Identification of a new DMD gene deletion by ectopic transcript analysis

The analysis of DMD gene deletions by multiplex PCR in Indonesian DMD/BMD patients: the era of personalized medicine

Objective

Duchenne/Becker muscular dystrophy (DMD/BMD) is the most common genetic neuromuscular disease in children, resulting from a defect in the DMD gene located on Xp21.2. The new emerging treatment using exon skipping strategy is tailored to specific mutations, thus molecular diagnostics are particularly important. This study aimed to detect the DMD gene deletion in Indonesian DMD/BMD patients and analyze the potential amenability by exon skipping therapy.

Results

Thirty-four male patients were enrolled in this study, 23 of them (67.6%) underwent muscle biopsy and showed the absence or partially expressed dystrophin protein in immunohistochemistry staining. All patients had very high serum CK levels (10.529 ± 9.97 IU/L). Multiplex PCR revealed the DMD gene deletions in 15 (44.1%) cases. Seventy-eight percent of deletions were clustered in the hot-spot region of exon 43 to 52. Furthermore, seven (20.5%) patients were potentially amenable to exon skipping treatment. Therefore, multiplex PCR is one feasible method to detect DMD gene deletion in Indonesian DMD/BMD patients that can further determine the potential amenability of exon skipping therapy. In addition, this study is the first report of DMD gene deletion analysis in Indonesia.

Optimization of Internally Deleted Dystrophin Constructs

Duchenne muscular dystrophy (DMD) is a severe, genetic muscle disease caused by the absence of the sarcolemmal protein dystrophin. Gene replacement therapy is considered a potential strategy for the treatment of DMD, aiming to restore the missing protein. Although the elements of the dystrophin molecule have been identified and studies in transgenic mdx mice have explored the importance of a number of these structural domains, the resulting modified dystrophin protein products that have been developed so far are only partially characterized in relation to their structure and function in vivo. To optimize a dystrophin cDNA construct for therapeutic application we designed and produced four human minidystrophins within the packaging capacity of lentiviral vectors. Two novel minidystrophins retained the centrally located neuronal nitric oxide synthase (nNOS)-anchoring domain in order to achieve sarcolemmal nNOS restoration, which is lost in most internally deleted dystrophin constructs. Functionality of the resulting truncated dystrophin proteins was investigated in muscle of adult dystrophin-deficient mdx mice followed by a battery of detailed immunohistochemical and morphometric tests. This initial assessment aimed to determine the overall suitability of various constructs for cloning into lentiviral vectors for ex vivo gene delivery to stem cells for future preclinical studies.

Cellular kinetics of neuroblastoma and the role of surgery

Neuroblastoma is known for its peculiar cellular kinetics, which has provoked some controversy regarding surgical treatment. Highly sensitive exploration systems using reverse transcription polymerase chain reaction (RT-PCR) methods have been developed to detect neuroblastoma cells. In our series of 49 patients with advanced neuroblastoma, circulating tumor cells (CTC) were detected by this system in 55.6% of the stage 4 patients who were examined, suggesting that the primary lesion may release tumor cells into the peripheral blood. The Kaplan-Meier survival rate was significantly lower among the patients with CTC or chemotherapy-insensitive bone marrow micrometastasis, compared with those without detectable micrometastasis (33.8 vs. 87.5%, P < 0.05). In contrast, a stage 3 patient with MYCN amplification exhibited drastic local relapse without systemic dissemination of the disease. Two patients were positive for CTC without an identifiable primary site. These observations indicate that the local growth of the primary tumor and tumor cell dissemination may be regulated by different molecular mechanisms in neuroblastomas. MYCN amplification seemed to be more closely associated with localized tumor growth but was minimally correlated with CTC positivity. High-risk neuroblastoma may include two separate subgroups characterized by different cellular kinetics: a local risk cohort and a systemic risk cohort. Surgical strategies for neuroblastoma should be determined with taking this cellular kinetics into consideration.

Diagnostic strategy for the detection of dystrophin gene mutations in asian patients and carriers using immortalized cell lines

Duchenne muscular dystrophy and Becker muscular dystrophy are X-linked recessive diseases of muscle degeneration caused by mutations in the dystrophin gene. More than half of our local Asian patients have point mutations that cannot be detected by conventional multiplex polymerase chain reaction deletion screening. This study aimed to develop mutational screening and carrier detection for Duchenne and Becker muscular dystrophy using protein truncation analysis from Epstein-Barr virus-transformed lymphocyte cell lines. Messenger ribonucleic acid was extracted from fresh lymphocytes and Epstein-Barr virus-transformed lymphocyte cell lines of 14 patients. Reverse transcriptase polymerase chain reaction was performed in 11 overlapping segments, followed by in vitro protein translation and truncation analysis. DNA sequencing was carried out for the corresponding complementary DNA regions, which showed aberrant truncated protein products. Carrier studies using this method were also performed for two families. Half of the patients had frame-shifting deletions, and the remaining seven patients showed point mutations, of which four were novel. These mutations were detected in messenger ribonucleic acid extracted from both fresh lymphocytes and Epstein-Barr virus-transformed lymphocyte cell lines. Carrier status was confirmed in one family and was found to be negative in the other family studied. Protein truncation analysis is an efficient method of screening truncating point mutations from immortalized lymphocyte cell lines from patients. This approach not only serves to prove the pathogenicity of both deletion- and nondeletion-type mutations; it is also effective for carrier detection. The use of such cell lines obviates the need for repeated blood and muscle sampling in patients and offers a perpetual source of messenger ribonucleic acid that can be used long after the patient's demise.

Surgical treatment of neuroblastoma with micrometastasis

BACKGROUND/PURPOSE

The aim of this study was to define the role of surgery in neuroblastoma with micrometastasis, which is detectable only by the polymerase chain reaction (PCR) method.

METHODS

Fifty samples (peripheral blood 9, bone marrow 41) were harvested sequentially from 27 neuroblastoma patients, and the micrometastases were examined using the previously described single-step PCR method. The results were reviewed with the clinical courses.

RESULTS

Radical surgery was performed in 9 patients with bone marrow micrometastasis. Event-free survival was obtained in 2 patients with stage IV disease (25.0%) for a follow-up period of 2 to 6 years in this group. Both patients received intraoperative radiation and subsequent autologous bone marrow transplantation (ABMT) using purged marrow. Radical surgery was performed in 18 patients without micrometastasis, and 6 of 9 advanced patients (66.7%) survived without the disease including 4 patients who received unpurged stem cell transplantation.

CONCLUSIONS

Persistent micrometastasis in bone marrow should be considered predictive as a poor prognostic factor in neuroblastoma. Intensive local control with surgery and radiation is important for the patients with micrometastasis and should be followed by ABMT using purged marrow. Unpurged marrow may be safely used if the single-step PCR detects no micrometastasis.

Meta-PCR: a novel method for creating chimeric DNA molecules and increasing the productivity of mutation scanning techniques

Many mutation scanning techniques are capable of locating mutations in DNA fragments much larger than the average exon. We have developed a system called Meta-PCR that can maximize the length of sequence scanned by these techniques, improving their productivity and realizing their full potential. Meta-PCR is a simple, versatile, and powerful method for generating chimeric DNA molecules. Currently, up to five PCR amplifiable fragments can be combined to form a single linear amplimer. The Meta-PCR reaction is self-assembling and takes place in two coupled stages carried out in a single reaction vessel. The order of fragments is reproducible and determined by primer design. We have developed two Meta-PCR assays, one comprising exons 6-10 of the Neurofibromatosis type 2 (NF2) gene and the second exons 8-12 of the human mismatch repair gene, hMLH1. We verified by direct sequencing that the order and sequence of the component exons in the Meta-PCR products is as predicted. Meta-PCR products from seven previously ascertained heterozygotes for NF2 mutations were directly sequenced. All seven mutations were clearly visible as mixed bases at the expected nucleotide, confirming that Meta-PCR faithfully reproduces the original sample genotype. We have evaluated the downstream use of the NF2 Meta-PCR products in fluorescent solid-phase chemical cleavage of mismatches (CCM). Meta-PCR products from eleven NF2 mutant heterozygotes were screened retrospectively for piperidine cleavage after hydroxylamine or potassium permanganate modification of mismatched bases. Ten of the 11 mutants were detected by visible cleavage. One mutation predicted to be cleaved after potassium permanganate modification was not detected. However, we were able to attribute this false negative to a failure in the CCM method. Meta-PCR is likely to be useful to clinical molecular diagnostic laboratories, helping them to fulfill demand for rapid and accurate screening for point mutations in large multi-exon genes.

X-linked dilated cardiomyopathy. Novel mutation of the dystrophin gene

We report on a family with a severe form of X-linked dilated cardiomyopathy (DCM). Two brothers, the elder requiring heart transplantation, and a maternal cousin presented elevated creatine kinase levels, increased right ventricular diameters and electrocardiographic abnormalities. All complained of exertional cramping myalgia, but none had muscle weakness or a pathological electromyogram. Muscle biopsies of these individuals revealed a mild myopathic picture with atrophic type I and hypertrophic type II fibers. Immunofluorescence using N- and C-terminal antibodies (dys-2, dys-3) against the dystrophin protein showed preserved, but reduced intensity of staining of the sarcolemmal membranes. Using the same two antibodies, Western blot analyses revealed a dystrophin molecule of the expected molecular weight, which was quantitatively reduced by 80%. However, the dys-1 antibody, directed against the mid rod region of the dystrophin protein, did not react with dystrophin both on Western blot and immunofluorescence. Linkage analysis with polymorphic markers of the dystrophin gene revealed an identical haplotype at the 5' region in all affected individuals (two point lod score of 1.93, phi = 0). A deletion of exons 48, 45-53, 2-7 and 1 including the promoter region of the dystrophin gene, as described in rare cases with similar clinical signs could be excluded by multiplex PCR and Southern blot analyses of this DCM family. In addition, a major splice-mutation of dystrophin mRNA was excluded by RT-PCR of skeletal and heart muscle tissue. Therefore, we conclude that a novel mutation in the 5' region of the dystrophin gene phenotypically leads to this severe form of DCM. Extensive analyses of the dystrophin gene, in particular of the sequences coding for the antigenic determinants of the dys-1 antibody in the mid rod region, may identify the molecular cause of this monogenetic form of DCM.

Microlesions and polymorphisms in the Duchenne/Becker muscular dystrophy gene

One third of mutations responsible for Duchenne or Becker muscular dystrophy (DMD/BMD) represent point mutations or other small sequence alterations not readily detectable by Southern blot analysis or multiplex amplification. Here, we report results of a comprehensive point mutation search that yielded seven new sequence variations and one novel polymorphism. We also summarize known mutations, polymorphisms and other small nucleotide variations in the DMD gene. To date, 12 nonsense mutations, two missense mutations, six microdeletions and one microinsertion have been reported in the coding sequence and a further six mutations in splice sites all of which were made responsible for the disease. Twelve polymorphisms with frequencies suitable for diagnostic purposes have been detected. A further 28 differences from the published sequence of the coding sequence or the promoter region are described.

Detection of carriers of deletions in the dystrophin gene in Bulgarian DMD-BMD families

Analysis of Bulgarian Duchenne/Becker muscular dystrophy (DMD/BMD) patients has demonstrated that deletions spanning exon 4 or exon 48 of the dystrophin gene account for about half of all patients, and that female relatives from these families constitute nearly 40% of all patients who require diagnosis of carrier status. We propose a relatively simple and inexpensive assay for the detection of deletion carriers based on a duplex PCR with radioactive 5' end labeling of one of the PCR primers for each exon. The PCR amplification is performed under conditions of exponential relationship between template DNA and the amount of PCR product obtained, thus facilitating gene dosage. The quantification of the products, and especially the use of a coefficient estimating of the relative proportion of each exon in the total densitometric area, provide a reliable differentiation between carriers and non-carriers.

Ectopic (illegitimate) transcription: new possibilities for the analysis and diagnosis of human genetic disease

By means of the Polymerase Chain Reaction (PCR), 'ectopic' or 'illegitimate' transcripts from any gene may be amplified from any tissue or cell type. RNA transcript analysis is therefore no longer dependent upon possession of the often inaccessible 'expressing' tissue. We review here the applications of ectopic transcript analysis to mutation detection and characterization, analysis of RNA splicing and the study of the genotype-phenotype relationship.

Brain- and muscle-type promoters of the dystrophin gene are selected in peripheral lymphocytes and Epstein Barr virus-transformed lymphoblastoid [correction of lymphoplastoid] cells

Promoter-specific transcripts of the dystrophin gene in peripheral lymphocytes and Epstein Barr virus-transformed lymphoblastoid cells were analysed using reverse transcription-nested polymerase chain reaction. Two DNA fragments, corresponding to the alternative first exons transcribed from either brain- or muscle-type promoters, were both amplified from cDNA prepared from normal lymphocytes and lymphoblastoid cells. The nucleotide sequences of the amplified products were 100% homologous to the 5' termini of the cDNA of brain- and muscle-type dystrophins, respectively. Neither fragment was amplified from the lymphoblastoid cells of a patient with Duchenne muscular dystrophy, who has a partial deletion involving the brain- and muscle-type promoters in the dystrophin gene. These findings showed that the brain-type as well as the muscle-type promoter of the dystrophin gene was active in lymphocytes and lymphoblastoid cells.

Molecular genetic analysis of 67 patients with Duchenne/Becker muscular dystrophy

A total of 56 Duchenne muscular dystrophy (DMD) patients and 11 Becker muscular dystrophy (BMD) patients was analyzed by extended "multiplex" amplification of the DMD/BMD gene; deletions were found in 60% of these patients. The data obtained were used to test the frameshift hypothesis and to compare the distribution of familial versus isolated cases. A significant correlation was found between deletions and isolated cases. Additional experiments were performed in order to determine the deletion breakpoints more precisely. These data are a prerequisite for carrier analysis in the respective families by detection or exclusion of aberrant cDNA fragments derived from ectopic lymphocyte RNA. This diagnostic technique is illustrated by 5 examples.