1
|
Jovanović A, Tošić N, Marjanović I, Komazec J, Zukić B, Nikitović M, Ilić R, Grujičić D, Janić D, Pavlović S. Germline Variants in Cancer Predisposition Genes in Pediatric Patients with Central Nervous System Tumors. Int J Mol Sci 2023; 24:17387. [PMID: 38139220 PMCID: PMC10744041 DOI: 10.3390/ijms242417387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/04/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Central nervous system (CNS) tumors comprise around 20% of childhood malignancies. Germline variants in cancer predisposition genes (CPGs) are found in approximately 10% of pediatric patients with CNS tumors. This study aimed to characterize variants in CPGs in pediatric patients with CNS tumors and correlate these findings with clinically relevant data. Genomic DNA was isolated from the peripheral blood of 51 pediatric patients and further analyzed by the next-generation sequencing approach. Bioinformatic analysis was done using an "in-house" gene list panel, which included 144 genes related to pediatric brain tumors, and the gene list panel Neoplasm (HP:0002664). Our study found that 27% of pediatric patients with CNS tumors have a germline variant in some of the known CPGs, like ALK, APC, CHEK2, ELP1, MLH1, MSH2, NF1, NF2 and TP53. This study represents the first comprehensive evaluation of germline variants in pediatric patients with CNS tumors in the Western Balkans region. Our results indicate the necessity of genomic research to reveal the genetic basis of pediatric CNS tumors, as well as to define targets for the application and development of innovative therapeutics that form the basis of the upcoming era of personalized medicine.
Collapse
Affiliation(s)
- Aleksa Jovanović
- Pediatric Oncology Department, National Cancer Research Center, 11000 Belgrade, Serbia; (A.J.); (D.J.)
| | - Nataša Tošić
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (N.T.); (I.M.); (J.K.); (B.Z.)
| | - Irena Marjanović
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (N.T.); (I.M.); (J.K.); (B.Z.)
| | - Jovana Komazec
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (N.T.); (I.M.); (J.K.); (B.Z.)
| | - Branka Zukić
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (N.T.); (I.M.); (J.K.); (B.Z.)
| | - Marina Nikitović
- Pediatric Radiation Oncology Department, National Cancer Research Center, 11000 Belgrade, Serbia;
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (R.I.); (D.G.)
| | - Rosanda Ilić
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (R.I.); (D.G.)
- Neurooncology Department, Neurosurgery Clinic, University Clinical Centre of Serbia, 11000 Belgrade, Serbia
| | - Danica Grujičić
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (R.I.); (D.G.)
- Neurooncology Department, Neurosurgery Clinic, University Clinical Centre of Serbia, 11000 Belgrade, Serbia
| | - Dragana Janić
- Pediatric Oncology Department, National Cancer Research Center, 11000 Belgrade, Serbia; (A.J.); (D.J.)
| | - Sonja Pavlović
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (N.T.); (I.M.); (J.K.); (B.Z.)
| |
Collapse
|
2
|
Ghalavand MA, Asghari A, Farhadi M, Taghizadeh-Hesary F, Garshasbi M, Falah M. The genetic landscape and possible therapeutics of neurofibromatosis type 2. Cancer Cell Int 2023; 23:99. [PMID: 37217995 DOI: 10.1186/s12935-023-02940-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/07/2023] [Indexed: 05/24/2023] Open
Abstract
Neurofibromatosis type 2 (NF2) is a genetic condition marked by the development of multiple benign tumors in the nervous system. The most common tumors associated with NF2 are bilateral vestibular schwannoma, meningioma, and ependymoma. The clinical manifestations of NF2 depend on the site of involvement. Vestibular schwannoma can present with hearing loss, dizziness, and tinnitus, while spinal tumor leads to debilitating pain, muscle weakness, or paresthesias. Clinical diagnosis of NF2 is based on the Manchester criteria, which have been updated in the last decade. NF2 is caused by loss-of-function mutations in the NF2 gene on chromosome 22, leading the merlin protein to malfunction. Over half of NF2 patients have de novo mutations, and half of this group are mosaic. NF2 can be managed by surgery, stereotactic radiosurgery, monoclonal antibody bevacizumab, and close observation. However, the nature of multiple tumors and the necessity of multiple surgeries over the lifetime, inoperable tumors like meningiomatosis with infiltration of the sinus or in the area of the lower cranial nerves, the complications caused by the operation, the malignancies induced by radiotherapy, and inefficiency of cytotoxic chemotherapy due to the benign nature of NF-related tumors have led a march toward exploring targeted therapies. Recent advances in genetics and molecular biology have allowed identifying and targeting of underlying pathways in the pathogenesis of NF2. In this review, we explain the clinicopathological characteristics of NF2, its genetic and molecular background, and the current knowledge and challenges of implementing genetics to develop efficient therapies.
Collapse
Affiliation(s)
- Mohammad Amin Ghalavand
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Alimohamad Asghari
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Skull Base Research Center, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Farhadi
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Farzad Taghizadeh-Hesary
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Radiation Oncology Department, Iran University of Medical Sciences, Tehran, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Masoumeh Falah
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
3
|
Tritto V, Eoli M, Paterra R, Redaelli S, Moscatelli M, Rusconi F, Riva P. Characterization of 22q12 Microdeletions Causing Position Effect in Rare NF2 Patients with Complex Phenotypes. Int J Mol Sci 2022; 23:ijms231710017. [PMID: 36077416 PMCID: PMC9456353 DOI: 10.3390/ijms231710017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/11/2022] [Accepted: 08/25/2022] [Indexed: 11/18/2022] Open
Abstract
Neurofibromatosis type 2 is an autosomal dominant tumor-prone disorder mainly caused by NF2 point mutations or intragenic deletions. Few individuals with a complex phenotype and 22q12 microdeletions have been described. The 22q12 microdeletions’ pathogenic effects at the genetic and epigenetic levels are currently unknown. We here report on 22q12 microdeletions’ characterization in three NF2 patients with different phenotype complexities. A possible effect of the position was investigated by in silico analysis of 22q12 topologically associated domains (TADs) and regulatory elements, and by expression analysis of 12 genes flanking patients’ deletions. A 147 Kb microdeletion was identified in the patient with the mildest phenotype, while two large deletions of 561 Kb and 1.8 Mb were found in the other two patients, showing a more severe symptomatology. The last two patients displayed intellectual disability, possibly related to AP1B1 gene deletion. The microdeletions change from one to five TADs, and the 22q12 chromatin regulatory landscape, according to the altered expression levels of four deletion-flanking genes, including PIK3IP1, are likely associated with an early ischemic event occurring in the patient with the largest deletion. Our results suggest that the identification of the deletion extent can provide prognostic markers, predictive of NF2 phenotypes, and potential therapeutic targets, thus overall improving patient management.
Collapse
Affiliation(s)
- Viviana Tritto
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20054 Segrate, Italy
| | - Marica Eoli
- Unità di Neuro-Oncologia Molecolare, Fondazione IRCCS, Istituto Neurologico Carlo Besta, 20133 Milan, Italy
- Correspondence: (M.E.); (P.R.)
| | - Rosina Paterra
- Unità di Neuro-Oncologia Molecolare, Fondazione IRCCS, Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Serena Redaelli
- Dipartimento di Medicina e Chirurgia, University of Milano-Bicocca, 20900 Monza, Italy
| | - Marco Moscatelli
- Unità di Neuroradiologia, Fondazione IRCCS, Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Francesco Rusconi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20054 Segrate, Italy
| | - Paola Riva
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20054 Segrate, Italy
- Correspondence: (M.E.); (P.R.)
| |
Collapse
|
4
|
Sadler KV, Rowlands CF, Smith PT, Hartley CL, Bowers NL, Roberts NY, Harris JL, Wallace AJ, Gareth Evans D, Messiaen LM, Smith MJ. Re-evaluation of Missense Variant Classifications in NF2. Hum Mutat 2022; 43:643-654. [PMID: 35332608 PMCID: PMC9323416 DOI: 10.1002/humu.24370] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 02/18/2022] [Accepted: 03/21/2022] [Indexed: 11/20/2022]
Abstract
Missense variants in the NF2 gene result in variable NF2 disease presentation. Clinical classification of missense variants often represents a challenge, due to lack of evidence for pathogenicity and function. This study provides a summary of NF2 missense variants, with variant classifications based on currently available evidence. NF2 missense variants were collated from pathology‐associated databases and existing literature. Association for Clinical Genomic Sciences Best Practice Guidelines (2020) were followed in the application of evidence for variant interpretation and classification. The majority of NF2 missense variants remain classified as variants of uncertain significance. However, NF2 missense variants identified in gnomAD occurred at a consistent rate across the gene, while variants compiled from pathology‐associated databases displayed differing rates of variation by exon of NF2. The highest rate of NF2 disease‐associated variants was observed in exon 7, while lower rates were observed toward the C‐terminus of the NF2 protein, merlin. Further phenotypic information associated with variants, alongside variant‐specific functional analysis, is necessary for more definitive variant interpretation. Our data identified differences in frequency of NF2 missense variants by exon between gnomAD population data and NF2 disease‐associated variants, suggesting a potential genotype‐phenotype correlation; further work is necessary to substantiate this.
Collapse
Affiliation(s)
- Katherine V Sadler
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), Manchester, UK.,Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Charlie F Rowlands
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), Manchester, UK.,Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Philip T Smith
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), Manchester, UK
| | - Claire L Hartley
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), Manchester, UK
| | - Naomi L Bowers
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), Manchester, UK
| | - Nicola Y Roberts
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), Manchester, UK
| | - Jade L Harris
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), Manchester, UK
| | - Andrew J Wallace
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), Manchester, UK
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), Manchester, UK.,Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Ludwine M Messiaen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Miriam J Smith
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), Manchester, UK.,Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| |
Collapse
|