Chromosome 17 loss-of-heterozygosity studies in benign and malignant tumors in neurofibromatosis type 1.

Neurofibromatosis type 1 (NF1) is a common autosomal dominant condition characterized by benign tumor (neurofibroma) growth and increased risk of malignancy. Dermal neurofibromas, arising from superficial nerves, are primarily of cosmetic significance, whereas plexiform neurofibromas, typically larger and associated with deeply placed nerves, extend into contiguous tissues and may cause serious functional impairment. Malignant peripheral nerve sheath tumors (MPNSTs) seem to arise from plexiform neurofibromas. The NF1 gene, on chromosome segment 17q11.2, encodes a protein that has tumor suppressor function. Loss of heterozygosity (LOH) for NF1 has been reported in some neurofibromas and NF1 malignancies, but plexiform tumors have been poorly represented. Also, the studies did not always employ the same markers, preventing simple comparison of the frequency and extent of LOH among different tumor types. Our chromosome 17 LOH analysis in a cohort of three tumor types was positive for NF1 allele loss in 2/15 (13%) dermal neurofibromas, 4/10 (40%) plexiform neurofibromas, and 3/5 (60%) MPNSTs. Although the region of loss varied, the p arm (including TP53) was lost only in malignant tumors. The losses in the plexiform tumors all included sequences distal to NF1. No subtle TP53 mutations were found in any tumors. This study also reports the identification of both NF1 "hits" in plexiform tumors, further supporting the tumor suppressor role of the NF1 gene in this tumor type.

Constitutional and mosaic large NF1 gene deletions in neurofibromatosis type 1.

A set of neurofibromatosis type 1 (NF1) patients was screened for large NF1 gene deletions by comparing patient and parent genotypes at 10 intragenic polymorphic loci. Of 67 patient/parent sets (47 new mutation patients and 20 familial cases), five (7.5%) showed loss of heterozygosity (LOH), indicative of NF1 gene deletion. These five patients did not have severe NF1 manifestations, mental retardation, or dysmorphic features, in contrast to previous reports of large NF1 deletions. All five deletions were de novo and occurred on the maternal chromosome. However, two patients showed partial LOH, consistent with somatic mosaicism for the deletion, suggesting that mosaicism may be more frequent in NF1 than previously recognised (and may have bearing on clinical severity). We suggest that large NF1 deletions (1) are not always associated with unusual clinical features, (2) tend to occur more frequently on maternal alleles, and (3) are an important mechanism for constitutional and somatic mutations in NF1 patients.

Four frameshift mutations in neurofibromatosis type 1 caused by small insertions.

We have been using heteroduplex analysis to assay individual exons within the NF1 gene in an effort to identify disease causing constitutional mutations in neurofibromatosis type 1 patients. Here we report the identification and characterisation of four insertional NF1 frameshift mutations in an analysis of exons 28-39 in a set of 78 patients. These include three 1 base pair insertions and one 2 base pair insertion. Three of these mutations can be attributed to replication slippage errors, while the mechanism behind the fourth may be related to formation of secondary structure during replication. It may be of significance that a majority of the previously reported small insertions in NF1 also lie within exons 28-39.

Identification of mutations in two major mRNA isoforms of the Chediak-Higashi syndrome gene in human and mouse.

Chediak-Higashi syndrome is an autosomal recessive, immune deficiency disorder of human (CHS) and mouse (beige, bg) that is characterized by abnormal intracellular protein transport to, and from, the lysosome. Recent reports have described the identification of homologous genes that are mutated in human CHS and bg mice. Here we report the sequences of two major mRNA isoforms of the CHS gene in human and mouse. These isoforms differ both in size and in sequence at the 3' end of their coding domains, with the smaller isoform (approximately 5.8 kb) arising from incomplete splicing and reading through an intron. These mRNAs also differ in tissue distribution of transcription and in predicted biological properties. Novel mutations were identified within the region of the coding domain common to both isoforms in three CHS patients: C-->T transitions that generated stop codons (R50X and Q1029X) were found in two patients, and a novel frameshift mutation (deletion of nucleotides 3073 and 3074 of the coding domain) was found in a third. Northern blots of lymphoblastoid mRNA from CHS patients revealed loss of the largest transcript (approximately 13.5 kb) in two of seven CHS patients, while the small mRNA was undiminished in abundance. These results suggest that the small isoform alone cannot complement Chediak-Higashi syndrome.

Somatic mosaicism in a patient with neurofibromatosis type 1.

Using loss of heterozygosity analysis, a method designed to detect moderate to large gene deletions, we have identified a new-mutation neurofibromatosis type 1 (NF1) patient who is somatically mosaic for a large maternally derived deletion in the NF1 gene region. The deletion extends at least from exon 4 near the 5' end of the gene to intron 39 near the 3' end. The gene-coding region is, therefore, mostly or entirely deleted, encompassing a loss of > or = 100 kb. We hypothesize that the deletion occurred at a relatively early developmental timepoint, since signs of NF1 in this patient are not confined to a specific body region, as seen in "segmental" NF, and since both mesodermally and ectodermally derived cells are affected. This report provides the first molecular evidence of somatic mosaicism in NF1 and, taken together with a recent report of germ-line mosaicism in NF1, adds credence to the concept that mosaicism plays an important role in phenotypic and genetic aspects of NF1 and may even be a relatively common phenomenon.

Benign neurofibromas in type 1 neurofibromatosis (NF1) show somatic deletions of the NF1 gene.

Neurofibromatosis type 1 (NF1) is one of the most common human autosomal dominant diseases. NF1 is characterized by café-au-lait spots (CLS), axillary freckles and Lisch nodules of the iris. Another hallmark of NF1 is the development of neurofibromas, benign tumours that arise from peripheral nerve sheaths. NF1 patients also have an increased incidence of certain malignant tumours. Malignancies in NF1 are believed to follow the 'two-hit' hypothesis, in which one allele is constitutionally inactivated while the other allele is subsequently inactivated ('second hit') at the somatic level. This hypothesis has not, however, been fully tested in the aetiology of benign neurofibromas. This is a crucial issue since it addresses not only the basic mechanism behind the genesis of neurofibromas, but may also indicate a mechanism common to many or all NF1 features. Using both NF1 intragenic polymorphisms as well as markers from flanking and more distal regions of chromosome 17, we have investigated loss of heterozygosity (LOH) in 22 neurofibromas from five unrelated NF1 patients. Eight of these tumours revealed somatic deletions involving NF1, indicating that inactivation of NF1 is associated with at least some neurofibromas.

Two NF1 mutations: frameshift in the GAP-related domain, and loss of two codons toward the 3' end of the gene.

Neurofibromatosis type 1 (NF1) is one of the most common autosomal dominant disorders, and is due to mutations within the NF1 gene on chromosome 17q11.2. Only the middle 400 amino acids of the associated protein (neurofibromin) have a known function, comprising a GTPase-activating-protein (GAP) domain. The large gene size and the fact that approximately half of cases are due to new mutation render mutation analysis difficult. NF1 direct mutation characterization is important for development of DNA diagnostic procedures, analysis of phenotype/genotype correlations, and delineation of functions for specific domains of neurofibromin. We report two mutations detected using PCR amplification of individual exons followed by heteroduplex analysis. One is a single base deletion in exon 24 which is predicted to result in a protein truncated early in the GAP-related domain. The other is a 6-bp deletion in exon 39 which is predicted to result in loss of two amino acids in the mature protein near the carboxy-terminus. The exon 24 mutant allele was shown to be expressed by RNA PCR analysis. The exon 39 mutation suggests that those two amino acids are important in neurofibromin function, perhaps indicating a functional domain.

Characterization of a single base-pair deletion in neurofibromatosis type 1.

The gene which is responsible for neurofibromatosis type 1 (NF1) is located on chromosome 17 (17q11.2). The NF1 gene is approximately 350 kilobases (kb) long and exhibits an extremely high mutation rate; therefore, most patients are expected to have unique mutations. To date, relatively few mutations have been well characterized. We report here a de novo single base pair (bp) deletion in one NF1 allele in a patient diagnosed with NF1 and leukemia. We further characterized this mutation at the RNA level by allele-specific oligonucleotide (ASO) hybridization which demonstrated that the mutant allele is transcribed.

Isolation and characterization of radiation-reduced hybrids containing portions of the proximal long arm of the human X chromosome: identification of hybrids containing the Menkes' disease locus.

The proximal long arm of the human X chromosome (Xcen----Xq13) encompasses an estimated 23 megabases of DNA and contains numerous identified genetic loci. In order to generate a highly enriched source of DNA from this region, radiation-reduced human-hamster hybrids were constructed and screened to identify those that contained at least part of proximal Xq. Eight such hybrids were identified and characterized by Southern blot and fluorescence in situ hybridization analyses to determine more precisely the human DNA complement in each. One hybrid contains the entire proximal long arm and will be useful for mapping Xcen----Xq13 in its entirety and for localizing genes within this region. Another hybrid contains a smaller portion of the proximal long arm that includes the region reported to contain the gene for Menkes' disease.

Mycoplasma pneumoniae DNA gyrase genes.

We have identified a clone from a lambda EMBL3 library containing a 19kb insert of Mycoplasma pneumoniae DNA which includes the genes that encode both subunits of DNA gyrase. The gyrB gene and the 5' end of the gyrA gene have been subcloned into M13. The gyrB gene is 1953bp in length and overlaps the gyrA gene by a single base. The nucleotide sequence of these subclones has significant homology to previously reported gyrase genes. In terms of the size of the gyrB gene and its proximity to the gyrA gene, M. pneumoniae is more similar to Bacillus subtilis than to Escherichia coli.

A physical map of the Mycoplasma genitalium genome.

We report the construction of a physical map of the genome of the human pathogen Mycoplasma genitalium through the use of pulse-field gel electrophoresis. The small size and relative simplicity of this genome permit the arrangement of restriction fragments without having to construct linking clones. The size of the genome has been calculated to be approximately 600 kb and several important genetic determinants have been assigned specific loci on the map.

Prevalence of novel repeat sequences in and around the P1 operon in the genome of Mycoplasma pneumoniae.

The presence of numerous different repetitive elements in the genome of Mycoplasma pneumoniae has been documented by several laboratories. One which we previously identified, denoted as SDC1, has now been further characterized, verified to be distinct from those discussed in previous publications and shown to lack homology to several other species of Mycoplasma when tested under our stringency conditions. As many as eight versions of the SDC1-type repeat, which is more than 400 bp long, are scattered throughout the genome of M. pneumoniae. The prototype for SDC1 is found within a gene encoding a putative 130-kDa membrane-binding protein lying just downstream from the gene encoding the cytadhesin protein P1. In fact, all of the reported M. pneumoniae repetitive elements have at least one representative either within or adjacent to the P1 operon; many if not all of these lie within open reading frames. The function of these repetitive elements is still unclear.