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Chen Y, Fu Y, Koczkowska M, Callens T, Gomes A, Liu J, Bradley W, Brown B, Shaw B, D’Agostino D, Fu C, Wallis D. Genotype-Phenotype Correlation in Neurofibromatosis Type 1: Evidence for a Mild Phenotype Associated with Splicing Variants Leading to In-Frame Skipping of NF1 Exon 24 [19a]. Cancers (Basel) 2024; 16:2406. [PMID: 39001468 PMCID: PMC11240586 DOI: 10.3390/cancers16132406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024] Open
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant neurocutaneous disorder caused by loss-of-function variants in the NF1 gene. As of 20 November 2023, over 5000 distinct pathogenic or likely pathogenic variants have been reported in public databases. However, only a few NF1 genotype-phenotype correlations have been established so far. In this study, we present findings on 40 individuals with NF1, comprising 26 unrelated probands and 14 affected relatives, who carry one of nine NF1 heterozygous pathogenic splicing variants, all of which result in the in-frame skipping of exon 24 [19a] (NM_000267.3:r.3114_3197del, p.Asn1039_Arg1066del). These variants include c.3114-2A>G, c.3114-1G>A, c.3196A>G, c.3197G>A, c.3197G>T, c.3197+1G>A, c.3197+1G>T, c.3197+2T>C, and c.3197+3A>T. Among individuals with these variants, none exhibit externally visible plexiform neurofibromas, histopathologically confirmed cutaneous or subcutaneous neurofibromas, symptomatic spinal neurofibromas, or symptomatic optic pathway gliomas. The most prevalent, and sometimes sole, clinical feature observed in this cohort is multiple café-au-lait macules, with or without skinfold freckles: 85% and 60.5% of the individuals display six or more café-au-lait macules and freckles, respectively. In comparison to established NF1 genotype-phenotype correlations, these patients demonstrate highly similar clinical presentations to those associated with the NF1 pathogenic variant c.2970_2972del (p.Met992del), known for resulting in the mildest clinical features. Despite the generally mild phenotype, cognitive impairment, developmental delay, and/or learning difficulties are still observed in 33.3% of these patients, suggesting that learning challenges remain a prominent aspect of the phenotypic presentation in these individuals and necessitate specialized care. This newly established genotype-phenotype correlation will assist clinicians in improving the management of patients harboring NF1 exon 24 [19a] skipping variants and provide a new therapeutic target for NF1 treatment.
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Affiliation(s)
- Yunjia Chen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.K.); (T.C.); (A.G.); (J.L.); (W.B.); (B.B.); (B.S.); (C.F.); (D.W.)
| | - Yulong Fu
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.K.); (T.C.); (A.G.); (J.L.); (W.B.); (B.B.); (B.S.); (C.F.); (D.W.)
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Magdalena Koczkowska
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.K.); (T.C.); (A.G.); (J.L.); (W.B.); (B.B.); (B.S.); (C.F.); (D.W.)
- 3P-Medicine Laboratory, Medical University of Gdansk, 80-211 Gdansk, Poland
| | - Tom Callens
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.K.); (T.C.); (A.G.); (J.L.); (W.B.); (B.B.); (B.S.); (C.F.); (D.W.)
| | - Alicia Gomes
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.K.); (T.C.); (A.G.); (J.L.); (W.B.); (B.B.); (B.S.); (C.F.); (D.W.)
| | - Jian Liu
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.K.); (T.C.); (A.G.); (J.L.); (W.B.); (B.B.); (B.S.); (C.F.); (D.W.)
| | - William Bradley
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.K.); (T.C.); (A.G.); (J.L.); (W.B.); (B.B.); (B.S.); (C.F.); (D.W.)
| | - Bryce Brown
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.K.); (T.C.); (A.G.); (J.L.); (W.B.); (B.B.); (B.S.); (C.F.); (D.W.)
| | - Brandon Shaw
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.K.); (T.C.); (A.G.); (J.L.); (W.B.); (B.B.); (B.S.); (C.F.); (D.W.)
| | - Daniela D’Agostino
- Division of Medical Genetics, Departments of Medicine and Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada;
| | - Chuanhua Fu
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.K.); (T.C.); (A.G.); (J.L.); (W.B.); (B.B.); (B.S.); (C.F.); (D.W.)
| | - Deeann Wallis
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.K.); (T.C.); (A.G.); (J.L.); (W.B.); (B.B.); (B.S.); (C.F.); (D.W.)
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Functional Assays Combined with Pre-mRNA-Splicing Analysis Improve Variant Classification and Diagnostics for Individuals with Neurofibromatosis Type 1 and Legius Syndrome. Hum Mutat 2023. [DOI: 10.1155/2023/9628049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Neurofibromatosis type 1 (NF1) and Legius syndrome (LS) are caused by inactivating variants in NF1 and SPRED1. NF1 encodes neurofibromin (NF), a GTPase-activating protein (GAP) for RAS that interacts with the SPRED1 product, Sprouty-related protein with an EVH (Ena/Vasp homology) domain 1 (SPRED1). Obtaining a clinical and molecular diagnosis of NF1 or LS can be challenging due to the phenotypic diversity, the size and complexity of the NF1 and SPRED1 loci, and uncertainty over the effects of some NF1 and SPRED1 variants on pre-mRNA splicing and/or protein expression and function. To improve NF1 and SPRED1 variant classification and establish pathogenicity for NF1 and SPRED1 variants identified in individuals with NF1 or LS, we analyzed patient RNA by RT-PCR and performed in vitro exon trap experiments and estimated NF and SPRED1 protein expression, RAS GAP activity, and interaction. We obtained evidence to support pathogenicity according to American College of Medical Genetics guidelines for 73/114 variants tested, demonstrating the utility of functional approaches for NF1 and SPRED1 variant classification and NF and LS diagnostics.
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Identification of Germinal Neurofibromin Hotspots. Biomedicines 2022; 10:biomedicines10082044. [PMID: 36009591 PMCID: PMC9405573 DOI: 10.3390/biomedicines10082044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/19/2022] [Indexed: 11/29/2022] Open
Abstract
Neurofibromin is engaged in many cellular processes and when the proper protein functioning is impaired, it causes neurofibromatosis type 1 (NF1), one of the most common inherited neurological disorders. Recent advances in sequencing and screening of the NF1 gene have increased the number of detected variants. However, the correlation of these variants with the clinic remains poorly understood. In this study, we analyzed 4610 germinal NF1 variants annotated in ClinVar and determined on exon level the mutational spectrum and potential pathogenic regions. Then, a binomial and sliding windows test using 783 benign and 938 pathogenic NF1 variants were analyzed against functional and structural regions of neurofibromin. The distribution of synonymous, missense, and frameshift variants are statistically significant in certain regions of neurofibromin suggesting that the type of variant and its associated phenotype may depend on protein disorder. Indeed, there is a negative correlation between the pathogenic fraction prediction and the disorder data, suggesting that the higher an intrinsically disordered region is, the lower the pathogenic fraction is and vice versa. Most pathogenic variants are associated to NF1 and our analysis suggests that GRD, CSRD, TBD, and Armadillo1 domains are hotspots in neurofibromin. Knowledge about NF1 genotype–phenotype correlations can provide prognostic guidance and aid in organ-specific surveillance.
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Leier A, Moore M, Liu H, Daniel M, Hyde AM, Messiaen L, Korf BR, Selvakumaran J, Ciszewski L, Lambert L, Foote J, Wallace MR, Kesterson RA, Dickson G, Popplewell L, Wallis D. Targeted exon skipping of NF1 exon 17 as a therapeutic for neurofibromatosis type I. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 28:261-278. [PMID: 35433111 PMCID: PMC8983316 DOI: 10.1016/j.omtn.2022.03.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/12/2022] [Indexed: 12/14/2022]
Abstract
We investigated the feasibility of utilizing an exon-skipping approach as a genotype-dependent therapeutic for neurofibromatosis type 1 (NF1) by determining which NF1 exons might be skipped while maintaining neurofibromin protein expression and GTPase activating protein (GAP)-related domain (GRD) function. Initial in silico analysis predicted exons that can be skipped with minimal loss of neurofibromin function, which was confirmed by in vitro assessments utilizing an Nf1 cDNA-based functional screening system. Skipping of exons 17 or 52 fit our criteria, as minimal effects on protein expression and GRD activity were noted. Antisense phosphorodiamidate morpholino oligomers (PMOs) were utilized to skip exon 17 in human cell lines with patient-specific pathogenic variants in exon 17, c.1885G>A, and c.1929delG. PMOs restored functional neurofibromin expression. To determine the in vivo significance of exon 17 skipping, we generated a homozygous deletion of exon 17 in a novel mouse model. Mice were viable and exhibited a normal lifespan. Initial studies did not reveal the presence of tumor development; however, altered nesting behavior and systemic lymphoid hyperplasia was noted in peripheral lymphoid organs. Alterations in T and B cell frequencies in the thymus and spleen were identified. Hence, exon skipping should be further investigated as a therapeutic approach for NF1 patients with pathogenic variants in exon 17, as homozygous deletion of exon 17 is consistent with at least partial function of neurofibromin.
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Affiliation(s)
- André Leier
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Marc Moore
- Centre of Biomedical Science, Department of Biological Sciences, Royal Holloway - University of London, Egham, Surrey TW20 0EX, UK
| | - Hui Liu
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Michael Daniel
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Alexis M. Hyde
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ludwine Messiaen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Bruce R. Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jamuna Selvakumaran
- Centre of Biomedical Science, Department of Biological Sciences, Royal Holloway - University of London, Egham, Surrey TW20 0EX, UK
| | - Lukasz Ciszewski
- Centre of Biomedical Science, Department of Biological Sciences, Royal Holloway - University of London, Egham, Surrey TW20 0EX, UK
| | - Laura Lambert
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jeremy Foote
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Margaret R. Wallace
- Department of Molecular Genetics and Microbiology, and UF Health Cancer Center, University of Florida, Gainesville, FL 32611, USA
| | - Robert A. Kesterson
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - George Dickson
- Centre of Biomedical Science, Department of Biological Sciences, Royal Holloway - University of London, Egham, Surrey TW20 0EX, UK
| | - Linda Popplewell
- Centre of Biomedical Science, Department of Biological Sciences, Royal Holloway - University of London, Egham, Surrey TW20 0EX, UK
| | - Deeann Wallis
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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5
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Awad EK, Moore M, Liu H, Ciszewski L, Lambert L, Korf BR, Popplewell L, Kesterson RA, Wallis D. Restoration of Normal NF1 Function with Antisense Morpholino Treatment of Recurrent Pathogenic Patient-Specific Variant c.1466A>G; p.Y489C. J Pers Med 2021; 11:jpm11121320. [PMID: 34945792 PMCID: PMC8705852 DOI: 10.3390/jpm11121320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/04/2021] [Accepted: 11/19/2021] [Indexed: 12/11/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant genetic disorder with almost 3000 different disease-causing variants within the NF1 gene identified. Up to 44% of these variants cause splicing errors to occur within pre-mRNA. A recurrent variant in exon 13, c.1466A>G; p.Y489C (Y489C) results in the creation of an intragenic cryptic splice site, aberrant splicing, a 62 base pair deletion from the mRNA, and subsequent frameshift. We investigated the ability of phosphorodiamidate morpholino oligomers (PMOs) to mask this variant on the RNA level, thus restoring normal splicing. To model this variant, we have developed a human iPS cell line homozygous for the variant using CRISPR/Cas9. PMOs were designed to be 25 base pairs long, and to cover the mutation site so it could not be read by splicing machinery. Results from our in vitro testing showed restoration of normal splicing in the RNA and restoration of full length neurofibromin protein. In addition, we observe the restoration of neurofibromin functionality through GTP-Ras and pERK/ERK testing. The results from this study demonstrate the ability of a PMO to correct splicing errors in NF1 variants at the RNA level, which could open the door for splicing corrections for other variants in this and a variety of diseases.
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Affiliation(s)
- Elias K. Awad
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (E.K.A.); (H.L.); (L.L.); (B.R.K.); (R.A.K.)
| | - Marc Moore
- Centre of Biomedical Sciences, Department of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK; (M.M.); (L.C.); (L.P.)
| | - Hui Liu
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (E.K.A.); (H.L.); (L.L.); (B.R.K.); (R.A.K.)
| | - Lukasz Ciszewski
- Centre of Biomedical Sciences, Department of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK; (M.M.); (L.C.); (L.P.)
| | - Laura Lambert
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (E.K.A.); (H.L.); (L.L.); (B.R.K.); (R.A.K.)
| | - Bruce R. Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (E.K.A.); (H.L.); (L.L.); (B.R.K.); (R.A.K.)
| | - Linda Popplewell
- Centre of Biomedical Sciences, Department of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK; (M.M.); (L.C.); (L.P.)
| | - Robert A. Kesterson
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (E.K.A.); (H.L.); (L.L.); (B.R.K.); (R.A.K.)
| | - Deeann Wallis
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (E.K.A.); (H.L.); (L.L.); (B.R.K.); (R.A.K.)
- Correspondence: ; Tel.: +1-205-934-2794; Fax: +1-205-975-4418
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6
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Long A, Liu H, Liu J, Daniel M, Bedwell DM, Korf B, Kesterson RA, Wallis D. Analysis of patient-specific NF1 variants leads to functional insights for Ras signaling that can impact personalized medicine. Hum Mutat 2021; 43:30-41. [PMID: 34694046 DOI: 10.1002/humu.24290] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 01/04/2023]
Abstract
We have created a panel of 29 NF1 variant complementary DNAs (cDNAs) representing missense variants, many with clinically relevant phenotypes, in-frame deletions, splice variants, and nonsense variants. We have determined the functional consequences of the variants, assessing their ability to produce mature neurofibromin and restore Ras signaling activity in NF1 null (-/-) cells. cDNAs demonstrate variant-specific differences in neurofibromin protein levels, suggesting that some variants lead to neurofibromatosis type 1 (NF1) gene or protein instability or enhanced degradation. When expressed at high levels, some variant proteins are still able to repress Ras activity, indicating that the NF1 phenotype may be due to low protein abundance. In contrast, other variant proteins are incapable of repressing Ras activity, indicating that some do not functionally engage Ras and stimulate GTPase activity. We observed that effects on protein abundance and Ras activity can be mutually exclusive. These assays allow us to categorize variants by functional effects, may help to classify variants of unknown significance, and may have future implications for more directed therapeutics.
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Affiliation(s)
- Ashlee Long
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Hui Liu
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jian Liu
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Michael Daniel
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - David M Bedwell
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Bruce Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Robert A Kesterson
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Deeann Wallis
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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7
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Bergoug M, Doudeau M, Godin F, Mosrin C, Vallée B, Bénédetti H. Neurofibromin Structure, Functions and Regulation. Cells 2020; 9:cells9112365. [PMID: 33121128 PMCID: PMC7692384 DOI: 10.3390/cells9112365] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 12/13/2022] Open
Abstract
Neurofibromin is a large and multifunctional protein encoded by the tumor suppressor gene NF1, mutations of which cause the tumor predisposition syndrome neurofibromatosis type 1 (NF1). Over the last three decades, studies of neurofibromin structure, interacting partners, and functions have shown that it is involved in several cell signaling pathways, including the Ras/MAPK, Akt/mTOR, ROCK/LIMK/cofilin, and cAMP/PKA pathways, and regulates many fundamental cellular processes, such as proliferation and migration, cytoskeletal dynamics, neurite outgrowth, dendritic-spine density, and dopamine levels. The crystallographic structure has been resolved for two of its functional domains, GRD (GAP-related (GTPase-activating protein) domain) and SecPH, and its post-translational modifications studied, showing it to be localized to several cell compartments. These findings have been of particular interest in the identification of many therapeutic targets and in the proposal of various therapeutic strategies to treat the symptoms of NF1. In this review, we provide an overview of the literature on neurofibromin structure, function, interactions, and regulation and highlight the relationships between them.
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Brosseau JP, Liao CP, Le LQ. Translating current basic research into future therapies for neurofibromatosis type 1. Br J Cancer 2020; 123:178-186. [PMID: 32439933 PMCID: PMC7374719 DOI: 10.1038/s41416-020-0903-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 03/25/2020] [Accepted: 05/01/2020] [Indexed: 12/12/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is a hereditary tumour syndrome that predisposes to benign and malignant tumours originating from neural crest cells. Biallelic inactivation of the tumour-suppressor gene NF1 in glial cells in the skin, along a nerve plexus or in the brain results in the development of benign tumours: cutaneous neurofibroma, plexiform neurofibroma and glioma, respectively. Despite more than 40 years of research, only one medication was recently approved for treatment of plexiform neurofibroma and no drugs have been specifically approved for the management of other tumours. Work carried out over the past several years indicates that inhibiting different cellular signalling pathways (such as Hippo, Janus kinase/signal transducer and activator of transcription, mitogen-activated protein kinase and those mediated by sex hormones) in tumour cells or targeting cells in the microenvironment (nerve cells, macrophages, mast cells and T cells) might benefit NF1 patients. In this review, we outline previous strategies aimed at targeting these signalling pathways or cells in the microenvironment, agents that are currently in clinical trials, and the latest advances in basic research that could culminate in the development of novel therapeutics for patients with NF1.
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Affiliation(s)
- Jean-Philippe Brosseau
- Department of Dermatology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390-9069, USA.
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada.
| | - Chung-Ping Liao
- 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.
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9
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Leier A, Bedwell DM, Chen AT, Dickson G, Keeling KM, Kesterson RA, Korf BR, Marquez Lago TT, Müller UF, Popplewell L, Zhou J, Wallis D. Mutation-Directed Therapeutics for Neurofibromatosis Type I. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 20:739-753. [PMID: 32408052 PMCID: PMC7225739 DOI: 10.1016/j.omtn.2020.04.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/20/2020] [Accepted: 04/23/2020] [Indexed: 02/07/2023]
Abstract
Significant advances in biotechnology have led to the development of a number of different mutation-directed therapies. Some of these techniques have matured to a level that has allowed testing in clinical trials, but few have made it to approval by drug-regulatory bodies for the treatment of specific diseases. While there are still various hurdles to be overcome, recent success stories have proven the potential power of mutation-directed therapies and have fueled the hope of finding therapeutics for other genetic disorders. In this review, we summarize the state-of-the-art of various therapeutic approaches and assess their applicability to the genetic disorder neurofibromatosis type I (NF1). NF1 is caused by the loss of function of neurofibromin, a tumor suppressor and downregulator of the Ras signaling pathway. The condition is characterized by a variety of phenotypes and includes symptoms such as skin spots, nervous system tumors, skeletal dysplasia, and others. Hence, depending on the patient, therapeutics may need to target different tissues and cell types. While we also discuss the delivery of therapeutics, in particular via viral vectors and nanoparticles, our main focus is on therapeutic techniques that reconstitute functional neurofibromin, most notably cDNA replacement, CRISPR-based DNA repair, RNA repair, antisense oligonucleotide therapeutics including exon skipping, and nonsense suppression.
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Affiliation(s)
- Andre Leier
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David M Bedwell
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ann T Chen
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
| | - George Dickson
- Centre of Biomedical Sciences, Department of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - Kim M Keeling
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Robert A Kesterson
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Ulrich F Müller
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Linda Popplewell
- Centre of Biomedical Sciences, Department of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - Jiangbing Zhou
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
| | - Deeann Wallis
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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10
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Optic Pathway Glioma in Type 1 Neurofibromatosis: Review of Its Pathogenesis, Diagnostic Assessment, and Treatment Recommendations. Cancers (Basel) 2019; 11:cancers11111790. [PMID: 31739524 PMCID: PMC6896195 DOI: 10.3390/cancers11111790] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/12/2019] [Accepted: 11/12/2019] [Indexed: 12/13/2022] Open
Abstract
Type 1 neurofibromatosis (NF1) is a dominantly inherited condition predisposing to tumor development. Optic pathway glioma (OPG) is the most frequent central nervous system tumor in children with NF1, affecting approximately 15-20% of patients. The lack of well-established prognostic markers and the wide clinical variability with respect to tumor progression and visual outcome make the clinical management of these tumors challenging, with significant differences among distinct centers. We reviewed published articles on OPG diagnostic protocol, follow-up and treatment in NF1. Cohorts of NF1 children with OPG reported in the literature and patients prospectively collected in our center were analyzed with regard to clinical data, tumor anatomical site, diagnostic workflow, treatment and outcome. In addition, we discussed the recent findings on the pathophysiology of OPG development in NF1. This review provides a comprehensive overview about the clinical management of NF1-associated OPG, focusing on the most recent advances from preclinical studies with genetically engineered models and the ongoing clinical trials.
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11
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Affinity Purification of NF1 Protein-Protein Interactors Identifies Keratins and Neurofibromin Itself as Binding Partners. Genes (Basel) 2019; 10:genes10090650. [PMID: 31466283 PMCID: PMC6770187 DOI: 10.3390/genes10090650] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/09/2019] [Accepted: 08/19/2019] [Indexed: 12/23/2022] Open
Abstract
Neurofibromatosis Type 1 (NF1) is caused by pathogenic variants in the NF1 gene encoding neurofibromin. Definition of NF1 protein–protein interactions (PPIs) has been difficult and lacks replication, making it challenging to define binding partners that modulate its function. We created a novel tandem affinity purification (TAP) tag cloned in frame to the 3’ end of the full-length murine Nf1 cDNA (mNf1). We show that this cDNA is functional and expresses neurofibromin, His-Tag, and can correct p-ERK/ERK ratios in NF1 null HEK293 cells. We used this affinity tag to purify binding partners with Strep-Tactin®XT beads and subsequently, identified them via mass spectrometry (MS). We found the tagged mNf1 can affinity purify human neurofibromin and vice versa, indicating that neurofibromin oligomerizes. We identify 21 additional proteins with high confidence of interaction with neurofibromin. After Metacore network analysis of these 21 proteins, eight appear within the same network, primarily keratins regulated by estrogen receptors. Previously, we have shown that neurofibromin levels negatively regulate keratin expression. Here, we show through pharmacological inhibition that this is independent of Ras signaling, as the inhibitors, selumetinib and rapamycin, do not alter keratin expression. Further characterization of neurofibromin oligomerization and binding partners could aid in discovering new neurofibromin functions outside of Ras regulation, leading to novel drug targets.
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Carnes RM, Mobley JA, Crossman DK, Liu H, Korf BR, Kesterson RA, Wallis D. Multi-Omics Profiling for NF1 Target Discovery in Neurofibromin (NF1) Deficient Cells. Proteomics 2019; 19:e1800334. [PMID: 30908848 DOI: 10.1002/pmic.201800334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 02/27/2019] [Indexed: 01/07/2023]
Abstract
Loss of NF1 is an oncogenic driver. In efforts to define pathways responsible for the development of neurofibromas and other cancers, transcriptomic and proteomic changes are evaluated in a non-malignant NF1 null cell line. NF1 null HEK293 cells were created using CRISPR/Cas9 technology and they are compared to parental cells that express neurofibromin. A total of 1222 genes and 132 proteins are found to be differentially expressed. The analysis is integrated to identify eight transcripts/proteins that are differentially regulated in both analyses. Metacore Pathway analysis identifies Neurogenesis NGF/TrkA MAPK-mediated signaling alterations. Next, the data set is compared with other published studies that involve analysis of cells or tumors deficient for NF1 and it is found that 141 genes recur in the sample and others; only thirteen of these genes recur in two or more studies. Genes/proteins of interest are validated via q-RT-PCR or Western blot. It is shown that KRT8 and 14-3-3σ protein levels respond to exogenously introduced mNf1 cDNA. Hence, transcripts/proteins that respond to neurofibromin levels are identified and they can potentially be used as biomarkers.
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Affiliation(s)
- Rachel M Carnes
- Department of Genetics, University of Alabama at Birmingham, 35294, Birmingham, AL, USA
| | - James A Mobley
- Department of Surgery, University of Alabama at Birmingham, 35294, Birmingham, AL, USA
| | - David K Crossman
- Department of Genetics, University of Alabama at Birmingham, 35294, Birmingham, AL, USA
| | - Hui Liu
- Department of Genetics, University of Alabama at Birmingham, 35294, Birmingham, AL, USA
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, 35294, Birmingham, AL, USA
| | - Robert A Kesterson
- Department of Genetics, University of Alabama at Birmingham, 35294, Birmingham, AL, USA
| | - Deeann Wallis
- Department of Genetics, University of Alabama at Birmingham, 35294, Birmingham, AL, USA
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Ferner RE, Bakker A, Elgersma Y, Evans DGR, Giovannini M, Legius E, Lloyd A, Messiaen LM, Plotkin S, Reilly KM, Schindeler A, Smith MJ, Ullrich NJ, Widemann B, Sherman LS. From process to progress-2017 International Conference on Neurofibromatosis 1, Neurofibromatosis 2 and Schwannomatosis. Am J Med Genet A 2019; 179:1098-1106. [PMID: 30908866 DOI: 10.1002/ajmg.a.61112] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 02/09/2019] [Indexed: 12/19/2022]
Abstract
The neurofibromatoses are inherited, tumor suppressor disorders that are characterized by multiple, benign peripheral nerve sheath tumors and other nervous system tumors. Each disease is associated with a distinct genetic mutation and with a different pathogenesis and clinical course. Neurofibromatosis 1 (NF1) is common and epitomized by multiple neurofibromas with widespread complications. NF2 and schwannomatosis are rare diseases that are typified by multiple schwannomas that are particularly painful in people with schwannomatosis. Since 1985, the Children's Tumor Foundation (formerly the National Neurofibromatosis Foundation) has hosted an international Neurofibromatosis Conference, bringing together international participants who are focused on NF research and clinical care. The 2017 Conference, held in Washington, DC, was among the largest gatherings of NF researchers to date and included presentations from clinicians and basic scientists, highlighting new data regarding the molecular and cellular mechanisms underlying each of these diseases as well as results from clinical studies and clinical trials. This article summarizes the findings presented at the meeting and represents the current state-of-the art for NF research.
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Affiliation(s)
- Rosalie E Ferner
- Department of Neurology, Neurofibromatosis Centre, Guy's and St. Thomas' NHS Foundation Trust, and King's College London, London, UK
| | | | - Ype Elgersma
- Department of Neuroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - D Gareth R Evans
- Centre for Genomic Medicine, St. Mary's Hospital, Manchester, UK.,Manchester Academic Health Sciences Centre (MAHSC), Division of Evolution and Genomic Science, University of Manchester, Manchester, UK
| | - Marco Giovannini
- Department of Head and Neck Surgery, University of California, Los Angeles
| | - Eric Legius
- Department of Human Genetics, University Hospital Leuven, Leuven, Herestraat, Belgium
| | - Alison Lloyd
- Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Ludwine M Messiaen
- Medical Genomics Laboratory, Department of Genetics, University of Alabama, Birmingham, Alabama
| | - Scott Plotkin
- Department of Neurology and Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Karlyne M Reilly
- Rare Tumors Initiative, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland
| | - Aaron Schindeler
- Orthopaedic Research & Biotechnology, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Miriam J Smith
- Centre for Genomic Medicine, St. Mary's Hospital, Manchester, UK.,Manchester Academic Health Sciences Centre (MAHSC), Division of Evolution and Genomic Science, University of Manchester, Manchester, UK
| | - Nicole J Ullrich
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Brigitte Widemann
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Larry S Sherman
- Division of Neuroscience, Oregon National Primate Research Center, and Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
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Trevisson E, Morbidoni V, Forzan M, Daolio C, Fumini V, Parrozzani R, Cassina M, Midena E, Salviati L, Clementi M. The Arg1038Gly missense variant in the NF1 gene causes a mild phenotype without neurofibromas. Mol Genet Genomic Med 2019; 7:e616. [PMID: 30843352 PMCID: PMC6503065 DOI: 10.1002/mgg3.616] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/16/2019] [Accepted: 02/11/2019] [Indexed: 01/08/2023] Open
Abstract
Background Neurofibromatosis type 1 (NF1) is an autosomal dominant condition caused by inactivating mutations of the NF1 gene. The wide allelic heterogeneity of this condition, with more than 3,000 pathogenic variants reported so far, is paralleled by its high clinical variability, which is observed even within the same family. The definition of genotype–phenotype correlations has been hampered by the complexity of the NF1 gene and, although a few exceptions have been recognized, the clinical course remains unpredictable in most patients. Methods Sequencing of NF1 in patients with cafè‐au‐lait spots identified the c.3112A>G variant. RNA analysis and a minigene assay were employed to investigate splicing. Results Here we report a novel genotype–phenotype correlation in NF1: the identification of the missense variant NM_000267.3:c.3112A>G p.(Arg1038Gly) in seven individuals from two unrelated families with a mild phenotype. All the patients manifest cafè‐au‐lait spots without neurofibromas or other NF1–associated complications, and Noonan syndrome features in most cases. The missense variant was not previously reported in available databases, segregates with the phenotype and involves a highly conserved residue. Both a minigene assay and patient's RNA analysis excluded an effect on splicing. Conclusion Our data support the correlation of the p.Arg1038Gly missense substitution with the cutaneous phenotype without neurofibromas or other complications. This finding may have relevant implications for patients and genetic counseling, but also to get insights into the function of neurofibromin.
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Affiliation(s)
- Eva Trevisson
- Department of Women's and Children's Health, Clinical Genetics Unit, University of Padova, Padova, Italy.,Laboratorio di Genetica Clinica ed Epidemiologica, Istituto di Ricerca Pediatrica, IRP, Padova, Italy
| | - Valeria Morbidoni
- Department of Women's and Children's Health, Clinical Genetics Unit, University of Padova, Padova, Italy.,Laboratorio di Genetica Clinica ed Epidemiologica, Istituto di Ricerca Pediatrica, IRP, Padova, Italy
| | - Monica Forzan
- Department of Women's and Children's Health, Clinical Genetics Unit, University of Padova, Padova, Italy.,Laboratorio di Genetica Clinica ed Epidemiologica, Istituto di Ricerca Pediatrica, IRP, Padova, Italy
| | | | - Valentina Fumini
- Department of Women's and Children's Health, Clinical Genetics Unit, University of Padova, Padova, Italy
| | | | - Matteo Cassina
- Department of Women's and Children's Health, Clinical Genetics Unit, University of Padova, Padova, Italy
| | - Edoardo Midena
- Department of Neurosciences, University of Padova, Padova, Italy.,IRCCS-Fondazione Bietti, Rome, Italy
| | - Leonardo Salviati
- Department of Women's and Children's Health, Clinical Genetics Unit, University of Padova, Padova, Italy.,Laboratorio di Genetica Clinica ed Epidemiologica, Istituto di Ricerca Pediatrica, IRP, Padova, Italy
| | - Maurizio Clementi
- Department of Women's and Children's Health, Clinical Genetics Unit, University of Padova, Padova, Italy.,Laboratorio di Genetica Clinica ed Epidemiologica, Istituto di Ricerca Pediatrica, IRP, Padova, Italy
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Cui Y, Morrison H. Construction of cloning-friendly minigenes for mammalian expression of full-length human NF1 isoforms. Hum Mutat 2018; 40:187-192. [DOI: 10.1002/humu.23681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/23/2018] [Accepted: 11/06/2018] [Indexed: 01/17/2023]
Affiliation(s)
- Yan Cui
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI); Jena Germany
| | - Helen Morrison
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI); Jena Germany
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Isakov O, Wallis D, Evans DG, Ben-Shachar S. Exhaustive non-synonymous variants functionality prediction enables high resolution characterization of the neurofibromin architecture. EBioMedicine 2018; 36:508-516. [PMID: 30274822 PMCID: PMC6197713 DOI: 10.1016/j.ebiom.2018.09.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/11/2018] [Accepted: 09/21/2018] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Neurofibromatosis type I (NF1) is caused by heterozygous loss-of-function variants in the NF1 gene encoding neurofibromin which serves as a tumor suppressor that inhibits RAS signaling and regulates cell proliferation and differentiation. While, the only well-established functional domain in the NF1 protein is the GAP-related domain (GRD), most of the identified non-truncating disease-causing variants are located outside of this domain, supporting the existence of other important disease-associated domains. Identifying these domains may reveal novel functions of NF1. METHODS By implementing inferential statistics combined with machine-learning methods, we developed a novel NF1-specific functional prediction model that focuses on nonsynonymous single nucleotide variants (SNVs). The model enables annotating all possible NF1 nonsynonymous variants, thus mapping the range of pathogenic non-truncating variants at the codon level across the NF1 gene. FINDINGS The generated model demonstrates high absolute prediction value for missense and splice-site variations (area under the ROC curve of 0.96) outperforming 14 other established models. By reviewing the entire dataset of nonsynonymous variants, two novel domains (Armadillo type fold 1 and 2) were identified as being associated with pathogenicity (OR 1.86; CI 1.04 to 3.34 and OR 2.08; CI 1.08 to 4.04, respectively; P < .05). Specific exons and codons associated with increased pathogenicity were also detected along the gene inside and outside the GRD domain. INTERPRETATION The developed model, enabled better prediction of pathogenicity for variants in NF1 gene, as well as elucidation of novel NF1-associated domains in addition to the GRD. FUND: This work was partially supported by the Kahn foundation. DGE is supported by the all Manchester NIHR Biomedical Research Centre (IS-brC-1215-20007).
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Affiliation(s)
- Ofer Isakov
- Department of Internal Medicine "T", Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Deeann Wallis
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States.
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Science, University of Manchester, Manchester University Hospitals NHS Foundation Trust, Manchester, UK.
| | - Shay Ben-Shachar
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Gilbert Israeli Neurofibromatosis Center, Tel-Aviv Medical Center, Tel-Aviv, Israel.
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