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Báez-Flores J, Rodríguez-Martín M, Lacal J. The therapeutic potential of neurofibromin signaling pathways and binding partners. Commun Biol 2023; 6:436. [PMID: 37081086 PMCID: PMC10119308 DOI: 10.1038/s42003-023-04815-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/05/2023] [Indexed: 04/22/2023] Open
Abstract
Neurofibromin controls many cell processes, such as growth, learning, and memory. If neurofibromin is not working properly, it can lead to health problems, including issues with the nervous, skeletal, and cardiovascular systems and cancer. This review examines neurofibromin's binding partners, signaling pathways and potential therapeutic targets. In addition, it summarizes the different post-translational modifications that can affect neurofibromin's interactions with other molecules. It is essential to investigate the molecular mechanisms that underlie neurofibromin variants in order to provide with functional connections between neurofibromin and its associated proteins for possible therapeutic targets based on its biological function.
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Affiliation(s)
- Juan Báez-Flores
- Laboratory of Functional Genetics of Rare Diseases, Department of Microbiology and Genetics, University of Salamanca (USAL), 37007, Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), 37007, Salamanca, Spain
| | - Mario Rodríguez-Martín
- Laboratory of Functional Genetics of Rare Diseases, Department of Microbiology and Genetics, University of Salamanca (USAL), 37007, Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), 37007, Salamanca, Spain
| | - Jesus Lacal
- Laboratory of Functional Genetics of Rare Diseases, Department of Microbiology and Genetics, University of Salamanca (USAL), 37007, Salamanca, Spain.
- Institute of Biomedical Research of Salamanca (IBSAL), 37007, Salamanca, Spain.
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2
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Heatley SL, Page EC, Eadie LN, McClure BJ, Rehn J, Yeung DT, Osborn M, Revesz T, Kirby M, White DL. Case Report: Precision Medicine Target Revealed by In Vitro Modeling of Relapsed, Refractory Acute Lymphoblastic Leukemia From a Child With Neurofibromatosis. Front Oncol 2022; 12:851572. [PMID: 35515133 PMCID: PMC9065550 DOI: 10.3389/fonc.2022.851572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/09/2022] [Indexed: 11/30/2022] Open
Abstract
Children with neurofibromatosis have a higher risk of developing juvenile myelomonocytic leukemia and acute myeloid leukemia, but rarely develop B-cell acute lymphoblastic leukemia (B-ALL). Through in-vitro modeling, a novel NF1 p.L2467 frameshift (fs) mutation identified in a relapsed/refractory Ph-like B-ALL patient with neurofibromatosis demonstrated cytokine independence and increased RAS signaling, indicative of leukemic transformation. Furthermore, these cells were sensitive to the MEK inhibitors trametinib and mirdametinib. Bi-allelic NF1 loss of function may be a contributing factor to relapse and with sensitivity to MEK inhibitors, suggests a novel precision medicine target in the setting of neurofibromatosis patients with B-ALL.
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Affiliation(s)
- Susan L Heatley
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia.,Faculty of Health & Medical Science, University of Adelaide, Adelaide, SA, Australia.,Australian & New Zealand Children's Haematology/Oncology Group, Clayton, VIC, Australia
| | - Elyse C Page
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia.,Faculty of Science, University of Adelaide, Adelaide, SA, Australia
| | - Laura N Eadie
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia.,Faculty of Health & Medical Science, University of Adelaide, Adelaide, SA, Australia
| | - Barbara J McClure
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia.,Faculty of Health & Medical Science, University of Adelaide, Adelaide, SA, Australia
| | - Jacqueline Rehn
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia.,Faculty of Health & Medical Science, University of Adelaide, Adelaide, SA, Australia
| | - David T Yeung
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia.,Faculty of Health & Medical Science, University of Adelaide, Adelaide, SA, Australia.,Dept of Haematology, Royal Adelaide Hospital, Adelaide, SA, Australia.,Australasian Leukaemia & Lymphoma Group, Richmond, VIC, Australia
| | - Michael Osborn
- Faculty of Health & Medical Science, University of Adelaide, Adelaide, SA, Australia.,Australian & New Zealand Children's Haematology/Oncology Group, Clayton, VIC, Australia.,Australasian Leukaemia & Lymphoma Group, Richmond, VIC, Australia.,Dept of Haematology & Oncology, Women's & Children's Hospital, Adelaide, SA, Australia
| | - Tamas Revesz
- Faculty of Health & Medical Science, University of Adelaide, Adelaide, SA, Australia.,Australian & New Zealand Children's Haematology/Oncology Group, Clayton, VIC, Australia.,Dept of Haematology & Oncology, Women's & Children's Hospital, Adelaide, SA, Australia
| | - Maria Kirby
- Australian & New Zealand Children's Haematology/Oncology Group, Clayton, VIC, Australia.,Dept of Haematology & Oncology, Women's & Children's Hospital, Adelaide, SA, Australia
| | - Deborah L White
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia.,Faculty of Health & Medical Science, University of Adelaide, Adelaide, SA, Australia.,Australian & New Zealand Children's Haematology/Oncology Group, Clayton, VIC, Australia.,Faculty of Science, University of Adelaide, Adelaide, SA, Australia.,Australasian Leukaemia & Lymphoma Group, Richmond, VIC, Australia.,Australian Genomics Health Alliance, Parkville, VIC, Australia
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3
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Leite Rocha D, Ashton-Prolla P, Rosset C. Reviewing the occurrence of large genomic rearrangements in patients with inherited cancer predisposing syndromes: importance of a comprehensive molecular diagnosis. Expert Rev Mol Diagn 2022; 22:319-346. [PMID: 35234551 DOI: 10.1080/14737159.2022.2049247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Hereditary cancer predisposition syndromes are caused by germline pathogenic or likely pathogenic variants in cancer predisposition genes (CPG). The majority of pathogenic variants in CPGs are point mutations, but large gene rearrangements (LGRs) are present in several CPGs. LGRs can be much more difficult to characterize and perhaps they may have been neglected in molecular diagnoses. AREAS COVERED We aimed to evaluate the frequencies of germline LGRs in studies conducted in different populations worldwide through a qualitative systematic review based on an online literature research in PubMed. Two reviewers independently extracted data from published studies between 2009 and 2020. In total, 126 studies from 37 countries and 5 continents were included in the analysis. The number of studies in different continents ranged from 3 to 48 and for several countries there was an absolute lack of information. Asia and Europe represented most of the studies, and LGR frequencies varied from 3.04 to 15.06% in different continents. MLPA was one of the methods of choice in most studies (93%). EXPERT OPINION The LGR frequencies found in this review reinforce the need for comprehensive molecular testing regardless of the population of origin and should be considered by genetic counseling providers.
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Affiliation(s)
- Débora Leite Rocha
- Laboratório de Medicina Genômica, Serviço de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, CEP: 90035-930, Porto Alegre, Rio Grande do Sul, Brazil
| | - Patrícia Ashton-Prolla
- Laboratório de Medicina Genômica, Serviço de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, CEP: 90035-930, Porto Alegre, Rio Grande do Sul, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil. Av. Bento Gonçalves, 9500 - Prédio 43312 M, CEP: 91501-970, Caixa Postal 1505, Porto Alegre, Rio Grande do Sul, Brazil.,Serviço de Genética Médica, HCPA, Rio Grande do Sul, Brazil. Rua Ramiro Barcelos, 2350, CEP: 90035-930, Porto Alegre, Rio Grande do Sul, Brazil
| | - Clévia Rosset
- Laboratório de Medicina Genômica, Serviço de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, CEP: 90035-930, Porto Alegre, Rio Grande do Sul, Brazil
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4
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Kehrer-Sawatzki H, Wahlländer U, Cooper DN, Mautner VF. Atypical NF1 Microdeletions: Challenges and Opportunities for Genotype/Phenotype Correlations in Patients with Large NF1 Deletions. Genes (Basel) 2021; 12:genes12101639. [PMID: 34681033 PMCID: PMC8535936 DOI: 10.3390/genes12101639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 09/30/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022] Open
Abstract
Patients with neurofibromatosis type 1 (NF1) and type 1 NF1 deletions often exhibit more severe clinical manifestations than patients with intragenic NF1 gene mutations, including facial dysmorphic features, overgrowth, severe global developmental delay, severe autistic symptoms and considerably reduced cognitive abilities, all of which are detectable from a very young age. Type 1 NF1 deletions encompass 1.4 Mb and are associated with the loss of 14 protein-coding genes, including NF1 and SUZ12. Atypical NF1 deletions, which do not encompass all 14 protein-coding genes located within the type 1 NF1 deletion region, have the potential to contribute to the delineation of the genotype/phenotype relationship in patients with NF1 microdeletions. Here, we review all atypical NF1 deletions reported to date as well as the clinical phenotype observed in the patients concerned. We compare these findings with those of a newly identified atypical NF1 deletion of 698 kb which, in addition to the NF1 gene, includes five genes located centromeric to NF1. The atypical NF1 deletion in this patient does not include the SUZ12 gene but does encompass CRLF3. Comparative analysis of such atypical NF1 deletions suggests that SUZ12 hemizygosity is likely to contribute significantly to the reduced cognitive abilities, severe global developmental delay and facial dysmorphisms observed in patients with type 1 NF1 deletions.
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Affiliation(s)
- Hildegard Kehrer-Sawatzki
- Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany
- Correspondence: ; Tel.: +49-731-500-65421
| | - Ute Wahlländer
- Kliniken des Bezirks Oberbayern (KBO), Children Clinical Center Munich, 81377 Munich, Germany;
| | - David N. Cooper
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff CF14 4XN, UK;
| | - Victor-Felix Mautner
- Department of Neurology, University Hospital Hamburg Eppendorf, 20246 Hamburg, Germany;
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5
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Kehrer-Sawatzki H, Cooper DN. Classification of NF1 microdeletions and its importance for establishing genotype/phenotype correlations in patients with NF1 microdeletions. Hum Genet 2021; 140:1635-1649. [PMID: 34535841 PMCID: PMC8553723 DOI: 10.1007/s00439-021-02363-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/01/2021] [Indexed: 01/12/2023]
Abstract
An estimated 5–11% of patients with neurofibromatosis type-1 (NF1) harbour large deletions encompassing the NF1 gene and flanking regions. These NF1 microdeletions are subclassified into type 1, 2, 3 and atypical deletions which are distinguishable from each other by their extent and by the number of genes included within the deletion regions as well as the frequency of mosaicism with normal cells. Most common are type-1 NF1 deletions which encompass 1.4-Mb and 14 protein-coding genes. Type-1 deletions are frequently associated with overgrowth, global developmental delay, cognitive disability and dysmorphic facial features which are uncommon in patients with intragenic pathogenic NF1 gene variants. Further, patients with type-1 NF1 deletions frequently exhibit high numbers of neurofibromas and have an increased risk of malignant peripheral nerve sheath tumours. Genes located within the type-1 NF1 microdeletion interval and co-deleted with NF1 are likely to act as modifiers responsible for the severe disease phenotype in patients with NF1 microdeletions, thereby causing the NF1 microdeletion syndrome. Genotype/phenotype correlations in patients with NF1 microdeletions of different lengths are important to identify such modifier genes. However, these correlations are critically dependent upon the accurate characterization of the deletions in terms of their extent. In this review, we outline the utility as well as the shortcomings of multiplex ligation-dependent probe amplification (MLPA) to classify the different types of NF1 microdeletion and indicate the importance of high-resolution microarray analysis for correct classification, a necessary precondition to identify those genes responsible for the NF1 microdeletion syndrome.
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Affiliation(s)
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
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6
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Rubino F, Eichberg DG, Shah AH, Luther EM, Lu VM, Saad AG, Kahn D, Komotar RJ, Ivan ME. When "Peripheral" Becomes "Central": Primary and Secondary Malignant Intracerebral Nerve Sheath Tumor: A Case Report and a Systematic Review. Neurosurgery 2021; 88:1074-1087. [PMID: 33647973 DOI: 10.1093/neuros/nyab043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/03/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The intracerebral occurrence of malignant peripheral nerve sheath tumors (MPNSTs) is exceedingly rare, and despite aggressive treatments, local recurrence and poor prognosis are very frequent. Like other brain tumors, these tumors could be primary or secondary, making the term "peripheral" an imprecise term for a primary brain tumor. OBJECTIVE To analyze the reported cases of primary and secondary cerebral MPSNTs in terms of diagnosis, treatment, and overall survival. Additionally, we present a case of malignant intracerebral nerve sheath tumor (MINST) treated with radical surgery and radiotherapy. METHODS Using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, one database (PubMed) and crossed references were queried for MPNST with brain metastasis and primary MINSTs from 1971 to 2020. Data regarding demographic features, primary tumor site, risk factors, brain location of the lesion, treatment applied, and overall survival were extracted. RESULTS A total of 55 patients were selected (including the reported case): 29 patients were secondary brain MPNST and 26 patients were primary MINST. The mean age was 41.8 ± 22 and 31.2 ± 23 yr, respectively. All brain metastases of MPNST (100%) had a primary tumor elsewhere in the body at the time of diagnosis. The overall survival was significantly shorter in patients with a secondary brain MPNST compared to MINST (P = .002). CONCLUSION We present a comprehensive analysis of every reported primary and secondary intracerebral MPNST. The prognosis in terms of survival is worst in the last one despite aggressive treatment. The lack of a primary MPNST in screening tests is sufficient to confirm a MINST at time of diagnosis.
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Affiliation(s)
- Franco Rubino
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Lois Pope Life Center, Miami, Florida, USA
| | - Daniel G Eichberg
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Lois Pope Life Center, Miami, Florida, USA
| | - Ashish H Shah
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Lois Pope Life Center, Miami, Florida, USA
| | - Evan M Luther
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Lois Pope Life Center, Miami, Florida, USA
| | - Victor M Lu
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Lois Pope Life Center, Miami, Florida, USA
| | - Ali G Saad
- Department of Pathology, University of Miami Miller School of Medicine, Lois Pope Life Center, Miami, Florida, USA
| | - David Kahn
- Department of Hematology and Medical Oncology, 21st Century Oncology Inc, Margate, Florida, USA
| | - Ricardo J Komotar
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Lois Pope Life Center, Miami, Florida, USA.,Sylvester Comprehensive Cancer Center, Miami, Florida, USA
| | - Michael E Ivan
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Lois Pope Life Center, Miami, Florida, USA.,Sylvester Comprehensive Cancer Center, Miami, Florida, USA
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7
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Büki G, Zsigmond A, Czakó M, Szalai R, Antal G, Farkas V, Fekete G, Nagy D, Széll M, Tihanyi M, Melegh B, Hadzsiev K, Bene J. Genotype-Phenotype Associations in Patients With Type-1, Type-2, and Atypical NF1 Microdeletions. Front Genet 2021; 12:673025. [PMID: 34168676 PMCID: PMC8217751 DOI: 10.3389/fgene.2021.673025] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/12/2021] [Indexed: 11/23/2022] Open
Abstract
Neurofibromatosis type 1 is a tumor predisposition syndrome inherited in autosomal dominant manner. Besides the intragenic loss-of-function mutations in NF1 gene, large deletions encompassing the NF1 gene and its flanking regions are responsible for the development of the variable clinical phenotype. These large deletions titled as NF1 microdeletions lead to a more severe clinical phenotype than those observed in patients with intragenic NF1 mutations. Around 5-10% of the cases harbor large deletion and four major types of NF1 microdeletions (type 1, 2, 3 and atypical) have been identified so far. They are distinguishable in term of their size and the location of the breakpoints, by the frequency of somatic mosaicism with normal cells not harboring the deletion and by the number of the affected genes within the deleted region. In our study genotype-phenotype analyses have been performed in 17 mostly pediatric patients with NF1 microdeletion syndrome identified by multiplex ligation-dependent probe amplification after systematic sequencing of the NF1 gene. Confirmation and classification of the NF1 large deletions were performed using array comparative genomic hybridization, where it was feasible. In our patient cohort 70% of the patients possess type-1 deletion, one patient harbors type-2 deletion and 23% of our cases have atypical NF1 deletion. All the atypical deletions identified in this study proved to be novel. One patient with atypical deletion displayed mosaicism. In our study NF1 microdeletion patients presented dysmorphic facial features, macrocephaly, large hands and feet, delayed cognitive development and/or learning difficulties, speech difficulties, overgrowth more often than patients with intragenic NF1 mutations. Moreover, neurobehavior problems, macrocephaly and overgrowth were less frequent in atypical cases compared to type-1 deletion. Proper diagnosis is challenging in certain patients since several clinical manifestations show age-dependency. Large tumor load exhibited more frequently in this type of disorder, therefore better understanding of genotype-phenotype correlations and progress of the disease is essential for individuals suffering from neurofibromatosis to improve the quality of their life. Our study presented additional clinical data related to NF1 microdeletion patients especially for pediatric cases and it contributes to the better understanding of this type of disorder.
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Affiliation(s)
- Gergely Büki
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Anna Zsigmond
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary
| | - Márta Czakó
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Renáta Szalai
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Gréta Antal
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary
| | - Viktor Farkas
- 1st Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - György Fekete
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Dóra Nagy
- Department of Medical Genetics, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Márta Széll
- Department of Medical Genetics, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Marianna Tihanyi
- Genetic Laboratory, Szent Rafael Hospital of Zala County, Zalaegerszeg, Hungary
| | - Béla Melegh
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary.,Full member of the European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No. 739547, Pécs, Hungary
| | - Kinga Hadzsiev
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Judit Bene
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary.,Full member of the European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No. 739547, Pécs, Hungary
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8
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Güneş N, Yeşil G, Geyik F, Kasap B, Celkan T, Kebudi R, Tüysüz B. Neurofibromatosis type 1: Expanded variant spectrum with multiplex ligation-dependent probe amplification and genotype-phenotype correlation in 138 Turkish patients. Ann Hum Genet 2021; 85:155-165. [PMID: 33877690 DOI: 10.1111/ahg.12422] [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: 01/09/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To investigate the variant spectrum and genotype-phenotype correlations in a Turkish cohort with Neurofibromatosis Type-1 (NF1). MATERIALS AND METHODS We retrospectively investigated the clinical and molecular data of 138 NF1 patients from 129 families who had been followed-up for a median of 3.9 (1.25-18.5) years. RESULTS NF1 sequencing revealed 73 different intragenic variants, 19 of which were novel. Seven large deletions were detected by multiplex ligation-dependent probe amplification (MLPA) analyses. The total detection rate of pathogenic NF1 variants was found to be 87.1%. Comparing age groups, cutaneous neurofibromas, freckling, and Lisch nodules were more prevalent in patients older than 12 years (p > .05). Optic glioma detected in 17.3% of the patients and was significantly more common before the age of 6 (p > .001). Other solid tumors developed in 5% of the patients. There was no genotype-phenotype correlation between patients with truncating and nontruncating variants. However, six out of seven patients with large deletions had significant developmental delay, one patient with the c.2970_2972delAAT (p.Met992del) variant had only typical pigmentary features, and another patient with the c.4267A > G (p.Lys1423Glu) variant had CALMs, freckling, neurofibromas, and Noonan-like phenotype. CONCLUSIONS We described 19 novel variants and seven large deletions in NF1. Applying MLPA assay in NF1 is useful in expanding the molecular diagnosis. Although very limited genotype-phenotype correlation has been reported in NF1, the fact that specific phenotypic findings were observed in our patients with large deletions and two intragenic variants supports the studies published recently.
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Affiliation(s)
- Nilay Güneş
- Cerrahpaşa Medical Faculty, Department of Pediatric Genetics, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Gözde Yeşil
- Faculty of Medicine, Department of Medical Genetics, Bezmialem Vakif University, Istanbul, Turkey
| | - Filiz Geyik
- Cerrahpaşa Medical Faculty, Department of Pediatric Genetics, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Büşra Kasap
- Cerrahpaşa Medical Faculty, Department of Pediatric Genetics, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Tiraje Celkan
- Cerrahpaşa Medical Faculty, Department of Pediatric Oncology, Istanbul University-Cerrahpaşa, Istanbul
| | - Rejin Kebudi
- Department of Pediatric Oncology, Istanbul University, Oncology Institute, Istanbul, Turkey
| | - Beyhan Tüysüz
- Cerrahpaşa Medical Faculty, Department of Pediatric Genetics, Istanbul University-Cerrahpaşa, Istanbul, Turkey
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9
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Scala M, Schiavetti I, Madia F, Chelleri C, Piccolo G, Accogli A, Riva A, Salpietro V, Bocciardi R, Morcaldi G, Di Duca M, Caroli F, Verrico A, Milanaccio C, Viglizzo G, Traverso M, Baldassari S, Scudieri P, Iacomino M, Piatelli G, Minetti C, Striano P, Garrè ML, De Marco P, Diana MC, Capra V, Pavanello M, Zara F. Genotype-Phenotype Correlations in Neurofibromatosis Type 1: A Single-Center Cohort Study. Cancers (Basel) 2021; 13:cancers13081879. [PMID: 33919865 PMCID: PMC8070780 DOI: 10.3390/cancers13081879] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Neurofibromatosis type 1 (NF1) is a complex disorder characterized by a multisystem involvement and cancer predisposition. It is caused by genetic variants in NF1, a large tumor suppressor gene encoding a cytoplasmatic protein (neurofibromin) with a regulatory role in essential cellular processes. Genotype–phenotype correlations in NF1 patients are so far elusive. We retrospectively reviewed clinical, radiological, and genetic data of 583 individuals with at least 1 National Institutes of Health (NIH) criterion for NF1 diagnosis, including 365 subjects fulfilling criteria for the diagnosis. Novel genotype–phenotype correlations were identified through uni- and multivariate statistical analysis. Missense variants negatively correlated with neurofibromas. Skeletal abnormalities were associated with frameshift variants and whole gene deletions. The c.3721C>T; p.(R1241*) variant positively correlated with structural brain alterations, whereas the c.6855C>A; p.(Y2285*) variant was associated with a higher prevalence of Lisch nodules and endocrinological disorders. These novel NF1 genotype–phenotype correlations may have a relevant role in the implementation of patients’ care. Abstract Neurofibromatosis type 1 (NF1) is a proteiform genetic condition caused by pathogenic variants in NF1 and characterized by a heterogeneous phenotypic presentation. Relevant genotype–phenotype correlations have recently emerged, but only few pertinent studies are available. We retrospectively reviewed clinical, instrumental, and genetic data from a cohort of 583 individuals meeting at least 1 diagnostic National Institutes of Health (NIH) criterion for NF1. Of these, 365 subjects fulfilled ≥2 NIH criteria, including 235 pediatric patients. Genetic testing was performed through cDNA-based sequencing, Next Generation Sequencing (NGS), and Multiplex Ligation-dependent Probe Amplification (MLPA). Uni- and multivariate statistical analysis was used to investigate genotype–phenotype correlations. Among patients fulfilling ≥ 2 NIH criteria, causative single nucleotide variants (SNVs) and copy number variations (CNVs) were detected in 267/365 (73.2%) and 20/365 (5.5%) cases. Missense variants negatively correlated with neurofibromas (p = 0.005). Skeletal abnormalities were associated with whole gene deletions (p = 0.05) and frameshift variants (p = 0.006). The c.3721C>T; p.(R1241*) variant positively correlated with structural brain alterations (p = 0.031), whereas Lisch nodules (p = 0.05) and endocrinological disorders (p = 0.043) were associated with the c.6855C>A; p.(Y2285*) variant. We identified novel NF1 genotype–phenotype correlations and provided an overview of known associations, supporting their potential relevance in the implementation of patient management.
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Affiliation(s)
- Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy; (M.S.); (C.C.); (A.A.); (A.R.); (V.S.); (R.B.); (P.S.); (C.M.); (P.S.); (F.Z.)
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (G.P.); (G.M.); (M.T.); (M.C.D.)
| | - Irene Schiavetti
- Department of Health Sciences, Section of Biostatistics, University of Genova, 16132 Genoa, Italy;
| | - Francesca Madia
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (F.M.); (M.D.D.); (F.C.); (S.B.); (M.I.); (P.D.M.); (V.C.)
| | - Cristina Chelleri
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy; (M.S.); (C.C.); (A.A.); (A.R.); (V.S.); (R.B.); (P.S.); (C.M.); (P.S.); (F.Z.)
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (G.P.); (G.M.); (M.T.); (M.C.D.)
| | - Gianluca Piccolo
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (G.P.); (G.M.); (M.T.); (M.C.D.)
| | - Andrea Accogli
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy; (M.S.); (C.C.); (A.A.); (A.R.); (V.S.); (R.B.); (P.S.); (C.M.); (P.S.); (F.Z.)
| | - Antonella Riva
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy; (M.S.); (C.C.); (A.A.); (A.R.); (V.S.); (R.B.); (P.S.); (C.M.); (P.S.); (F.Z.)
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (G.P.); (G.M.); (M.T.); (M.C.D.)
| | - Vincenzo Salpietro
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy; (M.S.); (C.C.); (A.A.); (A.R.); (V.S.); (R.B.); (P.S.); (C.M.); (P.S.); (F.Z.)
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (G.P.); (G.M.); (M.T.); (M.C.D.)
| | - Renata Bocciardi
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy; (M.S.); (C.C.); (A.A.); (A.R.); (V.S.); (R.B.); (P.S.); (C.M.); (P.S.); (F.Z.)
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (F.M.); (M.D.D.); (F.C.); (S.B.); (M.I.); (P.D.M.); (V.C.)
| | - Guido Morcaldi
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (G.P.); (G.M.); (M.T.); (M.C.D.)
| | - Marco Di Duca
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (F.M.); (M.D.D.); (F.C.); (S.B.); (M.I.); (P.D.M.); (V.C.)
| | - Francesco Caroli
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (F.M.); (M.D.D.); (F.C.); (S.B.); (M.I.); (P.D.M.); (V.C.)
| | - Antonio Verrico
- Neuro-Oncology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (A.V.); (C.M.); (M.L.G.)
| | - Claudia Milanaccio
- Neuro-Oncology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (A.V.); (C.M.); (M.L.G.)
| | | | - Monica Traverso
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (G.P.); (G.M.); (M.T.); (M.C.D.)
| | - Simona Baldassari
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (F.M.); (M.D.D.); (F.C.); (S.B.); (M.I.); (P.D.M.); (V.C.)
| | - Paolo Scudieri
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy; (M.S.); (C.C.); (A.A.); (A.R.); (V.S.); (R.B.); (P.S.); (C.M.); (P.S.); (F.Z.)
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (F.M.); (M.D.D.); (F.C.); (S.B.); (M.I.); (P.D.M.); (V.C.)
| | - Michele Iacomino
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (F.M.); (M.D.D.); (F.C.); (S.B.); (M.I.); (P.D.M.); (V.C.)
| | - Gianluca Piatelli
- Neurosurgery Department, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy;
| | - Carlo Minetti
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy; (M.S.); (C.C.); (A.A.); (A.R.); (V.S.); (R.B.); (P.S.); (C.M.); (P.S.); (F.Z.)
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (G.P.); (G.M.); (M.T.); (M.C.D.)
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy; (M.S.); (C.C.); (A.A.); (A.R.); (V.S.); (R.B.); (P.S.); (C.M.); (P.S.); (F.Z.)
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (G.P.); (G.M.); (M.T.); (M.C.D.)
| | - Maria Luisa Garrè
- Neuro-Oncology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (A.V.); (C.M.); (M.L.G.)
| | - Patrizia De Marco
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (F.M.); (M.D.D.); (F.C.); (S.B.); (M.I.); (P.D.M.); (V.C.)
| | - Maria Cristina Diana
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (G.P.); (G.M.); (M.T.); (M.C.D.)
| | - Valeria Capra
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (F.M.); (M.D.D.); (F.C.); (S.B.); (M.I.); (P.D.M.); (V.C.)
| | - Marco Pavanello
- Neurosurgery Department, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy;
- Correspondence:
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy; (M.S.); (C.C.); (A.A.); (A.R.); (V.S.); (R.B.); (P.S.); (C.M.); (P.S.); (F.Z.)
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (F.M.); (M.D.D.); (F.C.); (S.B.); (M.I.); (P.D.M.); (V.C.)
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10
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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.
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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
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11
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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.
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12
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Bianchessi D, Ibba MC, Saletti V, Blasa S, Langella T, Paterra R, Cagnoli GA, Melloni G, Scuvera G, Natacci F, Cesaretti C, Finocchiaro G, Eoli M. Simultaneous Detection of NF1, SPRED1, LZTR1, and NF2 Gene Mutations by Targeted NGS in an Italian Cohort of Suspected NF1 Patients. Genes (Basel) 2020; 11:genes11060671. [PMID: 32575496 PMCID: PMC7349720 DOI: 10.3390/genes11060671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 12/30/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) displays overlapping phenotypes with other neurocutaneous diseases such as Legius Syndrome. Here, we present results obtained using a next generation sequencing (NGS) panel including NF1, NF2, SPRED1, SMARCB1, and LZTR1 genes on Ion Torrent. Together with NGS, the Multiplex Ligation-Dependent Probe Amplification Analysis (MLPA) method was performed to rule out large deletions/duplications in NF1 gene; we validated the MLPA/NGS approach using Sanger sequencing on DNA or RNA of both positive and negative samples. In our cohort, a pathogenic variant was found in 175 patients; the pathogenic variant was observed in NF1 gene in 168 cases. A SPRED1 pathogenic variant was also found in one child and in a one year old boy, both NF2 and LZTR1 pathogenic variants were observed; in addition, we identified five LZTR1 pathogenic variants in three children and two adults. Six NF1 pathogenic variants, that the NGS analysis failed to identify, were detected on RNA by Sanger. NGS allows the identification of novel mutations in five genes in the same sequencing run, permitting unambiguous recognition of disorders with overlapping phenotypes with NF1 and facilitating genetic counseling and a personalized follow-up.
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Affiliation(s)
- Donatella Bianchessi
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
| | - Maria Cristina Ibba
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
| | - Veronica Saletti
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (V.S.); (G.M.)
| | - Stefania Blasa
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza dell’Ateneo Nuovo, 1, 20126 Milan, Italy
| | - Tiziana Langella
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
- Molecular Immunology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian, 20133 Milan, Italy
| | - Rosina Paterra
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
| | - Giulia Anna Cagnoli
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, via Francesco Sforza 28, 20122 Milan, Italy; (G.A.C.); (F.N.); (C.C.)
| | - Giulia Melloni
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (V.S.); (G.M.)
| | - Giulietta Scuvera
- Pediatric Highly Intensive Care Unit, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, via Francesco Sforza 28, 20122 Milan, Italy;
| | - Federica Natacci
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, via Francesco Sforza 28, 20122 Milan, Italy; (G.A.C.); (F.N.); (C.C.)
| | - Claudia Cesaretti
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, via Francesco Sforza 28, 20122 Milan, Italy; (G.A.C.); (F.N.); (C.C.)
| | - Gaetano Finocchiaro
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
| | - Marica Eoli
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
- Correspondence:
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13
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Jarhelle E, Riise Stensland HMF, Hansen GÅM, Skarsfjord S, Jonsrud C, Ingebrigtsen M, Strømsvik N, Van Ghelue M. Identifying sequence variants contributing to hereditary breast and ovarian cancer in BRCA1 and BRCA2 negative breast and ovarian cancer patients. Sci Rep 2019; 9:19986. [PMID: 31882575 PMCID: PMC6934654 DOI: 10.1038/s41598-019-55515-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/26/2019] [Indexed: 12/21/2022] Open
Abstract
Families with breast and ovarian cancer are often tested for disease associated sequence variants in BRCA1 and BRCA2. Pathogenic sequence variants (PVs) in these two genes are known to increase breast and ovarian cancer risks in females. However, in most families no PVs are detected in these two genes. Currently, several studies have identified other genes involved in hereditary breast and ovarian cancer (HBOC). To identify genetic risk factors for breast and ovarian cancer in a Norwegian HBOC cohort, 101 breast and/or ovarian cancer patients negative for PVs and variants of unknown clinical significance (VUS) in BRCA1/2 were screened for PVs in 94 genes using next-generation sequencing. Sixteen genes were closely scrutinized. Nine different deleterious germline PVs/likely pathogenic variants (LPVs) were identified in seven genes in 12 patients: three in ATM, and one in CHEK2, ERCC5, FANCM, RAD51C, TP53 and WRN. Additionally, 32 different VUSs were identified and these require further characterization. For carriers of PV/LPV in many of these genes, there are no national clinical management programs in Norway. The diversity of genetic risk factors possibly involved in cancer development show the necessity for more knowledge to improve the clinical follow-up of this genetically diverse patient group.
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Affiliation(s)
- Elisabeth Jarhelle
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway. .,Department of Clinical Medicine, University of Tromsø, Tromsø, Norway. .,Northern Norway Family Cancer Center, Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway.
| | - Hilde Monica Frostad Riise Stensland
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway.,Northern Norway Family Cancer Center, Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway
| | - Geir Åsmund Myge Hansen
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway.,Northern Norway Family Cancer Center, Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway
| | - Siri Skarsfjord
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway
| | - Christoffer Jonsrud
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway.,Northern Norway Family Cancer Center, Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway
| | - Monica Ingebrigtsen
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway
| | - Nina Strømsvik
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway.,Northern Norway Family Cancer Center, Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway.,Department of Health and Caring Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | - Marijke Van Ghelue
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway. .,Department of Clinical Medicine, University of Tromsø, Tromsø, Norway. .,Northern Norway Family Cancer Center, Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway.
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14
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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.
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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:
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15
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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.
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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
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16
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Molecular genetic diagnosis of Tunisian Glanzmann thrombasthenia patients reveals a common nonsense mutation in the ITGA2B gene that seems to be specific for the studied population. Blood Coagul Fibrinolysis 2018; 29:689-696. [DOI: 10.1097/mbc.0000000000000779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Wu-Chou YH, Hung TC, Lin YT, Cheng HW, Lin JL, Lin CH, Yu CC, Chen KT, Yeh TH, Chen YR. Genetic diagnosis of neurofibromatosis type 1: targeted next- generation sequencing with Multiple Ligation-Dependent Probe Amplification analysis. J Biomed Sci 2018; 25:72. [PMID: 30290804 PMCID: PMC6172719 DOI: 10.1186/s12929-018-0474-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/26/2018] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Neurofibromatosis type 1 (NF1) is a dominantly inherited tumor predisposition syndrome that targets the peripheral nervous system. It is caused by mutations of the NF1 gene which serve as a negative regulator of the cellular Ras/MAPK (mitogen-activated protein kinases) signaling pathway. Owing to the complexity in some parts of clinical diagnoses and the need for better understanding of its molecular relationships, a genetic characterization of this disorder will be helpful in the clinical setting. METHODS In this study, we present a customized targeted gene panel of NF1/KRAS/BRAF/p53 and SPRED1 genes combined with Multiple Ligation-Dependent Probe Amplification analysis for the NF1 mutation screening in a cohort of patients clinically suspected as NF1. RESULTS In this study, we identified 73 NF1 mutations and two BRAF novel variants from 100 NF1 patients who were suspected as having NF1. These genetic alterations are heterogeneous and distribute in a complicated way without clustering in either cysteine-serine-rich domain or within the GAP-related domain. We also detected fifteen multi-exon deletions within the NF1 gene by MLPA Analysis. CONCLUSIONS Our results suggested that a genetic screening using a NGS panel with high coverage of Ras-signaling components combined with Multiple Ligation-Dependent Probe Amplification analysis will enable differential diagnosis of patients with overlapping clinical features.
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Affiliation(s)
- Yah-Huei Wu-Chou
- Human Molecular Genetics Laboratory, Department of Medical Research, Chang Gung Memorial Hospital, No.5, Fushing Street, Kweishan, Taoyuan, Taiwan.
| | - Tzu-Chao Hung
- Human Molecular Genetics Laboratory, Department of Medical Research, Chang Gung Memorial Hospital, No.5, Fushing Street, Kweishan, Taoyuan, Taiwan
| | - Yin-Ting Lin
- Human Molecular Genetics Laboratory, Department of Medical Research, Chang Gung Memorial Hospital, No.5, Fushing Street, Kweishan, Taoyuan, Taiwan
| | - Hsing-Wen Cheng
- Human Molecular Genetics Laboratory, Department of Medical Research, Chang Gung Memorial Hospital, No.5, Fushing Street, Kweishan, Taoyuan, Taiwan
| | - Ju-Li Lin
- Division of Genetics and Endocrinology, Department of Pediatrics, Chang Gung University College of Medicine and Chang Gung Children's and Memorial Hospital, No.5, Fushing Street, Kweishan, Taoyuan, Taiwan
| | - Chih-Hung Lin
- Department of Plastic & Reconstructive Surgery, Chang Gung Memorial Hospital, Kweishan, Taoyuan, Taiwan
| | - Chung-Chih Yu
- Department of Plastic & Reconstructive Surgery, Chang Gung Memorial Hospital, Kweishan, Taoyuan, Taiwan
| | - Kuo-Ting Chen
- Department of Plastic & Reconstructive Surgery, Chang Gung Memorial Hospital, Kweishan, Taoyuan, Taiwan
| | - Tu-Hsueh Yeh
- Neuroscience Research Center, Department of Neurology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yu-Ray Chen
- Department of Plastic & Reconstructive Surgery, Chang Gung Memorial Hospital, Kweishan, Taoyuan, Taiwan.
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18
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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.
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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
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19
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Clinical characteristics and NF1 gene mutation analysis of three successive generations in three different Indian families with neurofibromatosis type 1 and peripheral nerve sheath tumours. J Clin Neurosci 2018; 53:62-68. [PMID: 29680440 DOI: 10.1016/j.jocn.2018.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 03/05/2018] [Accepted: 04/02/2018] [Indexed: 11/21/2022]
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20
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Stella A, Lastella P, Loconte DC, Bukvic N, Varvara D, Patruno M, Bagnulo R, Lovaglio R, Bartolomeo N, Serio G, Resta N. Accurate Classification of NF1 Gene Variants in 84 Italian Patients with Neurofibromatosis Type 1. Genes (Basel) 2018; 9:genes9040216. [PMID: 29673180 PMCID: PMC5924558 DOI: 10.3390/genes9040216] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/27/2018] [Accepted: 04/03/2018] [Indexed: 11/16/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is one of the most common autosomal dominant genetic diseases. It is caused by mutations in the NF1 gene encoding for the large protein, neurofibromin. Genetic testing of NF1 is cumbersome because 50% of cases are sporadic, and there are no mutation hot spots. In addition, the most recognizable NF1 clinical features—café-au-lait (CALs) spots and axillary and/or inguinal freckling—appear early in childhood but are rather non-specific. Thus, the identification of causative variants is extremely important for early diagnosis, especially in paediatric patients. Here, we aimed to identify the underlying genetic defects in 72 index patients referred to our centre for NF1. Causative mutations were identified in 58 subjects, with 29 being novel changes. We evaluated missense and non-canonical splicing mutations with both protein and splicing prediction algorithms. The ratio of splicing mutations detected was higher than that reported in recent patients’ series and in the Human Gene Mutation Database (HGMD). After applying in silico predictive tools to 41 previously reported missense variants, we demonstrated that 46.3% of these putatively missense mutations were forecasted to alter splicing instead. Our data suggest that mutations affecting splicing can be frequently underscored if not analysed in depth. We confirm that hamartomas can be useful for diagnosing NF1 in children. Lisch nodules and cutaneous neurofibromas were more frequent in patients with frameshifting mutations. In conclusion, we demonstrated that comprehensive in silico analysis can be a highly specific method for predicting the nature of NF1 mutations and may help in assuring proper patient care.
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Affiliation(s)
- Alessandro Stella
- Laboratorio di Genetica Medica, Dipartimento di Scienze Biomediche e Oncologia Umana, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy.
| | - Patrizia Lastella
- Centro di Malattie Rare, Azienda Ospedaliero-Universitario Policlinico di Bari, 70124 Bari, Italy.
| | - Daria Carmela Loconte
- Laboratorio di Genetica Medica, Dipartimento di Scienze Biomediche e Oncologia Umana, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy.
| | - Nenad Bukvic
- Laboratorio di Genetica Medica, Dipartimento di Scienze Biomediche e Oncologia Umana, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy.
| | - Dora Varvara
- Azienda Ospedaliero-Universitario Policlinico di Bari, 70124 Bari, Italy.
| | - Margherita Patruno
- Laboratorio di Genetica Medica, Dipartimento di Scienze Biomediche e Oncologia Umana, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy.
| | - Rosanna Bagnulo
- Laboratorio di Genetica Medica, Dipartimento di Scienze Biomediche e Oncologia Umana, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy.
| | - Rosaura Lovaglio
- Laboratorio di Genetica Medica, Dipartimento di Scienze Biomediche e Oncologia Umana, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy.
| | - Nicola Bartolomeo
- Sezione di Igiene, Dipartimento di Scienze Biomediche e Oncologia Umana, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy.
| | - Gabriella Serio
- Sezione di Igiene, Dipartimento di Scienze Biomediche e Oncologia Umana, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy.
| | - Nicoletta Resta
- Laboratorio di Genetica Medica, Dipartimento di Scienze Biomediche e Oncologia Umana, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy.
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21
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Rossitti HM, Söderkvist P, Gimm O. Extent of surgery for phaeochromocytomas in the genomic era. Br J Surg 2018; 105:e84-e98. [DOI: 10.1002/bjs.10744] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/15/2017] [Accepted: 10/01/2017] [Indexed: 12/14/2022]
Abstract
Abstract
Background
Germline mutations are present in 20–30 per cent of patients with phaeochromocytoma. For patients who develop bilateral disease, complete removal of both adrenal glands (total adrenalectomy) will result in lifelong adrenal insufficiency with an increased risk of death from adrenal crisis. Unilateral/bilateral adrenal-sparing surgery (subtotal adrenalectomy) offers preservation of cortical function and independence from steroids, but leaves the adrenal medulla in situ and thus at risk of developing new and possibly malignant disease. Here, present knowledge about how tumour genotype relates to clinical behaviour is reviewed, and application of this knowledge when choosing the extent of adrenalectomy is discussed.
Methods
A literature review was undertaken of the penetrance of the different genotypes in phaeochromocytomas, the frequency of bilateral disease and malignancy, and the underlying pathophysiological mechanisms, with emphasis on explaining the clinical phenotypes of phaeochromocytomas and their associated syndromes.
Results
Patients with bilateral phaeochromocytomas most often have multiple endocrine neoplasia type 2 (MEN2) or von Hippel–Lindau disease (VHL) with high-penetrance mutations for benign disease, whereas patients with mutations in the genes encoding SDHB (succinate dehydrogenase subunit B) or MAX (myelocytomatosis viral proto-oncogene homologue-associated factor X) are at increased risk of malignancy.
Conclusion
Adrenal-sparing surgery should be the standard approach for patients who have already been diagnosed with MEN2 or VHL when operating on the first side, whereas complete removal of the affected adrenal gland(s) is generally recommended for patients with SDHB or MAX germline mutations. Routine assessment of a patient's genotype, even after the first operation, can be crucial for adopting an appropriate strategy for follow-up and future surgery.
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Affiliation(s)
- H M Rossitti
- Department of Clinical and Experimental Medicine, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - P Söderkvist
- Department of Clinical and Experimental Medicine, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - O Gimm
- Department of Clinical and Experimental Medicine, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
- Department of Surgery, County Council of Östergötland, Linköping, Sweden
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22
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Bonatti F, Adorni A, Matichecchia A, Mozzoni P, Uliana V, Pisani F, Garavelli L, Graziano C, Gnoli M, Carli D, Bigoni S, Boschi E, Martorana D, Percesepe A. Patterns of Novel Alleles and Genotype/Phenotype Correlations Resulting from the Analysis of 108 Previously Undetected Mutations in Patients Affected by Neurofibromatosis Type I. Int J Mol Sci 2017; 18:ijms18102071. [PMID: 28961165 PMCID: PMC5666753 DOI: 10.3390/ijms18102071] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/29/2017] [Accepted: 09/26/2017] [Indexed: 11/16/2022] Open
Abstract
Neurofibromatosis type I, a genetic disorder due to mutations in the NF1 gene, is characterized by a high mutation rate (about 50% of the cases are de novo) but, with the exception of whole gene deletions associated with a more severe phenotype, no specific hotspots and few solid genotype/phenotype correlations. After retrospectively re-evaluating all NF1 gene variants found in the diagnostic activity, we studied 108 patients affected by neurofibromatosis type I who harbored mutations that had not been previously reported in the international databases, with the aim of analyzing their type and distribution along the gene and of correlating them with the phenotypic features of the affected patients. Out of the 108 previously unreported variants, 14 were inherited by one of the affected parents and 94 were de novo. Twenty-nine (26.9%) mutations were of uncertain significance, whereas 79 (73.2%) were predicted as pathogenic or probably pathogenic. No differential distribution in the exons or in the protein domains was observed and no statistically significant genotype/phenotype correlation was found, confirming previous evidences.
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Affiliation(s)
| | - Alessia Adorni
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy.
| | | | - Paola Mozzoni
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy.
| | - Vera Uliana
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy.
| | - Francesco Pisani
- Children's Neuropsycological Services, University Hospital of Parma, 43126 Parma, Italy.
| | - Livia Garavelli
- Clinical Genetics, IRCCS S. Maria Nuova Hospital, Reggio 42123 Emilia, Italy.
| | - Claudio Graziano
- Medical Genetics, S. Orsola-Malpighi University Hospital, 40138 Bologna, Italy.
| | - Maria Gnoli
- Medical Genetics and Skeletal Rare Diseases, Istituto Ortopedico Rizzoli, 40126 Bologna, Italy.
| | - Diana Carli
- Medical Genetics, Città della Salute e della Scienza University Hospital, 10126 Torino, Italy.
| | - Stefania Bigoni
- UOL Medical Genetics, University of Ferrara, 44121 Ferrara, Italy.
| | - Elena Boschi
- Plastic Surgery, University Hospital of Parma, 43126 Parma, Italy.
| | - Davide Martorana
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy.
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23
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Ulusal SD, Gürkan H, Atlı E, Özal SA, Çiftdemir M, Tozkır H, Karal Y, Güçlü H, Eker D, Görker I. Genetic Analyses of the NF1 Gene in Turkish Neurofibromatosis Type I Patients and Definition of three Novel Variants. Balkan J Med Genet 2017; 20:13-20. [PMID: 28924536 PMCID: PMC5596817 DOI: 10.1515/bjmg-2017-0008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Neurofibromatosis Type I (NF1) is a multi systemic autosomal dominant neurocutaneous disorder predisposing patients to have benign and/or malignant lesions predominantly of the skin, nervous system and bone. Loss of function mutations or deletions of the NF1 gene is responsible for NF1 disease. Involvement of various pathogenic variants, the size of the gene and presence of pseudogenes makes it difficult to analyze. We aimed to report the results of 2 years of multiplex ligation-dependent probe amplification (MLPA) and next generation sequencing (NGS) for genetic diagnosis of NF1 applied at our genetic diagnosis center. The MLPA, semiconductor sequencing and Sanger sequencing were performed in genomic DNA samples from 24 unrelated patients and their affected family members referred to our center suspected of having NF1. In total, three novel and 12 known pathogenic variants and a whole gene deletion were determined. We suggest that next generation sequencing is a practical tool for genetic analysis of NF1. Deletion/duplication analysis with MLPA may also be helpful for patients clinically diagnosed to carry NF1 but do not have a detectable mutation in NGS.
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Affiliation(s)
- S D Ulusal
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - H Gürkan
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - E Atlı
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - S A Özal
- Department of Opthalmology, Trakya University Faculty of Medicine, Edirne, Turkey
| | - M Çiftdemir
- Department of Orthopedics and Traumatology, Trakya University Faculty of Medicine, Edirne, Turkey
| | - H Tozkır
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Y Karal
- Department of Pediatric Neurology, Trakya University Faculty of Medicine, Edirne, Turkey
| | - H Güçlü
- Department of Opthalmology, Trakya University Faculty of Medicine, Edirne, Turkey
| | - D Eker
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - I Görker
- Department of Child and Adolescent Psychiatry, Trakya University Faculty of Medicine, Edirne, Turkey
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24
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Calì F, Chiavetta V, Ruggeri G, Piccione M, Selicorni A, Palazzo D, Bonsignore M, Cereda A, Elia M, Failla P, Figura MG, Fiumara A, Maitz S, Luana Mandarà GM, Mattina T, Ragalmuto A, Romano C, Ruggieri M, Salluzzo R, Saporoso A, Schepis C, Sorge G, Spanò M, Tortorella G, Romano V. Mutation spectrum of NF1 gene in Italian patients with neurofibromatosis type 1 using Ion Torrent PGM™ platform. Eur J Med Genet 2016; 60:93-99. [PMID: 27838393 DOI: 10.1016/j.ejmg.2016.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 10/26/2016] [Accepted: 11/06/2016] [Indexed: 01/06/2023]
Abstract
Neurofibromatosis type 1 (NF1) is caused by mutations of the NF1 gene and is one of the most common human autosomal dominant disorders. The patient shows different signs on the skin and other organs from early childhood. The best known are six or more café au lait spots, axillary or inguinal freckling, increased risk of developing benign nerve sheath tumours and plexiform neurofibromas. Mutation detection is complex, due to the large gene size, the large variety of mutations and the presence of pseudogenes. Using Ion Torrent PGM™ Platform, 73 mutations were identified in 79 NF1 Italian patients, 51% of which turned out to be novel mutations. Pathogenic status of each variant was classified using "American College of Medical Genetics and Genomics" guidelines criteria, thus enabling the classification of 96% of the variants identified as being pathogenic. The use of Next Generation Sequencing has proven to be effective as for costs, and time for analysis, and it allowed us to identify a patient with NF1 mosaicism. Furthermore, we designed a new approach aimed to quantify the mosaicism percentage using electropherogram of capillary electrophoresis performed on Sanger method.
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Affiliation(s)
- Francesco Calì
- Laboratorio di Genetica Molecolare, UOC Laboratorio di Genetica Medica, Associazione Oasi Maria SS, IRCCS, Troina, EN, Italy.
| | - Valeria Chiavetta
- Laboratorio di Genetica Molecolare, UOC Laboratorio di Genetica Medica, Associazione Oasi Maria SS, IRCCS, Troina, EN, Italy
| | - Giuseppa Ruggeri
- Laboratorio di Genetica Molecolare, UOC Laboratorio di Genetica Medica, Associazione Oasi Maria SS, IRCCS, Troina, EN, Italy
| | - Maria Piccione
- Azienda Ospedali Riuniti Villa Sofia Cervello, Università degli Studi di Palermo, Palermo, Italy
| | - Angelo Selicorni
- UOS Genetica Pediatrica, Fondazione MBBM, AOS Gerardo, Monza, Italy; UOC Pediatria ASST Lariana, Como, Italy
| | - Daniela Palazzo
- Azienda Ospedali Riuniti Villa Sofia Cervello, Università degli Studi di Palermo, Palermo, Italy
| | - Maria Bonsignore
- UOC di Neuropsichiatria Infantile, Dipartimento Materno Infantile, Policlinico Universitario "G. Martino", Messina, Italy
| | - Anna Cereda
- UOC Pediatria Ospedale Papa Giovanni XXIII Bergamo, Italy
| | - Maurizio Elia
- Dipartimento per il Ritardo Mentale, Associazione Oasi Maria SS, IRCCS, Troina, EN, Italy
| | - Pinella Failla
- Dipartimento per il Ritardo Mentale, Associazione Oasi Maria SS, IRCCS, Troina, EN, Italy
| | - Maria Grazia Figura
- Dipartimento per il Ritardo Mentale, Associazione Oasi Maria SS, IRCCS, Troina, EN, Italy
| | - Agata Fiumara
- Dipartimento di Medicina Clinica e Sperimentale, Sezione di Pediatria e Neuropsichiatria Infantile, Università degli Studi di Catania, Catania, Italy
| | - Silvia Maitz
- UOS Genetica Pediatrica, Fondazione MBBM, AOS Gerardo, Monza, Italy
| | | | - Teresa Mattina
- Dipartimento di Medicina Clinica e Sperimentale, Sezione di Pediatria e Neuropsichiatria Infantile, Università degli Studi di Catania, Catania, Italy
| | - Alda Ragalmuto
- Laboratorio di Genetica Molecolare, UOC Laboratorio di Genetica Medica, Associazione Oasi Maria SS, IRCCS, Troina, EN, Italy
| | - Corrado Romano
- Dipartimento per il Ritardo Mentale, Associazione Oasi Maria SS, IRCCS, Troina, EN, Italy
| | - Martino Ruggieri
- Dipartimento di Medicina Clinica e Sperimentale, Sezione di Pediatria e Neuropsichiatria Infantile, Università degli Studi di Catania, Catania, Italy
| | - Roberto Salluzzo
- Laboratorio di Genetica Molecolare, UOC Laboratorio di Genetica Medica, Associazione Oasi Maria SS, IRCCS, Troina, EN, Italy
| | - Antonino Saporoso
- UOC di Neuropsichiatria Infantile, Dipartimento Materno Infantile, Policlinico Universitario "G. Martino", Messina, Italy
| | - Carmelo Schepis
- Dipartimento per il Ritardo Mentale, Associazione Oasi Maria SS, IRCCS, Troina, EN, Italy
| | - Giovanni Sorge
- Dipartimento di Medicina Clinica e Sperimentale, Sezione di Pediatria e Neuropsichiatria Infantile, Università degli Studi di Catania, Catania, Italy
| | - Maria Spanò
- UOC di Neuropsichiatria Infantile, Dipartimento Materno Infantile, Policlinico Universitario "G. Martino", Messina, Italy
| | - Gaetano Tortorella
- UOC di Neuropsichiatria Infantile, Dipartimento Materno Infantile, Policlinico Universitario "G. Martino", Messina, Italy
| | - Valentino Romano
- Dipartimento di Fisica e Chimica, Università degli Studi di Palermo, Palermo, Italy
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