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Perez-Becerril C, Evans DG, Smith MJ. Pathogenic noncoding variants in the neurofibromatosis and schwannomatosis predisposition genes. Hum Mutat 2021; 42:1187-1207. [PMID: 34273915 DOI: 10.1002/humu.24261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/16/2021] [Accepted: 07/13/2021] [Indexed: 11/11/2022]
Abstract
Neurofibromatosis type 1 (NF1), type 2 (NF2), and schwannomatosis are a group of autosomal dominant disorders that predispose to the development of nerve sheath tumors. Pathogenic variants (PVs) that cause NF1 and NF2 are located in the NF1 and NF2 loci, respectively. To date, most variants associated with schwannomatosis have been identified in the SMARCB1 and LZTR1 genes, and a missense variant in the DGCR8 gene was recently reported to predispose to schwannomas. In spite of the high detection rate for PVs in NF1 and NF2 (over 90% of non-mosaic germline variants can be identified by routine genetic screening) underlying PVs for a proportion of clinical cases remain undetected. A higher proportion of non-NF2 schwannomatosis cases have no detected PV, with PVs currently only identified in around 70%-86% of familial cases and 30%-40% of non-NF2 sporadic schwannomatosis cases. A number of variants of uncertain significance have been observed for each disorder, many of them located in noncoding, regulatory, or intergenic regions. Here we summarize noncoding variants in this group of genes and discuss their established or potential role in the pathogenesis of NF1, NF2, and schwannomatosis.
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Affiliation(s)
- Cristina Perez-Becerril
- Division of Evolution and Genomic Science, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, UK
| | - D Gareth Evans
- Division of Evolution and Genomic Science, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Miriam J Smith
- Division of Evolution and Genomic Science, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, UK
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Jentarra GM, Rice SG, Olfers S, Rajan C, Saffen DM, Narayanan V. Skewed allele-specific expression of the NF1 gene in normal subjects: a possible mechanism for phenotypic variability in neurofibromatosis type 1. J Child Neurol 2012; 27:695-702. [PMID: 22068829 DOI: 10.1177/0883073811423439] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Neurofibromatosis type 1 is an autosomal dominant disorder characterized by neurocutaneous abnormalities, learning disabilities, and attention-deficit disorder. Neurofibromatosis type 1 symptom severity can be highly variable even within families where all affected members carry the same mutation. We hypothesized that variation in the expression of the normal NF1 allele may be a mechanism that participates in producing variable phenotypes. We performed allelic expression imbalance assays on healthy control individuals to estimate the prevalence of skewed allelic expression of the NF1 gene. Approximately 30% of individuals in our sample population showed significant skewing of allelic expression away from the expected 50:50 ratio, indicating that differential regulation of the NF1 alleles occurs in a high proportion of individuals. Differences of up to 25% in allele-specific expression of the NF1 alleles were identified. In individuals with Neurofibromatosis type 1, who carry a mutant allele (haploinsufficient), this degree of expression skewing may be sufficient to modulate the phenotype.
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Affiliation(s)
- Garilyn M Jentarra
- Neurology Research Department, Barrow Neurological Institute, Phoenix, AZ 85013, USA
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Harder A, Titze S, Herbst L, Harder T, Guse K, Tinschert S, Kaufmann D, Rosenbaum T, Mautner VF, Windt E, Wahlländer-Danek U, Wimmer K, Mundlos S, Peters H. Monozygotic Twins With Neurofibromatosis Type 1 (NF1) Display Differences in Methylation ofNF1Gene Promoter Elements, 5' Untranslated region, Exon and Intron 1. Twin Res Hum Genet 2012; 13:582-94. [DOI: 10.1375/twin.13.6.582] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Neurofibromatosis type 1 (NF1) is a common autosomal dominant disorder caused by heterozygotic inactivation of the NF1 tumor suppressor gene at 17q11.2. The associated phenotypes are highly variable, and modifying genes have been proposed to explain at least in part the intriguing expressivity. Given that haploinsufficiency of the NF1 gene product neurofibromin is responsible for some of the clinical manifestations, variations in expression of the wildtype NF1 allele might modify the phenotype. We therefore investigated epigenetic molecular modifications that could result in variable expression of the normal NF1 allele. To exclude confounding by DNA sequence variations, we analyzed monozygotic twin pairs with NF1 who presented with several discordant features. We fine-mapped the methylation pattern of a nearly 1 kb NF1 promoter region in lymphocytes of 8 twin pairs. All twin pairs showed significant intra-pair differences in methylation, especially of specific promoter subregions such as 5'UTR, exon 1 and intron 1 (+7 to +622), transcription factor binding sites and promoter elements like NF1HCS. Furthermore, we detected significant intra-pair differences in cytosine methylation for the region from -249 to -234 with regard to discordance for optic glioma with a higher grade of methylation in glioma cases. In conclusion, our findings of epigenetic differences of the NF1 promoter in leukocytes within mono zygotic twin pairs may serve as a proof of principle for other tissues. The results point towards a role of methylation patterns of the normal NF1 allele for expression differences and for modification of the NF1 phenotype.
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Jouhilahti EM, Peltonen S, Heape AM, Peltonen J. The pathoetiology of neurofibromatosis 1. THE AMERICAN JOURNAL OF PATHOLOGY 2011; 178:1932-9. [PMID: 21457932 PMCID: PMC3081157 DOI: 10.1016/j.ajpath.2010.12.056] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 12/01/2010] [Accepted: 12/10/2010] [Indexed: 01/13/2023]
Abstract
Although a mutation in the NF1 gene is the only factor required to initiate the neurocutaneous-skeletal neurofibromatosis 1 (NF1) syndrome, the pathoetiology of the multiple manifestations of this disease in different organ systems seems increasingly complex. The wide spectrum of different clinical phenotypes and their development, severity, and prognosis seem to result from the cross talk between numerous cell types, cell signaling networks, and cell-extracellular matrix interactions. The bi-allelic inactivation of the NF1 gene through a "second hit" seems to be of crucial importance to the development of certain manifestations, such as neurofibromas, café-au-lait macules, and glomus tumors. In each case, the second hit involves only one cell type, which is subsequently clonally expanded in a discrete lesion. Neurofibromas, which are emphasized in this review, and cutaneous neurofibromas in particular, are known to contain a subpopulation of NF1-diploinsufficient Schwann cells and a variety of NF1-haploinsufficient cell types. A recent study identified a multipotent precursor cell population with an NF1(+/-) genotype that resides in human cutaneous neurofibromas and that has been suggested to play a role in their pathogenesis.
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Affiliation(s)
- Eeva-Mari Jouhilahti
- Department of Cell Biology and Anatomy, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Sirkku Peltonen
- Department of Dermatology, University of Turku and Turku University Hospital, Turku, Finland
| | - Anthony M. Heape
- Department of Anatomy and Cell Biology, Institute of Biomedicine, University of Oulu, Oulu, Finland
| | - Juha Peltonen
- Department of Cell Biology and Anatomy, Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Dermatology, University of Turku and Turku University Hospital, Turku, Finland
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Pitulescu ME, Teichmann M, Luo L, Kessel M. TIPT2 and geminin interact with basal transcription factors to synergize in transcriptional regulation. BMC BIOCHEMISTRY 2009; 10:16. [PMID: 19515240 PMCID: PMC2702275 DOI: 10.1186/1471-2091-10-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Accepted: 06/10/2009] [Indexed: 12/20/2022]
Abstract
BACKGROUND The re-replication inhibitor Geminin binds to several transcription factors including homeodomain proteins, and to members of the polycomb and the SWI/SNF complexes. RESULTS Here we describe the TATA-binding protein-like factor-interacting protein (TIPT) isoform 2, as a strong binding partner of Geminin. TIPT2 is widely expressed in mouse embryonic and adult tissues, residing both in cyto- and nucleoplasma, and enriched in the nucleolus. Like Geminin, also TIPT2 interacts with several polycomb factors, with the general transcription factor TBP (TATA box binding protein), and with the related protein TBPL1 (TRF2). TIPT2 synergizes with geminin and TBP in the activation of TATA box-containing promoters, and with TBPL1 and geminin in the activation of the TATA-less NF1 promoter. Geminin and TIPT2 were detected in the chromatin near TBP/TBPL1 binding sites. CONCLUSION Together, our study introduces a novel transcriptional regulator and its function in cooperation with chromatin associated factors and the basal transcription machinery.
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Affiliation(s)
- Mara E Pitulescu
- Department of Molecular Cell Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
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Thompson W, Conlan S, McCue LA, Lawrence CE. Using the Gibbs Motif Sampler for phylogenetic footprinting. Methods Mol Biol 2008; 395:403-24. [PMID: 17993688 DOI: 10.1007/978-1-59745-514-5_25] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
The Gibbs Motif Sampler (Gibbs) is a software package used to predict conserved elements in biopolymer sequences. Although the software can be used to locate conserved motifs in protein sequences, its most common use is the prediction of transcription factor binding sites (TFBSs) in promoters upstream of gene sequences. We will describe approaches that use Gibbs to locate TFBSs in a collection of orthologous nucleotide sequences, i.e., phylogenetic footprinting. To illustrate this technique, we present examples that use Gibbs to detect binding sites for the transcription factor LexA in orthologous sequence data from representative species belonging to two different proteobacterial divisions.
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KELLY BB, HEDLUND E, KIM C, ISHIGURO H, ISACSON O, CHIKARAISHI DM, KIM KS, FENG G. A tyrosine hydroxylase-yellow fluorescent protein knock-in reporter system labeling dopaminergic neurons reveals potential regulatory role for the first intron of the rodent tyrosine hydroxylase gene. Neuroscience 2006; 142:343-54. [PMID: 16876957 PMCID: PMC2610443 DOI: 10.1016/j.neuroscience.2006.06.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2006] [Revised: 06/14/2006] [Accepted: 06/16/2006] [Indexed: 11/20/2022]
Abstract
Degeneration of the dopaminergic neurons of the substantia nigra is a hallmark of Parkinson's disease. To facilitate the study of the differentiation and maintenance of this population of dopaminergic neurons both in vivo and in vitro, we generated a knock-in reporter line in which the yellow fluorescent protein (YFP) replaced the first exon and the first intron of the tyrosine hydroxylase (TH) gene in one allele by homologous recombination. Expression of YFP under the direct control of the entire endogenous 5' upstream region of the TH gene was predicted to closely match expression of TH from the wild type allele, thus marking functional dopaminergic neurons. We found that YFP was expressed in dopaminergic neurons differentiated in vitro from the knock-in mouse embryonic stem cell line and in dopaminergic brain regions in knock-in mice. Surprisingly, however, YFP expression did not overlap completely with TH expression, and the degree of overlap varied in different TH-expressing brain regions. Thus, the reporter gene did not identify functional TH-expressing cells with complete accuracy. A DNaseI hypersensitivity assay revealed a cluster of hypersensitivity sites in the first intron of the TH gene, which was deleted by insertion of the reporter gene, suggesting that this region may contain cis-acting regulatory sequences. Our results suggest that the first intron of the rodent TH gene may be important for accurate expression of TH.
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Affiliation(s)
- B. B. KELLY
- Department of Neurobiology, Box 3209, Duke University Medical Center, Durham, NC 27710, USA
| | - E. HEDLUND
- Udall Parkinson’s Disease Research Center of Excellence, McLean Hospital/Harvard Medical School, MA 02478, USA
- Molecular Neurobiology Laboratory, McLean Hospital/Harvard Medical School, Belmont, MA 02478, USA
- Neuroregeneration Laboratory, McLean Hospital/Harvard Medical School, Belmont, MA 02478, USA
| | - C. KIM
- Udall Parkinson’s Disease Research Center of Excellence, McLean Hospital/Harvard Medical School, MA 02478, USA
- Molecular Neurobiology Laboratory, McLean Hospital/Harvard Medical School, Belmont, MA 02478, USA
| | - H. ISHIGURO
- Carna Bioscience, KIBC 511, 5-5-2, Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Hyogo, Japan
| | - O. ISACSON
- Udall Parkinson’s Disease Research Center of Excellence, McLean Hospital/Harvard Medical School, MA 02478, USA
- Neuroregeneration Laboratory, McLean Hospital/Harvard Medical School, Belmont, MA 02478, USA
| | - D. M. CHIKARAISHI
- Department of Neurobiology, Box 3209, Duke University Medical Center, Durham, NC 27710, USA
| | - K.-S. KIM
- Udall Parkinson’s Disease Research Center of Excellence, McLean Hospital/Harvard Medical School, MA 02478, USA
- Molecular Neurobiology Laboratory, McLean Hospital/Harvard Medical School, Belmont, MA 02478, USA
| | - G. FENG
- Department of Neurobiology, Box 3209, Duke University Medical Center, Durham, NC 27710, USA
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
- Correspondence to: G. Feng, Department of Neurobiology, Box 3209, Duke University Medical Center, Durham, NC 27710, USA. Tel: +1-919-668-1657; fax: +1-919-668-1891. E-mail address: (G. Feng)
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