1
|
Miyagishima KJ, Qiao F, Stasheff SF, Nadal-Nicolás FM. Visual Deficits and Diagnostic and Therapeutic Strategies for Neurofibromatosis Type 1: Bridging Science and Patient-Centered Care. Vision (Basel) 2024; 8:31. [PMID: 38804352 PMCID: PMC11130890 DOI: 10.3390/vision8020031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/29/2024] Open
Abstract
Neurofibromatosis type 1 (NF1) is an inherited autosomal dominant disorder primarily affecting children and adolescents characterized by multisystemic clinical manifestations. Mutations in neurofibromin, the protein encoded by the Nf1 tumor suppressor gene, result in dysregulation of the RAS/MAPK pathway leading to uncontrolled cell growth and migration. Neurofibromin is highly expressed in several cell lineages including melanocytes, glial cells, neurons, and Schwann cells. Individuals with NF1 possess a genetic predisposition to central nervous system neoplasms, particularly gliomas affecting the visual pathway, known as optic pathway gliomas (OPGs). While OPGs are typically asymptomatic and benign, they can induce visual impairment in some patients. This review provides insight into the spectrum and visual outcomes of NF1, current diagnostic techniques and therapeutic interventions, and explores the influence of NF1-OPGS on visual abnormalities. We focus on recent advancements in preclinical animal models to elucidate the underlying mechanisms of NF1 pathology and therapies targeting NF1-OPGs. Overall, our review highlights the involvement of retinal ganglion cell dysfunction and degeneration in NF1 disease, and the need for further research to transform scientific laboratory discoveries to improved patient outcomes.
Collapse
Affiliation(s)
- Kiyoharu J. Miyagishima
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.J.M.); (F.Q.); (S.F.S.)
| | - Fengyu Qiao
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.J.M.); (F.Q.); (S.F.S.)
| | - Steven F. Stasheff
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.J.M.); (F.Q.); (S.F.S.)
- Center for Neuroscience and Behavioral Medicine, Gilbert Neurofibromatosis Institute, Children’s National Health System, Washington, DC 20010, USA
- Neurology Department, George Washington University School of Medicine, Washington, DC 20037, USA
| | - Francisco M. Nadal-Nicolás
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.J.M.); (F.Q.); (S.F.S.)
| |
Collapse
|
2
|
Fukunaga N, Hayashi T, Yamada Y, Mizobuchi K, Ohta A, Nakano T. A novel stop-gain NF1 variant in neurofibromatosis type 1 and bilateral optic atrophy without optic gliomas. Ophthalmic Genet 2024; 45:186-192. [PMID: 37599594 DOI: 10.1080/13816810.2023.2245464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/25/2023] [Accepted: 08/01/2023] [Indexed: 08/22/2023]
Abstract
BACKGROUND Neurofibromatosis type 1 (NF1) is a multisystem disorder that primarily affects the skin and peripheral nervous system and is caused by chromosomal abnormalities and mostly truncating variants in the NF1 gene. Ocular complications such as Lisch nodules and optic pathway gliomas (OPGs) can occur in NF1 patients. Herein, we report a novel NF1 variant in an NF1 patient with bilateral optic atrophy. METHODS Ophthalmological examinations and genetic analyses were performed using targeted next-generation sequencing (NGS). RESULTS A 14-year-old girl diagnosed with NF1 visited our hospital with decreased visual acuity (VA). The patient had no family history of NF1 or visual impairment. Brain and orbital magnetic resonance imaging revealed no remarkable findings. Ophthalmoscopy revealed temporal pallor of the optic discs, which was confirmed by optical coherence tomography findings of significant thinning of the circumpapillary retinal nerve fiber layer in both eyes. At 23 years of age, the decimal-corrected VA had deteriorated to 0.2 in the right eye and 0.1 in the left eye. Additionally, the targeted NGS panel revealed a novel heterozygous stop-gain variant (p.Tyr628Ter) in the NF1 gene; however, no pathogenic variants in OPA1 or the mitochondrial DNA were identified. CONCLUSIONS A patient with NF1 without OPGs developed bilateral optic atrophy and carried a novel de novo stop-gain variant of NF1. Although the relationship between NF1 variants and bilateral optic atrophy remains unclear, further investigations are required.
Collapse
Affiliation(s)
- Naoko Fukunaga
- Department of Ophthalmology, Katsushika Medical Center, The Jikei University School of Medicine, Tokyo, Japan
| | - Takaaki Hayashi
- Department of Ophthalmology, Katsushika Medical Center, The Jikei University School of Medicine, Tokyo, Japan
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
| | - Yuki Yamada
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
| | - Kei Mizobuchi
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
| | - Arihito Ohta
- Department of Dermatology, The Jikei University School of Medicine, Tokyo, Japan
| | - Tadashi Nakano
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
| |
Collapse
|
3
|
Na B, Shah S, Nghiemphu PL. Cancer Predisposition Syndromes in Neuro-oncology. Semin Neurol 2024; 44:16-25. [PMID: 38096910 DOI: 10.1055/s-0043-1777702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Although most primary central and peripheral nervous system (NS) tumors occur sporadically, there are a subset that may arise in the context of a cancer predisposition syndrome. These syndromes occur due to a pathogenic mutation in a gene that normally functions as a tumor suppressor. With increased understanding of the molecular pathogenesis of these tumors, more people have been identified with a cancer predisposition syndrome. Identification is crucial, as this informs surveillance, diagnosis, and treatment options. Moreover, relatives can also be identified through genetic testing. Although there are many cancer predisposition syndromes that increase the risk of NS tumors, in this review, we focus on three of the most common cancer predisposition syndromes, neurofibromatosis type 1, neurofibromatosis type 2, and tuberous sclerosis complex type 1 and type 2, emphasizing the clinical manifestations, surveillance guidelines, and treatment options.
Collapse
Affiliation(s)
- Brian Na
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, California
| | - Shilp Shah
- Department of Bioengineering, UCLA Samueli School of Engineering, Los Angeles, California
| | | |
Collapse
|
4
|
Castro-Pérez E, Singh M, Sadangi S, Mela-Sánchez C, Setaluri V. Connecting the dots: Melanoma cell of origin, tumor cell plasticity, trans-differentiation, and drug resistance. Pigment Cell Melanoma Res 2023; 36:330-347. [PMID: 37132530 PMCID: PMC10524512 DOI: 10.1111/pcmr.13092] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 02/17/2023] [Accepted: 04/17/2023] [Indexed: 05/04/2023]
Abstract
Melanoma, a lethal malignancy that arises from melanocytes, exhibits a multiplicity of clinico-pathologically distinct subtypes in sun-exposed and non-sun-exposed areas. Melanocytes are derived from multipotent neural crest cells and are present in diverse anatomical locations, including skin, eyes, and various mucosal membranes. Tissue-resident melanocyte stem cells and melanocyte precursors contribute to melanocyte renewal. Elegant studies using mouse genetic models have shown that melanoma can arise from either melanocyte stem cells or differentiated pigment-producing melanocytes depending on a combination of tissue and anatomical site of origin and activation of oncogenic mutations (or overexpression) and/or the repression in expression or inactivating mutations in tumor suppressors. This variation raises the possibility that different subtypes of human melanomas (even subsets within each subtype) may also be a manifestation of malignancies of distinct cells of origin. Melanoma is known to exhibit phenotypic plasticity and trans-differentiation (defined as a tendency to differentiate into cell lineages other than the original lineage from which the tumor arose) along vascular and neural lineages. Additionally, stem cell-like properties such as pseudo-epithelial-to-mesenchymal (EMT-like) transition and expression of stem cell-related genes have also been associated with the development of melanoma drug resistance. Recent studies that employed reprogramming melanoma cells to induced pluripotent stem cells have uncovered potential relationships between melanoma plasticity, trans-differentiation, and drug resistance and implications for cell or origin of human cutaneous melanoma. This review provides a comprehensive summary of the current state of knowledge on melanoma cell of origin and the relationship between tumor cell plasticity and drug resistance.
Collapse
Affiliation(s)
- Edgardo Castro-Pérez
- Center for Cellular and Molecular Biology of Diseases, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), City of Knowledge, Panama City, Panama
- Department of Genetics and Molecular Biology, University of Panama, Panama City, Panama
| | - Mithalesh Singh
- Department of Dermatology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, U.S.A
| | - Shreyans Sadangi
- Department of Dermatology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, U.S.A
| | - Carmen Mela-Sánchez
- Department of Genetics and Molecular Biology, University of Panama, Panama City, Panama
| | - Vijayasaradhi Setaluri
- Department of Dermatology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, U.S.A
- William S. Middleton VA Hospital, Madison, WI, U.S.A
| |
Collapse
|
5
|
Rhodes SD, McCormick F, Cagan RL, Bakker A, Staedtke V, Ly I, Steensma MR, Lee SY, Romo CG, Blakeley JO, Sarin KY. RAS Signaling Gone Awry in the Skin: The Complex Role of RAS in Cutaneous Neurofibroma Pathogenesis, Emerging Biological Insights. J Invest Dermatol 2023; 143:1358-1368. [PMID: 37245145 PMCID: PMC10409534 DOI: 10.1016/j.jid.2023.01.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 05/29/2023]
Abstract
Cutaneous neurofibromas (cNFs) are the most common tumor in people with the rasopathy neurofibromatosis type 1. They number in hundreds or even thousands throughout the body, and currently, there are no effective interventions to prevent or treat these skin tumors. To facilitate the identification of novel and effective therapies, essential studies including a more refined understanding of cNF biology and the role of RAS signaling and downstream effector pathways responsible for cNF initiation, growth, and maintenance are needed. This review highlights the current state of knowledge of RAS signaling in cNF pathogenesis and therapeutic development for cNF treatment.
Collapse
Affiliation(s)
- Steven D Rhodes
- Division of Hematology-Oncology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA; Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA; Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA; Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Ross L Cagan
- School of Cancer Sciences, University of Glasgow, Glasgow, Scotland
| | | | - Verena Staedtke
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ina Ly
- Stephen E. and Catherine Pappas Center for Neuro-Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Matthew R Steensma
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan, USA; Helen DeVos Children's Hospital, Spectrum Health System, Grand Rapids, Michigan, USA; College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Sang Y Lee
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Carlos G Romo
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jaishri O Blakeley
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kavita Y Sarin
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA.
| |
Collapse
|
6
|
Spolia A, Angural A, Sharma V, Razdan S, Dhar MK, Mahajan A, Verma V, Pandita KK, Sharma S, Rai E. Cost-effective Whole Exome Sequencing discovers pathogenic variant causing Neurofibromatosis type 1 in a family from Jammu and Kashmir, India. Sci Rep 2023; 13:7852. [PMID: 37188759 DOI: 10.1038/s41598-023-34941-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 05/10/2023] [Indexed: 05/17/2023] Open
Abstract
Neurofibromatosis type 1 (NF1) is a multisystemic hereditary disorder associated with an increased risk of benign and malignant tumor formation predominantly on the skin, bone, and peripheral nervous system. It has been reported that out of all the NF1 cases, more than 95% cases develop the disease due to heterozygous loss-of-function variants in Neurofibromin (NF1) gene. However, identification of NF1 causative variants by presently recommended method of gene-targeted Sanger sequencing is challenging and cost-intensive due to the large size of the NF1gene with 60 exons spanning about 350 kb. Further, conducting the genetic studies is difficult in low resource regions and among families with the limited financial capabilities, restricting them from availing diagnostic as well as proper disease management measures. Here, we studied a three-generation family from Jammu and Kashmir state in India, with multiple affected family members showing clinical indications of NF1. We combinedly used two applications, Whole Exome Sequencing (WES) and Sanger sequencing, for this study and discovered a nonsense variant NM_000267.3:c.2041C>T (NP_000258.1:p.Arg681Ter*) in exon 18 of NF1 gene in a cost effective manner. In silico analyses further substantiated the pathogenicity of this novel variant. The study also emphasized on the role of Next Generation Sequencing (NGS) as a cost-effective method for the discovery of pathogenic variants in disorders with known phenotypes found in large sized candidate genes. The current study is the first study based on the genetic characterization of NF1 from Jammu and Kashmir-India, highlighting the importance of the described methodology adopted for the identification and understanding of the disease in low resource region. The early diagnosis of genetic disorders would open the door to appropriate genetic counseling, reducing the disease burden in the affected families and the general population at large.
Collapse
Affiliation(s)
- Akshi Spolia
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Kakryal, Jammu and Kashmir, 182320, India
| | - Arshia Angural
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Kakryal, Jammu and Kashmir, 182320, India
- Department of Medical Genetics, JSS Medical College and JSS Hospital, JSS Academy of Higher Education and Research, Mysuru, Karnataka, 570015, India
| | - Varun Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Kakryal, Jammu and Kashmir, 182320, India
- NMC Genetics India Pvt Ltd, Gurugram, 122002, Haryana, India
| | - Sushil Razdan
- Bhagwati Nagar, House No.:7, 180016, Jammu and Kashmir, India
| | - Manoj K Dhar
- School of Biotechnology, University of Jammu, Jammu and Kashmir, 180006, India
| | - Ankit Mahajan
- School of Biotechnology, University of Jammu, Jammu and Kashmir, 180006, India
| | - Vijeshwar Verma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Kakryal, Jammu and Kashmir, 182320, India
| | - Kamal K Pandita
- Health Clinic, Swarn Vihar, Muthi, 181205, Jammu and Kashmir, India
| | - Swarkar Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Kakryal, Jammu and Kashmir, 182320, India.
- Centre for Molecular Biology, Central University of Jammu, Jammu and Kashmir, 181143, India.
| | - Ekta Rai
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Kakryal, Jammu and Kashmir, 182320, India.
| |
Collapse
|
7
|
Alesi V, Genovese S, Lepri FR, Catino G, Loddo S, Orlando V, Di Tommaso S, Morgia A, Martucci L, Di Donato M, Digilio MC, Dallapiccola B, Novelli A, Capolino R. Deep Intronic LINE-1 Insertions in NF1: Expanding the Spectrum of Neurofibromatosis Type 1-Associated Rearrangements. Biomolecules 2023; 13:biom13050725. [PMID: 37238595 DOI: 10.3390/biom13050725] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Neurofibromatosis type 1 is an autosomal-dominant condition caused by NF1 gene inactivation. Clinical diagnosis is corroborated by genetic tests on gDNA and cDNA, which are inconclusive in approximately 3-5% of cases. Genomic DNA approaches may overlook splicing-affecting intronic variants and structural rearrangements, especially in regions enriched in repetitive sequences. On the other hand, while cDNA-based methods provide direct information about the effect of a variant on gene transcription, they are hampered by non-sense-mediated mRNA decay and skewed or monoallelic expression. Moreover, analyses on gene transcripts in some patients do not allow tracing back to the causative event, which is crucial for addressing genetic counselling, prenatal monitoring, and developing targeted therapies. We report on a familial NF1, caused by an insertion of a partial LINE-1 element inside intron 15, leading to exon 15 skipping. Only a few cases of LINE-1 insertion have been reported so far, hampering gDNA studies because of their size. Often, they result in exon skipping, and their recognition of cDNA may be difficult. A combined approach, based on Optical Genome Mapping, WGS, and cDNA studies, enabled us to detect the LINE-1 insertion and test its effects. Our results improve knowledge of the NF1 mutational spectrum and highlight the importance of custom-built approaches in undiagnosed patients.
Collapse
Affiliation(s)
- Viola Alesi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Silvia Genovese
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Francesca Romana Lepri
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Giorgia Catino
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Sara Loddo
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Valeria Orlando
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Silvia Di Tommaso
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Alessandra Morgia
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Licia Martucci
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Maddalena Di Donato
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Maria Cristina Digilio
- Medical Genetics Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
- Genetics and Rare Disease Research Division, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Disease Research Division, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Rossella Capolino
- Medical Genetics Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
- Genetics and Rare Disease Research Division, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| |
Collapse
|
8
|
Pálla S, Anker P, Farkas K, Plázár D, Kiss S, Marschalkó P, Szalai Z, Bene J, Hadzsiev K, Maróti Z, Kalmár T, Medvecz M. Co-occurrence of neurofibromatosis type 1 and pseudoachondroplasia - a first case report. BMC Pediatr 2023; 23:110. [PMID: 36890482 PMCID: PMC9993747 DOI: 10.1186/s12887-023-03920-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/17/2023] [Indexed: 03/10/2023] Open
Abstract
BACKGROUND Neurofibromatosis type 1 and pseudoachondroplasia are both rare autosomal dominant disorders, caused by pathogenic mutations in NF1 and COMP genes, respectively. Both neurofibromin 1 and cartilage oligomeric matrix protein (COMP) play a role in the development of the skeleton. Carrying both germline mutations has not been previously reported; however, it can affect the developing phenotype. CASE PRESENTATION The index patient, an 8-year-old female presented with several skeletal and dermatologic anomalies resembling the coexistence of multiple syndromes. Her mother had dermatologic symptoms characteristic for neurofibromatosis type 1, and her father presented with distinct skeletal anomalies. NGS-based analysis revealed a heterozygous pathogenic mutation in genes NF1 and COMP in the index patient. A previously unreported heterozygous variant was detected for the NF1 gene. The sequencing of the COMP gene revealed a previously reported, pathogenic heterozygous variant that is responsible for the development of the pseudoachondroplasia phenotype. CONCLUSIONS Here, we present the case of a young female carrying pathogenic NF1 and COMP mutations, diagnosed with two distinct heritable disorders, neurofibromatosis type 1 and pseudoachondroplasia. The coincidence of two monogenic autosomal dominant disorders is rare and can pose a differential diagnostic challenge. To the best of our knowledge, this is the first reported co-occurrence of these syndromes.
Collapse
Affiliation(s)
- Sára Pálla
- Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, Budapest, 1085, Hungary
| | - Pálma Anker
- Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, Budapest, 1085, Hungary
| | - Klára Farkas
- Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, Budapest, 1085, Hungary
| | - Dóra Plázár
- Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, Budapest, 1085, Hungary
| | - Sándor Kiss
- Department of Orthopaedics, Semmelweis University, Budapest, 1085, Hungary
| | - Péter Marschalkó
- Department of Paediatric Orthopaedics, Heim Pál National Children's Institute, Budapest, 1089, Hungary
| | - Zsuzsanna Szalai
- Department of Paediatric Dermatology, Heim Pál National Children's Institute, Budapest, 1089, Hungary
| | - Judit Bene
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, 7623, Hungary
| | - Kinga Hadzsiev
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, 7623, Hungary
| | - Zoltán Maróti
- Genetic Diagnostic Laboratory, Department of Pediatrics, Faculty of Medicine, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, 6726, Hungary
| | - Tibor Kalmár
- Genetic Diagnostic Laboratory, Department of Pediatrics, Faculty of Medicine, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, 6726, Hungary
| | - Márta Medvecz
- Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, Budapest, 1085, Hungary.
| |
Collapse
|
9
|
Paterra R, Bettinaglio P, Borghi A, Mangano E, Tritto V, Cesaretti C, Schettino C, Bordoni R, Santoro C, Avignone S, Moscatelli M, Melone MAB, Saletti V, Piluso G, Natacci F, Riva P, Eoli M. A Translational Approach to Spinal Neurofibromatosis: Clinical and Molecular Insights from a Wide Italian Cohort. Cancers (Basel) 2022; 15:cancers15010059. [PMID: 36612057 PMCID: PMC9817775 DOI: 10.3390/cancers15010059] [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: 11/04/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Spinal neurofibromatosis (SNF), a phenotypic subclass of neurofibromatosis 1 (NF1), is characterized by bilateral neurofibromas involving all spinal roots. In order to deepen the understanding of SNF’s clinical and genetic features, we identified 81 patients with SNF, 55 from unrelated families, and 26 belonging to 19 families with at least 1 member affected by SNF, and 106 NF1 patients aged >30 years without spinal tumors. A comprehensive NF1 mutation screening was performed using NGS panels, including NF1 and several RAS pathway genes. The main features of the SNF subjects were a higher number of internal neurofibromas (p < 0.001), nerve root swelling (p < 0.001), and subcutaneous neurofibromas (p = 0.03), while hyperpigmentation signs were significantly less frequent compared with the classical NF1-affected cohorts (p = 0.012). Fifteen patients underwent neurosurgical intervention. The histological findings revealed neurofibromas in 13 patients and ganglioneuromas in 2 patients. Phenotypic variability within SNF families was observed. The proportion of missense mutations was higher in the SNF cases than in the classical NF1 group (21.40% vs. 7.5%, p = 0.007), conferring an odds ratio (OR) of 3.34 (CI = 1.33−10.78). Two unrelated familial SNF cases harbored in trans double NF1 mutations that seemed to have a subclinical worsening effect on the clinical phenotype. Our study, with the largest series of SNF patients reported to date, better defines the clinical and genetic features of SNF, which could improve the management and genetic counseling of NF1.
Collapse
Affiliation(s)
- Rosina Paterra
- Molecular Neuroncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20122 Milano, Italy
| | - Paola Bettinaglio
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Segrate, 20122 Milan, Italy
| | - Arianna Borghi
- Molecular Neuroncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20122 Milano, Italy
| | - Eleonora Mangano
- Institute of Biomedical Technologies (ITB) National Research Center (CNR), ITB-CNR, Segrate, 20122 Milan, Italy
| | - Viviana Tritto
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Segrate, 20122 Milan, Italy
| | - Claudia Cesaretti
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, 20122 Milano, Italy
| | - Carla Schettino
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania “Luigi Vanvitelli”, 81100 Naples, Italy
| | - Roberta Bordoni
- Institute of Biomedical Technologies (ITB) National Research Center (CNR), ITB-CNR, Segrate, 20122 Milan, Italy
| | - Claudia Santoro
- Neurofibromatosis Referral Center, Department of Woman, Child and of General and Specialized Surgery, and Clinic of Child and Adolescent Neuropsychiatry, Department of Mental Health, Physical and Preventive Medicine, University of Campania “Luigi Vanvitelli”, 81100 Naples, Italy
| | - Sabrina Avignone
- Neuroradiology Department, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, 20122 Milano, Italy
| | - Marco Moscatelli
- Neuroradiology Department, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milano, Italy
| | - Mariarosa Anna Beatrice Melone
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania “Luigi Vanvitelli”, 81100 Naples, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Temple University, Philadelphia, PA 19122, USA
| | - Veronica Saletti
- Developmental Neurology Unit, Mariani Foundation Center for Complex Disabilities, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Giulio Piluso
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Naples, Italy
| | - Federica Natacci
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, 20122 Milano, Italy
| | - Paola Riva
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Segrate, 20122 Milan, Italy
- Correspondence: (P.R.); (M.E.); Tel.: +39-02-503130462 (P.R.); +39-02-23942285 (M.E.)
| | - Marica Eoli
- Molecular Neuroncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20122 Milano, Italy
- Correspondence: (P.R.); (M.E.); Tel.: +39-02-503130462 (P.R.); +39-02-23942285 (M.E.)
| |
Collapse
|
10
|
Comparison of In Silico Tools for Splice-Altering Variant Prediction Using Established Spliceogenic Variants: An End-User’s Point of View. Int J Genomics 2022; 2022:5265686. [PMID: 36275637 PMCID: PMC9584665 DOI: 10.1155/2022/5265686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/18/2022] [Accepted: 08/10/2022] [Indexed: 11/18/2022] Open
Abstract
Assessing the impact of variants of unknown significance on splicing has become a critical issue and a bottleneck, especially with the widespread implementation of whole-genome or exome sequencing. Although multiple in silico tools are available, the interpretation and application of these tools are difficult and practical guidelines are still lacking. A streamlined decision-making process can facilitate the downstream RNA analysis in a more efficient manner. Therefore, we evaluated the performance of 8 in silico tools (Splice Site Finder, MaxEntScan, Splice-site prediction by neural network, GeneSplicer, Human Splicing Finder, SpliceAI, Splicing Predictions in Consensus Elements, and SpliceRover) using 114 NF1 spliceogenic variants, experimentally validated at the mRNA level. The change in the predicted score incurred by the variant of the nearest wild-type splice site was analyzed, and for type II, III, and IV splice variants, the change in the prediction score of de novo or cryptic splice site was also analyzed. SpliceAI and SpliceRover, tools based on deep learning, outperformed all other tools, with AUCs of 0.972 and 0.924, respectively. For de novo and cryptic splice sites, SpliceAI outperformed all other tools and showed a sensitivity of 95.7% at an optimal cut-off of 0.02 score change. Our results show that deep learning algorithms, especially those of SpliceAI, are validated at a significantly higher rate than other in silico tools for clinically relevant NF1 variants. This suggests that deep learning algorithms outperform traditional probabilistic approaches and classical machine learning tools in predicting the de novo and cryptic splice sites.
Collapse
|
11
|
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.
Collapse
|
12
|
Functional restoration of mouse Nf1 nonsense alleles in differentiated cultured neurons. J Hum Genet 2022; 67:661-668. [PMID: 35945271 DOI: 10.1038/s10038-022-01072-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 11/09/2022]
Abstract
Neurofibromatosis type 1 (NF1), one of the most common autosomal dominant genetic disorders, is caused by mutations in the NF1 gene. NF1 patients have a wide variety of manifestations with a subset at high risk for the development of tumors in the central nervous system (CNS). Nonsense mutations that result in the synthesis of truncated NF1 protein (neurofibromin) are strongly associated with CNS tumors. Therapeutic nonsense suppression with small molecule drugs is a potentially powerful approach to restore the expression of genes harboring nonsense mutations. Ataluren is one such drug that has been shown to restore full-length functional protein in several models of nonsense mutation diseases, as well as in patients with nonsense mutation Duchenne muscular dystrophy. To test ataluren's potential applicability to NF1 nonsense mutations associated with CNS tumors, we generated a homozygous Nf1R683X/R683X-3X-FLAG mouse embryonic stem (mES) cell line which recapitulates an NF1 patient nonsense mutation (c.2041 C > T; p.Arg681X). We differentiated Nf1R683X/R683X-3X-FLAG mES cells into cortical neurons in vitro, treated the cells with ataluren, and demonstrated that ataluren can promote readthrough of the nonsense mutation at codon 683 of Nf1 mRNA in neural cells. The resulting full-length protein is able to reduce the cellular level of hyperactive phosphorylated ERK (pERK), a RAS effector normally suppressed by the NF1 protein.
Collapse
|
13
|
Genotype-Phenotype Correlations in Neurofibromatosis Type 1: Identification of Novel and Recurrent NF1 Gene Variants and Correlations with Neurocognitive Phenotype. Genes (Basel) 2022; 13:genes13071130. [PMID: 35885913 PMCID: PMC9316015 DOI: 10.3390/genes13071130] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 02/01/2023] Open
Abstract
Neurofibromatosis type 1 (NF1) is one of the most common genetic tumor predisposition syndrome, caused by mutations in the NF1. To date, few genotype-phenotype correlations have been discerned in NF1, due to a highly variable clinical presentation. We aimed to study the molecular spectrum of NF1 and genotype-phenotype correlations in a monocentric study cohort of 85 NF1 patients (20 relatives, 65 sporadic cases). Clinical data were collected at the time of the mutation analysis and reviewed for accuracy in this investigation. An internal phenotypic categorization was applied. The 94% of the patients enrolled showed a severe phenotype with at least one systemic complication and a wide range of associated malignancies. Spine deformities were the most common complications in this cohort. We also reported 66 different NF1 mutations, of which 7 are novel mutations. Correlation analysis identified a slight significant inverse correlation between age at diagnosis and delayed acquisition of psychomotor skills with residual multi-domain cognitive impairment. Odds ratio with 95% confidence interval showed a higher prevalence of learning disabilities in patients carrying frameshift mutations. Overall, our results aim to offer an interesting contribution to studies on the genotype–phenotype of NF1 and in genetic management and counselling.
Collapse
|
14
|
Primary Benign Tumors of the Spinal Canal. World Neurosurg 2022; 164:178-198. [PMID: 35552036 DOI: 10.1016/j.wneu.2022.04.135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 11/23/2022]
Abstract
Benign tumors that grow in the spinal canal are heterogeneous neoplasms with low incidence; from these, meningiomas and nerve sheath tumors (neurofibromas and schwannomas) account for 60%-70% of all primary spinal tumors. Benign spinal canal tumors provoke nonspecific clinical manifestations, mostly related to the affected level of the spinal cord. These tumors present a challenge for the patient and healthcare professionals, for they are often difficult to diagnose and the high frequency of posttreatment complications. In this review, we describe the epidemiology, risk factors, clinical features, diagnosis, histopathology, molecular biology, and treatment of extramedullary benign meningiomas, osteoid osteomas, osteoblastomas, aneurysmal bone cysts, osteochondromas, neurofibromas, giant cell tumors of the bone, eosinophilic granulomas, hemangiomas, lipomas, and schwannomas located in the spine, as well as possible future targets that could lead to an improvement in their management.
Collapse
|
15
|
Keegan NP, Wilton SD, Fletcher S. Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. Front Genet 2022; 12:806946. [PMID: 35140743 PMCID: PMC8819188 DOI: 10.3389/fgene.2021.806946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding pre-mRNA splicing is crucial to accurately diagnosing and treating genetic diseases. However, mutations that alter splicing can exert highly diverse effects. Of all the known types of splicing mutations, perhaps the rarest and most difficult to predict are those that activate pseudoexons, sometimes also called cryptic exons. Unlike other splicing mutations that either destroy or redirect existing splice events, pseudoexon mutations appear to create entirely new exons within introns. Since exon definition in vertebrates requires coordinated arrangements of numerous RNA motifs, one might expect that pseudoexons would only arise when rearrangements of intronic DNA create novel exons by chance. Surprisingly, although such mutations do occur, a far more common cause of pseudoexons is deep-intronic single nucleotide variants, raising the question of why these latent exon-like tracts near the mutation sites have not already been purged from the genome by the evolutionary advantage of more efficient splicing. Possible answers may lie in deep intronic splicing processes such as recursive splicing or poison exon splicing. Because these processes utilize intronic motifs that benignly engage with the spliceosome, the regions involved may be more susceptible to exonization than other intronic regions would be. We speculated that a comprehensive study of reported pseudoexons might detect alignments with known deep intronic splice sites and could also permit the characterisation of novel pseudoexon categories. In this report, we present and analyse a catalogue of over 400 published pseudoexon splice events. In addition to confirming prior observations of the most common pseudoexon mutation types, the size of this catalogue also enabled us to suggest new categories for some of the rarer types of pseudoexon mutation. By comparing our catalogue against published datasets of non-canonical splice events, we also found that 15.7% of pseudoexons exhibit some splicing activity at one or both of their splice sites in non-mutant cells. Importantly, this included seven examples of experimentally confirmed recursive splice sites, confirming for the first time a long-suspected link between these two splicing phenomena. These findings have the potential to improve the fidelity of genetic diagnostics and reveal new targets for splice-modulating therapies.
Collapse
Affiliation(s)
- Niall P. Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Niall P. Keegan,
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| |
Collapse
|
16
|
Muthusamy K, El-Jabali A, Ongie LJ, Dhamija R, Babovic-Vuksanovic D. Neurofibromatosis 1 in the setting of dual diagnosis: Diagnostic and management conundrums. Am J Med Genet A 2021; 188:911-918. [PMID: 34797032 DOI: 10.1002/ajmg.a.62575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/27/2021] [Accepted: 10/29/2021] [Indexed: 11/07/2022]
Abstract
Neurofibromatosis type 1 (NF1) is a common neurocutaneous disorder characterized by development of pigmentary skin changes, neurogenic tumors, and other manifestations involving multiple organ systems. Penetrance is complete, though expressivity is quite variable even among the family members. Given that NF1 is a common hereditary condition, existence of a second genetic disorder in NF1 patients is not unexpected. During comprehensive evaluations of individuals with NF1, we encountered 11 patients with dual diagnosis who contributed to phenotypic complexity and challenges for long-term management. Examples include Prader-Willi Syndrome, Autosomal Dominant Polycystic Kidney Disease, Down syndrome, infantile myofibromatosis, Craniosynostosis, cleft lip and palate, 47,XYY, 22q11.2 duplication, 15q13.3 deletion syndrome, and BRCA2- and ATM- related cancer predisposition syndromes. Presence of dysmorphism, developmental delay, atypical tumors, and family history of other genetic disorders including cancers appears as determinants to consider a second genetic etiology and helps to differentiate from an extreme phenotypic spectrum of NF1. Clinicians should have high index of suspicion to exclude coexisting disorders, as apart from providing comprehensive medical care. This also has potential implications in genetic counseling. Long-term effects of the synergistic mechanisms leading to phenotypic complexity and patient outcomes are yet to be characterized, with follow-up needed.
Collapse
Affiliation(s)
- Karthik Muthusamy
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Laura J Ongie
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Radhika Dhamija
- Department of Clinical Genomics, Mayo Clinic, Phoenix, Arizona, USA.,Department of Neurology, Mayo Clinic, Phoenix, Arizona, USA
| | - Dusica Babovic-Vuksanovic
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA.,Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
17
|
Ha C, Kim JW, Jang JH. Performance Evaluation of SpliceAI for the Prediction of Splicing of NF1 Variants. Genes (Basel) 2021; 12:1308. [PMID: 34573290 PMCID: PMC8472818 DOI: 10.3390/genes12091308] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 12/16/2022] Open
Abstract
Neurofibromatosis type 1, characterized by neurofibromas and café-au-lait macules, is one of the most common genetic disorders caused by pathogenic NF1 variants. Because of the high proportion of splicing mutations in NF1, identifying variants that alter splicing may be an essential issue for laboratories. Here, we investigated the sensitivity and specificity of SpliceAI, a recently introduced in silico splicing prediction algorithm in conjunction with other in silico tools. We evaluated 285 NF1 variants identified from 653 patients. The effect on variants on splicing alteration was confirmed by complementary DNA sequencing followed by genomic DNA sequencing. For in silico prediction of splicing effects, we used SpliceAI, MaxEntScan (MES), and Splice Site Finder-like (SSF). The sensitivity and specificity of SpliceAI were 94.5% and 94.3%, respectively, with a cut-off value of Δ Score > 0.22. The area under the curve of SpliceAI was 0.975 (p < 0.0001). Combined analysis of MES/SSF showed a sensitivity of 83.6% and specificity of 82.5%. The concordance rate between SpliceAI and MES/SSF was 84.2%. SpliceAI showed better performance for the prediction of splicing alteration for NF1 variants compared with MES/SSF. As a convenient web-based tool, SpliceAI may be helpful in clinical laboratories conducting DNA-based NF1 sequencing.
Collapse
Affiliation(s)
| | | | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Korea; (C.H.); (J.-W.K.)
| |
Collapse
|
18
|
Perez-Becerril C, Evans DG, Smith MJ. Pathogenic noncoding variants in the neurofibromatosis and schwannomatosis predisposition genes. Hum Mutat 2021; 42:1187-1207. [PMID: 34273915 DOI: 10.1002/humu.24261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/16/2021] [Accepted: 07/13/2021] [Indexed: 11/11/2022]
Abstract
Neurofibromatosis type 1 (NF1), type 2 (NF2), and schwannomatosis are a group of autosomal dominant disorders that predispose to the development of nerve sheath tumors. Pathogenic variants (PVs) that cause NF1 and NF2 are located in the NF1 and NF2 loci, respectively. To date, most variants associated with schwannomatosis have been identified in the SMARCB1 and LZTR1 genes, and a missense variant in the DGCR8 gene was recently reported to predispose to schwannomas. In spite of the high detection rate for PVs in NF1 and NF2 (over 90% of non-mosaic germline variants can be identified by routine genetic screening) underlying PVs for a proportion of clinical cases remain undetected. A higher proportion of non-NF2 schwannomatosis cases have no detected PV, with PVs currently only identified in around 70%-86% of familial cases and 30%-40% of non-NF2 sporadic schwannomatosis cases. A number of variants of uncertain significance have been observed for each disorder, many of them located in noncoding, regulatory, or intergenic regions. Here we summarize noncoding variants in this group of genes and discuss their established or potential role in the pathogenesis of NF1, NF2, and schwannomatosis.
Collapse
Affiliation(s)
- Cristina Perez-Becerril
- Division of Evolution and Genomic Science, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, UK
| | - D Gareth Evans
- Division of Evolution and Genomic Science, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Miriam J Smith
- Division of Evolution and Genomic Science, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, UK
| |
Collapse
|
19
|
Cruz TZ, Ferreira-Pinto PHC, Brito ACG, Ururahy L, Sanchez JT, Nigri F. Ganglioglioma of the cervicothoracic spinal cord in a patient with neurofibromatosis type 1: A case report. Surg Neurol Int 2021; 12:313. [PMID: 34345454 PMCID: PMC8326088 DOI: 10.25259/sni_192_2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/26/2021] [Indexed: 11/25/2022] Open
Abstract
Background: Gangliogliomas are rare tumors of the central nervous system. They are usually located intracranially and rarely in the spinal cord. There is no clear correlation between this tumor and neurofibromatosis type 1 (NF1) with only four cases described. The aim of this article is to describe one more case and add data to the literature regarding this rare association. Case Description: An 8-year-old boy with NF1 presented progressive asymmetrical paraparesis (Grade 4 medical research council scale on the right leg and Grade 3 on the left leg). The cervicothoracic spinal magnetic resonance imaging demonstrated an intramedullary lesion from C4 to T4 vertebrae. The patient underwent a microsurgical resection. A partial resection was performed due to a drop in the motor evoked potential signal amplitude during dissection. Pathology report revealed a ganglioglioma (World Health Organization Grade I). Postoperatively, the patient evolved with worsening of the paraparesis. A few weeks later, he has improved his preoperative functional neurological state (better strength and gait). Adjuvant radiotherapy was not used. The patient is being followed up at the neurosurgery outpatient clinic. Conclusion: This is another case of spinal ganglioglioma associated with NF1. The tumor must be included in the differential diagnosis of patients with NF1 and spinal lesions. Complete microsurgical resection remains the standard treatment for spinal gangliogliomas, however, in this specific case, it was decided to leave a portion of the tumor to prevent neurological damage. The prognosis and treatment of this condition associated with NF1 remains to be determined.
Collapse
Affiliation(s)
- Thainá Zanon Cruz
- Departament of Surgical Specialities and Neurosurgery, Neurosurgery Teaching and Assistance Unit, Pedro Ernesto University Hospital, Rio de Janeiro, Brazil
| | - Pedro Henrique Costa Ferreira-Pinto
- Departament of Surgical Specialities and Neurosurgery, Neurosurgery Teaching and Assistance Unit, Pedro Ernesto University Hospital, Rio de Janeiro, Brazil
| | | | - Leandro Ururahy
- Departament of Surgical Specialities and Neurosurgery, Neurosurgery Teaching and Assistance Unit, Pedro Ernesto University Hospital, Rio de Janeiro, Brazil
| | - Jefferson Trivino Sanchez
- Departament of Surgical Specialities and Neurosurgery, Neurosurgery Teaching and Assistance Unit, Pedro Ernesto University Hospital, Rio de Janeiro, Brazil
| | - Flavio Nigri
- Departament of Surgical Specialities and Neurosurgery, Neurosurgery Teaching and Assistance Unit, Pedro Ernesto University Hospital, Rio de Janeiro, Brazil
| |
Collapse
|
20
|
Ranalli M, Boni A, Caroleo AM, Del Baldo G, Rinelli M, Agolini E, Rossi S, Miele E, Colafati GS, Boccuto L, Alessi I, De Ioris MA, Cacchione A, Capolino R, Carai A, Vennarini S, Mastronuzzi A. Molecular Characterization of Medulloblastoma in a Patient with Neurofibromatosis Type 1: Case Report and Literature Review. Diagnostics (Basel) 2021; 11:diagnostics11040647. [PMID: 33918520 PMCID: PMC8067061 DOI: 10.3390/diagnostics11040647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/27/2021] [Accepted: 03/28/2021] [Indexed: 12/31/2022] Open
Abstract
Brain tumors are the most common solid neoplasms of childhood. They are frequently reported in children with Neurofibromatosis type 1 (NF1). The most frequent central nervous system malignancies described in NF1 are optic pathway gliomas and brainstem gliomas. Medulloblastoma (MB) in NF1 patients is extremely rare, and to our knowledge, only 10 cases without molecular characterization are described in the literature to date. We report the case of a 14-year-old girl with NF1 that came to our attention for an incidental finding of a lesion arising from cerebellar vermis. The mass was completely resected, revealing a localized classic medulloblastoma (MB), subgroup 4. She was treated as a standard-risk MB with a dose-adapted personalized protocol. The treatment proved to be effective, with minor toxicity. Brain and spine MRI one year after diagnosis confirmed the complete remission of the disease. To our knowledge, this is the only case of MB reported in a patient with NF1 with molecular characterization by the methylation profile. The association between NF1 and MB, although uncommon, may not be an accidental occurrence.
Collapse
Affiliation(s)
- Marco Ranalli
- Department of Pediatrics, Sapienza University, Viale Regina Elena 324, 00161 Rome, Italy; (M.R.); (A.B.); (E.M.)
| | - Alessandra Boni
- Department of Pediatrics, Sapienza University, Viale Regina Elena 324, 00161 Rome, Italy; (M.R.); (A.B.); (E.M.)
| | - Anna Maria Caroleo
- Department of Onco-Hematology and Cell and Gene Therapy, Bambino Gesù Children’s Hospital (IRCCS), 00165 Rome, Italy; (A.M.C.); (G.D.B.); (I.A.); (M.A.D.I.); (A.C.)
| | - Giada Del Baldo
- Department of Onco-Hematology and Cell and Gene Therapy, Bambino Gesù Children’s Hospital (IRCCS), 00165 Rome, Italy; (A.M.C.); (G.D.B.); (I.A.); (M.A.D.I.); (A.C.)
| | - Martina Rinelli
- Laboratory of Medical Genetics, Bambino Gesù Children’s Hospital (IRCCS), 00165 Rome, Italy; (M.R.); (E.A.)
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Bambino Gesù Children’s Hospital (IRCCS), 00165 Rome, Italy; (M.R.); (E.A.)
| | - Sabrina Rossi
- Pathology Unit, Department of Laboratories, Bambino Gesù Children’s Hospital (IRCCS), 00165 Rome, Italy;
| | - Evelina Miele
- Department of Pediatrics, Sapienza University, Viale Regina Elena 324, 00161 Rome, Italy; (M.R.); (A.B.); (E.M.)
| | - Giovanna Stefania Colafati
- Neuroradiology Unit, Department of Imaging, Bambino Gesù Children’s Hospital (IRCCS), 00165 Rome, Italy;
| | - Luigi Boccuto
- School of Nursing, College of Behavioral, Social and Health Sciences Healthcare Genetics Interdisciplinary Doctoral Program, Clemson University, Clemson, SC 29631, USA;
| | - Iside Alessi
- Department of Onco-Hematology and Cell and Gene Therapy, Bambino Gesù Children’s Hospital (IRCCS), 00165 Rome, Italy; (A.M.C.); (G.D.B.); (I.A.); (M.A.D.I.); (A.C.)
| | - Maria Antonietta De Ioris
- Department of Onco-Hematology and Cell and Gene Therapy, Bambino Gesù Children’s Hospital (IRCCS), 00165 Rome, Italy; (A.M.C.); (G.D.B.); (I.A.); (M.A.D.I.); (A.C.)
| | - Antonella Cacchione
- Department of Onco-Hematology and Cell and Gene Therapy, Bambino Gesù Children’s Hospital (IRCCS), 00165 Rome, Italy; (A.M.C.); (G.D.B.); (I.A.); (M.A.D.I.); (A.C.)
| | - Rossella Capolino
- Medical Genetics Unit, Bambino Gesù Children Hospital, Bambino Gesù Children’s Hospital (IRCCS), 00165 Rome, Italy;
| | - Andrea Carai
- Neurosurgery Unit, Department of Neurosciences, Bambino Gesù Children’s Hospital (IRCCS), 00165 Rome, Italy;
| | - Sabina Vennarini
- Proton Therapy Center, Hospital of Trento, Azienda Provinciale per I Servizi Sanitari (APSS), 38122 Trento, Italy;
| | - Angela Mastronuzzi
- Department of Onco-Hematology and Cell and Gene Therapy, Bambino Gesù Children’s Hospital (IRCCS), 00165 Rome, Italy; (A.M.C.); (G.D.B.); (I.A.); (M.A.D.I.); (A.C.)
- Correspondence:
| |
Collapse
|
21
|
Zhang ZYO, Wu YY, Cai XY, Fang WL, Xiao FL. Molecular Diagnosis of Neurofibromatosis by Multigene Panel Testing. Front Genet 2021; 12:603195. [PMID: 33767727 PMCID: PMC7985060 DOI: 10.3389/fgene.2021.603195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 02/02/2021] [Indexed: 11/13/2022] Open
Abstract
Neurofibromatosis (NF) is an autosomal genetic disorder for which early and definite clinical diagnoses are difficult. To identify the diagnosis, five affected probands with suspected NF from unrelated families were included in this study. Molecular analysis was performed using multigene panel testing and Sanger sequencing. Ultradeep sequencing was used to analyze the mutation rate in the tissues from the proband with mosaic mutations. Three different pathogenic variants of the NF1 gene were found in three probands who mainly complained of café-au-lait macules (CALMs), including one frameshift variant c.5072_5073insTATAACTGTAACTCCTGGGTCAGGGAGTACACCAA:p.Tyr1692Ilefs in exon 37, one missense variant c.3826C > T:p.Arg1276Ter in exon 28, and one splicing variant c.4110 + 1G > T at the first base downstream of the 3′-end of exon 30. One NF1 gene mosaic variant was found in a proband who complained of cutaneous neurofibroma with the frameshift variant c.495_498del:p.Thr165fs in exon 5, and ultradeep sequencing showed the highest mutation rate of 10.81% in cutaneous neurofibromas. A frameshift variant, c.36_39del:p.Ser12fs in exon 1 of the NF2 gene, was found in a proband who presented with skin plaques and intracranial neurogenic tumors. All of these pathogenic variants were heterozygous, one was not reported, and one not in Chinese before. This study expands the pathogenic variant spectrum of NF and demonstrates the clinical diagnosis.
Collapse
Affiliation(s)
- Zeng-Yun-Ou Zhang
- Department of Dermatology, First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Yuan-Yuan Wu
- Department of Dermatology, First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Xin-Ying Cai
- Department of Dermatology, First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Wen-Liang Fang
- Clinical College, Anhui Medical University, Hefei, China
| | - Feng-Li Xiao
- Department of Dermatology, First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China.,The Center for Scientific Research of Anhui Medical University, Hefei, China
| |
Collapse
|
22
|
Morbidoni V, Baschiera E, Forzan M, Fumini V, Ali DS, Giorgi G, Buson L, Desbats MA, Cassina M, Clementi M, Salviati L, Trevisson E. Hybrid Minigene Assay: An Efficient Tool to Characterize mRNA Splicing Profiles of NF1 Variants. Cancers (Basel) 2021; 13:cancers13050999. [PMID: 33673681 PMCID: PMC7957615 DOI: 10.3390/cancers13050999] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 02/08/2023] Open
Abstract
Neurofibromatosis type 1 (NF1) is caused by heterozygous loss of function mutations in the NF1 gene. Although patients are diagnosed according to clinical criteria and few genotype-phenotype correlations are known, molecular analysis remains important. NF1 displays allelic heterogeneity, with a high proportion of variants affecting splicing, including deep intronic alleles and changes outside the canonical splice sites, making validation problematic. Next Generation Sequencing (NGS) technologies integrated with multiplex ligation-dependent probe amplification (MLPA) have largely overcome RNA-based techniques but do not detect splicing defects. A rapid minigene-based system was set up to test the effects of NF1 variants on splicing. We investigated 29 intronic and exonic NF1 variants identified in patients during the diagnostic process. The minigene assay showed the coexistence of multiple mechanisms of splicing alterations for seven variants. A leaky effect on splicing was documented in one de novo substitution detected in a sporadic patient with a specific phenotype without neurofibromas. Our splicing assay proved to be a reliable and fast method to validate novel NF1 variants potentially affecting splicing and to detect hypomorphic effects that might have phenotypic consequences, avoiding the requirement of patient's RNA.
Collapse
Affiliation(s)
- Valeria Morbidoni
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Elisa Baschiera
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Monica Forzan
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Valentina Fumini
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Dario Seif Ali
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Gianpietro Giorgi
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Lisa Buson
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Maria Andrea Desbats
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Matteo Cassina
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Maurizio Clementi
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Leonardo Salviati
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Eva Trevisson
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
- Correspondence: ; Tel.: + 39-(04)-9821-1402
| |
Collapse
|
23
|
Ozarslan B, Russo T, Argenziano G, Santoro C, Piccolo V. Cutaneous Findings in Neurofibromatosis Type 1. Cancers (Basel) 2021; 13:463. [PMID: 33530415 PMCID: PMC7865571 DOI: 10.3390/cancers13030463] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/02/2021] [Accepted: 01/14/2021] [Indexed: 12/15/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is a complex autosomal dominant disorder associated with germline mutations in the NF1 tumor suppressor gene. NF1 belongs to a class of congenital anomaly syndromes called RASopathies, a group of rare genetic conditions caused by mutations in the Ras/mitogen-activated protein kinase pathway. Generally, NF1 patients present with dermatologic manifestations. In this review the main features of café-au-lait macules, freckling, neurofibromas, juvenile xanthogranuloma, nevus anemicus and other cutaneous findings will be discussed.
Collapse
Affiliation(s)
| | - Teresa Russo
- Dermatology Unit, University of Campania Luigi Vanvitelli, 80100 Naples, Italy; (T.R.); (G.A.)
| | - Giuseppe Argenziano
- Dermatology Unit, University of Campania Luigi Vanvitelli, 80100 Naples, Italy; (T.R.); (G.A.)
| | - Claudia Santoro
- Department of Woman, Neurofibromatosis Referral Centre, Child and of General and Specialised Surgery, University of Campania Luigi Vanvitelli, 80100 Naples, Italy;
| | - Vincenzo Piccolo
- Dermatology Unit, University of Campania Luigi Vanvitelli, 80100 Naples, Italy; (T.R.); (G.A.)
| |
Collapse
|
24
|
Evaluation of clinical findings and neurofibromatosis type 1 bright objects on brain magnetic resonance images of 60 Turkish patients with NF1 gene variants. Neurol Sci 2021; 42:2045-2057. [PMID: 33443663 DOI: 10.1007/s10072-020-04988-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/11/2020] [Indexed: 12/13/2022]
Abstract
Neurofibromatosis type 1 (NF1) is caused by mutations in the NF1 gene. This retrospective study aims to evaluate the clinical manifestations and brain magnetic resonance images (MRI) analysis in 60 genetically confirmed NF1 patients. The results of next-generation sequencing (NGS), Sanger sequencing, and MLPA of NF1 gene were evaluated. A total of 54 different variants were identified. Fourteen out of them were novel variants (25.9%). Patients who complied with NIH criteria had most frequently frameshift variants (11/32 patients), and those with only CALMs had missense variants (9/28 patients). Neurofibromatosis type 1 bright objects (NBOs) on T2-weighted MRI were detected in 42 patients (42/56; 75%). These brain lesions were detected mostly in basal ganglia and in cerebellar vermis. NBOs were detected more in the patients who complied with NIH criteria (80.6%) compared to those who were only CALMs (68%). While frameshift variants (33.3%) were the most common type variants in the patients who had NBOs, the most common variants were splicing (35.7%) and missense (35.7%) variants in the patients whose MRIs were normal. Frameshift variants (11/28 patients; 39.3%) were the most common in the patients with more than one brain locus involvement. Therefore, we consider that frameshift variants may be associated with increased incidence of NBOs and involvement of more than one brain locus. In addition, NBOs may occur less frequently in the patients with splicing variants. To our knowledge, this is the first study evaluated the relationship between NF1 gene variants and NBOs. Future studies may help us understand the etiology of NBOs.
Collapse
|
25
|
Osum SH, Coutts AW, Duerre DJ, Tschida BR, Kirstein MN, Fisher J, Bell WR, Delpuech O, Smith PD, Widemann BC, Moertel CL, Largaespada DA, Watson AL. Selumetinib normalizes Ras/MAPK signaling in clinically relevant neurofibromatosis type 1 minipig tissues in vivo. Neurooncol Adv 2021; 3:vdab020. [PMID: 33978635 PMCID: PMC8095338 DOI: 10.1093/noajnl/vdab020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The MEK1/2 inhibitor selumetinib was recently approved for neurofibromatosis type 1 (NF1)-associated plexiform neurofibromas, but outcomes could be improved and its pharmacodynamic evaluation in other relevant tissues is limited. The aim of this study was to assess selumetinib tissue pharmacokinetics (PK) and pharmacodynamics (PD) using a minipig model of NF1. METHODS WT (n = 8) and NF1 (n = 8) minipigs received a single oral dose of 7.3 mg/kg selumetinib. Peripheral blood mononuclear cells (PBMCs), cerebral cortex, optic nerve, sciatic nerve, and skin were collected for PK analysis and PD analysis of extracellular regulated kinase phosphorylation (p-ERK) inhibition and transcript biomarkers (DUSP6 & FOS). RESULTS Key selumetinib PK parameters aligned with those observed in human patients. Selumetinib concentrations were higher in CNS tissues from NF1 compared to WT animals. Inhibition of ERK phosphorylation was achieved in PBMCs (mean 60% reduction), skin (95%), and sciatic nerve (64%) from all minipigs, whereas inhibition of ERK phosphorylation in cerebral cortex was detected only in NF1 animals (71%). Basal p-ERK levels were significantly higher in NF1 minipig optic nerve compared to WT and were reduced to WT levels (60%) with selumetinib. Modulation of transcript biomarkers was observed in all tissues. CONCLUSIONS Selumetinib reduces MAPK signaling in tissues clinically relevant to NF1, effectively normalizing p-ERK to WT levels in optic nerve but resulting in abnormally low levels of p-ERK in the skin. These results suggest that selumetinib exerts activity in NF1-associated CNS tumors by normalizing Ras/MAPK signaling and may explain common MEK inhibitor-associated dermatologic toxicities.
Collapse
Affiliation(s)
- Sara H Osum
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | | | | | | | - Mark N Kirstein
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota, USA
| | - James Fisher
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota, USA
| | - W Robert Bell
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
- Division of Neuropathology, Department of Lab Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Oona Delpuech
- Oncology R&D, AstraZeneca, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Paul D Smith
- Oncology R&D, AstraZeneca, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Brigitte C Widemann
- Pediatric Oncology Branch, Rare Tumor Initiative, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | | | - David A Largaespada
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | | |
Collapse
|
26
|
Joynt AT, Evans TA, Pellicore MJ, Davis-Marcisak EF, Aksit MA, Eastman AC, Patel SU, Paul KC, Osorio DL, Bowling AD, Cotton CU, Raraigh KS, West NE, Merlo CA, Cutting GR, Sharma N. Evaluation of both exonic and intronic variants for effects on RNA splicing allows for accurate assessment of the effectiveness of precision therapies. PLoS Genet 2020; 16:e1009100. [PMID: 33085659 PMCID: PMC7605713 DOI: 10.1371/journal.pgen.1009100] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 11/02/2020] [Accepted: 09/08/2020] [Indexed: 12/21/2022] Open
Abstract
Elucidating the functional consequence of molecular defects underlying genetic diseases enables appropriate design of therapeutic options. Treatment of cystic fibrosis (CF) is an exemplar of this paradigm as the development of CFTR modulator therapies has allowed for targeted and effective treatment of individuals harboring specific genetic variants. However, the mechanism of these drugs limits effectiveness to particular classes of variants that allow production of CFTR protein. Thus, assessment of the molecular mechanism of individual variants is imperative for proper assignment of these precision therapies. This is particularly important when considering variants that affect pre-mRNA splicing, thus limiting success of the existing protein-targeted therapies. Variants affecting splicing can occur throughout exons and introns and the complexity of the process of splicing lends itself to a variety of outcomes, both at the RNA and protein levels, further complicating assessment of disease liability and modulator response. To investigate the scope of this challenge, we evaluated splicing and downstream effects of 52 naturally occurring CFTR variants (exonic = 15, intronic = 37). Expression of constructs containing select CFTR intronic sequences and complete CFTR exonic sequences in cell line models allowed for assessment of RNA and protein-level effects on an allele by allele basis. Characterization of primary nasal epithelial cells obtained from individuals harboring splice variants corroborated in vitro data. Notably, we identified exonic variants that result in complete missplicing and thus a lack of modulator response (e.g. c.2908G>A, c.523A>G), as well as intronic variants that respond to modulators due to the presence of residual normally spliced transcript (e.g. c.4242+2T>C, c.3717+40A>G). Overall, our data reveals diverse molecular outcomes amongst both exonic and intronic variants emphasizing the need to delineate RNA, protein, and functional effects of each variant in order to accurately assign precision therapies. Genetic variants that impact pre-mRNA splicing are a common cause of genetic disease and have varying downstream molecular consequences. As a result, precision therapies that function at the protein level are not always effective for these variants and thus careful assessment is necessary. Here we evaluate RNA-level effects of 52 variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene and show that study of splicing and its consequences allows for more accurate assignment of precision therapies.
Collapse
Affiliation(s)
- Anya T. Joynt
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Taylor A. Evans
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Matthew J. Pellicore
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Emily F. Davis-Marcisak
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Melis A. Aksit
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alice C. Eastman
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Shivani U. Patel
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Kathleen C. Paul
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Derek L. Osorio
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alyssa D. Bowling
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Calvin U. Cotton
- Departments of Pediatrics, Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Karen S. Raraigh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Natalie E. West
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Christian A. Merlo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Garry R. Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (GRC); (NS)
| | - Neeraj Sharma
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (GRC); (NS)
| |
Collapse
|
27
|
Riccardi C, Perrone L, Napolitano F, Sampaolo S, Melone MAB. Understanding the Biological Activities of Vitamin D in Type 1 Neurofibromatosis: New Insights into Disease Pathogenesis and Therapeutic Design. Cancers (Basel) 2020; 12:E2965. [PMID: 33066259 PMCID: PMC7602022 DOI: 10.3390/cancers12102965] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/18/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023] Open
Abstract
Vitamin D is a fat-soluble steroid hormone playing a pivotal role in calcium and phosphate homeostasis as well as in bone health. Vitamin D levels are not exclusively dependent on food intake. Indeed, the endogenous production-occurring in the skin and dependent on sun exposure-contributes to the majority amount of vitamin D present in the body. Since vitamin D receptors (VDRs) are ubiquitous and drive the expression of hundreds of genes, the interest in vitamin D has tremendously grown and its role in different diseases has been extensively studied. Several investigations indicated that vitamin D action extends far beyond bone health and calcium metabolism, showing broad effects on a variety of critical illnesses, including cancer, infections, cardiovascular and autoimmune diseases. Epidemiological studies indicated that low circulating vitamin D levels inversely correlate with cutaneous manifestations and bone abnormalities, clinical hallmarks of neurofibromatosis type 1 (NF1). NF1 is an autosomal dominant tumour predisposition syndrome causing significant pain and morbidity, for which limited treatment options are available. In this context, vitamin D or its analogues have been used to treat both skin and bone lesions in NF1 patients, alone or combined with other therapeutic agents. Here we provide an overview of vitamin D, its characteristic nutritional properties relevant for health benefits and its role in NF1 disorder. We focus on preclinical and clinical studies that demonstrated the clinical correlation between vitamin D status and NF1 disease, thus providing important insights into disease pathogenesis and new opportunities for targeted therapy.
Collapse
Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy;
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini 5, I-80131 Naples, Italy; (L.P.); (F.N.); (S.S.)
| | - Lorena Perrone
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini 5, I-80131 Naples, Italy; (L.P.); (F.N.); (S.S.)
| | - Filomena Napolitano
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini 5, I-80131 Naples, Italy; (L.P.); (F.N.); (S.S.)
| | - Simone Sampaolo
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini 5, I-80131 Naples, Italy; (L.P.); (F.N.); (S.S.)
| | - Mariarosa Anna Beatrice Melone
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini 5, I-80131 Naples, Italy; (L.P.); (F.N.); (S.S.)
- Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, Temple University, BioLife Building (015-00), 1900 North 12th Street, Philadelphia, PA 19122-6078, USA
| |
Collapse
|
28
|
Neurofibromatosis type 1: New developments in genetics and treatment. J Am Acad Dermatol 2020; 84:1667-1676. [PMID: 32771543 DOI: 10.1016/j.jaad.2020.07.105] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 07/26/2020] [Accepted: 07/28/2020] [Indexed: 12/12/2022]
Abstract
Neurofibromatosis type 1 is the most common neurocutaneous syndrome, with a frequency of 1 in 2500 persons. Diagnosis is paramount in the pretumor stage to provide proper anticipatory guidance for a number of neoplasms, both benign and malignant. Loss-of-function mutations in the NF1 gene result in truncated and nonfunctional production of neurofibromin, a tumor suppressor protein involved in downregulating the RAS signaling pathway. New therapeutic and preventive options include tyrosine kinase inhibitors, mTOR inhibitors, interferons, and radiofrequency therapy. This review summarizes recent updates in genetics, mutation analysis assays, and treatment options targeting aberrant genetic pathways. We also propose modified diagnostic criteria and provide an algorithm for surveillance of patients with neurofibromatosis type 1.
Collapse
|
29
|
Foiadelli T, Naso M, Licari A, Orsini A, Magistrali M, Trabatti C, Luzzi S, Mosconi M, Savasta S, Marseglia GL. Advanced pharmacological therapies for neurofibromatosis type 1-related tumors. ACTA BIO-MEDICA : ATENEI PARMENSIS 2020; 91:101-114. [PMID: 32608378 PMCID: PMC7975824 DOI: 10.23750/abm.v91i7-s.9961] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 06/23/2020] [Indexed: 11/23/2022]
Abstract
Neurofibromatosis Type 1 (NF1) is an autosomal dominant tumor-predisposition disorder that is caused by a heterozygous loss of function variant in the NF1 gene, which encodes a protein called neurofibromin. The absence of neurofibromin causes increased activity in the Rat sarcoma protein (RAS) signalling pathway, which results in an increased growth and cell proliferation. As a result, both oncological and non-oncological comorbidities contribute to a high morbidity and mortality in these patients. Optic pathways gliomas, plexiform neurofibromas and malignant peripheral nerve sheath tumor (MPNST) are the most frequent NF1-associated tumors. The treatment of these complications is often challenging, since surgery may not be feasible due to the location, size, and infiltrative nature of these tumors, and standard chemotherapy or radiotherapy are burdened by significant toxicity and risk for secondary malignancies. For these reasons, following the novel discoveries of the pathophysiological mechanisms that lead to cell proliferation and tumorigenesis in NF1 patients, emerging drugs targeting specific signalling pathways (i.e. the MEK/ERK cascade), have been developed with promising results.
Collapse
Affiliation(s)
- Thomas Foiadelli
- Pediatric Clinic, Department of Pediatrics, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy.
| | - Matteo Naso
- Pediatric Clinic, Department of Pediatrics, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy.
| | - Amelia Licari
- Pediatric Clinic, Department of Pediatrics, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy.
| | - Alessandro Orsini
- Pediatric Neurology, Pediatric Department, Azienda Ospedaliera Universitaria Pisana, University of Pisa, Italy.
| | - Mariasole Magistrali
- Pediatric Clinic, Department of Pediatrics, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy.
| | - Chiara Trabatti
- Pediatric Clinic, Department of Pediatrics, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy.
| | - Sabino Luzzi
- Neurosurgery Unit, Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy; Neurosurgery Unit, Department of Surgical Sciences, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
| | - Mario Mosconi
- Orthopaedic and Traumatology Unit, Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy.
| | - Salvatore Savasta
- Pediatric Clinic, Department of Pediatrics, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy.
| | - Gian Luigi Marseglia
- Pediatric Clinic, Department of Pediatrics, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy.
| |
Collapse
|
30
|
Li J, Liu L, Zhang Q, Huang Y, Zhang Y, Gan X, Liu S, Yue Z, Wei Y. A novel TJP1-ROS1 fusion in malignant peripheral nerve sheath tumor responding to crizotinib: A case report. Medicine (Baltimore) 2020; 99:e20725. [PMID: 32590748 PMCID: PMC7328986 DOI: 10.1097/md.0000000000020725] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
RATIONALE Malignant peripheral nerve sheath tumor (MPNST) is a rare sarcoma. Owing to the lack of specific histological criteria, immunohistochemical, and molecular diagnostic markers, several differential diagnoses must be considered. Advances in molecular testing can provide significant insights for management of rare tumor. PATIENT CONCERNS The patient was a 50-year-old man with a history of lumpectomy on the right back 30 years ago. He felt a stabbing pain at the right iliac fossa and went to the local hospital. DIAGNOSIS By immunohistochemistry, the tumor cells stained positively for S-100 (focal +), CD34 (strong +++) and Ki-67 (20%), and negatively for smooth muscle actin, pan-cytokeratin, neurofilament, pan-cytokeratin-L, GFAP, CD31, STAT6, ERG, myogenin, and MyoD1. Combined with the histopathology and immunohistochemistry results, our initial diagnosis was solitary fibrous tumor (SFT) or MPNST. The tissue biopsy was sent for next-generation sequencing. neurofibromatosis type 1 Q1395Hfs*22 somatic mutation, neurofibromatosis type 1 D483Tfs*15 germline mutation, and amplifications of BTK, MDM2, ATF1, BMPR1A, EBHA2, GNA13, PTPN11, RAD52, RPTOR, and SOX9, as well as TJP1-ROS1 fusion, CDKN2A-IL1RAPL2 fusion and CDKN2A/UBAP1 rearrangement were identified. Given that NAB2-STAT6 fusion, a specific biomarker of SFT, was not identified in our patient's tumor, the SFT was excluded by through genetic testing results. Therefore, our finally diagnosis was a MPNST by 2 or more pathologists. INTERVENTIONS AND OUTCOMES Subsequently, the patient received crizotinib therapy for 2 months and showed stable disease. However, after crizotinib continued treatment for 4 months, the patient's disease progressed. Soon after, the patient stopped crizotinib treatment and died in home. LESSONS To our knowledge, this is the first report of the TJP1-ROS1 fusion, which expands the list of gene fusions and highlights new targets for targeted therapy. Also, our case underlines the value of multi-gene panel next-generation sequencing for diagnosis of MPNST.
Collapse
Affiliation(s)
| | - Lingxiang Liu
- Department of Medical Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Peces R, Mena R, Martín Y, Hernández C, Peces C, Tellería D, Cuesta E, Selgas R, Lapunzina P, Nevado J. Co-occurrence of neurofibromatosis type 1 and optic nerve gliomas with autosomal dominant polycystic kidney disease type 2. Mol Genet Genomic Med 2020; 8:e1321. [PMID: 32533764 PMCID: PMC7434601 DOI: 10.1002/mgg3.1321] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/25/2020] [Accepted: 04/27/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD) and neurofibromatosis type 1 (NF1) are both autosomal dominant disorders with a high rate of novel mutations. However, the two disorders have distinct and well-delineated genetic, biochemical, and clinical findings. Only a few cases of coexistence of ADPKD and NF1 in a single individual have been reported, but the possible implications of this association are unknown. METHODS We report an ADPKD male belonging to a family of several affected members in three generations associated with NF1 and optic pathway gliomas. The clinical diagnosis of ADPKD and NF1 was performed by several image techniques. RESULTS Linkage analysis of ADPKD family was consistent to the PKD2 locus by a nonsense mutation, yielding a truncated polycystin-2 by means of next-generation sequencing. The diagnosis of NF1 was confirmed by mutational analysis of this gene showing a 4-bp deletion, resulting in a truncated neurofibromin, as well. The impact of this association was investigated by analyzing putative genetic interactions and by comparing the evolution of renal size and function in the proband with his older brother with ADPKD without NF1 and with ADPKD cohorts. CONCLUSION Despite the presence of both conditions there was not additive effect of NF1 and PKD2 in terms of the severity of tumor development and/or ADPKD progression.
Collapse
Affiliation(s)
- Ramón Peces
- Servicio de Nefrología, Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma, Madrid, Spain
| | - Rocío Mena
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Yolanda Martín
- Servicio de Genética, Hospital Universitario Ramón y Cajal, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Concepción Hernández
- Servicio de Genética, Hospital Universitario Ramón y Cajal, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Carlos Peces
- Area de Tecnologías de la Información, SESCAM, Toledo, Spain
| | - Dolores Tellería
- Servicio de Genética, Hospital Universitario Ramón y Cajal, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Emilio Cuesta
- Servicio de Radiología, Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma, Madrid, Spain
| | - Rafael Selgas
- Servicio de Nefrología, Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma, Madrid, Spain
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Julián Nevado
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| |
Collapse
|
32
|
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.
Collapse
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.
| |
Collapse
|
33
|
Lalor L, Davies OMT, Basel D, Siegel DH. Café au lait spots: When and how to pursue their genetic origins. Clin Dermatol 2020; 38:421-431. [PMID: 32972601 DOI: 10.1016/j.clindermatol.2020.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Café au lait spots are common birthmarks seen sporadically and in association with several genetic syndromes. Dermatologists are often asked to evaluate these birthmarks both by other physicians and by parents. In some cases, it is challenging to know when and how to pursue further evaluation. Diagnostic challenges may come in the form of the appearance of the individual lesions, areas and patterns of cutaneous involvement, and associated features (or lack thereof). In this review, we aim to clarify when and how to evaluate the child with multiple or patterned café au lait spots and to explain some emerging concepts in our understanding of the genetics of these lesions.
Collapse
Affiliation(s)
- Leah Lalor
- Department of Dermatology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
| | - Olivia M T Davies
- Department of Dermatology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Donald Basel
- Division of Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Dawn H Siegel
- Department of Dermatology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| |
Collapse
|
34
|
Mucaki EJ, Shirley BC, Rogan PK. Expression Changes Confirm Genomic Variants Predicted to Result in Allele-Specific, Alternative mRNA Splicing. Front Genet 2020; 11:109. [PMID: 32211018 PMCID: PMC7066660 DOI: 10.3389/fgene.2020.00109] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/30/2020] [Indexed: 12/11/2022] Open
Abstract
Splice isoform structure and abundance can be affected by either noncoding or masquerading coding variants that alter the structure or abundance of transcripts. When these variants are common in the population, these nonconstitutive transcripts are sufficiently frequent so as to resemble naturally occurring, alternative mRNA splicing. Prediction of the effects of such variants has been shown to be accurate using information theory-based methods. Single nucleotide polymorphisms (SNPs) predicted to significantly alter natural and/or cryptic splice site strength were shown to affect gene expression. Splicing changes for known SNP genotypes were confirmed in HapMap lymphoblastoid cell lines with gene expression microarrays and custom designed q-RT-PCR or TaqMan assays. The majority of these SNPs (15 of 22) as well as an independent set of 24 variants were then subjected to RNAseq analysis using the ValidSpliceMut web beacon (http://validsplicemut.cytognomix.com), which is based on data from the Cancer Genome Atlas and International Cancer Genome Consortium. SNPs from different genes analyzed with gene expression microarray and q-RT-PCR exhibited significant changes in affected splice site use. Thirteen SNPs directly affected exon inclusion and 10 altered cryptic site use. Homozygous SNP genotypes resulting in stronger splice sites exhibited higher levels of processed mRNA than alleles associated with weaker sites. Four SNPs exhibited variable expression among individuals with the same genotypes, masking statistically significant expression differences between alleles. Genome-wide information theory and expression analyses (RNAseq) in tumor exomes and genomes confirmed splicing effects for 7 of the HapMap SNP and 14 SNPs identified from tumor genomes. q-RT-PCR resolved rare splice isoforms with read abundance too low for statistical significance in ValidSpliceMut. Nevertheless, the web-beacon provides evidence of unanticipated splicing outcomes, for example, intron retention due to compromised recognition of constitutive splice sites. Thus, ValidSpliceMut and q-RT-PCR represent complementary resources for identification of allele-specific, alternative splicing.
Collapse
Affiliation(s)
- Eliseos J Mucaki
- Department of Biochemistry, University of Western Ontario, London, ON, Canada
| | | | - Peter K Rogan
- Department of Biochemistry, University of Western Ontario, London, ON, Canada.,CytoGnomix, London, ON, Canada.,Department of Oncology University of Western Ontario, London, ON, Canada.,Department of Computer Science, University of Western Ontario, London, ON, Canada
| |
Collapse
|
35
|
Ravindran DM, Ravi S, Santhanakrishnan M, Sk B. LASER Assisted Excision of Solitary Neurofibroma in the Gingiva. Cureus 2020; 12:e7118. [PMID: 32257664 PMCID: PMC7105066 DOI: 10.7759/cureus.7118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Neurofibromatosis (NF) is a genetic disorder that presents as benign tumours of the nervous system originating from the nerve sheath. It is of three types: Type I, Type II and Schwannomatosis. Type I Neurofibromatosis or von Recklinghausen's disease is the most common type of neurofibromatosis seen and it accounts for 90% of all cases seen. It can be seen as light brown pigmentation spots (Café-au-lait) on the skin and multiple small tumours among the nerves. Oral manifestations of NF are very rare and can be seen as sessile lesion in the tongue or the gingiva. The major complaints of the oral manifestations include difficulty in speech and mastication which it results in progression of periodontal disease. Here, we present a case report of Type I NF which presented as a sessile lesion in the right maxillary gingiva, for which we performed an excisional biopsy using LASER.
Collapse
Affiliation(s)
- Deepak M Ravindran
- Periodontology, Sri Ramachandra Institute of Higher Education and Research, Chennai, IND
| | - Shravanthy Ravi
- Periodontology, Sri Ramachandra Institute of Higher Education and Research, Chennai, IND
| | | | - Balaji Sk
- Periodontology, Sri Ramachandra Institute of Higher Education and Research, Chennai, IND
| |
Collapse
|
36
|
Adashek JJ, Kato S, Lippman SM, Kurzrock R. The paradox of cancer genes in non-malignant conditions: implications for precision medicine. Genome Med 2020; 12:16. [PMID: 32066498 PMCID: PMC7027240 DOI: 10.1186/s13073-020-0714-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/30/2020] [Indexed: 02/07/2023] Open
Abstract
Next-generation sequencing has enabled patient selection for targeted drugs, some of which have shown remarkable efficacy in cancers that have the cognate molecular signatures. Intriguingly, rapidly emerging data indicate that altered genes representing oncogenic drivers can also be found in sporadic non-malignant conditions, some of which have negligible and/or low potential for transformation to cancer. For instance, activating KRAS mutations are discerned in endometriosis and in brain arteriovenous malformations, inactivating TP53 tumor suppressor mutations in rheumatoid arthritis synovium, and AKT, MAPK, and AMPK pathway gene alterations in the brains of Alzheimer's disease patients. Furthermore, these types of alterations may also characterize hereditary conditions that result in diverse disabilities and that are associated with a range of lifetime susceptibility to the development of cancer, varying from near universal to no elevated risk. Very recently, the repurposing of targeted cancer drugs for non-malignant conditions that are associated with these genomic alterations has yielded therapeutic successes. For instance, the phenotypic manifestations of CLOVES syndrome, which is characterized by tissue overgrowth and complex vascular anomalies that result from the activation of PIK3CA mutations, can be ameliorated by the PIK3CA inhibitor alpelisib, which was developed and approved for breast cancer. In this review, we discuss the profound implications of finding molecular alterations in non-malignant conditions that are indistinguishable from those driving cancers, with respect to our understanding of the genomic basis of medicine, the potential confounding effects in early cancer detection that relies on sensitive blood tests for oncogenic mutations, and the possibility of reverse repurposing drugs that are used in oncology in order to ameliorate non-malignant illnesses and/or to prevent the emergence of cancer.
Collapse
Affiliation(s)
- Jacob J Adashek
- Department of Internal Medicine, University of South Florida, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Shumei Kato
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, University of California San Diego Moores Cancer Center, Health Sciences Drive, La Jolla, CA, 92093, USA
| | - Scott M Lippman
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, University of California San Diego Moores Cancer Center, Health Sciences Drive, La Jolla, CA, 92093, USA
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, University of California San Diego Moores Cancer Center, Health Sciences Drive, La Jolla, CA, 92093, USA.
| |
Collapse
|
37
|
Bergqvist C, Servy A, Valeyrie-Allanore L, Ferkal S, Combemale P, Wolkenstein P. Neurofibromatosis 1 French national guidelines based on an extensive literature review since 1966. Orphanet J Rare Dis 2020; 15:37. [PMID: 32014052 PMCID: PMC6998847 DOI: 10.1186/s13023-020-1310-3] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/17/2020] [Indexed: 12/13/2022] Open
Abstract
Neurofibromatosis type 1 is a relatively common genetic disease, with a prevalence ranging between 1/3000 and 1/6000 people worldwide. The disease affects multiple systems with cutaneous, neurologic, and orthopedic as major manifestations which lead to significant morbidity or mortality. Indeed, NF1 patients are at an increased risk of malignancy and have a life expectancy about 10-15 years shorter than the general population. The mainstay of management of NF1 is a patient-centered longitudinal care with age-specific monitoring of clinical manifestations, aiming at the early recognition and symptomatic treatment of complications as they occur. Protocole national de diagnostic et de soins (PNDS) are mandatory French clinical practice guidelines for rare diseases required by the French national plan for rare diseases. Their purpose is to provide health care professionals with guidance regarding the optimal diagnostic and therapeutic management of patients affected with a rare disease; and thus, harmonizing their management nationwide. PNDS are usually developed through a critical literature review and a multidisciplinary expert consensus. The purpose of this article is to present the French guidelines on NF1, making them even more available to the international medical community. We further dwelled on the emerging new evidence that might have therapeutic potential or a strong impact on NF1 management in the coming feature. Given the complexity of the disease, the management of children and adults with NF1 entails the full complement healthcare providers and communication among the various specialties.
Collapse
Affiliation(s)
- Christina Bergqvist
- Faculty of medicine, Université Paris-Est Creteil (UPEC), F-94010 Créteil Cedex, France
- Assistance Publique-Hôpital Paris (AP-HP), Hôpital Henri-Mondor, Service de Dermatologie, F-94010 Créteil, France
| | - Amandine Servy
- Assistance Publique-Hôpital Paris (AP-HP), Hôpital Henri-Mondor, Service de Dermatologie, F-94010 Créteil, France
| | - Laurence Valeyrie-Allanore
- INSERM, Centre d’Investigation Clinique 006, Referral Center of Neurofibromatosis, Assistance Publique-Hôpital Paris (AP-HP), Hôpital Henri-Mondor, F-94010 Créteil, France
| | - Salah Ferkal
- INSERM, Centre d’Investigation Clinique 006, Referral Center of Neurofibromatosis, Assistance Publique-Hôpital Paris (AP-HP), Hôpital Henri-Mondor, F-94010 Créteil, France
| | - Patrick Combemale
- Rhône-Alpes Auvergne Competence Center for the treatment of Neurofibromatosis type 1, Léon Bérard Comprehensive Cancer Center, Hôpitaux Universitaires de Lyon, Université de Lyon, F-69008 Lyon, France
| | - Pierre Wolkenstein
- Faculty of medicine, Université Paris-Est Creteil (UPEC), F-94010 Créteil Cedex, France
- Assistance Publique-Hôpital Paris (AP-HP), Hôpital Henri-Mondor, Service de Dermatologie, F-94010 Créteil, France
- INSERM, Centre d’Investigation Clinique 006, Referral Center of Neurofibromatosis, Assistance Publique-Hôpital Paris (AP-HP), Hôpital Henri-Mondor, F-94010 Créteil, France
| |
Collapse
|
38
|
Lobbous M, Bernstock JD, Coffee E, Friedman GK, Metrock LK, Chagoya G, Elsayed G, Nakano I, Hackney JR, Korf BR, Nabors LB. An Update on Neurofibromatosis Type 1-Associated Gliomas. Cancers (Basel) 2020; 12:E114. [PMID: 31906320 PMCID: PMC7017116 DOI: 10.3390/cancers12010114] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/26/2019] [Accepted: 12/29/2019] [Indexed: 12/22/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant tumor predisposition syndrome that affects children and adults. Individuals with NF1 are at high risk for central nervous system neoplasms including gliomas. The purpose of this review is to discuss the spectrum of intracranial gliomas arising in individuals with NF1 with a focus on recent preclinical and clinical data. In this review, possible mechanisms of gliomagenesis are discussed, including the contribution of different signaling pathways and tumor microenvironment. Furthermore, we discuss the recent notable advances in the developing therapeutic landscape for NF1-associated gliomas including clinical trials and collaborative efforts.
Collapse
Affiliation(s)
- Mina Lobbous
- Division of Neuro Oncology, Department of Neurology, University of Alabama at Birmingham, 510 20th Street South, Faculty Office Tower Suite 1020 Birmingham, Birmingham, AL 35294, USA; (E.C.)
| | - Joshua D. Bernstock
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
| | - Elizabeth Coffee
- Division of Neuro Oncology, Department of Neurology, University of Alabama at Birmingham, 510 20th Street South, Faculty Office Tower Suite 1020 Birmingham, Birmingham, AL 35294, USA; (E.C.)
| | - Gregory K. Friedman
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (G.K.F.); (L.K.M.)
| | - Laura K. Metrock
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (G.K.F.); (L.K.M.)
| | - Gustavo Chagoya
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (G.C.); (G.E.); (I.N.)
| | - Galal Elsayed
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (G.C.); (G.E.); (I.N.)
| | - Ichiro Nakano
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (G.C.); (G.E.); (I.N.)
| | - James R. Hackney
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Bruce R. Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Louis B. Nabors
- Division of Neuro Oncology, Department of Neurology, University of Alabama at Birmingham, 510 20th Street South, Faculty Office Tower Suite 1020 Birmingham, Birmingham, AL 35294, USA; (E.C.)
| |
Collapse
|
39
|
Identification of a Novel NF1 Frameshift Variant in a Chinese Family with Neurofibromatosis Type 1. BIOMED RESEARCH INTERNATIONAL 2019; 2019:2721357. [PMID: 31886188 PMCID: PMC6925767 DOI: 10.1155/2019/2721357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 10/23/2019] [Accepted: 11/01/2019] [Indexed: 11/27/2022]
Abstract
Neurofibromatosis type 1 (NF1) is a progressive neurocutaneous disorder in humans, mainly characterized by café-au-lait macules (CALMs) and neurofibromas. NF1 is caused by variants of the neurofibromin 1 gene (NF1), which encodes a Ras-GTPase-activating protein called neurofibromin. NF1 variants may result in loss of neurofibromin function and elevation of cell proliferation and tumor formation. In this study, a Chinese NF1 family with an autosomal dominant inheritance pattern was recruited. Exome sequencing and Sanger sequencing were performed to discover the causative variant responsible for the family, followed by molecular analysis of effect of the mutated NF1 protein on Ras activity. A novel frameshift variant c.541dupC (p.(Gln181Profs∗20)) in the NF1 gene was identified in all three affected family members. The variant cosegregated with the disease phenotypes in the pedigree and was absent in 100 healthy controls. Bioinformatic analysis showed that the variant c.541dupC (p.(Gln181Profs∗20)) was pathogenic. The further molecular analysis verified the cells expressing NF1 variant p.(Gln181Profs∗20) partially enhanced Ras activity and elevated cell proliferation and tumor formation due to loss of neurofibromin function caused by the variant. Taken together, the data strongly advocate the c.541dupC (p.(Gln181Profs∗20)) variant as the underlying genetic cause of the Chinese family with NF1. Moreover, our findings broaden the spectrum of NF1 variants and provide molecular insights into the pathogenesis of NF1.
Collapse
|
40
|
Castellanos E, Rosas I, Negro A, Gel B, Alibés A, Baena N, Pineda M, Pi G, Pintos G, Salvador H, Lázaro C, Blanco I, Vilageliu L, Brems H, Grinberg D, Legius E, Serra E. Mutational spectrum by phenotype: panel‐based NGS testing of patients with clinical suspicion of RASopathy and children with multiple café‐au‐lait macules. Clin Genet 2019; 97:264-275. [DOI: 10.1111/cge.13649] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/19/2019] [Accepted: 09/25/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Elisabeth Castellanos
- Hereditary Cancer Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC)Germans Trias & Pujol Research Institute (IGTP) Barcelona Spain
| | - Inma Rosas
- Hereditary Cancer Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC)Germans Trias & Pujol Research Institute (IGTP) Barcelona Spain
| | - Alex Negro
- Hereditary Cancer Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC)Germans Trias & Pujol Research Institute (IGTP) Barcelona Spain
| | - Bernat Gel
- Hereditary Cancer Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC)Germans Trias & Pujol Research Institute (IGTP) Barcelona Spain
| | - Andreu Alibés
- Cancer Genetics and Epigenetics GroupProgram of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias & Pujol Research Institute (IGTP) Barcelona Spain
| | - Neus Baena
- Genetics Laboratory of the UDIAT‐CDParc Tauli Health Corporation Barcelona Spain
| | - Mercè Pineda
- Neuropaediatrics UnitHospital Sant Joan de Déu Barcelona Spain
| | - Graciela Pi
- Neuropaediatrics UnitLa Ribera Hospital Valencia Spain
| | - Guillem Pintos
- Department of PediatricsGermans Trias i Pujol University Hospital and Research Institute (IGTP), Universitat de Barcelona Barcelona Spain
| | - Hector Salvador
- Paediatrics Oncology UnitHospital Sant Joan de Déu Barcelona Spain
| | - Conxi Lázaro
- Hereditary Cancer ProgramCatalan Institute of Oncology (ICO‐IDIBELL‐ONCOBELL), L'Hospitalet de Llobregat Barcelona Spain
- Centro de Investigación Biomédica en RED (CIBERONC)Instituto de Salud Carlos III Madrid Spain
| | - Ignacio Blanco
- Clinical Genetics and Genetic Counseling ProgramGermans Trias i Pujol Hospital Barcelona Spain
| | - Lluïsa Vilageliu
- Department of Genetics, Microbiology and Statistics, Facultat de BiologiaUniversitat de Barcelona (UB), IBUB, IRSJD, CIBERER Barcelona Spain
| | - Hilde Brems
- Laboratory for Neurofibromatosis Research, Department of Human GeneticsKU Leuven University Hospital Leuven Belgium
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Facultat de BiologiaUniversitat de Barcelona (UB), IBUB, IRSJD, CIBERER Barcelona Spain
| | - Eric Legius
- Laboratory for Neurofibromatosis Research, Department of Human GeneticsKU Leuven University Hospital Leuven Belgium
| | - Eduard Serra
- Hereditary Cancer Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC)Germans Trias & Pujol Research Institute (IGTP) Barcelona Spain
- Centro de Investigación Biomédica en RED (CIBERONC)Instituto de Salud Carlos III Madrid Spain
| |
Collapse
|
41
|
Melloni G, Eoli M, Cesaretti C, Bianchessi D, Ibba MC, Esposito S, Scuvera G, Morcaldi G, Micheli R, Piozzi E, Avignone S, Chiapparini L, Pantaleoni C, Natacci F, Finocchiaro G, Saletti V. Risk of Optic Pathway Glioma in Neurofibromatosis Type 1: No Evidence of Genotype-Phenotype Correlations in A Large Independent Cohort. Cancers (Basel) 2019; 11:cancers11121838. [PMID: 31766501 PMCID: PMC6966666 DOI: 10.3390/cancers11121838] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/17/2019] [Accepted: 11/18/2019] [Indexed: 11/16/2022] Open
Abstract
The occurrence of optic pathway gliomas (OPGs) in children with neurofibromatosis type 1 (NF1) still raises many questions regarding screening and surveillance because of the lack of robust prognostic factors. Recent studies of an overall cohort of 381 patients have suggested that the genotype may be the main determinant of the development of OPG, with the risk being higher in patients harbouring NF1 mutations in the 5’ tertile and the cysteine/serine-rich domain. In an attempt to confirm this hypothesis, we used strict criteria to select a large independent cohort of 309 NF1 patients with defined constitutional NF1 mutations and appropriate brain images (255 directly enrolled and 54 as a result of a literature search). One hundred and thirty-two patients had OPG and 177 did not. The association of the position (tertiles and functional domains) and type of NF1 mutation with the development of OPG was analysed using the χ2 test and Fisher’s exact probability test; odds ratios (ORs) with 95% confidence intervals were calculated, and Bonferroni’s correction for multiple comparisons was applied; multiple logistic regression was also used to study genotype–phenotype associations further. Our findings show no significant correlation between the site/type of NF1 mutation and the risk of OPG, and thus do not support the hypothesis that certain constitutional mutations provide prognostic information in this regard. In addition, we combined our cohort with a previously described cohort of 381 patients for a total of 690 patients and statistically re-analysed the results. The re-analysis confirmed that there were no correlations between the site (tertile and domain) and the risk of OPG, thus further strengthening our conclusions.
Collapse
Affiliation(s)
- Giulia Melloni
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20121 Milan, Italy; (G.M.); (S.E.); (C.P.)
| | - Marica Eoli
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20121 Milan, Italy; (M.E.); (D.B.); (M.C.I.); (G.F.)
| | - Claudia Cesaretti
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, via Francesco Sforza 28, 20122 Milan, Italy; (C.C.); (F.N.)
| | - Donatella Bianchessi
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20121 Milan, Italy; (M.E.); (D.B.); (M.C.I.); (G.F.)
| | - Maria Cristina Ibba
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20121 Milan, Italy; (M.E.); (D.B.); (M.C.I.); (G.F.)
| | - Silvia Esposito
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20121 Milan, Italy; (G.M.); (S.E.); (C.P.)
| | - Giulietta Scuvera
- Department of Pathophysiology and Transplantation, Pediatric Highly Intensive Care Unit, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, via Francesco Sforza 28, 20122 Milan, Italy;
| | - Guido Morcaldi
- Paediatric Neurology and Neuromuscular Disorders, University of Genoa and Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genoa, Italy;
| | - Roberto Micheli
- Pediatric Neuropsychiatry, Spedali Civili of Brescia, Piazzale Spedali Civili 1, 25125 Brescia, Italy;
| | - Elena Piozzi
- Pediatric Department, ASST Grande Ospedale Metropolitano Niguarda, Piazza Ospedale Maggiore 3, 20162 Milan, Italy;
| | - Sabrina Avignone
- Neuroradiology Department, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, University of Milan, via Francesco Sforza 28, 20122 Milan, Italy;
| | - Luisa Chiapparini
- Neuroradiology Department, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20121 Milan, Italy;
| | - Chiara Pantaleoni
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20121 Milan, Italy; (G.M.); (S.E.); (C.P.)
| | - Federica Natacci
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, via Francesco Sforza 28, 20122 Milan, Italy; (C.C.); (F.N.)
| | - Gaetano Finocchiaro
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20121 Milan, Italy; (M.E.); (D.B.); (M.C.I.); (G.F.)
| | - Veronica Saletti
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20121 Milan, Italy; (G.M.); (S.E.); (C.P.)
- Correspondence:
| |
Collapse
|
42
|
Pacot L, Burin des Roziers C, Laurendeau I, Briand-Suleau A, Coustier A, Mayard T, Tlemsani C, Faivre L, Thomas Q, Rodriguez D, Blesson S, Dollfus H, Muller YG, Parfait B, Vidaud M, Gilbert-Dussardier B, Yardin C, Dauriat B, Derancourt C, Vidaud D, Pasmant E. One NF1 Mutation may Conceal Another. Genes (Basel) 2019; 10:genes10090633. [PMID: 31443423 PMCID: PMC6769760 DOI: 10.3390/genes10090633] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/10/2019] [Accepted: 08/20/2019] [Indexed: 01/01/2023] Open
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant disease with complete penetrance but high variable expressivity. NF1 is caused by loss-of-function mutations in the NF1 gene, a negative regulator of the RAS-MAPK pathway. The NF1 gene has one of the highest mutation rates in human disorders, which may explain the outbreak of independent de novo variants in the same family. Here, we report the co-occurrence of pathogenic variants in the NF1 and SPRED1 genes in six families with NF1 and Legius syndrome, using next-generation sequencing. In five of these families, we observed the co-occurrence of two independent NF1 variants. All NF1 variants were classified as pathogenic, according to the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG-AMP) guidelines. In the sixth family, one sibling inherited a complete deletion of the NF1 gene from her mother and carried a variant of unknown significance in the SPRED1 gene. This variant was also present in her brother, who was diagnosed with Legius syndrome, a differential diagnosis of NF1. This work illustrates the complexity of molecular diagnosis in a not-so-rare genetic disease.
Collapse
Affiliation(s)
- Laurence Pacot
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Cyril Burin des Roziers
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Ingrid Laurendeau
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Audrey Briand-Suleau
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Audrey Coustier
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
| | - Théodora Mayard
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
| | - Camille Tlemsani
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Laurence Faivre
- Inserm, UMR 1231, Génétique des Anomalies du Développement, Université de Bourgogne, 21079 Dijon, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d'Enfants, 21079 Dijon, France
| | - Quentin Thomas
- Inserm, UMR 1231, Génétique des Anomalies du Développement, Université de Bourgogne, 21079 Dijon, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d'Enfants, 21079 Dijon, France
| | - Diana Rodriguez
- Department of Child Neurology and National Reference Center for Neurogenetic Disorders, Armand Trousseau Hospital, GHUEP, AP-HP, INSERM U1141, 75012 Paris, France
- GRC n°19 ConCer-LD, Sorbonne Université, 75012 Paris, France
| | - Sophie Blesson
- Service de Génétique, CHRU de Tours, 37044 Tours, France
| | - Hélène Dollfus
- Centre de référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), Hôpital Civil, 67091 Strasbourg, France
- Service de Génétique Médicale, Hôpital de Hautepierre, 67200 Strasbourg, France
- Laboratoire de Génétique Médicale, INSERM U1112, 67000 Strasbourg, France
| | | | - Béatrice Parfait
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Michel Vidaud
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | | | - Catherine Yardin
- Department of Cytogenetics and clinical genetics, Limoges University Hospital, 87042 Limoges, France
- UMR 7252, Limoges University, CNRS, XLIM, 87000 Limoges, France
| | - Benjamin Dauriat
- Department of Cytogenetics and clinical genetics, Limoges University Hospital, 87042 Limoges, France
| | - Christian Derancourt
- EA 4537, Antilles University, 97261 Fort-de-France, Martinique, France
- DRCI, Martinique University Hospital, 97261 Fort-de-France, Martinique, France
| | - Dominique Vidaud
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Eric Pasmant
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France.
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France.
| |
Collapse
|
43
|
Wang W, Qin W, Ge H, Kong X, Xie C, Tang Y, Li M. Clinical and molecular characteristics of thirty NF1 variants in Chinese patients with neurofibromatosis type 1. Mol Biol Rep 2019; 46:4349-4359. [PMID: 31201679 DOI: 10.1007/s11033-019-04888-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/15/2019] [Indexed: 01/29/2023]
Abstract
Neurofibromatosis type 1 (NF1) is a common autosomal dominant tumor-predisposition disorder that mainly impacts the nervous system and skin. Since the full clinical presentation of NF1 depends on age, it can be difficult to make an early and definite diagnosis in paediatric patients without family history who only exhibited multiple cafè-au-lait spots, highlighting the need for mutational analysis. A combination of techniques was conducted in 30 families with NF1, including multi-gene panels, direct sequencing, cDNA sequencing and multiplex ligation-dependent probe amplification. Thirty variants were identified in 36 patients from the 30 families, among which ten variants were novel. As a result, we confirmed that the combination of techniques were highly accurate and sensitive for identifying pathogenic variants in patients clinically suspected of having NF1, in particular, for patients who only present with multiple cafè-au-lait spots.
Collapse
Affiliation(s)
- Wen Wang
- Departments of Dermatology and Venereology, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Weibing Qin
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, Guangzhou, China
| | - Hongsong Ge
- Departments of Dermatology, Anhui Provincial Children's Hospital, Hefei, Anhui, China
| | | | - Chao Xie
- Department of Paediatrics, The First People's Hospital of Hefei, Hefei, Anhui, China
| | - Yunge Tang
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, Guangzhou, China.
| | - Ming Li
- Departments of Dermatology, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| |
Collapse
|
44
|
Baraban E, Sadigh S, Rosenbaum J, Van Arnam J, Bogusz AM, Mehr C, Bagg A. Cyclin D1 expression and novel mutational findings in Rosai-Dorfman disease. Br J Haematol 2019; 186:837-844. [PMID: 31172509 DOI: 10.1111/bjh.16006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/16/2019] [Indexed: 12/13/2022]
Abstract
Rosai-Dorfman disease (RDD) is an enigmatic histiocytic disorder classically diagnosed by a distinctive combination of pathological features: emperipolesis, or migration of intact haematological cells through the voluminous cytoplasm of lesional histiocytes, and expression of S100 by these histiocytes. The pathogenesis has long been elusive until the recent detection of recurrent and mutually exclusive mutations in several oncogenes in the mitogen-activated protein kinase (MAPK) pathway. Based on these findings, we investigated a cohort of 21 RDD patients and found that the lesional histiocytes in 86% (18/21) of patients exhibited strong and diffuse nuclear Cyclin D1 expression, which not only may provide a diagnostic marker for this sometimes pathologically challenging disease, but also probably reflects constitutive MAPK pathway activation because we additionally identified phosphorylated-ERK expression in 90% (19/21) of cases. Further, we performed massively parallel sequencing on a subset (6/18) of the CyclinD1 positive cases, identifying several mutations that have not been previously reported in RDD. Taken together, our findings bolster the concept of RDD as a disease of MAPK activation in a substantial percentage of cases and enhance the current understanding of the pathogenesis of RDD.
Collapse
Affiliation(s)
- Ezra Baraban
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Sam Sadigh
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Jason Rosenbaum
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - John Van Arnam
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Agata M Bogusz
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Chelsea Mehr
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Adam Bagg
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
45
|
Iwanowski P, Kowalska M, Prendecki M, Dorszewska J, Kozubski W, Rydzanicz M, Płoski R, Losy J. Primary progressive multiple sclerosis and neurofibromatosis type 1. Mult Scler Relat Disord 2019; 32:66-69. [PMID: 31048186 DOI: 10.1016/j.msard.2019.04.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Multiple sclerosis (MS) is a common inflammatory demyelinating disease of the central nervous system. The clinical phenotype is probably modified by interactions from genetic and environmental factors. Neurofibromatosis type 1 (NF1) is an autosomal dominant neurocutaneous disease. NF1 gene mutations lead to clinical manifestation in the peripheral and central nervous system. Coexistence of MS and NF1 is a rare condition. OBJECTIVE To report the case of the patient with primary progressive MS (PPMS) and NF1. METHODS A retrospective analysis of a patient who has undergone whole exome sequencing confirmed by Sanger sequencing. RESULTS We reported a novel de novo c.6817delC deletion and rs1801052 polymorphism in NF1 gene associated with NF1 symptoms, as well as numerous polymorphisms in SPG7, SPG15, SPG39 genes responsible for benign spastic paraplegia. CONCLUSION Co-occurrence of PPMS and NF1 may be a consequence of genetic changes.
Collapse
Affiliation(s)
- Piotr Iwanowski
- Chair and Department of Neurology, Poznan University of Medical Sciences, 49 Przybyszewskiego Street, 60-355 Poznan, Poland.
| | - Marta Kowalska
- Laboratory of Neurobiology, Department of Neurology, Poznan University of Medical Sciences, 49 Przybyszewskiego Street, 60-355 Poznan, Poland
| | - Michał Prendecki
- Laboratory of Neurobiology, Department of Neurology, Poznan University of Medical Sciences, 49 Przybyszewskiego Street, 60-355 Poznan, Poland
| | - Jolanta Dorszewska
- Laboratory of Neurobiology, Department of Neurology, Poznan University of Medical Sciences, 49 Przybyszewskiego Street, 60-355 Poznan, Poland
| | - Wojciech Kozubski
- Chair and Department of Neurology, Poznan University of Medical Sciences, 49 Przybyszewskiego Street, 60-355 Poznan, Poland
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, 3c Pawinskiego St., 02-106 Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, 3c Pawinskiego St., 02-106 Warsaw, Poland
| | - Jacek Losy
- Department of Clinical Neuroimmunology, Chair and Department of Neurology, Poznan University of Medical Sciences, 49 Przybyszewskiego Street, 60-355 Poznan, Poland
| |
Collapse
|
46
|
Scheffzek K, Shivalingaiah G. Ras-Specific GTPase-Activating Proteins-Structures, Mechanisms, and Interactions. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a031500. [PMID: 30104198 DOI: 10.1101/cshperspect.a031500] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ras-specific GTPase-activating proteins (RasGAPs) down-regulate the biological activity of Ras proteins by accelerating their intrinsic rate of GTP hydrolysis, basically by a transition state stabilizing mechanism. Oncogenic Ras is commonly not sensitive to RasGAPs caused by interference of mutants with the electronic or steric requirements of the transition state, resulting in up-regulation of activated Ras in respective cells. RasGAPs are modular proteins containing a helical catalytic RasGAP module surrounded by smaller domains that are frequently involved in the subcellular localization or contributing to regulatory features of their host proteins. In this review, we summarize current knowledge about RasGAP structure, mechanism, regulation, and dual-substrate specificity and discuss in some detail neurofibromin, one of the most important negative Ras regulators in cellular growth control and neuronal function.
Collapse
Affiliation(s)
- Klaus Scheffzek
- Division of Biological Chemistry (Biocenter), Medical University of Innsbruck, A-6020 Innsbruck, Austria
| | - Giridhar Shivalingaiah
- Division of Biological Chemistry (Biocenter), Medical University of Innsbruck, A-6020 Innsbruck, Austria
| |
Collapse
|
47
|
Isakson SH, Rizzardi AE, Coutts AW, Carlson DF, Kirstein MN, Fisher J, Vitte J, Williams KB, Pluhar GE, Dahiya S, Widemann BC, Dombi E, Rizvi T, Ratner N, Messiaen L, Stemmer-Rachamimov AO, Fahrenkrug SC, Gutmann DH, Giovannini M, Moertel CL, Largaespada DA, Watson AL. Genetically engineered minipigs model the major clinical features of human neurofibromatosis type 1. Commun Biol 2018; 1:158. [PMID: 30302402 PMCID: PMC6168575 DOI: 10.1038/s42003-018-0163-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/07/2018] [Indexed: 12/13/2022] Open
Abstract
Neurofibromatosis Type 1 (NF1) is a genetic disease caused by mutations in Neurofibromin 1 (NF1). NF1 patients present with a variety of clinical manifestations and are predisposed to cancer development. Many NF1 animal models have been developed, yet none display the spectrum of disease seen in patients and the translational impact of these models has been limited. We describe a minipig model that exhibits clinical hallmarks of NF1, including café au lait macules, neurofibromas, and optic pathway glioma. Spontaneous loss of heterozygosity is observed in this model, a phenomenon also described in NF1 patients. Oral administration of a mitogen-activated protein kinase/extracellular signal-regulated kinase inhibitor suppresses Ras signaling. To our knowledge, this model provides an unprecedented opportunity to study the complex biology and natural history of NF1 and could prove indispensable for development of imaging methods, biomarkers, and evaluation of safety and efficacy of NF1-targeted therapies.
Collapse
Affiliation(s)
- Sara H Isakson
- Masonic Cancer Center, University of Minnesota, Room 3-129, Cancer Cardiovascular Research Building, 2231 6th Street SE, Minneapolis, MN, 55455, USA
| | - Anthony E Rizzardi
- Recombinetics Inc., 1246 University Avenue W., Suite 301, St. Paul, MN, 55104, USA
| | - Alexander W Coutts
- Recombinetics Inc., 1246 University Avenue W., Suite 301, St. Paul, MN, 55104, USA
| | - Daniel F Carlson
- Recombinetics Inc., 1246 University Avenue W., Suite 301, St. Paul, MN, 55104, USA
| | - Mark N Kirstein
- Masonic Cancer Center, University of Minnesota, Room 3-129, Cancer Cardiovascular Research Building, 2231 6th Street SE, Minneapolis, MN, 55455, USA.,Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Room 459, 717 Delaware Street SE, Minneapolis, MN, 55414, USA
| | - James Fisher
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Room 459, 717 Delaware Street SE, Minneapolis, MN, 55414, USA
| | - Jeremie Vitte
- Department of Head and Neck Surgery, David Geffen School of Medicine at UCLA and Jonsson Comprehensive Cancer Center (JCCC), University of California Los Angeles, 675 Charles E Young Drive S, MRL Room 2240, Los Angeles, CA, 90095, USA
| | - Kyle B Williams
- Masonic Cancer Center, University of Minnesota, Room 3-129, Cancer Cardiovascular Research Building, 2231 6th Street SE, Minneapolis, MN, 55455, USA
| | - G Elizabeth Pluhar
- Masonic Cancer Center, University of Minnesota, Room 3-129, Cancer Cardiovascular Research Building, 2231 6th Street SE, Minneapolis, MN, 55455, USA.,Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Sonika Dahiya
- Division of Neuropathology, Department of Pathology and Immunology, Washington University School of Medicine, 660S. Euclid Avenue, CB 8118, St. Louis, MO, 63110, USA
| | - Brigitte C Widemann
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, CRC 1-5750, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Eva Dombi
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, CRC 1-5750, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Tilat Rizvi
- Division of Experimental Hematology and Cancer Biology, Department of Pediatrics, Cincinnati Children's Hospital, University of Cincinnati, 3333 Burnet Avenue, ML 7013, Cincinnati, OH, 45229, USA
| | - Nancy Ratner
- Division of Experimental Hematology and Cancer Biology, Department of Pediatrics, Cincinnati Children's Hospital, University of Cincinnati, 3333 Burnet Avenue, ML 7013, Cincinnati, OH, 45229, USA
| | - Ludwine Messiaen
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Kaul Building, 720 20th Street South, Birmingham, AL, 35294, USA
| | - Anat O Stemmer-Rachamimov
- Department of Pathology, Massachusetts General Hospital, Warren Building, Room 333A, 55 Fruit Street, Boston, MA, 02114, USA
| | - Scott C Fahrenkrug
- Recombinetics Inc., 1246 University Avenue W., Suite 301, St. Paul, MN, 55104, USA
| | - David H Gutmann
- Department of Neurology, Washington University School of Medicine, Box 8111, 660S. Euclid Avenue, St. Louis, MO, 63110, USA
| | - Marco Giovannini
- Department of Head and Neck Surgery, David Geffen School of Medicine at UCLA and Jonsson Comprehensive Cancer Center (JCCC), University of California Los Angeles, 675 Charles E Young Drive S, MRL Room 2240, Los Angeles, CA, 90095, USA
| | - Christopher L Moertel
- Masonic Cancer Center, University of Minnesota, Room 3-129, Cancer Cardiovascular Research Building, 2231 6th Street SE, Minneapolis, MN, 55455, USA.,Department of Pediatrics, University of Minnesota, Room 3-129, Cancer Cardiovascular Research Building, 2231 6th Street SE, Minneapolis, MN, 55455, USA
| | - David A Largaespada
- Masonic Cancer Center, University of Minnesota, Room 3-129, Cancer Cardiovascular Research Building, 2231 6th Street SE, Minneapolis, MN, 55455, USA.,Department of Pediatrics, University of Minnesota, Room 3-129, Cancer Cardiovascular Research Building, 2231 6th Street SE, Minneapolis, MN, 55455, USA
| | - Adrienne L Watson
- Recombinetics Inc., 1246 University Avenue W., Suite 301, St. Paul, MN, 55104, USA.
| |
Collapse
|
48
|
Agrahari AK, Muskan M, George Priya Doss C, Siva R, Zayed H. Computational insights of K1444N substitution in GAP-related domain of NF1 gene associated with neurofibromatosis type 1 disease: a molecular modeling and dynamics approach. Metab Brain Dis 2018; 33:1443-1457. [PMID: 29804243 DOI: 10.1007/s11011-018-0251-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 05/17/2018] [Indexed: 12/18/2022]
Abstract
The NF1 gene encodes for neurofibromin protein, which is ubiquitously expressed, but most highly in the central nervous system. Non-synonymous SNPs (nsSNPs) in the NF1 gene were found to be associated with Neurofibromatosis Type 1 disease, which is characterized by the growth of tumors along nerves in the skin, brain, and other parts of the body. In this study, we used several in silico predictions tools to analyze 16 nsSNPs in the RAS-GAP domain of neurofibromin, the K1444N (K1423N) mutation was predicted as the most pathogenic. The comparative molecular dynamic simulation (MDS; 50 ns) between the wild type and the K1444N (K1423N) mutant suggested a significant change in the electrostatic potential. In addition, the RMSD, RMSF, Rg, hydrogen bonds, and PCA analysis confirmed the loss of flexibility and increase in compactness of the mutant protein. Further, SASA analysis revealed exchange between hydrophobic and hydrophilic residues from the core of the RAS-GAP domain to the surface of the mutant domain, consistent with the secondary structure analysis that showed significant alteration in the mutant protein conformation. Our data concludes that the K1444N (K1423N) mutant lead to increasing the rigidity and compactness of the protein. This study provides evidence of the benefits of the computational tools in predicting the pathogenicity of genetic mutations and suggests the application of MDS and different in silico prediction tools for variant assessment and classification in genetic clinics.
Collapse
Affiliation(s)
- Ashish Kumar Agrahari
- Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Meghana Muskan
- Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - C George Priya Doss
- Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
| | - R Siva
- Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar.
| |
Collapse
|
49
|
Palma Milla C, Lezana Rosales JM, López Montiel J, Andrés Garrido LD, Sánchez Linares C, Carmona Tamajón S, Torres Fernández C, Sánchez González P, Franco Freire S, Benito López C, López Siles J. Neurofibromatosis type I: mutation spectrum of NF1 in spanish patients. Ann Hum Genet 2018; 82:425-436. [PMID: 30014477 DOI: 10.1111/ahg.12272] [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] [Received: 01/15/2018] [Revised: 05/19/2018] [Accepted: 06/18/2018] [Indexed: 01/07/2023]
Abstract
Neurofibromatosis type I (NF1) is one of the most common genetic disorders in humans. NF1, a tumor predisposition syndrome, is caused by heterozygous pathogenic variants in the NF1 gene. Molecular genetic testing of NF1 is complex, especially because of the presence of a high number of partial pseudogenes, some of them with a high percentage of sequence identity. In this study, we have analyzed the largest cohort of NF1 Spanish patients (150 unrelated individuals suspected of having NF1 and 53 relatives, making a total of 203 individuals). Mutation analysis of the entire coding region was performed in all unrelated index patients. Additionally, the Multiplex Ligation-dependent Probe Amplification (MLPA) test of the NF1 gene and SPRED1 gene analysis (sequencing and MLPA test) was performed in some of the negative patients for NF1 point mutations. When fulfilling the National Institutes of Health (NIH) criterion for the clinical diagnosis of NF1, the detection rate was 79%. Among the 80 genetically confirmed NF1 probands, we detected 69 different pathogenic variants. Two mutations (3%) were gross deletions of the whole gene, the remaining 78 mutations (97%) were small changes spread among all NF1 exons. Among these 69 different mutations detected, 42 mutations were described elsewhere, and 27 mutations were novel mutations. When segregation was studied, 67% of mutations resulted de novo variants. No genetic mosaicism was detected on patients' parents.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Sara Franco Freire
- Hospital Regional Universitario de Málaga. U.G.C. de Laboratorio. Sección de Genética
| | - Carmen Benito López
- Hospital Regional Universitario de Málaga. U.G.C. de Laboratorio. Sección de Genética
| | | |
Collapse
|
50
|
Jia X, Madireddy L, Caillier S, Santaniello A, Esposito F, Comi G, Stuve O, Zhou Y, Taylor B, Kilpatrick T, Martinelli-Boneschi F, Cree BAC, Oksenberg JR, Hauser SL, Baranzini SE. Genome sequencing uncovers phenocopies in primary progressive multiple sclerosis. Ann Neurol 2018; 84:51-63. [PMID: 29908077 PMCID: PMC6119489 DOI: 10.1002/ana.25263] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 01/06/2023]
Abstract
Objective Primary progressive multiple sclerosis (PPMS) causes accumulation of neurological disability from disease onset without clinical attacks typical of relapsing multiple sclerosis (RMS). However, whether genetic variation influences the disease course remains unclear. We aimed to determine whether mutations causative of neurological disorders that share features with multiple sclerosis (MS) contribute to risk for developing PPMS. Methods We examined whole‐genome sequencing (WGS) data from 38 PPMS and 81 healthy subjects of European ancestry. We selected pathogenic variants exclusively found in PPMS patients that cause monogenic neurological disorders and performed two rounds of replication genotyping in 746 PPMS, 3,049 RMS, and 1,000 healthy subjects. To refine our findings, we examined the burden of rare, potentially pathogenic mutations in 41 genes that cause hereditary spastic paraplegias (HSPs) in PPMS (n = 314), secondary progressive multiple sclerosis (SPMS; n = 587), RMS (n = 2,248), and healthy subjects (n = 987) genotyped using the MS replication chip. Results WGS and replication studies identified three pathogenic variants in PPMS patients that cause neurological disorders sharing features with MS: KIF5A p.Ala361Val in spastic paraplegia 10; MLC1 p.Pro92Ser in megalencephalic leukodystrophy with subcortical cysts, and REEP1 c.606 + 43G>T in Spastic Paraplegia 31. Moreover, we detected a significant enrichment of HSP‐related mutations in PPMS patients compared to controls (risk ratio [RR] = 1.95; 95% confidence interval [CI], 1.27–2.98; p = 0.002), as well as in SPMS patients compared to controls (RR = 1.57; 95% CI, 1.18–2.10; p = 0.002). Importantly, this enrichment was not detected in RMS. Interpretation This study provides evidence to support the hypothesis that rare Mendelian genetic variants contribute to the risk for developing progressive forms of MS. Ann Neurol 2018;83:51–63
Collapse
Affiliation(s)
- Xiaoming Jia
- UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA.,Department of Neurology, University of California San Francisco, San Francisco, CA
| | - Lohith Madireddy
- UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA.,Department of Neurology, University of California San Francisco, San Francisco, CA
| | - Stacy Caillier
- UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA.,Department of Neurology, University of California San Francisco, San Francisco, CA
| | - Adam Santaniello
- UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA.,Department of Neurology, University of California San Francisco, San Francisco, CA
| | - Federica Esposito
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSpe), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy.,Department of Neurology and Neuro-rehabilitation, San Raffaele Scientific Institute, Milan, Italy
| | - Giancarlo Comi
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSpe), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy.,Department of Neurology and Neuro-rehabilitation, San Raffaele Scientific Institute, Milan, Italy
| | - Olaf Stuve
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical, Dallas, TX
| | - Yuan Zhou
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Bruce Taylor
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Trevor Kilpatrick
- Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, VIC, Australia
| | - Filippo Martinelli-Boneschi
- Laboratory of Genomics of Neurological Diseases and Department of Neurology, Policlinico San Donato Hospital and Scientific Institute, San Donato Milanese, Italy.,Department of Biomedical Sciences for Health, Università degli Studi di Milano, Milan, Italy.,Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSpe), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Bruce A C Cree
- UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA.,Department of Neurology, University of California San Francisco, San Francisco, CA
| | - Jorge R Oksenberg
- UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA.,Department of Neurology, University of California San Francisco, San Francisco, CA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA
| | - Stephen L Hauser
- UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA.,Department of Neurology, University of California San Francisco, San Francisco, CA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA
| | - Sergio E Baranzini
- UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA.,Department of Neurology, University of California San Francisco, San Francisco, CA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA.,Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, CA
| |
Collapse
|