Mutation detection in Leber's hereditary optic neuropathy by PCR with allele-specific priming

Molecular epidemiology of mtDNA mutations in 903 Chinese families suspected with Leber hereditary optic neuropathy

We report the molecular epidemiology of three primary mutations in mitochondrial DNA (mtDNA) responsible for Leber hereditary optic neuropathy (LHON) based on analysis of probands suspected with LHON from 903 Chinese families. Most of them had optic neuropathy of unknown cause, and only 128 had a family history of optic neuropathy. Mutations in the mtDNA were detected in 346 probands. Of the 346 cases, 340 were homoplasmic and only six were heteroplasmic; 284 were male and 62 were female; 120 had a family history and 226 were sporadic. G11778A, T14484C and G3460A mutations were detected in 312 (90.2%), 30, and four families, respectively. The majority (226/346, 65.3%) of all LHON cases in Chinese are sporadic. These 226 probands (29.2%) were identified from 775 probands with sporadic optic neuropathy. Affected male-to-female ratio was 4.6:1 for all probands but was 2.2:1 for family members. Average age at onset was 18.5 years, ranging from 4.5 to 47 years old.

Multiplex allele-specific target amplification based on PCR suppression

We have developed a strategy for multiplex PCR based on PCR suppression. PCR suppression allows DNA target amplification with only one sequence-specific primer per target and a second primer that is common for all targets. Therefore, an n-plex PCR would require only n + 1 primers. We have demonstrated uniform, efficient amplification of targeted sequences in 14-plex PCR. The high specificity of suppression PCR also provides multiplexed amplification with allele specificity. Multiplexed PCR was used to develop assays for genotyping DNA samples from cystic fibrosis-affected individuals. The new approach greatly simplifies primer design, significantly increases the PCR multiplexing level, and decreases the overall primer cost. In addition, this assay is more readily amenable to automation and is therefore suitable for high-throughput genetic diagnostics.

Role of the mitochondrial DNA and calmitine in myopathies

We present data on mitochondrial DNA deletions and mitochondrial diseases. The mechanism of their occurrence is discussed on the basis of deletion breakpoints and particularly with the slippage mispairing hypothesis. As the correlation between the genotypes and the phenotypes is not always straightforward, a classification of mitochondrial diseases is suggested according to the genotype (deletions, depletions and duplications, mutations affecting structural genes or tRNA genes) rather than the phenotype. The effect of mitochondrial DNA alterations on the expression of nuclear encoded proteins is presented, and the nucleus can be found to respond differently but in a coordinate way according to the kind of mitochondrial DNA alteration. The search for a nuclear gene affecting the expression of Leber's disease could not show any correlation between the alleles of TAP2 (transporter antigen peptide) and the expression of the disease. Finally, we present new data on another class of myopathies, namely Duchenne muscular dystrophy (DMD), where mitochondria could play an unexpected role in the metabolism of calcium. In some patients with DMD a mitochondrial calcium binding protein that is mainly located in the mitochondrial matrix and which is named 'calmitine' was found to disappear. We have thus cloned its cDNA and found that it was identical with to calsequestrine which is a high-capacity but low-affinity Ca2+ binding protein from the sarcoplasmic reticulum.

Mitochondrial DNA alterations and genetic diseases: a review

We review the main features of human mitochondrial function and structure, and in particular mitochondrial transcription, translation, and replication cycles. Furthermore, some pecularities such as mitochondria's high polymorphism, the existence of mitochondrial pseudogenes, and the various considerations to take into account when studying mitochondrial diseases will also be mentioned. Mitochondrial syndromes mostly affecting the nervous system have, during the past few years, been associated with mitochondrial DNA (mt DNA) alterations such as deletions, duplications, mutations and depletions. We suggest a possible classification of mitochondrial diseases according to the kind of mt DNA mutations: structural mitochondrial gene mutation as in LHON (Leber's Hereditary Optic Neuropathy) and NARP (Neurogenic muscle weakness, Ataxia and Retinitis Pigmentosa) as well as some cases of Leigh's syndrome; transfer RNA and ribosomal RNA mitochondrial gene mutation as in MELAS (Mitochondrial Encephalomyopathy, Lactic Acidosis and Strokelike Episodes) or MERRF (Myoclonic Epilepsy with Ragged Red Fibers) or deafness with aminoglycoside; structural with transfer RNA mitochondrial gene mutations as observed in large-scale deletions or duplications in Kearns-Sayre syndrome, Pearson's syndrome, diabetes mellitus with deafness, and CPEO (Chronic Progressive External Ophtalmoplegia). Depletions of the mt DNA may also be classified in this category. Even though mutations are generally maternally inherited, most of the deletions are sporadic. However, multiple deletions or depletions may be transmitted in a mendelan trait which suggests that nuclear gene products play a primary role in these processes. The relationship between a mutation and a particular phenotype is far from being fully understood. Gene dosage and energic threshold, which are tissue-specific, appear to be the best indicators. However, the recessive or dominant behavior of both the wild type or the mutated genome appears to play a significant role, which can be verified with in vitro studies.

Time-resolved fluorometry in the diagnosis of Leber hereditary optic neuroretinopathy

We have applied time-resolved fluorometry (TRF) to construct a DNA hybridization assay for the diagnosis of Leber hereditary optic neuroretinopathy (LHON). A rapid and reliable detection of the most prevalent mitochondrial DNA (mtDNA) point mutation associated with LHON is demonstrated. In addition, the TRF-method can be used in the quantification of heteroplasmy, a phenomenon commonly present in mtDNA mutations. The assay includes PCR amplification of a fragment encompassing the mutation site followed by hybridization reactions with allele-specific europium (Eu)-labelled oligonucleotide probes. A time-resolved fluorometer is used to measure the bound label. The TRF assay was successfully used to demonstrate the ND4/11778 mutation in patient samples. For quantification of heteroplasmy, synthetic target oligonucleotide mixtures with known ratios of wild-type and mutated sequences were used as standards to control the hybridization step. The assay allowed the detection of heteroplasmy ranging from 5 to 95%. This was also shown in a family with several heteroplasmic members.

Juvenile Kearns-Sayre syndrome initially misdiagnosed as a psychosomatic disorder

We have investigated a 15 year old girl with progressive external ophthalmoplegia, including bilateral ptosis and retinal rod and cone cell dysfunction with atypical retinal pigmentation, complicated by cerebellar ataxia, partial cardiac conduction block, and diabetes mellitus. In infancy she had a severe crisis of bone marrow depression, and as a child she suffered from hypersensitivity to light, increasing fatigue, and vertigo, signs that were initially though to be psychosomatic. Histological examination showed mitochondrial myopathy, and subsequent mitochondrial DNA (mtDNA) analysis showed a deletion of approximately 5500 base pairs in 35 to 40% of her muscle mtDNA. We therefore conclude that this patient has developed the Kearns-Sayre syndrome after a Pearson syndrome-like crisis in her first year of life.

Mutation-specific PCR: a rapid and inexpensive diagnostic method, as exemplified by mitochondrial DNA analysis in Leber's hereditary optic neuropathy

Mitochondrial DNA analyses were carried out on 30 individuals with clinically documented or suspected Leber's hereditary optic neuropathy (LHON). Three methods based on the polymerase chain reaction (PCR) were compared, all three aiming at detecting the G/C to A/T mutation of base pair 11,778 causing LHON. Two methods included restriction analysis with either Sfa NI or Mae III, while the third one relied on allele-specific amplification (ASA), using a mutation-specific primer. The results were completely consistent, showing the presence of the mutation in 18 and its absence in 12 cases. From these results it is concluded, that mutation-specific PCR is the diagnostic method of choice, because it obviates the need for subsequent restriction analysis, thus being faster and more cost-efficient. The general applicability of ASA makes this strategy universally useful for detection of specific mutations in the diagnostic analysis of genetic disease, and for typing of genetic polymorphisms or other sequence variations due to single-base differences.

Screening for the two most frequent mutations in Leber's hereditary optic neuropathy by duplex PCR based on allele-specific amplification

This report describes a rapid and inexpensive assay, which allows detection, in whole blood and by PCR alone, of the two most frequent mitochondrial DNA mutations causing Leber's hereditary optic neuropathy. The assay is based on allele-specific amplification, using primers with the mutation-specific base in the 3' position, and a deliberately introduced G-->C substitution of base no. four from the 3' end, which prevents amplification of the wild-type allele.

Amplimers with 3'-terminal phosphorothioate linkages resist degradation by vent polymerase and reduce Taq polymerase mispriming

The 3'-->5' exonuclease activity of Vent, a thermostable polymerase from Thermococcus litoralis, enhances DNA replication fidelity but also diverts PCR primers (amplimers) from targeted amplification by degrading their 3' termini. We demonstrate that amplimers with a 3-base 3'-terminal mismatch can be efficiently truncated by Vent to prime DNA polymerizations that compete with the specific amplification reaction. However, amplimers with phosphorothioate bonds joining their 3'-terminal residues are resistant to degradation and demonstrate greatly enhanced priming specificity. Slight destabilization of base-pairing by phosphorothioate bond-linked residues also diminishes extension of mispaired 3' amplimer termini in Taq polymerase-mediated amplifications.

Identification of a mutation in the gene encoding the alpha subunit of the stimulatory G protein of adenylyl cyclase in McCune-Albright syndrome

McCune-Albright syndrome (MAS) is characterized by polyostotic fibrous dysplasia, café-au-lait lesions, and a variety of endocrine disorders, including precocious puberty, hyperthyroidism, hypercortisolism, growth hormone excess, and hyperprolactinemia. The diverse metabolic abnormalities seen in MAS share the involvement of cells that respond to extracellular signals through activation of the hormone-sensitive adenylyl cyclase system (EC 4.6.1.1). Mutations that lead to constitutive activation of Gs alpha, the guanine nucleotide-binding regulatory protein that stimulates adenylyl cyclase activity, have been identified in a subset of human growth hormone-secreting pituitary tumors and human thyroid tumors. We report here the identification of a mutation in the gene encoding Gs alpha in a patient with MAS. Denaturing gradient gel electrophoresis was used to analyze amplified DNA fragments including exon 8 or exon 9 of the Gs alpha gene. In one subject with MAS a G-to-A transition was found in exon 8 of one of the two alleles encoding Gs alpha. This single-base substitution results in the replacement of arginine by histidine at position 201 of the mature Gs alpha protein. Semiquantitative analysis of amplified DNA indicated that the mutant allele was less prevalent than the wild-type allele in peripheral leukocytes and was present in very low levels in skin. These findings support the previous contention that the segmental distribution and variable expression of the cutaneous, skeletal, and endocrine manifestations of MAS reflect an underlying somatic mosaicism. Further, these results suggest that the molecular basis of MAS is a postzygotic mutation in Gs alpha that causes constitutive activation of adenylyl cyclase.

Mitochondrial DNA mutations in human diseases: a review

Human mitochondrial diseases have been associated recently with mitochondrial DNA mutations, duplications and deletions which impair the protein synthesis of the mitochondrial subunits of the respiratory chain complexes. A constant feature is the coincident presence of the mutated and wild type genomes which provide heteroplasmy. The clinical expression of these diseases depends on the relative expression of each kind of mitochondrial DNA in the various tissues, which in turn affects the production of ATP in these tissues. Research on nuclear gene products interfering with mtDNA or with its gene products is the next step towards understanding the etiology of these diseases.