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Mo J, Moye SL, McKay RM, Le LQ. Neurofibromin and suppression of tumorigenesis: beyond the GAP. Oncogene 2022; 41:1235-1251. [PMID: 35066574 PMCID: PMC9063229 DOI: 10.1038/s41388-021-02156-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/01/2021] [Accepted: 12/13/2021] [Indexed: 12/15/2022]
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant genetic disease and one of the most common inherited tumor predisposition syndromes, affecting 1 in 3000 individuals worldwide. The NF1 gene encodes neurofibromin, a large protein with RAS GTP-ase activating (RAS-GAP) activity, and loss of NF1 results in increased RAS signaling. Neurofibromin contains many other domains, and there is considerable evidence that these domains play a role in some manifestations of NF1. Investigating the role of these domains as well as the various signaling pathways that neurofibromin regulates and interacts with will provide a better understanding of how neurofibromin acts to suppress tumor development and potentially open new therapeutic avenues. In this review, we discuss what is known about the structure of neurofibromin, its interactions with other proteins and signaling pathways, its role in development and differentiation, and its function as a tumor suppressor. Finally, we discuss the latest research on potential therapeutics for neurofibromin-deficient neoplasms.
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Affiliation(s)
- Juan Mo
- Department of Dermatology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390-9069, USA
| | - Stefanie L Moye
- Department of Dermatology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390-9069, USA
| | - Renee M McKay
- Department of Dermatology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390-9069, USA
| | - Lu Q Le
- Department of Dermatology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390-9069, USA.
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390-9069, USA.
- UTSW Comprehensive Neurofibromatosis Clinic, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390-9069, USA.
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390-9069, USA.
- O'Donnell Brain Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390-9069, USA.
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3
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Woycinck Kowalski T, Brussa Reis L, Finger Andreis T, Ashton-Prolla P, Rosset C. Systems Biology Approaches Reveal Potential Phenotype-Modifier Genes in Neurofibromatosis Type 1. Cancers (Basel) 2020; 12:cancers12092416. [PMID: 32858845 PMCID: PMC7565824 DOI: 10.3390/cancers12092416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/18/2020] [Accepted: 07/20/2020] [Indexed: 12/18/2022] Open
Abstract
Neurofibromatosis type (NF1) is a syndrome characterized by varied symptoms, ranging from mild to more aggressive phenotypes. The variation is not explained only by genetic and epigenetic changes in the NF1 gene and the concept of phenotype-modifier genes in extensively discussed in an attempt to explain this variability. Many datasets and tools are already available to explore the relationship between genetic variation and disease, including systems biology and expression data. To suggest potential NF1 modifier genes, we selected proteins related to NF1 phenotype and NF1 gene ontologies. Protein–protein interaction (PPI) networks were assembled, and network statistics were obtained by using forward and reverse genetics strategies. We also evaluated the heterogeneous networks comprising the phenotype ontologies selected, gene expression data, and the PPI network. Finally, the hypothesized phenotype-modifier genes were verified by a random-walk mathematical model. The network statistics analyses combined with the forward and reverse genetics strategies, and the assembly of heterogeneous networks, resulted in ten potential phenotype-modifier genes: AKT1, BRAF, EGFR, LIMK1, PAK1, PTEN, RAF1, SDC2, SMARCA4, and VCP. Mathematical models using the random-walk approach suggested SDC2 and VCP as the main candidate genes for phenotype-modifiers.
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Affiliation(s)
- Thayne Woycinck Kowalski
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil; (T.W.K.); (L.B.R.); (T.F.A.); (P.A.-P.)
- Programa de Pós-Graduação em Genética e Biologia Molecular, PPGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Rio Grande do Sul, Brazil
- CESUCA - Faculdade Inedi, Cachoeirinha 94935-630, Rio Grande do Sul, Brazil
| | - Larissa Brussa Reis
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil; (T.W.K.); (L.B.R.); (T.F.A.); (P.A.-P.)
- Programa de Pós-Graduação em Genética e Biologia Molecular, PPGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Rio Grande do Sul, Brazil
| | - Tiago Finger Andreis
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil; (T.W.K.); (L.B.R.); (T.F.A.); (P.A.-P.)
- Programa de Pós-Graduação em Genética e Biologia Molecular, PPGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Rio Grande do Sul, Brazil
| | - Patricia Ashton-Prolla
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil; (T.W.K.); (L.B.R.); (T.F.A.); (P.A.-P.)
- Programa de Pós-Graduação em Genética e Biologia Molecular, PPGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Rio Grande do Sul, Brazil
- Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil
| | - Clévia Rosset
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil; (T.W.K.); (L.B.R.); (T.F.A.); (P.A.-P.)
- Unidade de Pesquisa Laboratorial, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil
- Correspondence: ; Tel.: +55-51-3359-7661
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Rodriguez FJ, Graham MK, Brosnan-Cashman JA, Barber JR, Davis C, Vizcaino MA, Palsgrove DN, Giannini C, Pekmezci M, Dahiya S, Gokden M, Noë M, Wood LD, Pratilas CA, Morris CD, Belzberg A, Blakeley J, Heaphy CM. Telomere alterations in neurofibromatosis type 1-associated solid tumors. Acta Neuropathol Commun 2019; 7:139. [PMID: 31462295 PMCID: PMC6712691 DOI: 10.1186/s40478-019-0792-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/19/2019] [Indexed: 12/29/2022] Open
Abstract
The presence of Alternative lengthening of telomeres (ALT) and/or ATRX loss, as well as the role of other telomere abnormalities, have not been formally studied across the spectrum of NF1-associated solid tumors. Utilizing a telomere-specific FISH assay, we classified tumors as either ALT-positive or having long (without ALT), short, or normal telomere lengths. A total of 426 tumors from 256 NF1 patients were evaluated, as well as 99 MPNST tumor samples that were sporadic or of unknown NF1 status. In the NF1-glioma dataset, ALT was present in the majority of high-grade gliomas: 14 (of 23; 60%) in contrast to only 9 (of 47; 19%) low-grade gliomas (p = 0.0009). In the subset of ALT-negative glioma cases, telomere lengths were estimated and we observed 17 (57%) cases with normal, 12 (40%) cases with abnormally long, and only 1 (3%) case with short telomeres. In the NF1-associated malignant nerve sheath tumor (NF1-MPNST) set (n = 75), ALT was present in 9 (12%). In the subset of ALT-negative NF1-MPNST cases, telomeres were short in 9 (38%), normal in 14 (58%) and long in 1 (3%). In the glioma set, overall survival was significantly decreased for patients with ALT-positive tumors (p < 0.0001). In the NF1-MPNST group, overall survival was superior for patients with tumors with short telomeres (p = 0.003). ALT occurs in a subset of NF1-associated solid tumors and is usually restricted to malignant subsets. In contrast, alterations in telomere lengths are more prevalent than ALT.
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Affiliation(s)
- Fausto J Rodriguez
- Departments of Pathology, Johns Hopkins University School of Medicine, Sheikh Zayed Tower, Room M2101, 1800 Orleans Street, Baltimore, MD, 21231, USA.
- Departments of Ophthalmology, Johns Hopkins University School of Medicine, Sheikh Zayed Tower, Room M2101, 1800 Orleans Street, Baltimore, MD, 21231, USA.
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Sheikh Zayed Tower, Room M2101, 1800 Orleans Street, Baltimore, MD, 21231, USA.
| | - Mindy K Graham
- Departments of Pathology, Johns Hopkins University School of Medicine, Sheikh Zayed Tower, Room M2101, 1800 Orleans Street, Baltimore, MD, 21231, USA
| | - Jacqueline A Brosnan-Cashman
- Departments of Pathology, Johns Hopkins University School of Medicine, Sheikh Zayed Tower, Room M2101, 1800 Orleans Street, Baltimore, MD, 21231, USA
| | - John R Barber
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Christine Davis
- Departments of Pathology, Johns Hopkins University School of Medicine, Sheikh Zayed Tower, Room M2101, 1800 Orleans Street, Baltimore, MD, 21231, USA
| | - M Adelita Vizcaino
- Departments of Pathology, Johns Hopkins University School of Medicine, Sheikh Zayed Tower, Room M2101, 1800 Orleans Street, Baltimore, MD, 21231, USA
| | - Doreen N Palsgrove
- Departments of Pathology, Johns Hopkins University School of Medicine, Sheikh Zayed Tower, Room M2101, 1800 Orleans Street, Baltimore, MD, 21231, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Sheikh Zayed Tower, Room M2101, 1800 Orleans Street, Baltimore, MD, 21231, USA
| | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Melike Pekmezci
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Sonika Dahiya
- Department of Pathology and Immunology, Washington University, St. Louis, MO, USA
| | | | - Michael Noë
- Departments of Pathology, Johns Hopkins University School of Medicine, Sheikh Zayed Tower, Room M2101, 1800 Orleans Street, Baltimore, MD, 21231, USA
| | - Laura D Wood
- Departments of Pathology, Johns Hopkins University School of Medicine, Sheikh Zayed Tower, Room M2101, 1800 Orleans Street, Baltimore, MD, 21231, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Sheikh Zayed Tower, Room M2101, 1800 Orleans Street, Baltimore, MD, 21231, USA
| | - Christine A Pratilas
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Sheikh Zayed Tower, Room M2101, 1800 Orleans Street, Baltimore, MD, 21231, USA
| | - Carol D Morris
- Department of Orthopedics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Allan Belzberg
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jaishri Blakeley
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Sheikh Zayed Tower, Room M2101, 1800 Orleans Street, Baltimore, MD, 21231, USA
- Departments of Neurology, Johns Hopkins University School of Medicine, Sheikh Zayed Tower, Room M2101, 1800 Orleans Street, Baltimore, MD, 21231, USA
| | - Christopher M Heaphy
- Departments of Pathology, Johns Hopkins University School of Medicine, Sheikh Zayed Tower, Room M2101, 1800 Orleans Street, Baltimore, MD, 21231, USA
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Abstract
INTRODUCTION Neurofibromatosis type 1 (NF1) is an autosomal dominantly inherited tumor predisposition syndrome with an incidence of one in 3000-4000 individuals with no currently effective therapies. The NF1 gene encodes neurofibromin, which functions as a negative regulator of RAS. NF1 is a chronic multisystem disorder affecting many different tissues. Due to cell-specific complexities of RAS signaling, therapeutic approaches for NF1 will likely have to focus on a particular tissue and manifestation of the disease. Areas covered: We discuss the multisystem nature of NF1 and the signaling pathways affected due to neurofibromin deficiency. We explore the cell-/tissue-specific molecular and cellular consequences of aberrant RAS signaling in NF1 and speculate on their potential as therapeutic targets for the disease. We discuss recent genomic, transcriptomic, and proteomic studies combined with molecular, cellular, and biochemical analyses which have identified several targets for specific NF1 manifestations. We also consider the possibility of patient-specific gene therapy approaches for NF1. Expert opinion: The emergence of NF1 genotype-phenotype correlations, characterization of cell-specific signaling pathways affected in NF1, identification of novel biomarkers, and the development of sophisticated animal models accurately reflecting human pathology will continue to provide opportunities to develop therapeutic approaches to combat this multisystem disorder.
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Affiliation(s)
- James A Walker
- a Center for Genomic Medicine , Massachusetts General Hospital, Harvard Medical School , Boston , MA , USA
| | - Meena Upadhyaya
- b Division of Cancer and Genetics , Cardiff University , Cardiff , UK
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Sharafi P, Ayter S. Possible modifier genes in the variation of neurofibromatosis type 1 clinical phenotypes. J Neurogenet 2018; 32:65-77. [PMID: 29644913 DOI: 10.1080/01677063.2018.1456538] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Neurofibromatosis type 1 (NF1) is the most common neurogenetic disorder worldwide, caused by mutations in the (NF1) gene. Although NF1 is a single-gene disorder with autosomal-dominant inheritance, its clinical expression is highly variable and unpredictable. NF1 patients have the highest known mutation rate among all human disorders, with no clear genotype-phenotype correlations. Therefore, variations in NF1 mutations may not correlate with the variations in clinical phenotype. Indeed, for the same mutation, some NF1 patients may develop severe clinical symptoms whereas others will develop a mild phenotype. Variations in the mutant NF1 allele itself cannot account for all of the disease variability, indicating a contribution of modifier genes, environmental factors, or their combination. Considering the gene structure and the interaction of neurofibromin protein with cellular components, there are many possible candidate modifier genes. This review aims to provide an overview of the potential modifier genes contributing to NF1 clinical variability.
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Affiliation(s)
- Parisa Sharafi
- a Faculty of Medicine , TOBB University of Economics and Technology , Ankara , Turkey
| | - Sükriye Ayter
- a Faculty of Medicine , TOBB University of Economics and Technology , Ankara , Turkey
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