Multiple transcripts of the neurofibromatosis type 1 gene in human brain and in brain tumours

Pathogenic noncoding variants in the neurofibromatosis and schwannomatosis predisposition genes

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.

Using antisense oligonucleotides for the physiological modulation of the alternative splicing of NF1 exon 23a during PC12 neuronal differentiation

Neurofibromatosis Type 1 (NF1) is a genetic condition affecting approximately 1:3500 persons worldwide. The NF1 gene codes for neurofibromin protein, a GTPase activating protein (GAP) and a negative regulator of RAS. The NF1 gene undergoes alternative splicing of exon 23a (E23a) that codes for 21 amino acids placed at the center of the GAP related domain (GRD). E23a-containing type II neurofibromin exhibits a weaker Ras-GAP activity compared to E23a-less type I isoform. Exon E23a has been related with the cognitive impairment present in NF1 individuals. We designed antisense Phosphorodiamidate Morpholino Oligomers (PMOs) to modulate E23a alternative splicing at physiological conditions of gene expression and tested their impact during PC12 cell line neuronal differentiation. Results show that any dynamic modification of the natural ratio between type I and type II isoforms disturbed neuronal differentiation, altering the proper formation of neurites and deregulating both the MAPK/ERK and cAMP/PKA signaling pathways. Our results suggest an opposite regulation of these pathways by neurofibromin and the possible existence of a feedback loop sensing neurofibromin-related signaling. The present work illustrates the utility of PMOs to study alternative splicing that could be applied to other alternatively spliced genes in vitro and in vivo.

Neurofibromin deficiency in mice causes exencephaly and is a modifier for Splotch neural tube defects

Neural tube defects are common and serious human congenital anomalies. These malformations have a multifactorial etiology and can be reproduced in mouse models by mutations of numerous individual genes and by perturbation of multiple environmental factors. The identification of specific genetic interactions affecting neural tube closure will facilitate our understanding of molecular pathways regulating normal neural development and will enhance our ability to predict and modify the incidence of spina bifida and other neural tube defects. Here, we report a genetic interaction between Nf1, encoding the intracellular signal transduction protein neurofibromin, and Pax3, a transcription factor gene mutated in the Splotch mouse. Both Pax3 and Nf1 are important for the development of neural crest-derived structures and the central nervous system. Splotch is an established model of folate-sensitive neural tube defects, and homozygous mutant embryos develop spina bifida and sometimes exencephaly. Neural development is grossly normal in heterozygotes and neural tube defects are not seen. In contrast, we found a low incidence of neural tube defects in heterozygous Splotch mice that also harbored a mutation in one Nf1 allele. All compound homozygotes had severe neural tube defects and died earlier in embryogenesis than either Nf1(-/-) or Sp(-/-) embryos. We also report occasional exencephaly in Nf1(-/-) mice and identify more subtle CNS abnormalities in normal-appearing Nf1(-/-) embryos. Though other genetic loci and environmental factors affect the incidence of neural tube defects in Splotch mice, these results establish Nf1 as the first known gene to act as a modifier of neural tube defects in Splotch.

Identification of a novel isoform of microphthalmia-associated transcription factor that is enriched in retinal pigment epithelium

Mutations at the mouse locus encoding microphthalmia-associated transcription factor (Mitf) affect the development of many cell types, including retinal pigment epithelium (RPE), melanocytes, mast cells, and osteoclasts. Here we have identified a novel Mitf isoform, Mitf-a, and its human homologue MITF-A by cDNA cloning. MITF-A consists of 520 amino acid residues and differs in the amino-terminus from authentic melanocyte-type MITF (MITF-M). MITF-A mRNA is widely expressed and represents a predominant MITF isoform in cultured RPE cells, whereas MITF-M mRNA is exclusively expressed in melanocytes and melanoma cells. In situ hybridization analysis suggested that Mitf-a mRNA is enriched in the prospective RPE of mouse embryo. Moreover, transient cotransfection assays suggested that MITF-A activated transcription of the tyrosinase and tyrosinase-related protein 1 genes. MITF-A/Mitf-a therefore may play an important role in melanogenesis in RPE.

cDNA cloning of a novel protein containing two zinc-finger domains that may function as a transcription factor for the human heme-oxygenase-1 gene

Heme oxygenase 1 is an essential enzyme in heme catabolism that cleaves heme to form biliverdin, iron, and carbon monoxide. The human heme-oxygenase-1 gene is transcriptionally activated through the cis-regulatory element (MTE), GTCATATGAC (positions -156 to -147), during 12-O-tetradecanoylphorbol 13-acetate (TPA)-induced differentiation of myelomonocytic cell lines, such as THP-1, to macrophages. MTE is responsible for the myelomonocytic-specific induction of heme-oxygenase-1 gene expression, and is bound by ubiquitous and myelomonocytic cell-line-restricted proteins. In this study, we cloned the cDNA segments coding for a portion of a protein that binds to MTE by a Southwestern procedure from a THP-1 cDNA expression library; we subsequently isolated putative full-length cDNAs by a conventional hybridization procedure. The deduced protein, termed MTB-Zf, consists of 1482 amino acid residues, has a molecular mass of about 162 kDa, and contains the two widely separated zinc-finger domains located near the N- and C-termini. MTB-Zf possesses other structural features characteristic of transcription factors, including a long stretch of acidic amino acids (amino acids 67 - 95), a proline-rich region (positions 733-849), a region rich in basic amino acids (positions 1161-1247), and a leucine repeat-like region (positions 486-514). We show that a portion of MTB-Zf, including an N-terminal zinc-finger domain, binds in vitro to MTE and that the transient coexpression of MTB-Zf cDNA leads to transactivation of the heme-oxygenase-1 gene promoter. Since the 6.5 kb MTB-Zf is expressed in various human cell lines of different lineages, MTB-Zf may represent a ubiquitous MTE-binding protein. Furthermore, the MTB-Zf gene has been mapped to human chromosome 1p35-36.1 by fluorescence in situ hybridization, a region which is frequently deleted in various solid tumors, including neurogenic tumors. We found remarkable differences in the expression patterns of MTB-Zf mRNA and two other hybridizable mRNAs of 5kb and 8.5 kb when human brain and primary brain tumors were compared. Both MTB-Zf and the 8.5-kb mRNAs were abundantly expressed in the five primary brain tumors examined, but only the 5-kb mRNA was detectable in the human brain. These results suggest that MTB-Zf is a transcription factor and may also play an important role in cell growth or differentiation.

Long RT-PCR of the entire 8.5-kb NF1 open reading frame and mutation detection on agarose gels

Previous approaches to mutation detection in mRNA from the neurofibromatosis 1 (NF1) locus have required the PCR amplification of five or more overlapping cDNA segments to screen the entire 8.5-kb open reading frame (ORF). Systematically, these assays do not detect deletions that span the region of overlap (usually 1-3 exons) of any two consecutive target segments. In such cases, amplification from the mutant region of the disease-causing allele fails because binding sites for the PCR primers are missing, but amplification from the normal allele proceeds, yielding only the normal product. To alleviate this problem, we have developed a protocol to reverse transcribe and amplify the entire protein-coding sequence of NF1 as a single PCR product, starting with total RNA from lymphoblast cell lines or from whole blood. The 8.7-kb RT-PCR product was prepared from nine NF1 patients with known deletions or insertions, ranging in size from a 30-bp deletion within 1 exon to a 2.4-kb deletion that removes 12 exons. Agarose gel analysis of the initial products detected deletions as small as 341 bp. Restriction endonuclease digestion with Asel and Fspl, followed by agarose gel electrophoresis, revealed the predicted abnormal bands in all nine patients. All mutant bands were identified readily by observers with no knowledge of the patients' mutations. This simple assay should detect a great variety of insertion/deletion mutations in the NF1mRNA internal to the primer binding sites, including all possible single and multiple exon dropouts and approximately 30% of all previously reported NF1 mutations.

The two types of mRNAs for neurofibromin isoforms produced by von Recklinghausen neurofibromatosis (NF1) gene: analysis in human astrocytic tumors

Two types of mRNAs for neurofibromin isoforms, which are produced by Von Recklinghausen neurofibromatosis (NF1) gene, have so far been identified. In the present study, we analyzed the differential expression of the two NF1 mRNAs in 16 cases of human astrocytic tumors and in surrounding normal tissues by the RNA-polymerase chain reaction. Astrocytic tumors predominantly expressed type II NF1 mRNA, whereas it was type I isoform that was predominantly expressed in the normal tissues. These results suggested that the increased type II NF1 protein might play an important role in the growth of astrocytic tumors.