal S, Modi, Apexa, Vaksman, Zalman, Farra, Lance M, Hyson, Eric, Noureddine, Moataz, Wei, Jun S, Smith, Malcolm A, Asgharzadeh, Shahab, Seeger, Robert C, Khan, Javed, Auvil, Jaime Guidry, Gerhard, Daniela S, Maris, John M, Diskin, Sharon J
• Format: Journal Article
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 01.09.2020
• Subjects: Adapter proteins; Autism; Breakpoints; Cell Line, Tumor; Children; Chromosome 11; Chromothripsis; Coding; Cohort Studies; DNA Breaks; DNA Copy Number Variations; Female; Genes, Tumor Suppressor; Genomes; Genomic Structural Variation; Genotyping; Humans; Localization; Male; Malignancy; N-Myc Proto-Oncogene Protein - genetics; Nerve Tissue Proteins - genetics; Neuroblastoma; Neuroblastoma - genetics; Neuroblastoma - pathology; Neuroblastoma cells; Neurogenesis - genetics; Phenotypes; Polymorphism, Single Nucleotide; Quantitative Trait Loci; Retinoic acid; Risk Assessment; RNA, Neoplasm; RNA-Seq; Single-nucleotide polymorphism; Sympathetic nervous system; Telomerase - genetics; Tumor Cells, Cultured; Tumor suppressor genes; Tumorigenesis; Tumors; Variation; Whole Genome Sequencing
• ISSN: 1088-9051; 1549-5469; 1549-5469
• DOI: 10.1101/gr.252106.119

Neuroblastoma is a malignancy of the developing sympathetic nervous system that accounts for 12% of childhood cancer deaths. Like many childhood cancers, neuroblastoma shows a relative paucity of somatic single-nucleotide variants (SNVs) and small insertions and deletions (indels) compared to adult cancers. Here, we assessed the contribution of somatic structural variation (SV) in neuroblastoma using a combination of whole-genome sequencing (WGS) of tumor-normal pairs ( = 135) and single-nucleotide polymorphism (SNP) genotyping of primary tumors ( = 914). Our study design allowed for orthogonal validation and replication across platforms. SV frequency, type, and localization varied significantly among high-risk tumors. nonamplified high-risk tumors harbored an increased SV burden overall, including a significant excess of tandem duplication events across the genome. Genes disrupted by SV breakpoints were enriched in neuronal lineages and associated with phenotypes such as autism spectrum disorder (ASD). The postsynaptic adapter protein-coding gene, , located on Chromosome 11q13, was disrupted by SVs in 14% of nonamplified high-risk tumors based on WGS and 10% in the SNP array cohort. Expression of was low across human-derived neuroblastoma cell lines and high-risk neuroblastoma tumors. Forced expression of in neuroblastoma cells resulted in significant growth inhibition ( = 2.6 × 10 to 3.4 × 10 ) and accelerated neuronal differentiation following treatment with all- retinoic acid ( = 3.1 × 10 to 2.4 × 10 ). These data further define the complex landscape of somatic structural variation in neuroblastoma and suggest that events leading to deregulation of neurodevelopmental processes, such as inactivation of , are key mediators of tumorigenesis in this childhood cancer.