Identification of five new mutations of PDS/SLC26A4 in Mediterranean families with hearing impairment.

Pendred syndrome is an autosomal-recessive disorder characterized by congenital sensorineural hearing loss combined with goiter. This disorder may account for up to 10% of cases of hereditary deafness. The disease gene (PDS/SLC26A4) has been mapped to chromosome 7q22-q31 and encodes a chloride-iodide transport protein. Mutations in this gene are also a cause of non-syndromic autosomal recessive hearing impairment (DFNB4). We have analyzed the PDS/SLC26A4 gene in Spanish and Italian families and we have detected five new mutations (X871M, T132I, IVS1-2A>G, Y556H and 406del5).

Erratum: Identification of five new mutations of PDS/SLC26A4 in Mediterranean families with hearing impairment.

Pendred syndrome is an autosomal-recessive disorder characterized by congenital sensorineural hearing loss combined with goiter. This disorder may account for up to 10% of cases of hereditary deafness. The disease gene (PDS/SLC26A4) has been mapped to chromosome 7q22-q31 and encodes a chloride-iodide transport protein. Mutations in this gene are also a cause of non-syndromic autosomal recessive hearing impairment (DFNB4). We have analyzed the PDS/SLC26A4 gene in Spanish and Italian families and we have detected five novel mutations (X781W, T132I, IVS2-2A>G, Y556H and 406del5).

Juvenile and adult hemochromatosis are distinct genetic disorders.

Juvenile Hemochromatosis (JH) is a rare genetic disorder that causes iron overload. JH clinical features are similar to those of hemochromatosis (HFE), but the clinical course is more severe and is characterized by an earlier onset and by a prevalence of cardiac symptoms and endocrine dysfunctions. Here we describe seven Italian patients belonging to five unrelated families with clinical features typical of JH. In four out of five families the parents were consanguineous. Analysis of HFE gene mutations in all the cases and nucleotide sequence of the gene in one case excluded this gene as responsible for JH. Segregation analysis of 6p markers closely associated with HFE in families with consanguineous parents clearly showed that JH is unlinked to 6p and thus genetically distinct from HFE.

Generation of a transcription map of a 1 Mbase region containing the HFE gene (6p22).

A transcription map was generated of a 1 Mb interval including the HFE gene on 6p22. Thirty-seven unique cDNA fragments were characterised following their retrieval from hybridisation of immobilised YACs to primary pools of cDNAs prepared from RNA of foetal brain, human liver, foetal human liver, placenta, and CaCo2 cell line. All cDNA fragments were positioned on the physical map on the basis of presence in aligned and overlapping YACs and cosmid clones of the region. The isolated cDNAs together with established or published sequence tagged sites (STSs) and markers provided sufficient landmark density to cover approximately 90% of the 1 Mb interval with cosmid clones. The precise localisation of two known genes (NPT1 and RING finger protein) was established. A minimum of 14 additional transcription units has also been integrated. Twenty-eight cDNA fragments showed no similarity with known sequences, but 20 of these detected discrete mRNAs upon northern analysis. Their characterisation is still under investigation. Eleven new polymorphisms were also identified and localised, and the HFE genomic structure was better defined. This integrated transcription map considerably extends a recently published map of the HFE region. It will be useful for the identification of genetic defects mapping to this region and for providing template resources for genomic sequencing.

Development of RNA-SSCP protocols for the identification and screening of CFTR mutations: identification of two new mutations.

A strategy is described that allows a rapid and accurate identification and screening of cystic fibrosis gene mutations. It consists of setting up and developing RNA single strand conformation polymorphism (rSSCP) protocols, a technique based on the large repertoire of secondary structure of single-stranded RNA. By incorporating the T7 phage promoter sequence into PCR primers, it is possible to carry out rSSCP and compare it to standard single-strand conformation polymorphism (SSCP). Several parallel tests indicate that rSSCP detects a higher fraction of single base changes, and is less time consuming than SSCP since it requires only one fairly short electrophoretic run. Using this technique we were able to identify two new splicing mutations in introns 5 (711 + 5G-->A) and 10 (1717-8G-->A) of the CFTR gene.

Detection of a neurofibromatosis type I (NF1) homologous sequence by PCR: implications for the diagnosis and screening of genetic diseases.

The neurofibromatosis type I (NF1) gene was extensively screened for mutations using single strand conformation polymorphism (SSCP) technology. During the analysis of the NF1 GAP-related domain, electrophoretically abnormal fragments were detected. Direct sequencing of these fragments allowed us to identify the presence of a NF1 highly homologous sequence (NF1HHS). A detailed analysis of a hybrid panel located this sequence on chromosome 15q24-->qter. An accurate search through several data banks demonstrated that this sequence is a new NF1 homologue. This report shows how it is possible to find homologous sequences at random, and subsequently to make wrong interpretations.

The motilin gene: subregional localisation, tissue expression, DNA polymorphisms and exclusion as a candidate gene for the HLA-associated immotile cilia syndrome.

The product of the human motilin gene (MLN) has an important role in regulating gastrointestinal motility. The precise chromosomal localisation and expression of this gene are still unresolved. Here, we report a detailed study assigning MLN to 6p21.3; MLN is tightly linked to the HLA-DQalpha locus. Moreover, MLN expression has been evaluated in a large series of tissues. Positive signals have been obtained for brain, bronchi and a gastrointestinal malignancy. Direct sequencing exon by exon of the codifying region, intron/exon boundaries and promoter has allowed the identification of three DNA polymorphisms, one of which corresponds to a common protein variant. The chromosomal localisation of MLN, and its expression in broncoepithelial cells suggests that this gene is involved in immotile-cilia syndrome (ICS) disease. Sequence and segregation analysis of the MLN gene carried out in two families, in which the disease locus was previously assigned to 6p21.3, exclude MLN as a candidate gene for the HLA-associated form of ICS.

A new complex polymorphic repeat close to the HLA-A and HLA-E loci.

We describe a complex polymorphic repeat discovered analyzing YAC 225B1, which spans the region between the HLA-A and HLA-E loci. The repeat consists of a variable number of the nucleotide A followed by a variable number of the trinucleotide AAG [(A)n(AAG)n]. Three different alleles were detected with an observed heterozygosity of 0.30.

Interstitial "de novo" tandem duplication of 7(q31.1-q35): first reported case.

A patient carrying a de novo 7q31-35 duplication is presented. The tandem duplication was confirmed by FISH analysis. The case seems to be the first in the literature and, in spite of the large size of the duplicated region, he shows mild facial dysmorphism and a moderate mental retardation. The clinical findings of the dup7q published cases are compared in order to define a possible common phenotype.

Molecular screening of genetic defects with RNA-SSCP analysis: the PKU and cystinuria model.

RNA single-strand conformation polymorphism (rSSCP) is a recently developed method for detecting genetic defects. This technique requires DNA amplification with a polymerase chain reaction making use of one T7 promoter-containing primer. Amplification products are subsequently transcribed in vitro and the labelled transcripts are analysed for single-strand conformation changes. rSSCP has been applied to mutation screening of the phenylalanine hydroxylase gene and rBAT cDNA, from PKU and cystinuric patients, respectively. Experimental evidence shows that 83% and 86% of screened PKU and cystinuric mutations, respectively, give rise to detectable rSSCP signals. Thus, results obtained show that RNA single-strand conformation polymorphism analysis is generally applicable and is a suitable technique for detecting genetic disease causing mutations, both in basic research and in clinical practice.

GABA (gamma-amino-butyric acid) neurotransmission: identification and fine mapping of the human GABAB receptor gene.

GABA (gamma-amino-butyric acid) receptors are a family of proteins involved in the GABAergic neurotransmission of the mammalian central nervous system (CNS). They have physiological importance and clinical relevance in several diseases. We report the identification, cloning, and fine mapping of the human cDNA for GABAB receptor. A 4.2-Kb cDNA containing an open reading frame for a predicted protein of 960 aa was isolated from a fetal brain cDNA library. It had a strong identity (91.5%) with the rat GABAB receptor (rGB1A) nucleotide sequence, that corresponded to 98.6% identity at the amino acid level. Expression of the GABAB at the transcription level was detected by Northern analysis in all brain areas examined. The GABAB receptor has been mapped to human chromosome 6p21.3 within the HLA class I region close to the HLA-F gene. Susceptibility loci for multiple sclerosis, epilepsy, and schizophrenia have been suggested to map in this region.

Cloning of a new gene (FB19) within HLA class I region.

A novel gene (named FB19) has been identified within the HLA class I region at human chromosome 6p21.3. A 4.5-kb cDNA containing a 2820-bp open reading frame for a predicted protein of 940 aa was identified. No homology with known gene was detected at the DNA level, while the predicted protein is characterized by a glycine-rich region followed by a domain of 35 residues that shows high homology with the CAT56 gene, another gene of MHC class I. A 4. 5-kb transcript was detected in several tissues and cell lines, clearly indicating a wide distribution of expression. Once its function is defined, it could be possible to investigate the relationship between the FB19 gene and the several diseases already mapped within the HLA class I region.

Hereditary hemochromatosis: generation of a transcription map within a refined and extended map of the HLA class I region.

Hereditary hemochromatosis, a common severe inherited disease, maps to the short arm of chromosome 6 close to the HLA-A locus. Recently, linkage data on Italian and French populations confirmed this location, while a similar analysis on Australian and British populations located the gene closer to D6S105, a marker residing telomeric of HLA-A. To increase our knowledge on the region of highest linkage disequilibrium in our population and possibly to identify the disease gene, a 1.2-Mb detailed physical and transcription map was generated, spanning the HLA class I region. Thirty-eight unique cDNA fragments, retrieved following the hybridization of immobilized YACs to primary pools of cDNAs prepared from RNA of fetal brain, adult brain, liver, placenta, and the CaCo2 cell line, were characterized. All cDNA fragments were positioned in a refined and extended map of the human major histocompatibility complex spanning from HLA-E to approximately 500 kb telomeric of HLA-F. The localization of known genes was refined, and a new gene from the RNA helicase superfamily was identified. Overall, 14 transcription units in addition to the HLA genes have been detected and integrated in the map. Thirteen cDNA fragments show no similarity with known sequences and could be candidates for the disease. Their characterization and assessment for involvement in hemochromatosis are still under investigation. Seven new polymorphisms, some tightly linked to the disease, were also identified and localized.

Mutation analysis of the HLA-H gene in Italian hemochromatosis patients.

Hemochromatosis (HH) is an inborn error of iron metabolism, frequent among Caucasians, characterized by progressive iron loading that, if untreated, causes high morbidity and death. HLA-H, a putative HH gene, has recently been isolated. The large majority of patients so far studied are homozygous for a single mutation, which results in a cysteine-to-tyrosine substitution at amino acid 282 of the protein. A second, less frequent, variant, His63Asp, has an undefined role in the pathogenesis of the disease. Here we report that the Cys282Tyr change accounts for 69% of HH chromosomes in a series of 75 unrelated Italian patients who fulfilled well-defined criteria for HH diagnosis. Sixty-four percent of patients were Cys282Tyr homozygous, 10% were heterozygous, and 21% carried the normal allele. The same mutation was rare in normal controls. The His63Asp variant was less frequent but had a similar frequency among affected and normal chromosomes. Subjects without two copies of the Cys282Tyr change were both isolated patients and individuals from families with a 6p-linked disease. Mutation analysis of the HLA-H gene, carried out by RNA-SSCP in the latter patients, did not reveal any significant nucleotide abnormality in coding sequences and intron-exon boundaries. The absence of mutations in HLA-H gene was confirmed in three cases by direct sequencing. Major deletions or rearrangements of the gene were excluded by Southern blotting. The existence of patients with clinical and histological features of HH, but without mutations in HLA-H gene, suggests that in Italy the disease is more heterogeneous than reported in northern Europe.

Screening of neurofibromatosis type 1 gene: identification of a large deletion and of an intronic variant.

Neurofibromatosis type 1 of von Recklinghausen is a common autosomal dominant disorder, characterized by peripheral neurofibromas, café-au-lait spots and Lisch nodules of the iris. The high mutation rate at the neurofibromatosis type 1 locus results in a wide range of molecular abnormalities. We have screened seven different exons of the neurofibromatosis type 1 gene, including those codifying for the GAP-related domain, using the RNA-Single Strand Conformation Polymorphism (RNA-SSCP) method in a series of 59 neurofibromatosis type 1 patients. We have also analyzed four intragenic repeats and one RFLP to detect hemizygosity and evaluate informativeness in at-risk families. One deletion and a new intronic normal variant have been detected. Thus the majority of Neurofibromatosis type 1 chromosomes have not been characterized, confirming difficulty in providing proper genetic counselling in neurofibromatosis type 1 families, even following extensive DNA analysis.

New polymorphisms and markers in the HLA class I region: relevance to hereditary hemochromatosis (HFE).

Hereditary hemochromatosis (HFE) is an inherited disorder whose gene lies in the proximity of the histocompatibility antigen (HLA) class I region, on 6p21.3. Despite efforts in refining the HFE region, a number of informative DNA markers, linked to the disease locus and amenable to use in an assay based on the polymerase chain reaction (PCR) is available. The gene content of this region is high, and the HFE gene has not so far been identified. We have used a strategy based on PCR protocols potentially able to detect both polymorphisms and expressed sequences. This approach has been applied to a 700-kb stretch (approximately) of DNA corresponding to the insert of a Centre d'Etude du Polymorphisme Humain yeast artificial chromosome (225 B1) of the possible candidate region. Five new polymorphisms have been detected among 20 specific fragments isolated. Four of them are tightly linked to the HFE locus. Because of the strong linkage disequilibrium with the disease demonstrated by these markers, they could represent starting points for the identification and characterization of the HFE gene. The remaining non-polymorphic fragments, being amplifiable and in most cases linked to NotI sites, may be useful starting points for the generation of a genomic contig of band 6p21.3 and for gene identification.

A recombination event close to HFE gene in hereditary hemochromatosis.

A candidate gene for Hereditary Hemochromatosis (HFE) has been recently cloned from a region 4 cM telomeric to HLA-A on the short arm of chromosome 6. This gene, defined HFE, is mutated in a high proportion of HFE patients. Positional cloning of HFE has been difficult, because of the extended region of linkage disequilibrium observed around the gene and of the rarity of recombination events in this DNA area. Here we describe a crossover in an Italian HFE patient which occurred close to the HFE gene in a restricted interval between D6S2221 and D6S2240-D6S2238 markers. The molecular analysis of this event and the segregation of the HFE mutations in the family are consistent with the position of the HFE gene telomeric to D6S2221.