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The primacy of NF1 loss as the driver of tumorigenesis in neurofibromatosis type 1-associated plexiform neurofibromas

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Abstract

Neurofibromatosis type 1 (NF1) is a common tumor-predisposition disorder due to germline mutations in the tumor suppressor gene NF1. A virtually pathognomonic finding of NF1 is the plexiform neurofibroma (PN), a benign, likely congenital tumor that arises from bi-allelic inactivation of NF1. PN can undergo transformation to a malignant peripheral nerve sheath tumor, an aggressive soft-tissue sarcoma. To better understand the non-NF1 genetic contributions to PN pathogenesis, we performed whole-exome sequencing, RNASeq profiling and genome-wide copy-number determination for 23 low-passage Schwann cell cultures established from surgical PN material with matching germline DNA. All resected tumors were derived from routine debulking surgeries. None of the tumors were considered at risk for malignant transformation at the time; for example, there was no pain or rapid growth. Deep (~500X) NF1 exon sequencing was also conducted on tumor DNA. Non-NF1 somatic mutation verification was performed using the Ampliseq/IonTorrent platform. We identified 100% of the germline NF1 mutations and found somatic NF1 inactivation in 74% of the PN. One individual with three PNs had different NF1 somatic mutations in each tumor. The median number of somatic mutations per sample, including NF1, was one (range 0–8). NF1 was the only gene that was recurrently somatically inactivated in multiple tumors. Gene Set Enrichment Analysis of transcriptome-wide tumor RNA sequencing identified five significant (FDR<0.01) and seven trending (0.01⩽FDR<0.02) gene sets related to DNA replication, telomere maintenance and elongation, cell cycle progression, signal transduction and cell proliferation. We found no recurrent non-NF1 locus copy-number variation in PN. This is the first multi-sample whole-exome and whole-transcriptome sequencing study of NF1-associated PN. Taken together with concurrent copy-number data, our comprehensive genetic analysis reveals the primacy of NF1 loss as the driver of PN tumorigenesis.

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Acknowledgements

Funding provided by the Intramural Research Programs of the National Human Genome Research Institute, the Center for Cancer Research of the National Cancer Institute and the Division of Cancer Epidemiology and Genetics of the National Cancer Institute. We thank the members of the NISC Comparative Sequencing Program: Betty Barnabas, PhD, Robert Blakesley, PhD, Gerry Bouffard, PhD, Shelise Brooks, BS, Holly Coleman, MSc, Mila Dekhtyar, MSc, Michael Gregory, MSc, Xiaobin Guan, PhD, Jyoti Gupta, MSc, Joel Han, BS, Shi-ling Ho, BS, Richelle Legaspi, MSc, Quino Maduro, BS, Cathy Masiello, MSc, Baishali Maskeri, PhD, Jenny McDowell, PhD, Casandra Montemayor, MSc, Morgan Park, PhD, Nancy Riebow, BS, Karen Schandler, MSc, Brian Schmidt, BS, Christina Sison, BS, Mal Stantripop, BS, James Thomas, PhD, Pam Thomas, PhD, Meg Vemulapalli, MSc, Alice Young, BA. We also thank the members of the NCI DCEG Cancer Genomics Research Laboratory: Michael Beerman, Aaron J Bouk, Seth Brodie, Laurie Burdett, Salma Chowdhury, Charles Chung, Nathan Cole, Michael Cullen, Casey Dagnall, Danielle Debacker, Sadie Frary, Chris Hautman, Belynda Hicks, Herb Higson, Keisha Hines-Harris, Amy Hutchinson, Kristie Jones, Eric Karlins, Sally Larson, Kerrie Lashley, Hyo Jung Lee, Shengchao Li, Tong Li, Wen Luo, Mike Malasky, Michelle Manning, Charles McCoy, Jason Mitchell, Adri O’Neil, Padma Ramya Packirisamy, Timothy Pelc, David Roberson, Aaron Rodriguez, Marianne Siler, Shalabh Suman, Kedest Teshome, Julio Tun, Sue Turner, Bill Utermahlen, Aurelie Vogt, Sarah Wagner, Mingyi Wang, Zhaoming Wang, Kathleen Wyatt, Qi Yang, Meredith Yeager, Sherry Yu, Xijun Zhang, Weiyin Zhou, Bin Zhu. MRW acknowledges funding from the Department of Defense (DAMD17-98-1-8609, DAMD17-00-1-0549), the National Institutes of Health (R29 NS31550), and the Children's Tumor Foundation supporting the development of the PN cultures over a 17-year span. Finally, we thank the patients who enlisted the help of their physicians to contribute tissues to research.

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Authors and Affiliations

  1. Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Cancer Institute, Rockville, MD, USA

    A Pemov & D R Stewart

  2. Department of Molecular Genetics and Microbiology, UF Genetics Institute, UF Health Cancer Center, University of Florida, Gainesville, FL, USA

    H Li & M R Wallace

  3. Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA

    R Patidar, S Sindiri, J S Wei & J Khan

  4. Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Rockville, MD, USA

    N F Hansen, A Elkahloun, S C Chandrasekharappa & J C Mullikin

  5. Division of Cancer Epidemiology and Genetics, Human Genetics Program, National Cancer Institute, Rockville, MD, USA

    S W Hartley

  6. NIH Intramural Sequencing Center, National Human Genome Research Institute, Rockville, MD, USA

    J C Mullikin

  7. Division of Cancer Epidemiology and Genetics, Cancer Genomics Research Laboratory, National Cancer Institute, Rockville, MD, USA

    J F Boland & S Bass

  8. Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA

    B C Widemann

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Pemov, A., Li, H., Patidar, R. et al. The primacy of NF1 loss as the driver of tumorigenesis in neurofibromatosis type 1-associated plexiform neurofibromas. Oncogene 36, 3168–3177 (2017). https://doi.org/10.1038/onc.2016.464

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