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a Author for correspondence. Fax 213-666-0489; e-mail lcwong{at}hsc.usc.edu
| Abstract |
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| Introduction |
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There are numerous mitochondria in each cell, usually hundreds to thousands, each having 210 copies of mitochondrial DNA (mtDNA) (3). Because virtually all the mtDNA of a fertilized egg are derived from the oocyte, maternal inheritance of mtDNA defines the mode of transmission of mtDNA disorders. A mutation in mtDNA may be present in all mtDNA copies (homoplasmy) or coexist with normal mtDNA copies (heteroplasmy). Usually, benign polymorphisms of mtDNA are homoplasmic and pathogenic mutations are heteroplasmic. The variable phenotypic expression of pathogenic mutations depends upon the degree of heteroplasmy and the energy requirements of the affected tissue. Accordingly, each tissue has a threshold concentration of mutant mtDNA that must be exceeded to cause respiratory chain dysfunction (4). This threshold concentration also varies among different mtDNA point mutations.
Because mitochondrial disorders affect a variety of organ systems, a diverse group of systemic diseases have been associated with mitochondrial mutations. Neurological manifestations of mitochondrial diseases include ophthalmoplegia, seizures, sensorineural hearing loss, myoclonus, optic neuropathy, pigmentary retinopathy, myopathy, ataxia, dementia, and peripheral neuropathy (3). Nonneurological systemic manifestations include cardiac conduction defects, cardiomyopathy, diabetes mellitus, hypoparathyroidism, cataracts, lactic acidosis, intestinal pseudoobstruction, and pancreatic dysfunction (3). Both large deletions and point mutations in mtDNA have been identified in patients with characteristic oxidative phosphorylation defects. The most common point mutations are A3243G, accounting for 80% of patients with mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS); A8344G, which underlies myoclonic epilepsy, ragged red fibers (MERRF); T8993G/C, leading to neuropathy, ataxia, retinitis pigmentosa (NARP); and G11778A, found in >50% of patients with Leber hereditary optic neuropathy (LHON). Genetic heterogeneity exists whereby different mutations may result in similar disease presentation. For example, A3243G, T3271C, T3291C, and C3256T can all present as a MELAS-like phenotype. Correspondingly, mitochondrial disease is also characterized by phenotypic pleiotropy whereby the identical point mutation may lead to different disease phenotypes. An example is the A3243G MELAS mutation, also found in some patients with maternally inherited diabetes/deafness (5).
To date, the mainstay of mitochondrial point mutation analysis has been PCR amplification of the mtDNA region of interest, followed by restriction enzyme analysis for each known mutation. However, given the complexity and heterogeneity of the mtDNA disorders, analysis of multiple point mutations is often desirable. In many cases, at the time when molecular diagnosis is requested, the clinical phenotype is nonspecific or evolving. Nevertheless, a definitive molecular diagnosis to rule out common mutations in mtDNA is necessary for effective patient management and genetic counseling. Analysis of several mutations by single PCR/restriction enzyme fragment length polymorphism (RFLP) is not practical. Here we describe a simple, sensitive, accurate, and cost-effective multiplex PCR/allele-specific oligonucleotide (ASO) method for the simultaneous screening of multiple point mutations in mtDNA.
| Patients and Methods |
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Genomic DNA was extracted from peripheral blood, muscle, hair
follicles, cheek cells, or paraffin-embedded tissues with published
procedures (6)(7)(8). Three mutation hot spots, including
tRNAleu(UUR), tRNAlys/ATPase, and
ND4 regions, were PCR-amplified with the three pairs of
primers listed in Table 1
. Ninety-six-well plates were used for multiplex PCR
amplification with Perkin-Elmer's 9600 thermal cycler. Each 100 µL
of PCR mixture contained 1x Promega PCR buffer; 1.5 mmol/L
MgCl2; 0.2 mmol/L of each dNTP; 0.5 µmol/L each of
primers mt1, mt12, mt3, mt8, LHON-F, and mt10; 1 U of Taq
DNA polymerase; and 100 ng of genomic DNA. The reaction mixture was
denatured at 94 °C for 5 min, followed by 25 cycles of 45 s of
denaturation at 94 °C, 1 min of reannealing at 55 °C, and 2 min
of extension at 72 °C. The PCR is completed by a final extension
cycle at 72 °C for 5 min. Two microliters of PCR product was spotted
onto a Biodyne B+ membrane. Dot blots were prepared for each of the
following normal and mutant probes: A3243, A8344, G11778, A3243G,
T3271C, A8344G, T8356C, T8993C, T8993G, G8363A, G3460A, T3394C, and
G11778A. The normal probes are used to ensure that each region has been
PCR-amplified. Eight rare point mutations were studied by hot pools I
and II. Hot pool I contained a mixture of mutant probes A3251G, A3252G,
A3260G, and A3302G. Hot pool II contained a mixture of mutant probes
T3250C, C3256T, T3291C, and C3303T. The sequences of the ASO probes for
various mutations are listed in Table 2
. Membrane preparation and hybridization conditions were those
of published procedures (9). The ASO probes were end
labeled with [
-32P]ATP with polynucleotide kinase.
Each dot blot was placed in a 15- or 50-mL disposable tube to be
hybridized with specific probe. Multiple tubes were put in a
hybridization bottle. The wash temperature varied with the melting
temperature (Tm) of each ASO probe and was
determined experimentally (Table 2
). The proportion of mutant mtDNA was
quantitatively analyzed according to published procedures
(7)(10)(11).
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| Results |
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| Discussion |
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Genetic heterogeneity complicates mitochondrial genotype/phenotype correlation. For instance, at least four different point mutations present as a MELAS-like syndrome, and at least 10 different point mutations have been found in patients with LHON. The A3243G mutation can have several different clinical manifestations, such as MELAS (14), diabetes and hearing loss with or without macular-pattern retinal dystrophy (5)(15)(16), and chronic progressive external ophthalmoplegia. The histologic and biochemical phenotype can be nonspecific. The clinical phenotype of patients with A3243G overlaps with that of patients with A8344G in that they may both have ragged red fibers and lactic acidosis. Thus, the mitochondrial disorders are a complex and heterogeneous group of genetic disorders. To rule out the most common point mutations in mtDNA, several point mutations causing MELAS, MERRF, NARP, Leigh, and (or) LHON syndromes may need to be evaluated. The individual analysis of multiple point mutations is time consuming, labor intensive, expensive, and not practical. The multiplex PCR/ASO method described here is direct, simple, accurate, sensitive, and cost effective. Accordingly, our turnaround time for the analysis of 18 point mutations is ~34 days. Complete molecular screening of mutations in mtDNA should also include Southern transfer analysis to detect large DNA deletions.
Because multiplex PCR amplifies the regions containing mutation hot spots, as new mutations in these regions are identified, the same blots can be stripped and reanalyzed with the new probes. This would permit efficient analysis of several specimens for the presence of the newly identified mutations. Currently, we have improved the multiplex PCR/ASO method to analyze 45 known point mutations in the mtDNA genome. The PCR products of mtDNA from all the patients are in the blots that can be easily reused in the future for the detection of any newly discovered mutations in these regions.
Molecular diagnosis is only part of a complete workup of mitochondrial disease. Patients highly suspected of mtDNA disorders on the basis of clinical, pedigree, and (or) laboratory information should receive a comprehensive evaluation including histochemical/electron microscopic studies, enzyme assays of electron transport chain, and mtDNA mutation analysis. In our experience, only ~7% of the specimens sent to our laboratory for DNA testing will have detectable pathogenic mutations by multiplex PCR/ASO and Southern analysis. Possibilities for further molecular characterization include single-strand conformation polymorphism analysis and direct sequencing of the entire mtDNA genome.
In the past, there has been uncertainty about the appropriate tissues to be tested for mtDNA mutations. Approximately 15% (300 of 2000) of the specimens tested are muscle tissue. Results of analysis of both blood and muscle specimens in 12 patients revealed that, in all cases, the blood contained a lower proportion of mutant mtDNA than muscle (17). Recently, we have looked at other noninvasive tissue specimens as alternatives. Among these are hair follicles and buccal mucosal cells. The results (17) indicate that although the percentage of mutant mtDNA fluctuates from tissue to tissue, in all patients analyzed, the mutant mtDNA for point mutations is consistently either present or absent in all three tissues (blood, hair follicles, and buccal cells) analyzed.
There is a bias in patient selection. Our laboratory is in a children's hospital. The majority of our patients have clinical presentations of MELAS, NARP, Leigh syndrome, and cardiomyopathy. mtDNA mutations that account for adult forms of myopathy, cardiomyopathy, MERRF, multisystem disorders, and mutations associated with aging such as Alzheimer and Parkinson diseases are apparently underrepresented.
| Acknowledgments |
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| Footnotes |
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1 Nonstandard abbreviations: nDNA, nuclear DNA; mtDNA, mitochondrial DNA; MELAS, mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes; MERRF, myoclonic epilepsy and ragged-red fibers; NARP, neuropathy, ataxia, retinitis pigmentosa; LHON, Leber hereditary optic neuropathy; RFLP, restriction fragment length polymorphism; and ASO, allele-specific oligonucleotide. ![]()
| References |
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