Whole Exome Sequencing Reveals the Order of Genetic Changes during Malignant Transformation and Metastasis in a Single Patient with NF1-plexiform Neurofibroma.
OBJECTIVE
Malignant peripheral nerve sheath tumors (MPNST) occur at increased frequency in individuals with neurofibromatosis type 1 (NF1), where they likely arise from benign plexiform neurofibroma precursors. While previous studies have used a variety of discovery approaches to discover genes associated with MPNST pathogenesis, it is currently unclear what molecular events are associated with the evolution of MPNST from plexiform neurofibroma.


METHODS
Whole-exome sequencing was performed on biopsy materials representing plexiform neurofibroma (n = 3), MPNST, and metastasis from a single individual with NF1 over a 14-year period. Additional validation cases were used to assess candidate genes involved in malignant progression, while a murine MPNST model was used for functional analysis.


RESULTS
There was an increasing proportion of cells with a somatic NF1 gene mutation as the tumors progressed from benign to malignant, suggesting a clonal process in MPNST development. Copy number variations, including loss of one copy of the TP53 gene, were identified in the primary tumor and the metastatic lesion, but not in benign precursor lesions. A limited number of genes with nonsynonymous somatic mutations (βIII-spectrin and ZNF208) were discovered, several of which were validated in additional primary and metastatic MPNST samples. Finally, increased βIII-spectrin expression was observed in the majority of MPNSTs, and shRNA-mediated knockdown reduced murine MPNST growth in vivo.


CONCLUSIONS
Collectively, the ability to track the molecular evolution of MPNST in a single individual with NF1 offers new insights into the sequence of genetic events important for disease pathogenesis and progression for future mechanistic study.
Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri.
Angela C
AC
Hirbe
Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri.
Sonika
S
Dahiya
Department of Genetics, The Genome Institute at Washington University, St. Louis, Missouri.
Christopher A
CA
Miller
Department of Genetics, The Genome Institute at Washington University, St. Louis, Missouri.
Tiandao
T
Li
Department of Genetics, The Genome Institute at Washington University, St. Louis, Missouri.
Robert S
RS
Fulton
Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri.
Xiaochun
X
Zhang
Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri.
Sandra
S
McDonald
Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri.
Katherine
K
DeSchryver
Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri.
Eric J
EJ
Duncavage
Rare Tumors Initiative, National Cancer Institute, Bethesda, Maryland. Division of Statistical Genomics, St. Louis, Missouri.
Jessica
J
Walrath
Rare Tumors Initiative, National Cancer Institute, Bethesda, Maryland. Division of Statistical Genomics, St. Louis, Missouri.
Karlyne M
KM
Reilly
Department of Pathology and.
Haley J
HJ
Abel
Neurological Surgery, UCSF School of Medicine, San Francisco, California.
Melike
M
Pekmezci
Neurological Surgery, UCSF School of Medicine, San Francisco, California. Department of Neurology, Washington University, St. Louis, Missouri.
Arie
A
Perry
Department of Genetics, The Genome Institute at Washington University, St. Louis, Missouri.
Timothy J
TJ
Ley
Department of Neurology, Washington University, St. Louis, Missouri. gutmannd@neuro.wustl.edu.
David H
DH
Gutmann
D000818:Animals; D001706:Biopsy; D002471:Cell Transformation, Neoplastic; D056915:DNA Copy Number Variations; D018450:Disease Progression; D059472:Exome; D016158:Genes, p53; D014644:Genetic Variation; D006801:Humans; D051379:Mice; D009154:Mutation; D009362:Neoplasm Metastasis; D009368:Neoplasm Transplantation; D018317:Nerve Sheath Neoplasms / Q000235:genetics*; D018318:Neurofibroma, Plexiform / Q000235:genetics*; D009456:Neurofibromatosis 1 / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D017422:Sequence Analysis, DNA; D013049:Spectrin / Q000737:chemistry
D013049:Spectrin