title: Massively parallel sequencing reveals an accumulation of de novo mutations and an activating mutation of LPAR1 in a patient with metastatic neuroblastoma.
abstract: Neuroblastoma is one of the most genomically heterogeneous childhood malignances studied to date, and the molecular events that occur during the course of the disease are not fully understood. Genomic studies in neuroblastoma have showed only a few recurrent mutations and a low somatic mutation burden. However, none of these studies has examined the mutations arising during the course of disease, nor have they systemically examined the expression of mutant genes. Here we performed genomic analyses on tumors taken during a 3.5 years disease course from a neuroblastoma patient (bone marrow biopsy at diagnosis, adrenal primary tumor taken at surgical resection, and a liver metastasis at autopsy). Whole genome sequencing of the index liver metastasis identified 44 non-synonymous somatic mutations in 42 genes (0.85 mutation/MB) and a large hemizygous deletion in the ATRX gene which has been recently reported in neuroblastoma. Of these 45 somatic alterations, 15 were also detected in the primary tumor and bone marrow biopsy, while the other 30 were unique to the index tumor, indicating accumulation of de novo mutations during therapy. Furthermore, transcriptome sequencing on the 3 tumors demonstrated only 3 out of the 15 commonly mutated genes (LPAR1, GATA2, and NUFIP1) had high level of expression of the mutant alleles, suggesting potential oncogenic driver roles of these mutated genes. Among them, the druggable G-protein coupled receptor LPAR1 was highly expressed in all tumors. Cells expressing the LPAR1 R163W mutant demonstrated a significantly increased motility through elevated Rho signaling, but had no effect on growth. Therefore, this study highlights the need for multiple biopsies and sequencing during progression of a cancer and combinatorial DNA and RNA sequencing approach for systematic identification of expressed driver mutations.
authors.affiliation: Oncogenomics Section, Pediatric Oncology Branch, Advanced Technology Center, National Cancer Institute, Bethesda, Maryland, United States of America.
authors.forename: Jun S
authors.initials: JS
authors.lastname: Wei
authors.forename: Peter
authors.initials: P
authors.lastname: Johansson
authors.forename: Li
authors.initials: L
authors.lastname: Chen
authors.forename: Young K
authors.initials: YK
authors.lastname: Song
authors.forename: Catherine
authors.initials: C
authors.lastname: Tolman
authors.forename: Samuel
authors.initials: S
authors.lastname: Li
authors.forename: Laura
authors.initials: L
authors.lastname: Hurd
authors.forename: Rajesh
authors.initials: R
authors.lastname: Patidar
authors.forename: Xinyu
authors.initials: X
authors.lastname: Wen
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Badgett
authors.forename: Adam T C
authors.initials: AT
authors.lastname: Cheuk
authors.forename: Jean-Claude
authors.initials: JC
authors.lastname: Marshall
authors.forename: Patricia S
authors.initials: PS
authors.lastname: Steeg
authors.forename: José P
authors.initials: JP
authors.lastname: Vaqué Díez
authors.forename: Yanlin
authors.initials: Y
authors.lastname: Yu
authors.forename: J Silvio
authors.initials: JS
authors.lastname: Gutkind
authors.forename: Javed
authors.initials: J
authors.lastname: Khan
mesh_terms: D000818:Animals; D005260:Female; D050989:GATA2 Transcription Factor / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D051379:Mice; D016297:Mutagenesis, Site-Directed; D009154:Mutation; D041681:NIH 3T3 Cells; D009447:Neuroblastoma / Q000175:diagnosis / Q000235:genetics*; D009687:Nuclear Proteins / Q000235:genetics; D016601:RNA-Binding Proteins / Q000235:genetics; D049368:Receptors, Lysophosphatidic Acid / Q000235:genetics*; D055815:Young Adult
chemical_list: D050989:GATA2 Transcription Factor; C494711:GATA2 protein, human; C403092:NUFIP1 protein, human; D009687:Nuclear Proteins; D016601:RNA-Binding Proteins; D049368:Receptors, Lysophosphatidic Acid