Detection of mitochondrial DNA mutations by temporal temperature gradient gel electrophoresis

BACKGROUND

A unique requirement for the molecular diagnosis of mitochondrial DNA (mtDNA) disorders is the ability to detect heteroplasmic mtDNA mutations and to distinguish them from homoplasmic sequence variations before further testing (e.g., sequencing) is performed. We evaluated the potential utility of temporal temperature gradient gel electrophoresis (TTGE) for these purposes in patients with suspected mtDNA mutations.

METHODS

DNA samples were selected from patients with known mtDNA mutations and patients suspected of mtDNA disorders without detectable mutations by routine analysis. Six regions of mtDNA were PCR amplified and analyzed by TTGE. Electrophoresis was carried out at 145 V with a constant temperature increment of 1.2 degrees C/h. Mutations were identified by direct sequencing of the PCR products and confirmed by PCR/allele-specific oligonucleotide or PCR/restriction fragment length polymorphism analysis.

RESULTS

In the experiments using patient samples containing various amounts of mutant mtDNA, TTGE detected as little as 4% mutant heteroplasmy and identified heteroplasmy in the presence of a homoplasmic polymorphism. In 109 specimens with 15 different known mutations, TTGE detected the presence of all mutations and distinguished heteroplasmic mutations from homoplasmic polymorphisms. When 11% of the mtDNA genome was analyzed by TTGE in 104 patients with clinically suspected mitochondrial disorders, 7 cases of heteroplasmy ( approximately 7%) were detected.

CONCLUSIONS

TTGE distinguishes heteroplasmic mutation from homoplasmic polymorphisms and appears to be a sensitive tool for detection of sequence variations and heteroplasmy in patients suspected of having mtDNA disorders.

Mitochondrial DNA deletion with Kearns Sayre syndrome in a child with Addison disease

Kearns Sayre syndrome (KSS) is a multisystem disorder with a confounding variety of clinical manifestations, including ocular myopathy, pigmentary retinopathy, heart block and ataxia. Endocrinopathies are common in KSS, including growth hormone deficiency, hypogonadism, diabetes mellitus and hypoparathyroidism. A variety of deletions of mitochondrial DNA (mtDNA) are found in most cases. We report on a 5-year-old boy with Addison disease in whom further investigation revealed a 4.9 kilobase mtDNA deletion and KSS. Later he developed severe lactic acidosis and expired.

CONCLUSION

The degree of mutant mtDNA heteroplasmy in various tissues on autopsy did not correlate well with the clinical manifestations, although this may be due at least in part to replacement with other tissue types. Our report is the first of non-autoimmune Addison disease in KSS and patients with KSS should be evaluated for adrenal insufficiency. Early recognition of adrenal insufficiency is crucial to prevent mortality from this cause.

Linkage disequilibrium and linkage analysis of the glucose-6-phosphatase gene

Recent studies have indicated that the four most common mutations account for 78% of mutant alleles in the glucose-6-phosphatase (G6Pase) gene. A significant fraction of mutant alleles remain unidentified. Thus, informative polymorphic markers are necessary for linkage analysis in carrier testing and prenatal diagnosis in families where mutations can not be identified. The common mutations appear to be ethnic-specific, suggesting that the individual mutations may have a common founder. With the recent discovery of the nucleotide 1176 polymorphism, we have studied whether these mutations are in linkage disequilibrium with the polymorphism. The results of polymerase chain reaction/allele-specific oligonucleotide analysis show that nucleotide 1 176 C is in linkage disequilibrium with mutations R83 C and R83H, and with the splicing mutation 727G-->T. The 1176T polymorphism is in linkage disequilibrium with 459insTA. A GT repeat polymorphism has also been found. However, its heterozygosity is low. The 1176 nucleotide polymorphic marker can be used in carrier and prenatal diagnosis of GSD1a families that have unidentified mutations and are informative for this marker.

3849 + 10 kb C --> T splicing mutation in Hispanic CF patients

Seven patients compound heterozygous for the 3849 + 10kb C --> T mutation in the CFTR gene were found among the 152 patients attending the CHLA CF Clinic. The frequency of this mutation accounts for 2.3 and 3.9% of thetotal and Hispanic CF alleles of CHLA patients. These are significantly higher than the 0.6% of the general CF population. The average age of diagnosis of this group of Hispanics is 3.1 years, which is much younger than that reported for CF patients of other ethnicities with the same mutation. Both pancreatic sufficient and pancreatic insufficient patients were observed. It is concluded that the 3849 + 10kb C --> T mutation is associated with a variable but potentially mild type of CF.

Yield of mtDNA mutation analysis in 2,000 patients

The multiplex polymerase chain reaction-allele specific oligonucleotides (PCR/ASO) dot blot hybridization method was used to detect 44 mitochondrial DNA point mutations in 2,000 patients suspected as having mitochondrial DNA disorders. These point mutations are classified into four categories. Category I consists of primary disease-causing, heteroplasmic point mutations. Homoplasmic nucleotide substitutions that have been reported to be possibly disease associated are in Category II. Homoplasmic nucleotide substitutions that are thought to be benign polymorphism are included in category III. The novel nucleotide substitutions recently discovered in our laboratory by single strand conformation polymorphism analysis are in category IV. Frequencies of these 44 nucleotide substitutions in 2,000 patients and 262 control individuals were studied. The results indicated that analysis of 12 recurrent disease-causing point mutations in category I identified 5.4% of the patients suspected as having mitochondrial DNA disorders. Since the mitochondrial disorders are a group of complex, heterogeneous, and multisystemic diseases, it is often difficult to confirm clinical diagnosis without molecular studies. Thus, the multiplex PCR/ASO method is an effective approach for initial screening of mtDNA mutations in patients suspected as having mitochondrial DNA disorders.

Molecular and biochemical basis of galactosemia

Galactosemia is a clinically heterogeneous autosomal recessive inborn error of metabolism caused by deficiency of galactose-1-phosphate uridylyltransferase (GALT). Despite the numerous point mutations identified in the GALT gene, the prevalence of these mutations in different ethnic groups has not been studied. Reports on genotype/phenotype correlation are not consistent due to the small sample sizes studied and the lack of a sensitive enzyme assay. We applied multiplex PCR/ASO dot blot analysis to screen 293 galactosemic patients for 17 known point mutations in exons 5, 6, and 10. Our data demonstrate that only 7 of these mutations were detected in our patients, accounting for 65% of the GALT mutant alleles. Although Q188R is the most common mutation in Caucasian and Hispanic patients, the S135L mutation is most common in African-Americans. Another mutation, F171S, was observed only among African-American patients. An improved, sensitive, and accurate method was used to measure GALT activity in patient's red blood cells. The results indicated that patients homozygous for Q188R have no enzyme activity while those homozygous for S135L had residual enzyme activity. Interestingly, both Q188R/S135L and S135L/F171S compound heterozygotes demonstrated zero enzyme activity. Overall, 85% of Q188R compound heterozygotes also did not have any enzyme activity, whereas the remaining Q188R and the majority of S135L compound heterozygotes expressed variable amounts of GALT activity. We speculate that heterodimeric subunit interaction plays an important role in determining the overall enzymatic activity. Various genotypes thus result in biochemical and clinical heterogeneity among the patients.

Instability of the (CTG)n repeat in congenital myotonic dystrophy

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Direct detection of multiple point mutations in mitochondrial DNA

Mitochondrial defects can be caused by mutations in nuclear or mitochondrial DNA. Large deletion/duplication and point mutations are the two major types of mitochondrial DNA (mtDNA) mutations. Comprehensive molecular diagnosis requires the analysis of multiple point mutations. We developed an effective multiplex PCR/allele-specific oligonucleotide (ASO) method to simultaneously screen multiple point mutations in mtDNA. The system involved three pairs of primers to amplify mutation "hot spots" at tRNA(leu(UUR)), tRNA(lys)/ATPase, and ND4 regions, followed by detection of point mutations with ASO probes. Over 2000 specimens were analyzed and the results were compared with those from previous studies with the PCR/restriction fragment length polymorphism method. Our data demonstrate that the multiplex PCR/ASO method is much more sensitive in the detection of low mutant heteroplasmy. It is simple and cost effective, especially if a large number of samples are to be screened for multiple point mutations.

Macular pattern retinal dystrophy, adult-onset diabetes, and deafness: a family study of A3243G mitochondrial heteroplasmy

PURPOSE

To correlate mitochondrial DNA (mtDNA) mutation with phenotypic expression in three members of a Finnish family with macroreticular pattern dystrophy, non-insulin-dependent diabetes mellitus, and deafness.

METHODS

A multiplex polymerase chain reaction/allele-specific oligonucleotide method was used to screen 10 mtDNA point mutations known to cause mitochondrial DNA disorders, often characterized by myopathy, retinopathy, or both. Quantitative analysis of mutant mitochondrial DNA was performed in three tissue types in each of three family members by determining the percentage of mutant mtDNA in blood, buccal cells, and hair follicles.

RESULTS

A heteroplasmic A3243G mtDNA point mutation was found in each of the three family members studied. Heteroplasmy refers to the coexistence of normal and mutant mitochondria in the same cell. The average percentage of mutant heteroplasmy ranged from 11% to 25%. The severity of disease symptoms did not appear to correlate with the average degree of mutant heteroplasmy in the three tissues analyzed.

CONCLUSIONS

Molecular confirmation in this family emphasizes the importance of mitochondrial DNA mutation analysis in patients with macular pattern retinal dystrophy and other mitochondrial associated nonocular disease, such as non-insulin-dependent diabetes mellitus and deafness. The detection of a disease-associated mitochondrial DNA mutation warrants genetic counseling, appropriate patient follow-up, and possibly the molecular testing of other at-risk family members.

Mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS) triggered by valproate therapy

We report in this study a patient who developed repeated convulsions as a result of valproate therapy. MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes) was subsequently diagnosed and a nucleotide 3243 A-->G mutation was detected in the mitochondrial DNA. This mutation predisposes the patient to the detrimental effects of valproate on oxidative phosphorylation.

CONCLUSION

We support the suggestion of Ponchaut et al. [14] that valproate should not be given to patients suspected of having mitochondrial diseases. In addition, for patients whose seizures worsen with valproate therapy, an inborn error of mitochondrial metabolism should be suspected. The underlying mitochondrial DNA defects should be sought for family screening and genetic counselling.

Prenatal diagnosis of glycogen storage disease type 1a by direct mutation detection

Current laboratory diagnosis for glycogen storage disease type 1a (GSD 1a) is established by functional enzyme assay to demonstrate the deficiency of glucose-6-phosphate phosphatase (G6Pase). This procedure requires liver biopsy and is impractical for routine prenatal diagnosis owing to the high morbidity of fetal liver biopsy. The accuracy of test results is dependent on the stability of the enzyme during specimen collection, shipment, and storage. Recently the gene for G6Pase has been cloned and the prevalent mutations in different ethnic groups have been identified. We have developed an allele-specific oligonucleotide (ASO) method to detect mutations in a large number of GSD 1a patients. In this paper we report the prenatal detection of mutations in the G6Pase gene using this simple, dependable, rapid, and non-invasive procedure. The turnaround time of this test can be as short as 48 h. A fetus was found to be a carrier using the ASO method and this was confirmed after birth. To our knowledge, this is the first GSD 1a prenatal case diagnosed by a DNA molecular method.

Genetic basis of glycogen storage disease type 1a: prevalent mutations at the glucose-6-phosphatase locus

Diagnosis of glycogen storage disease (GSD) type 1a currently is established by demonstrating the lack of glucose-6-phosphatase (G6Pase) activity in the patient's biopsied liver specimen. Recent cloning of the G6Pase gene and identification of mutations within the gene that causes GSD type 1a allow for the development of a DNA-based diagnostic method. Using SSCP analysis and DNA sequencing, we characterized the G6Pase gene of 70 unrelated patients with enzymatically confirmed diagnosis of GSD type 1a and detected mutations in all except 17 alleles (88%). Sixteen mutations were uncovered that were shown by expression to abolish or greatly reduce G6Pase activity and that therefore are responsible for the GSD type 1a disorder. R83C and Q347X are the most prevalent mutations found in Caucasians, 130X and R83C are most prevalent in Hispanics, and R83H is most prevalent in Chinese. The Q347X mutation has thus far been identified only in Caucasian patients, and the 130X mutation has been identified only in Hispanic patients. Our results demonstrate that the DNA-based analysis can accurately, rapidly, and noninvasively detect the majority of mutations in GSD type 1a. This DNA-based diagnosis now permits prenatal diagnosis among at-risk patients and serves as a database in screening and counseling patients clinically suspected of having this disease.

Characterization of the cDNA and the gene encoding murine adenylosuccinate lyase

Adenylosuccinate lyase catalyzes two similar reactions in the de novo purine biosynthetic pathway; the cleavage of succinylaminoimidazole carboxamide ribotide to aminoimidazole carboxamide ribotide and fumarate and the cleavage of adenylosuccinate to adenylate and fumarate. Adenylosuccinate lyase is also a participant in the purine nucleotide cycle which plays an important role in maintaining the AMP levels in muscle. In order to understand the structure/function and evolutionary relationships of the members of the fumarate gene family and to evaluate the possible existence of tissue specific isoforms of adenylosuccinate lyase, we have isolated and characterized the murine cDNA and gene encoding adenylosuccinate lyase. The cDNA has 94% and 87% identity to the human sequence at the amino acid and nucleotide levels respectively. The gene is about 27 kb and contains 13 exons. Comparison of the exon/intron structure of this gene with the argininosuccinate lyase gene did not suggest gene duplication or exon shuffling as a mechanism of evolution in the fumarate gene family.

Somatic mosaicism, germline expansions, germline reversions and intergenerational reductions in myotonic dystrophy males: small pool PCR analyses

In order to characterize the dynamics of CTG repeat instability in somatic and germline tissue from myotonic dystrophy (DM) males we have used small pool polymerase chain reaction (PCR) in a detailed quantitative analysis of repeat length variation. We demonstrate that the heterogeneous smear of CTG repeats observed in DM patients using standard analyses is comprised of multiple unresolved bands that may be dissected into discrete length alleles derived from single cells using single molecule PCR techniques. Analysis of somatic tissues demonstrates a bias toward increasing allele length and a lower boundary below which variant alleles are rare, consistent with a highly directional expansion pathway in the soma. Two sperm samples show extensive variation and a size increase bias, concordant with the phenomenon of anticipation. In addition, sperm analysis shows that large contractions, including reversions into the normal size range, are restricted to the germline. Detailed analysis of intergenerational 'reductions' paternally transmitted to two offspring suggests that some apparent reductions may be artifacts of somatic expansion in the parent. Our data indicate that in addition to germline variation, substantial somatic expansion can also contribute to the intergenerational differences usually observed in DM.

Somatic heterogeneity of the CTG repeat in myotonic dystrophy is age and size dependent

The most common form of adult muscular dystrophy, myotonic dystrophy (DM), is caused by the abnormal expansion of the CTG repeat, located in the 3' UTR of the DM gene. The expanded-CTG allele often presents as a diffused band on Southern blot analysis, suggesting somatic mosaicism. In order to study the somatic instability of the CTG repeat, we have investigated the dynamics of the size heterogeneity of the CTG expansion. Size heterogeneity is shown as a smear on Southern blot and is measured by the midpeak-width ratio of the expanded allele to the normal sized allele. The ratio is also corrected for compression in the higher-molecular-weight region. It is found that the size heterogeneity of the expanded-CTG repeats, of 173 DM patients, correlates well with the age of the patient (r = .81, P << .001). The older patients show larger size variation. This correlation is independent of the sex of either the patient or the transmitting parent. The size heterogeneity of the expansion, based on age groups, is also dependent on the size of the expanded trinucleotide repeat. However, obvious size heterogeneity is not observed in congenital cases, regardless of the size of expansion. Comparison of individual patient samples collected at two different times has confirmed that the degree of size heterogeneity increases with age and has revealed a subtle but definite upward shift in the size of the expanded-CTG allele. The progression of the CTG repeat toward larger expansion with age is further confirmed by small-pool PCR assay that resolved the heterogeneous fragments into discrete bands.(ABSTRACT TRUNCATED AT 250 WORDS)

CAG repeat size and clinical presentation in Huntington's disease

The specific mutation in Huntington's disease (HD) is an expansion of the unstable CAG trinucleotide repeat in the IT15 gene in chromosome 4p. We examined the relationship between the CAG repeat size and clinical presentation in 36 patients with suspected diagnosis of HD. Twelve patients had no relatives with documented HD, and five of them failed to show the expanded (>37) CAG repeats. The remaining 31 patients, including seven patients with atypical clinical features for HD (three without and four with family history of documented HD), were heterozygotes for the CAG repeat expansion. There were large CAG repeats (50 copies) in paternally transmitted HD cases with early onset (age 30 or earlier). The rate of disease progression was faster in paternally transmitted cases regardless of the CAG repeat length or age of onset. We conclude that (1) patients lacking the family history of HD frequently show no expansion of the CAG repeats, and (2) the sex of the affected parent influences both the CAG repeat size and the phenotypic expression of the HD gene in the offspring.

Chemical crosslinking and the stabilization of proteins and enzymes

The technique of chemical crosslinking has been used to enhance the stability of proteins and enzymes. In this procedure, the molecule is braced with chemical crosslinks either intramolecularly or intermolecularly to another species to reinforce its active structure. Various chemicals have been used for this purpose. The bifunctional reagents are the most prominent. These compounds are derived from group-specific reagents and may be classified into homobifunctional, heterobifunctional, and zero-length crosslinkers. Different physical and chemical characteristics have been incorporated into these chemicals. Their versatility holds great potential in preparing chemically, thermally, and mechanically stable proteins and enzymes for industrial applications.

Regulation of nuclear histone acetyltransferase by nucleic acids, histone.DNA complex, and chromatin

Nuclear histone acetyltransferase is found to be inhibited by various nucleic acids and components. Of the adenosine phosphates, the order of inhibitory potency is ATP greater than ADP greater than AMP. Among the nucleoside triphosphates, GTP seems to be the best inhibitor, followed by ATP, CTP, and UTP. Deoxymononucleotides have the same order of inhibition potential as their ribonucleotide counterparts, with inhibition constants in the low millimolar range. Oligonucleotides and polynucleotides are much better inhibitors than mononucleotides. The inhibition constants of the DNA molecules are size dependent. Molecules larger than 40 base pairs have inhibition constants less than 18 micrograms/ml, whereas molecules with decreasing numbers of base pairs have increasing magnitudes of inhibition constants. However, acetyltransferase has a lower affinity for free DNA molecules than for DNA.histone complexes as revealed by its interaction with DNA-Sepharose and histone.DNA-Sepharose columns. Furthermore, native chromatin depleted of endogenous histone acetyltransferase activity shows no inhibitory effect on the enzyme. Yet heated chromatin not only loses substrate activity but also becomes an inhibitor for the enzyme. Since unmodified sea urchin sperm chromatin has been shown to be a potent acetyltransferase inhibitor, it seems possible that DNA.histone complexes may be the true inhibitory species and that the conformational states of such complexes may serve as a regulatory mechanism in the control of the enzyme activity.