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p53 gene mutation analysis in tumors of patients exposed to alpha-particles.

The p53 gene was examined for point mutations in archived, alpha-radiation-associated lung and liver cancers. Lung tumors of 50 uranium miners in Germany were screened by restriction fragment length analysis for the putative hotspot mutation at codon 249 (Arg-->Met) previously detected in a significant fraction of miners from the Colorado Plateau, USA. This mutation has been proposed as a marker of radon exposure. None of the tumors we examined harbored the hotspot mutation. Five of the 50 tumors, however, did indeed harbor exon 7 mutations, as determined by subsequent mutation analysis of exon 7. These mutations were dispersed among various codons and may be attributable to heavy tobacco smoking in this cohort. In support of this interpretation, we found no mutations in exons 5-8 of the p53 gene in 13 iatrogenic liver cancers induced by injection of Thorotrast, an alpha-emitting radiocontrast agent. We propose that if the p53 tumor suppressor gene is a target for the carcinogenic action of alpha-particle radiation, loss of suppressor function may occur preferentially by mechanisms such as intrachromosomal deletions, rather than by base substitution mutations.

Aged↗

Mutation analysis and the correlation between genotype and phenotype of Arg778Leu mutation in chinese patients with Wilson disease.

BACKGROUND: The defective gene (ATP7B) that causes Wilson disease (WD) codes for a putative copper-transporting P-type adenosine triphosphatase. After cloning of ATP7B, the spectrum of mutations and their clinical consequences have been investigated in patients with WD in different ethnic populations. However, the spectrum of mutations and the correlation of genotype-phenotype in the Chinese population have not been extensively studied. OBJECTIVE: To investigate the characterization of mutations of ATP7B and the correlation between genotype and phenotype in the Chinese population. METHODS: We studied 60 unrelated healthy Chinese and 65 unrelated Chinese families, including 84 patients with WD and 126 parents. Genomic DNA was prepared from peripheral blood leukocytes using a salt-precipitation method. Polymerase chain reaction single-strand conformation polymorphism and subsequent direct sequencing were used to identify the mutations and polymorphisms of ATP7B. Statistical analysis was performed using t test or chi(2) test. RESULTS: We identified 18 mutations (7 novel) and 11 polymorphisms (3 novel). The novel mutations are -36C-->T, Trp650ter, Gln914ter, 2810delT, Thr935Met, Arg1041Pro, and Glu1173Lys. The novel polymorphisms are 1168A-->G (Ile390Val), 2785A-->G (Ile929Val), and 3316G-->A (Val1106Ile). Two mutations, Arg778Leu and Thr935Met, are relatively frequent, representing 37.7% and 10.0% of patients, respectively. To our knowledge, we are the first to report the correlation between the genotype and phenotype of Arg778Leu. The result shows that Arg778Leu homozygotes are associated with the early onset of WD with hepatic presentation. CONCLUSIONS: The Arg778Leu and Thr935Met mutations are hot spots in the Chinese population. The features of mutations of ATP7B differ between the Chinese and Western ethnic populations. The Arg778Leu mutation has severe effects on the function of ATP7B. These findings are valuable for developing a fast and effective method to diagnose the presence of the WD gene.

Adolescent↗

Targeted mutational analysis of the RyR2-encoded cardiac ryanodine receptor in sudden unexplained death: a molecular autopsy of 49 medical examiner/coroner's cases.

OBJECTIVE: To perform a molecular autopsy of the RyR2-encoded cardiac ryanodine receptor/calcium release channel in medical examiner/coroner's cases of sudden unexplained death (SUD). METHODS: From September 1998 to March 2004, 49 cases of SUD were referred by medical examiners/coroners to the Sudden Death Genomics Laboratory at the Mayo Clinic in Rochester, Minn, for a cardiac channel molecular autopsy. Mutational analysis of 18 exons of RyR2 implicated previously in the pathogenesis of catecholaminergic polymorphic ventricular tachycardia (CPVT) was performed on genomic DNA using polymerase chain reaction, denaturing high-performance liquid chromatography, and direct DNA sequencing. RESULTS: This cohort of 49 cases of SUD included 30 males, 13 with a family history of syncope, cardiac arrest, or sudden cardiac death (mean +/- SD age at death, 14.2 +/- 10.9 years). Six distinct RyR2 missense mutations (3 novel) were discovered in 7 cases (14%, 6 males, mean +/- SD age at death, 13.6 +/- 11.2 years) of SUD. The activities at the time of SUD were exertion (3), emotion (1), and unknown (3). The mutations, R420W, S2246L, N4097S, E4146K, T4158P, and R4497C, involved nonconservative amino acid substitutions in highly conserved residues across species and were not seen in 400 reference alleles. CONCLUSIONS: This study represents the first molecular autopsy of RyR2 in medical examiner-referred cases of SUD. A targeted analysis of only 18 of the 105 protein-encoding exons of the cardiac ryanodine receptor/calcium release channel revealed potential CPVT1-causing RyR2 mutations in 1 of every 7 cases of SUD. These findings suggest that postmortem genetic testing of RyR2 should be considered as a part of the comprehensive medicolegal autopsy investigation of a SUD case and that this potentially heritable and often elusive arrhythmia syndrome be scrutinized carefully in family members of those who experience SUD.

Adolescent↗

Mutational analysis of baculovirus capping enzyme Lef4 delineates an autonomous triphosphatase domain and structural determinants of divalent cation specificity.

The 464-amino acid baculovirus Lef4 protein is a bifunctional mRNA capping enzyme with triphosphatase and guanylyltransferase activities. The hydrolysis of 5'-triphosphate RNA and free NTPs by Lef4 is dependent on a divalent cation cofactor. RNA triphosphatase activity is optimal at pH 7.5 with either magnesium or manganese, yet NTP hydrolysis at neutral pH is activated only by manganese or cobalt. Here we show that Lef4 possesses an intrinsic magnesium-dependent ATPase with a distinctive alkaline pH optimum and a high K(m) for ATP (4 mm). Lef4 contains two conserved sequences, motif A ((8)IEKEISY(14)) and motif C ((180)LEYEF(184)), which define the fungal/viral/protozoal family of metal-dependent RNA triphosphatases. We find by mutational analysis that Glu(9), Glu(11), Glu(181), and Glu(183) are essential for phosphohydrolase chemistry and likely comprise the metal-binding site of Lef4. Conservative mutations E9D and E183D abrogate the magnesium-dependent triphosphatase activities of Lef4 and transform it into a strictly manganese-dependent RNA triphosphatase. Limited proteolysis of Lef4 and ensuing COOH-terminal deletion analysis revealed that the NH(2)-terminal 236-amino acid segment of Lef4 constitutes an autonomous triphosphatase catalytic domain.

Acid Anhydride Hydrolases↗

Androgen insensitivity syndrome (AIS): emotional reactions of parents and adult patients to the clinical diagnosis of AIS and its confirmation by androgen receptor gene mutation analysis.

The emotional reactions of parents and adult patients on disclosure of the clinical diagnosis of androgen insensitivity syndrome (AIS) and its later confirmation by gene mutation analysis were assessed. A semistructured interview and three questionnaires were used. Parents came from 18 different families with a total of 20 children (15 complete AIS, 5 partial AIS), 19 raised as girls, 1 as a boy. Ten adult women with complete AIS came from six families. The short-term reaction upon the clinical diagnosis was in the majority of both parents and adult patients associated with shock, grief, anger, and shame and in the mothers and adult patients with guilt. Emotional reactions were more long-lasting in mothers and adult patients than in fathers. The confirmation by DNA analysis did not alter the actual feelings of both parents. Adolescents with AIS should be informed completely - but in a step-by-step way - about their condition, since adult patients indicated that they had suffered from being not at all or misinformed about AIS in their adolescence.

Adult↗

Mutational analysis supports a role for multiple structural features in the C-terminal secretion signal of Escherichia coli haemolysin.

We have carried out an extensive mutational analysis of the C-terminal signal which targets the export of the 1024-residue haemolysin protein (HlyA) of Escherichia coli across both bacterial membranes into the surrounding medium. Over 60 variants of the HlyA C-terminal 53-amino-acid sequence were created by oligonucleotide-directed mutagenesis and fused to the HlyA N-terminal 830 residues. Transport of the HlyA derivatives by the HlyB/HlyD system was compared with the wild-type level and the data indicate that the HlyA C-terminal export signal lies within the last 48 amino acids and comprises three functional domains: an amphipathic, charged helix between residues 1,977 and R,996; a 13-amino-acid uncharged region from residue T,997 to S,1009; and an 8-amino-acid hydroxylated tail at the extreme C-terminus. Analogous features were found in the C-terminal sequences of an extended family of haemolysins, leukotoxins and proteases which are secreted by HlyB/HlyD-type translocators. In particular, all nine proteins which are secreted into the extracellular medium possess potential extended amphipathic helices. These results suggest a possible role for multiple regions of the HlyA C-terminal export signal in which the first two domains span the membranes and the third domain remains in the cytoplasm.

Amino Acid Sequence↗

A mutational analysis of the 5' HoxD genes: dissection of genetic interactions during limb development in the mouse.

Using gene targeting in mice, we have undertaken a systematic mutational analysis of the homeobox-containing 5' HoxD genes. In particular, we have characterized the limb defects observed in mice with independent targeted disruptions of hoxd-12 and hoxd-13. Animals defective for hoxd-12 are viable, fertile, and appear outwardly normal yet have minor autopodal defects in the forelimb which include a reduction in the bone length of metacarpals and phalanges, and a malformation of the distal carpal bone d4. The limb phenotypes observed in hoxd-13 mutant mice are more extensive, including strong reductions in length, complete absences, or improper segmentations of many metacarpal and phalangeal bones. Additionally, the d4 carpal bone is not properly formed and often produces an extra rudimentary digit. To examine the genetic interactions between the 5' HoxD genes, we bred these mutant strains with each other and with our previously characterized hoxd-11 mouse to produce a series of trans-heterozygotes. Skeletal analyses of these mice reveal that these genes interact in the formation of the vertebrate limb, since the trans-heterozygotes display phenotypes not present in the individual heterozygotes, including more severe carpal, metacarpal and phalangeal defects. Some of these phenotypes appear to be accounted for by a delay in the ossification events in the autopod, which lead to either the failure of fusion or the elimination of cartilaginous elements. Characteristically, these mutations lead to the overall truncation of digits II and V on the forelimb. Additionally, some trans-animals show the growth of an extra postaxial digit VI, which is composed of a bony element resembling a phalange. The results demonstrate that these genes interact in the formation of the limb. In addition to the previously characterized paralogous interactions, a multitude of interactions between Hox genes is used to finely sculpt the forelimb. The 5' Hox genes could therefore act as a major permissive genetic milieu that has been exploited by evolutionary adaptation to form the tetrapod limbs.

Animals↗

Mutational analysis of candidate genes in psychiatric disorders.

A genetic hypothesis for a disease presupposes the existence of variation in the DNA sequences of affected individuals. A series of techniques known together as "mutational analysis" can be applied towards identifying new sequence variations in selected genes. These techniques can screen a large series of individuals for mutations efficiently, so it is not necessary to determine the nucleotide sequence in every DNA sample. DNA samples suspected of harboring sequence variants are then sequenced. Denaturing gradient gel electrophoresis techniques, single stranded conformation polymorphism paradigms, and chemical cleavage of mismatches are 3 procedures widely used for the molecular screening of mutations today. We discuss each of these techniques for mutation screening.

Electrophoresis, Polyacrylamide Gel↗

Mutational analysis of the regulatory region of the Mycobacterium plasmid pAL5000.

The regulatory region of the Mycobacterium fortuitum plasmid pAL5000 was studied in vivo and in vitro by mutational analysis. This region comprises the origin of replication for the plasmid and the start point of transcription for the repA/B genes, which encode the two replication proteins RepA and RepB. In this region there are two binding sites for RepB: a low-affinity site which is probably the origin of replication and a high-affinity-site which overlaps the promoter and implies an autoregulated expression of RepB. The high-affinity site contains two 8 bp palindromes, as well as an inverted repeat structure. By introducing point mutations into each of these motifs and monitoring changes to RepB binding in a gel-retardation assay, it was shown that the central, GC-rich palindrome (the GC-box) is the most important motif for protein binding. Mutations in the second, AT-rich palindrome (the AT-box) had no effect on protein binding and the inverted repeat structure per se was not needed, though some single-base changes affected binding to one or other of the DNA strands. These mutations were subsequently tested in vivo for their effects on plasmid replication in Mycobacterium smegmatis. Any change to the GC-box abolished replication, but changes to the other motifs were dependent on the position of the changed base, again indicating that the inverted repeats are not essential and that the AT-box is part of the promoter and not primarily recognised by RepB. The mutated plasmids did not show any changes in copy number to that of the wild-type. The expression of RepB was boosted by introducing a stronger promoter upstream of the repA/B genes. The resulting plasmid was capable of increasing to a degree in trans the copy number of other plasmids carrying the ori region, but was unstable when present on its own in M.smegmatis.

Bacterial Proteins↗

Mutation analysis of the BRCA1 gene in ovarian cancers.

Germline mutations of the BRCA1 tumor suppressor gene on chromosome 17q are involved in a significant fraction of hereditary breast and ovarian cancers. Allelic deletions that include the BRCA1 locus are common in breast and ovarian cancers, implying that somatic mutations of this gene may play an important role in the more common sporadic forms of these tumors as well. The recent cloning of BRCA1 allows direct testing of this hypothesis. A combination of single strand conformation and sequencing analyses was used to examine the 22 coding exons and intronic splice donor and acceptor regions of BRCA1 for mutations in 115 unselected cases of epithelial ovarian carcinoma. Seven mutations were identified, all of which were present in the germlines of patients with remarkable family or medical histories of breast and/or ovarian cancer. Eighty-nine of these tumors were examined for loss of heterozygosity in the BRCA1 region of chromosome 17q, and 67% of the tumors studied exhibited allelic deletions that included this region. These data are consistent with the hypothesis that BRCA1 mutations are involved in the etiology of hereditary ovarian carcinomas but occur rarely in sporadic tumors, and that the frequent allelic loss on chromosome 17q in this cancer type reflects the involvement of an additional tumor suppressor gene(s).

Adult↗

Mutational analysis of the p63/p73L/p51/p40/CUSP/KET gene in human cancer cell lines using intronic primers.

After the identification of p73, a second homologue of the human p53 tumor suppressor gene has been reported and named p63/p73L/p51/p40/CUSP/KET. We have investigated the hypotheses that: (a) p63 is mutated in diverse types of human cancers; and (b) p63 functions in the same pathway as p53 and p73 in the process of carcinogenesis; therefore, mutations in these three genes would be mutually exclusive. We have analyzed the genomic structure of the p63 gene and have performed mutational analyses on 54 human cell lines using intronic primers flanking each exon. We have confirmed that the human p63 open reading frame encodes the same length of protein as murine p63 that was initially reported to be 39 amino acids longer than human p63. By mutational analysis, we have shown that DLD1 and SKOV3 cells have either heterozygous mutations or polymorphisms in the putative DNA binding domain of p63. In these cell lines, p63 is biallelically expressed. We conclude that mutations in the p63 gene are rare in human cell lines. The fact that DLD1 is abnormal for both p63 and p53 genes suggests that they may not be involved in the same tumor suppressor pathway.

Amino Acid Sequence↗

Mutation analysis of type II Gaucher disease in five Taiwanese children: identification of two novel mutations.

Gaucher disease (GD), one of the most prevalent lysosomal storage diseases, is caused by deficiency of lysosomal acid beta-glucosidase (GBA). It is divided into three types according to the presence and progression of neurologic symptoms. Of those, type II is relatively rare and most severe; patients usually die before the age of two years. Using polymerase chain reaction (PCR) and direct sequencing of GBA gene in five Taiwanese type II GD patients, we identified two novel mutations: G355D and three-nucleotide insertion in exon 7 of GBA. The latter resulted in an in-frame insertion of a methionine residue between Leu241 and Ser242. L444P, the second most common GD allele among non-Jewish Caucasian population, was found in all five type II GD patients (50%). Overall, 9 out of 10 GD alleles were identified in this study. Direct sequencing of all PCR products led to high detection rate of GD alleles and identification of the RecNci 1 alleles. In the future, high throughput sequencing will make it possible identifying more rare mutations in type II GD patients.

Base Sequence↗

Mutational analysis of the lambda int gene: DNA sequence of dominant mutations.

We have combined techniques of genetic and physical mapping with rapid DNA sequence analysis to identify the nucleotide change in lambda int mutations. These mutations define two dominant phenotypic classes: (i) recombination that is partially independent of accessory factors, and (ii) inhibition of wild-type Int by missense or nonsense proteins, i.e., negative complementation.

Bacteriophage lambda↗

Mutational analysis of the autoimmune regulator (AIRE) gene in sporadic autoimmune Addison's disease can reveal patients with unidentified autoimmune polyendocrine syndrome type I.

OBJECTIVE: To investigate whether patients with Addison's disease and polyendocrine syndromes have undiagnosed autoimmune polyendocrine syndrome type I (APS I). MATERIALS AND METHODS: Forty patients with clinical manifestations resembling APS I and with autoantibodies typical of this condition were screened for Norwegian autoimmune regulator (AIRE) gene mutations. RESULTS: A 30-year old man who had developed Addison' s disease at the age of 12, but had no other components of APS I, was homozygous for the 1094-1106 deletion mutation in exon 8 of the AIRE gene, the most common mutation found in Norway. CONCLUSIONS: APS I patients with milder and atypical phenotypes are difficult to diagnose on clinical grounds. Autoantibody analysis and mutational analysis of AIRE may therefore be helpful modalities for identifying these individuals.

Addison Disease↗

Clinical implications of mutation analysis in primary hyperoxaluria type 1.

BACKGROUND: Primary hyperoxaluria type 1 (PH1) is an inborn error of glyoxylate metabolism with an extensive clinical and genetic heterogeneity. Although over 50 disease-causing mutations have been identified, the relationship between genotype and clinical outcome remains unclear. The aim of this study was to determine this association in order to find clues for improvement of patient care. METHODS: AGXT mutation analysis and assessment of biochemical characteristics and clinical outcome were performed on patients from a Dutch PH1 cohort. RESULTS: Thirty-three of a cohort of 57 PH1 patients, identified in The Netherlands over a period of 30 years, were analyzed. Ten different mutations were found. The most common mutations were the Gly170Arg, Phe152Ile, and the 33insC mutations, with an allele frequency of 43%, 19%, and 15%, respectively. Homozygous Gly170Arg and Phe152Ile mutations were associated with pyridoxine responsiveness and a preserved renal function over time when treatment was timely initiated. All patients homozygous for the 33insC mutation had end-stage renal disease (ESRD) before the first year of age. In two unrelated patients, a new Val336Asp mutation was found coupled with the Gly170Arg mutation on the minor allele. We also found 3 patients homozygous for a novel Gly82Arg mutation with adverse outcome in 2 of them. CONCLUSION: Early detection of Gly170Arg and Phe152Ile mutations in PH1 has important clinical implications because of their association with pyridoxine responsiveness and clinical outcome. The association of a homozygous 33insC mutation with severe infantile ESRD, resulting in early deaths in 2 out of 3 cases, warrants a choice for prenatal diagnostics in affected families.

Adolescent↗

The molecular basis of Sjögren-Larsson syndrome: mutation analysis of the fatty aldehyde dehydrogenase gene.

Sjögren-Larsson syndrome (SLS) is an autosomal recessive disorder characterized by ichthyosis, mental retardation, spasticity, and deficient activity of fatty aldehyde dehydrogenase (FALDH). To define the molecular defects causing SLS, we performed mutation analysis of the FALDH gene in probands from 63 kindreds with SLS. Among these patients, 49 different mutations-including 10 deletions, 2 insertions, 22 amino acid substitutions, 3 nonsense mutations, 9 splice-site defects, and 3 complex mutations-were found. All of the patients with SLS were found to carry mutations. Nineteen of the missense mutations resulted in a severe reduction of FALDH enzyme catalytic activity when expressed in mammalian cells, but one mutation (798G-->C [K266N]) seemed to have a greater effect on mRNA stability. The splice-site mutations led to exon skipping or utilization of cryptic acceptor-splice sites. Thirty-seven mutations were private, and 12 mutations were seen in two or more probands of European or Middle Eastern descent. Four single-nucleotide polymorphisms (SNPs) were found in the FALDH gene. At least four of the common mutations (551C-->T, 682C-->T, 733G-->A, and 798+1delG) were associated with multiple SNP haplotypes, suggesting that these mutations originated independently on more than one occasion or were ancient SLS genes that had undergone intragenic recombination. Our results demonstrate that SLS is caused by a strikingly heterogeneous group of mutations in the FALDH gene and provide a framework for understanding the genetic basis of SLS and the development of DNA-based diagnostic tests.

Aldehyde Oxidoreductases↗

Mutational analysis of the encephalomyocarditis virus primary cleavage.

Sixteen substitution mutations of the conserved DvExNPGP sequence, implicated in cardiovirus and aphthovirus primary polyprotein cleavage, were created in encephalomyocarditis virus cDNA, expressed, and characterized for processing activity. Nearly all the mutations severely decreased the efficiency of the primary cleavage reaction during cell-free synthesis of viral precursors, indicating a stringent requirement for the natural sequence in this processing event. When representative mutations were tested in full-length genomic contexts, they were lethal and no revertants were observed. Not only were the primary cleavage reactions deficient in these polyproteins, but subsequent cleavage of P1 by endogenous or exogenous 3C pro was also impaired. This indicates that primary cleavage has a role in the proper processing of the viral capsid precursor.

Amino Acid Sequence↗