Identification of novel SLC3A1 gene mutations in Spanish cystinuria families and association with clinical phenotypes.

Cystinuria is an inherited metabolic disease characterized by an abnormal urinary excretion of cystine and dibasic amino acids, leading to kidney stone formation. Incidence of cystinuria in the Mediterranean Spanish population is one of the highest in the world. In view of the low prevalence of previously reported mutations in the SLC3A1 gene, analyses to identify novel variants were carried out on 20 cystinuria families. Additionally, we investigated the possible association between these molecular variants and clinical phenotypes. Genomic DNA from 48 cystinuria patients, 44 healthy relatives and 81 unrelated controls from the East Mediterranean coast of Spain was screened by conformation sensitive gel electrophoresis. Abnormal patterns were confirmed by nucleotide sequence determination and by further restriction fragment-length polymorphism. We only found 11 genetic variants within the SLC3A1 gene: five known polymorphisms (114C > A, 231T > A, 1136 + 3delT, 1332 + 7T > C and 1338G > A), four point mutations (M467T, R452W, I105R and Y461X), one single base pair deletion (1767delA) and one 2-bp insertion (1670insAT). Two of these genetic variants (I105R and 1670insAT) were described for the first time. All mutations but one were detected in families classified as Type I cystinuria due to the transmission pattern of the disease. Association analyses revealed that 231T > A (M467T), 1136 + 3delT and 1332 + 7T > C genetic variants were statistically related with urinary amino acid excretion in cystinuria patients. Although some molecular variants within the SLC3A1 gene were associated with clinical traits in cystinuria patients, the low detection rate of mutations in this gene strongly suggests that variation of the SLC3A1 is not the major genetic factor contributing to cystinuria in this Mediterranean population.

Gut neuroendocrine cells: relationship to the proliferative activity and apoptosis of mucous epitheliocytes in aging.

OBJECTIVES: Diffuse neuroendocrine system (DNES) cells regulate homeostasis via neurocrine, endocrine and paracrine mechanisms. Extensive effects of peptide hormones and biogenic amines necessitate studying of DNES cell biology in aging. In this connection, the functional morphology of gut neuroendocrine cells (NEC), proliferative activity and apoptosis of mucous epithelial cells in aging have been studied. MATERIAL AND METHODS: The study was performed on BALB/c-nu mice of 4, 21 and 34 months of age. NEC, proliferative activity and apoptosis of mucous epitheliocytes in stomach and duodenum have been studied by histochemical, immunohistochemical and morphometrical methods. RESULTS: The total number of NEC shows an increasing trend with advancing age. However, the different types of NEC elicit differential patterns. The total number of epithelial cell nuclei does not show any statistically significant difference during aging. The proliferative activity of mucous epitheliocytes also shows no difference among the three animal groups studied. On the contrary, the apoptotic index increases with advancing age. CONCLUSIONS: The results demonstrate that various gut NEC show differential behavior with age and their time-courses are dependent on the site of location (stomach or duodenum). The picture seems quite complex to allow a comprehensive interpretation, nonetheless it gives us some useful indications for further investigation. In fact, since the gut does not show evident gross age-related physiological changes, modifications with age in specific biological parameters can suggest the key mechanisms of compensative regulatory processes possibly acting during aging.

Role of thyroid hormone in craniofacial and eye development using a rat model.

Thyroid hormones (TH) are essential for somatic and neural development. Epidemiological studies have pointed to TH-dependent craniofacial features occurring during development. In an attempt to elucidate the precise role of TH in the developing eyes and adnexa (orbit, lids, nasolacrimal structures), we analysed the craniofacial and eyeball developmental characteristics in a rat model of congenital-neonatal hypothyroidism (HG), induced by combined chemical-surgical thyroidectomy. The heads and eyeballs from control and HG animals were obtained at key developmental stages and processed for scanning electron, light and transmission electron microscopy. On embryological day 13 (E13), significantly reduced values for head parameters (25% less), optic primordia area (0.053 +/- 0.0085 vs. 0.111 +/- 0.012 microm(2); p < 0.05) and volume (3.96 +/- 0.141 vs. 8.09 +/- 0.123 microm(3); p < 0.05) were found in the HG with respect to the controls. In addition, a delayed prenatal eye closure and postnatal eye opening took place in the treated rats. The photoreceptor and ganglion cell layer thickness displayed significantly lower values (p < 0.001) in HG, at each developmental time point. Postnatally, a delay in photoreceptor outer segment morphogenesis (in relation to retarded disc formation) and significantly lower values for ganglion cell nuclear volumes (p < 0.001) and nuclear pore density (p < 0.01) were observed in the TH-deficient animals. All data suggest that TH play a pivotal role in the development of the face and eye. Therefore, a series of defects due to a loss of TH actions involved in anterior-posterior development of the head and face and the loss of TH-dependent signals crucial for cell differentiation, migration, proliferation and establishment of definitive cell phenotypes in the eyes may appear. Gestational and neonatal screenings for thyroid functioning are suggested to paediatricians and ophthalmologists in order to prevent craniofacial malformations and visual abnormalities.

[Sensitivity, specificity and predictive value of the genetic analysis of SLC3A1 gene variants used for the diagnosis of cystinuria among the spanish population]. / Sensibilidad, especificidad y valor predictivo del análisis genético de variantes en el gen SLC3A1 aplicado al diagnóstico de cistinuria en población española.

OBJECTIVE: To test the clinical usefulness of the analysis of point mutations R452W, M467T, 114C > A, 231T > A, 1136 + 3delT and 1332 + 7T > C in the gene SLC3A1 as well as their possible haplotypes used for the diagnosis of cystinuria in the mediterranean spanish population. MATERIAL AND METHODS: A total of 48 patients with cystinuria, 44 relatives without cystinuria, and 81 healthy controls were studied. A genetic analysis was conducted in order to identify variants in the gene SLC3A1. The sensitivity, specificity, and predictive value for each genetic variant and for the possible haplotypes were calculated. RESULTS: The specificity of mutations M467T, R452W, and 231T > A used for the diagnosis of cystinuria in the general population or for the different subtypes of cystinuria in involved families, was higher than 90%; nevertheless, none of the analysed variants reached a sensitivity higher than 80%. In the study of haplotypes, the highest sensitivity was obtained with the haplotype CTTT (83.8%); however, its specificity and predictive value were low (20.6% and 53.4%, respectively). CONCLUSIONS: The studied genetic variants did not show enough clinical usefulness.

Sensibilidad, especificidad y valor predictivo del análisis genético de variantes en el gen SLC3A1 aplicado al diagnóstico de cistinuria en población española / Sensitivity, specificity and predictive value of the genetic analysis of SLC3A1 gene variants used for the diagnosis of cystinuria among the spanish population

Objetivo. Estimar la validez clínica del análisis de las mutaciones puntuales R452W, M467T, 114C > A, 231T > A, 1136 + 3delT y 1332 + 7T > C en el gen SLC3A1, así como de sus posibles haplotipos aplicados al diagnóstico de cistinuria en población mediterránea española. Material y métodos. Se han estudiado 48 pacientes con cistinuria, 44 familiares sin cistinuria y 81 controles sanos. Se realizó un análisis genético para la identificación de variantes en el gen SLC3A1. Se calculó la sensibilidad, especificidad y valor predictivo para cada variante genética y para los posibles haplotipos. Resultados. La especificidad de las mutaciones M467T, R452W y 231T > A aplicadas al diagnóstico de cistinuria en población general o para los diferentes subtipos de cistinuria en familias afectadas fue superior al 90 por ciento; sin embargo, ninguna variante analizada alcanzó una sensibilidad superior al 80 por ciento. En el estudio de haplotipos, la sensibilidad más alta se obtuvo con el haplotipo CTTT (83,8 por ciento); sin embargo, su especificidad y valor predictivo fueron bajos (20,6 por ciento y 53,4 por ciento, respectivamente).Conclusiones. Las variantes genéticas estudiadas no mostraron suficiente validez clínica (AU)

Association between M467T and 114 C-->A variants within the SLC3A1 gene and some phenotypical traits in cystinuria patients from Spain.

Cystinuria is an inherited metabolic disease characterized by an abnormal urinary excretion of cystine and dibasic amino acids. Formation of renal calculi, recurrent infections and renal failure are the main complications of this disease. The SLC3A1 gene, which codes for a dibasic amino acid transporter protein, is involved in the pathogenesis of cystinuria. We investigated the possible association between molecular variants (M467T, E483X, T216 M and 114 C-->A) within the SLC3A1 gene and some phenotypical traits in a Spanish area. The study population consisted of 45 cystinuria patients, 42 cystinuria relatives and 81 healthy control subjects. Only the M467T mutation was found in chromosomes of cystinuria patients and relatives. However, the 114 C-->A polymorphism was detected in cystinuria patients, in relatives and in control subjects but with different prevalences. Moreover, a statistically significant association between this polymorphism and urinary amino acid levels was found in cystinuria patients (P<0.05). Subjects with the C/C genotype showed significantly higher urinary levels of cystine, arginine and their sum as compared with carriers of the A allele (P<0.05). When multiple linear regression analysis was performed in cystinuria patients, the 114 C-->A polymorphism remained significantly associated (P=0.047) with cystine levels even after controlling for age, gender and the M467T mutation. Furthermore, we also found a statistically significant interaction term (P=0.028) between M467T and 114 C-->A in determining urinary cystine levels. According to our results, the 114 C-->A polymorphism might be a marker of a functional variant in the SLC3A1 gene or in other genes related to urinary amino acid excretion in cystinuria patients.

Adaptation of conformation-sensitive gel electrophoresis to an ALFexpress DNA sequencer to screen BRCA1 mutations.

Conformation-sensitive gel electrophoresis (CSGE) has been introduced as the most reliable method for the screening of large and multi-exon genes because of its simplicity, sensitivity and specificity. Based on heteroduplex formation and with the use of mildly denaturing solvents, it allows detection of single-base mutations with accuracy. This is important in genes such as BRCA1 and BRCA2, in which alterations span the entire gene. We have adapted the CSGE assay to a fluorescent platform--a DNA sequencer one-color technology--that reduces the time involved and enhances resolving power for the complete scanning of the BRCA genes. Electrophoresis has high sensitivity and is performed in less than three hours, and the gel does not require staining with ethidium bromide. Eighteen single-base and six frameshift mutations in the BRCA1 gene were analyzed. We compared the manual and fluorescent CSGE methods, and all mutations were detected with accuracy.

[Phenotypical manifestations of cystinuria: a study of 20 families in the Community of Valencia]. / Manifestaciones fenotípicas de la cistinuria: estudio de 20 familias en la Comunidad Valenciana.

BACKGROUND: The aim of this study was to classify phenotypically cystinuria patients in the Comunidad Valenciana using their genealogy and to study the large heterogeneity of the disease expression. SUBJECTS AND METHOD: From 29 patients diagnosed of cystinuria, 20 families were enrolled in the study. An urine sample of every subject was collected to quantify urine amino acids using high pressure liquid chromatography. We also looked for the presence of cystine crystals. Genetic analyses were carried out using PCR (Polymerase Chain Reaction), and RFLPs (Restriction Fragment Length Polymorphisms). Demographic and clinical characteristics were recorded in a standard questionnaire. RESULTS: From 20 families, 4 were classified Type I, 10 as Type non I, and 6 as Type unknown. Type I cystinuria patients showed the highest urinary levels of cystine and ornithine. We also found an association of cystine crystals and M467T mutation in SLC3A1 gene with Type I. However, we did not find a higher risk of nephrolithiasis associated to any family type. CONCLUSIONS: Phenotypical characterization of patients with cystinuria has showed the wide variability of phenotypical traits indeed in the same transmission pattern. This variability could be due to the genetic and environmental heterogeneity which has developed this pathology and modulated its evolution.

[Genetic and molecular study of cystinuria in the Valencian community]. / Estudio genético y molecular de la cistinuria en la Comunidad Valenciana.

BACKGROUND: The aim of this study has been to know the prevalence of the four most common mutations reported in SLC3A1 gene involved in human cystinuria, and to estimate the association with different phenotypic manifestations of this disease in population of the Valencian Community, Spain. PATIENTS AND METHODS: We have carried out a cross-sectional study with a control group in 16 families with one or more members diagnosed as cystinuric patients. 149 subjects (38 cystinuric patients, 39 relatives and 72 controls) were studied. Genetic analyses were carried out using PCR (polymerase chain reaction), RFLPs (restriction fragment length polymorphisms) and sequencing of PCR products. Parametric and non parametric tests were applied in the statistical analyses. RESULTS: None of the four mutations studied were found in the control group. M467T mutation was the most prevalent in cystinuric patients as well as in relatives, showing and allelic frequency of 0.06 and 0.03 respectively. Regarding to the association analysis between genotype and phenotype, we found that, in cystinuric subjects, urinary excretion of some dibasic amino acid was higher in those who carried M467T mutation (p < 0.05). The formation of cystine crystals was also higher in cystinuric patients who carried this mutation (p < 0.05). CONCLUSIONS: Prevalences of recurrent mutations reported up to now in SLC3A1 gene are very low in cystinuric subjects of the Valencian Community, Spain. Only mutation M467T has been found, without differences between cystinuric and their relatives, although in the first ones was associated with a more accurate phenotype manifestation of the disease.

Gene structure of the human mitochondrial outer membrane receptor Tom20 and evolutionary study of its family of processed pseudogenes.

The structure of the human gene encoding the mitochondrial outer membrane receptor Tom20 has been determined from overlapping clones obtained using PCR-based techniques. The 20kb human Tom20 gene (hTom20) consists of five exons separated by four introns. The 5' flanking region presents features common with other nuclear genes encoding mitochondrial proteins. Comparison with its homologs and putative homologs in other species has revealed common features in their TPR motifs and other relevant protein domains. Aspects concerning evolutionary origins of the family of processed pseudogenes of hTom20 are also discussed.

Identification of psi3Tom20, a novel processed pseudogene of the human Tom20 gene, and complete characterization of psi1Tom20 and psi2Tom20.

We report the identification and characterization of psi3Tom20, a novel processed pseudogene of the human Tom20 (hTom20) gene, which is 96.2% similarity with the hTom20 cDNA and is 5' and 3' truncated. In addition, we present the complete characterization of psi2Tom20 and psi2Tom20, the two other recently reported members of this pseudogene family. Comparison of the sequences of psi3Tom20 with that of the previously reported psi2Tom20 revealed and corrected an error in the previously determined sequence of psi2Tom20. A detailed analysis of these three pseudogenes, including their flanking regions, is presented. It suggests they probably arose from mRNAs that were polyadenylated at different sites. Possible mechanisms involved in their integration as retroposons are also discussed.

Antibiotic susceptibility assay for Staphylococcus aureus in biofilms developed in vitro.

Four slime-producing isolates of Staphylococcus aureus were used in an antibiotic susceptibility assay for biofilms developed on 96-well polystyrene tissue culture plates. The study involved 11 antibiotics, two biofilm ages (6 and 48 h), two biofilm growth media (tryptone soy broth (TSB) and delipidated milk) and three antibiotic concentrations (4 x MBC, 100 mg/L and 500 mg/L). ATP-bioluminescence was used for automated bacterial viability determination after a 24 h exposure to antibiotics, to avoid biofilm handling. Under the conditions applied, viability in untreated biofilms (controls) was lower when biofilm growth was attempted in milk rather than in TSB. Various antibiotics had a greater effect on viability when used at higher (> or =100 mg/L) antibiotic concentrations and on younger (6 h) biofilms. Increased antibiotic effect was observed in milk-grown rather than TSB-grown biofilms. Phosphomycin and cefuroxime, followed by rifampicin, cefazolin, novobiocin, vancomycin, penicillin, ciprofloxacin and tobramycin significantly affected biofilm cell viability at least under some of the conditions tested. Gentamicin and erythromycin had a non-significant effect on cell viability. Transmission electron microscopy revealed that cells at the inner biofilm layers tend to remain intact after antibiotic treatment and that TSB-grown biofilms favoured a uniformity of cell distribution and increased cell density in comparison with milk-grown biofilms. A reduced matrix distribution and enhanced cell density were observed as the biofilm aged. The S. aureus biofilm test discriminated antibiotics requiring shorter (3 h or 6 h) from those requiring longer (24 h) exposure and yielded results which may be complementary to those obtained by conventional tests.

Reference values of urinary excretion of cystine and dibasic aminoacids: classification of patients with cystinuria in the Valencian Community, Spain.

OBJECTIVE: Cystinuria is an autosomal-recessive disorder of the kidneys and small intestine affecting a luminal transport mechanism shared by cystine, ornithine, arginine, and lysine. Three different types of cystinuria can be distinguished according to the excretion of these amino acids in urine samples. We propose cutoff values from our population as references and we present a classification of cystinuric patients using quantitative amino acid chromatography in first morning urine samples. DESIGN AND METHODS: A random sample of forty healthy subjects belonging to general population of the Valencian Community were selected as control subjects. Cystine, lysine, arginine, and ornithine were quantified by reverse-phase HPLC. Seventy-two subjects, diagnosed previously as cystinuric by the cyanide-nitroprusside test were classified. Probands excreting more than 113.12 micromol cystine per mmol of creatinine (i.e., 1,000 micromol cystine per gram of creatinine) were classified as homozygotes. Parents of homozygotes in whom excretion of amino acids were normal were classified as heterozygotes type I. Those probands showing the excretion of at least one amino acid and the sum of urinary cystine plus the basic amino acids higher than the corresponding references ranges in our population were classified as heterozygotes type II or type III (heterozygotes non-type 1). RESULTS: We identified 24 homozygotes, 39 non-type I heterozygotes and 3 type I heterozygotes. The remaining 6 probands could not be classified. Means for cystine, lysine, arginine ornithine and their sum in homozygotes and heterozygotes non-type I were significantly (p < 0.001) in excess of the respective reference ranges. Moreover, means values in homozygotes were statistically different (p < 0.001) from heterozygotes non-type I. CONCLUSION: Urinary excretion of cystine per mmol creatinine allow us to distinguish heterozygotes from homozygotes. However, the best discriminator to distinguish non-type I heterozygotes from normal population might be the excretion of lysine per mmol creatinine. Additional studies including characterization of appropriate haplotypes should be carried out for a more precise identification of types of cystinuria.

Effects of polyamine levels on the degradation of short-lived and long-lived proteins in cultured L-132 human lung cells.

Biogenic polyamines have important regulatory functions in various biological processes and it has also been suggested that they could modulate intracellular protein degradation. For an overall assessment of the role of polyamines in this process, we have investigated the effect that the decrease in intracellular polyamine levels caused by inhibitors of polyamine biosynthesis brings about on the degradation of the pools of short- and long-lived proteins in cultured L-132 human lung cells. Treatment of cells with 100 microM (2R,5R)-delta-methyl acetylenic putrescine (MAP), a potent enzyme-activated irreversible inhibitor of ornithine decarboxylase, or with 100 microM MAP plus 50 microM N-butyl 1,3-diaminopropane, a specific inhibitor of spermine synthase, caused a similar decrease (65-70% of control) in the total intracellular levels of polyamines, although they affected the concentrations of spermidine and spermine differently. The effect of the two treatments on protein degradation was essentially the same. In polyamine-depleted cells we observed an inhibition of degradation in long-lived proteins of 16% (P<0.05), with a significant increase in the half-life (t12) of this pool from 100.5 to 120.1 h. This was concomitant with an increase of 26% (P<0. 05) in degradation in short-lived proteins, with a significant decrease in the t12 of this pool from 0.85 to 0.67 h. Recovery of polyamine levels by the addition of 50 microM spermidine to polyamine-depleted cells resulted in a restoration of the degradation rates in both pools of proteins. The way(s) by which polyamines could modulate proteolysis are discussed.

Identification of two processed psuedogenes of the human Tom20 gene.

The open reading frame (ORF) of the human Tom20 gene (hTom20) was amplified by PCR from a HeLa cDNA library using primers based on the sequence of HUMRSC145 and cloned into a pET15b vector. Amplification of human genomic DNA using these primers yielded a DNA fragment of the same size as that of the ORF of hTom20 cDNA. Sequencing of this fragment revealed that: (1) it has the same number of base pairs as the ORF of hTom20 cDNA (438 bp); and (2) the two sequences differ by 14 single base pair substitutions (97% similarity) causing eight changes in the amino acid sequence and two premature stop codons. Further amplification of human genomic DNA adaptor-ligated libraries using primers based on HUMRSC145 revealed three different sequence-related genomic regions; one corresponding to the fragment referred above, another corresponding to the hTom20 gene, and a third fragment of which the sequence differs from the ORF of hTom20 cDNA by only 22 base pair substitutions and a deletion of 4 bp. We conclude that, in addition to the hTom20 gene, there are two genomic DNA sequences (psi1Tom20 and psi2Tom20) that are processed pseudogenes of hTom20. Aspects concerning their evolutionary origin are discussed.

Type III Ehlers-Danlos syndrome and pregnancy.

We report a case of type III Ehlers-Danlos syndrome with a favourable outcome. We review the literature and do not consider that pregnancy in patients with type III Ehlers-Danlos Syndrome represents a high risk situation.

A novel extracellular matrix protein from tomato associated with lignified secondary cell walls.

A cDNA clone representing a novel cell wall protein was isolated from a tomato cDNA library. The deduced amino acid sequence shows that the encoded protein is very small (88 amino acids), contains an N-terminal hydrophobic signal peptide, and is enriched in lysine and tyrosine. We have designated this protein TLRP for tyrosine- and lysine-rich protein. RNA gel blot hybridization identified TLRP transcripts constitutively present in roots, stems, and leaves from tomato plants. The encoded protein seems to be highly insolubilized in the cell wall, and we present evidence that this protein is specifically localized in the modified secondary cell walls of the xylem and in cells of the sclerenchyma. In addition, the protein is localized in the protective periderm layer of the growing root. The highly localized deposition in cells destined to give support and protection to the plant indicates that this cell wall protein alone and/or in collaboration with other cell wall structural proteins may have a specialized structural function by mechanically strengthening the walls.

A structure-effect study of the induction by polyamines of the transport in vitro of the precursor of ornithine transcarbamylase.

Polyamines induce the transport in vitro of the precursor of ornithine transcarbamylase (pOTC) into isolated rat liver mitochondria by facilitating its functional binding to these organelles. Comparative studies of the effect on the in vitro transport of pOTC of polyamine derivatives and related compounds have allowed us to establish that: (i) at least two protonated amino groups per molecule are necessary to induce the pOTC transport; (ii) a distance of three -CH2- groups between the amino groups in diamines is enough to induce this effect, although no differences were observed with diamines having distances of three to eight -CH2- groups. Longer distances resulted in a marked decrease of the effect.

cDNA cloning of viroid-induced tomato pathogenesis-related protein P23. Characterization as a vacuolar antifungal factor.

A 23-kD pathogenesis-related protein (P23) is induced in tomato (Lycopersicon esculentum Mill, cv Rutgers) plants when infected with citrus exocortis viroid. This protein is homologous to the salt-induced tomato NP24 protein (I. Rodrigo, P. Vera, R. Frank, V. Conejero [1991] Plant Mol Biol 16: 931-934). Further characterization of P23 has shown that this protein accumulates in vacuoles in association with dense inclusion bodies. In vitro assays indicated that the purified P23 protein inhibits the growth of several phytopathogenic fungi. P23-coding cDNA clones were isolated from viroid-induced and ethylene-induced libraries. Southern analysis showed that at least two genes could encode P23 or P23-related products. The accumulation of P23 protein correlated with the accumulation of its mRNA. Sequence analysis revealed significant differences in both coding and downstream untranslated regions between the cDNA sequences corresponding to the viroid-induced P23 and the salt stress-induced NP24 proteins.