Human elongation factor EF-1 beta: cloning and characterization of the EF1 beta 5a gene and assignment of EF-1 beta isoforms to chromosomes 2,5,15 and X

We report here the isolation and characterization of a novel human elongation factor-1 beta (EF-1 beta) gene by cDNA selection from YAC mapping on chromosome 5q12-q14. This gene is specifically transcribed in fetal brain and in skeletal muscle and is characterized by a complete sequence homology with previously described EF-1 beta cDNAs. We also assigned the loci for three other EF-1 beta isoforms, to human chromosomes 2, 15 and X. The multiple chromosomal assignments of EF-1 beta loci demonstrates the genetic heterogeneity of human EF-1 beta peptides.

The myotonic dystrophy gene

The myotonic dystrophy gene codes for a protein kinase and contains a repeated trinucleotide motif (adenine-guanine-cytosine [AGC]) in its transcribed sequence. The repeat is polymorphic in the general population, varying in size from five to 37 AGC units in normal alleles. Myotonic dystrophy patients show expansions of the repeated sequence from over 50 elements up to several thousand units. There is a positive correlation between repeat size and clinical severity. The direct analysis of the AGC repeat size allows an easy confirmation of the clinical diagnosis of myotonic dystrophy in difficult cases and for prenatal counseling.

Chromosomal rearrangement segregating with adrenoleukodystrophy: a molecular analysis

The relationship between X chromosome-linked adrenoleukodystrophy and the red/green color pigment gene cluster on Xq28 was investigated in a large kindred. The DNA in a hemizygous male showed altered restriction fragment sizes compatible with at least a deletion extending from the 5' end of the color pigment genes. Segregation analysis using a DNA probe within the color pigment gene cluster showed significant linkage with adrenoleukodystrophy (logarithm of odds score of 3.19 at theta = 0.0). These data demonstrate linkage, rather than association, between a unique molecular rearrangement in the color pigment gene cluster and adrenoleukodystrophy. The DNA changes in this region are thus likely to be helpful for determining the location and identity of the responsible gene.

Identification of repeat sequence heterogeneity at the polymorphic short tandem repeat locus HUMTH01[AATG]n and reassignment of alleles in population analysis by using a locus-specific allelic ladder

An allelic ladder containing amplified sequences of seven alleles of the polymorphic human tyrosine hydroxylase locus, HUMTH01, was constructed and employed as a standard marker. Sequence analysis of each ladder component indicates that fragments differ by integral multiples of the AATG core repeat sequence characteristic of this locus. Individual alleles are designated "5" through "11," according to the number of complete reiterations of the core repeat contained within them. Comparison of the HUMTH01 allelic ladder with DNA samples amplified at this locus revealed core repeat length heterogeneity (i.e., deletions or insertions shorter than one core repeat) within the human population. In particular, a common allele was identified which migrates more quickly than allele 10, but more slowly than allele 9, on electrophoresis through a denaturing polyacrylamide gel. Sequence analysis of this allele, designated "10-1," reveals lack of a single adenine normally present in the seventh copy of the AATG. The allelic ladder was used to reevaluate previously published population data. Results of testing for Hardy-Weinberg equilibrium and population substructure were not altered significantly by these modifications.

Efficient adenoviral-mediated ornithine transcarbamylase expression in deficient mouse and human hepatocytes

100% of primary human hepatocytes infected with an adenoviral vector carrying beta-galactosidase expressed the exogenous gene. Expression was also achieved in > 40% of adult mouse hepatocytes in vivo. Normal levels of activity were achieved in mouse ornithine transcarbamylase (OTC)-deficient primary hepatocytes using another adenoviral vector carrying human OTC cDNA. Study of OTC-deficient primary human hepatocytes from a single patient confirmed the utility of adenoviral delivery of OTC. We describe adenoviral-mediated exogenous gene expression in human and mouse hepatocytes in vitro and in mouse liver in vivo. Data suggest that adenoviral vectors may be useful for correcting OTC deficiency.

Isolation of a Miller-Dieker lissencephaly gene containing G protein beta-subunit-like repeats

Lissencephaly (agyria-pachygyria) is a human brain malformation manifested by a smooth cerebral surface and abnormal neuronal migration. Identification of the gene(s) involved in this disorder would facilitate molecular dissection of normal events in brain development. Type 1 lissencephaly occurs either as an isolated abnormality or in association with dysmorphic facial appearance in patients with Miller-Dieker syndrome. About 15% of patients with isolated lissencephaly and more than 90% of patients with Miller-Dieker syndrome have microdeletions in a critical 350-kilobase region in chromosome 17p13.3 (ref. 6). These deletions are hemizygous, so haplo-insufficiency for a gene in this interval is implicated. Here we report the cloning of a gene (LIS-1, lissencephaly-1) in 17p13.3 that is deleted in Miller-Dieker patients. Non-overlapping deletions involving either the 5' or 3' end of the gene were found in two patients, identifying LIS-1 as the disease gene. The deduced amino-acid sequence shows significant homology to beta-subunits of heterotrimeric G proteins, suggesting that it could possibly be involved in a signal transduction pathway crucial for cerebral development.

Multiplex DNA amplification and solid-phase direct sequencing for mutation analysis at the hprt locus in Chinese hamster cells

We report here the development of multiplex in vitro DNA amplification and solid-phase direct exon sequencing for the analysis of mutations at the hypoxanthine-guanine phosphoribosyltransferase (hprt) locus in Chinese hamster cells. 18 representative HPRT-deficient mutants, derived either spontaneously, or after exposure to UV light or ionizing radiation, were analyzed. All 9 hprt exons were simultaneously amplified via the polymerase chain reaction (PCR) for rapid deletion detection. 5 mutants involve single- or multiple-exon deletions. Altered multiplex PCR patterns were detected in mutants Bsp-040, Bsp-065 and BGR-606. Subsequent direct sequence analysis reveals that Bsp-040 and Bsp-065 carry a 52-bp and a 13-bp intragenic DNA deletion in exon 3, respectively. BGR-606 contains a 223-bp insertion accompanied by a 10-bp deletion of intron sequence within exon 4 fragment. Other subtle DNA alterations identified by direct exon sequence analysis include single-base substitutions, small deletions and insertions, and RNA splicing mutations.

Trinucleotide repeats and genome variation

The recent cloning of several disease genes has identified the instability of trinucleotide repeats as a fundamental mechanism for variation within the human genome. This mutation mechanism explains the unique inheritance characteristics of the diseases it causes, and there is a significant potential that this mechanism is involved in the pathogenesis of other, as yet uncharacterized, genetic diseases.

Mdx transgenic mouse: restoration of recombinant dystrophin to the dystrophic muscle

We report the restoration of the 430-kD dystrophin in mdx, the mouse model of Duchenne muscular dystrophy, by expression of a single-copy recombinant dystrophin transgene. Muscle-specific expression was achieved using a creatine kinase promoter influenced by two enhancers. Immunostaining with anti-Xp21-coded dystrophin monoclonal antibodies showed that the recombinant dystrophin was localized to the muscle fiber membrane. However, there was variability in the level of dystrophin expression in various animals with aging, between fast and slow muscles, and within different regions of the same muscle. Curiously, recombinant dystrophin was relatively absent in the diaphragm muscle of these mdx transgenic animals. Our studies indicate that there is a direct correlation between the level of muscle fibers expressing recombinant dystrophin and the level of muscle fibers with peripheral nuclei, indicating an improvement in muscle pathology. These studies indicate that the regional expression of recombinant dystrophin in dystrophic muscle leads to regional restoration of normal muscle morphology.

Relationship between parental trinucleotide GCT repeat length and severity of myotonic dystrophy in offspring

OBJECTIVE

To assess the relationship between the GCT repeat number in the myotonic dystrophy gene and the clinical phenotype and examine its predictive utility in prenatal testing.

DESIGN

DNA from patients was examined for the length of the myotonic dystrophy GCT repeat region, using both Southern blot analysis and polymerase chain reaction. The results were compared with the clinical onset of disease, as well as with pregnancy outcomes.

SETTING

Patient samples were referred to the Kleberg DNA Diagnostic Laboratory at the Baylor College of Medicine for DNA analysis by geneticists and genetic counselors (84%), neurologists (10%), and obstetricians and other specialists (6%). Clinical features including onset of disease and family pedigrees were determined by the referring centers.

PATIENTS

A total of 241 patient samples from 118 families referred from primarily genetic or neurological centers for genetic linkage analysis or mutation analysis for myotonic dystrophy. This included 44 families referred for prenatal diagnosis.

MAIN OUTCOME MEASURES

A relationship between myotonic dystrophy disease onset and length of the GCT repeat allele, parental origin of the disease allele, and results of prenatal diagnosis predictions of disease status were measured.

RESULTS

There is a relationship between increasing repeat length and earlier clinical onset of disease. Essentially all (> 99%) myotonic mutations causing myotonic dystrophy are accounted for by GCT repeat amplification. Congenital myotonic dystrophy occurs with as few as 730 GCT repeats but only with alleles of maternal origin. Maternal GCT repeats were found as low as 75 (asymptomatic) that were amplified to result in a child with congenital myotonic dystrophy. Application of DNA diagnosis to 32 pregnancies provided an accurate method for identification of at-risk fetuses and allele enlargement.

CONCLUSIONS

The GCT repeat in myotonic dystrophy is highly mutable. The triplet repeat amplification is highly specific for mutations involving the myotonin protein kinase gene accounting for myotonic dystrophy. The quantitation of triplet repeats can be more sensitive than physical, ophthalmologic, and electromyography examinations since the mutation can be detected in patients without evidence of myotonic dystrophy clinical findings. The length of the triplet expansion is influenced by the sex of the transmitting parent and is related to the clinical onset of disease features. Prenatal measurement of the GCT triplet repeat has utility for families with myotonic dystrophy risk since mutant and normal repeats are distinguishable and the length of mutant repeat alleles is associated with clinical severity. Thus, GCT triplet measurement provides a highly accurate means of detecting the myotonic dystrophy mutation in patients and offers a new reproductive option for families at risk for myotonic dystrophy.

Restoration of dystrophin-associated proteins in skeletal muscle of mdx mice transgenic for dystrophin gene

Duchenne muscular dystrophy (DMD) patients and mdx mice are characterized by the absence of dystrophin, a membrane cytoskeletal protein. Dystrophin is associated with a large oligomeric complex of sarcolemmal glycoproteins, including dystroglycan which provides a linkage to the extracellular matrix component, laminin. The finding that all of the dystrophin-associated proteins (DAPs) are drastically reduced in DMD and mdx skeletal muscle supports the primary function of dystrophin as an anchor of the sarcolemmal glycoprotein complex to the subsarcolemmal cytoskeleton. These findings indicate that the efficacy of dystrophin gene therapy will depend not only on replacing dystrophin but also on restoring all of the DAPs in the sarcolemma. Here we have investigated the status of the DAPs in the skeletal muscle of mdx mice transgenic for the dystrophin gene. Our results demonstrate that transfer of dystrophin gene restores all of the DAPs together with dystrophin, suggesting that dystrophin gene therapy should be effective in restoring the entire dystrophin-glycoprotein complex.

Gene therapy of the immune system

Many applications of somatic gene therapy relate to the immune system. Several forms of inherited immunodeficiencies are candidates for treatment by gene transfer. Adenosine deaminase (ADA) deficiency causes a form of severe combined immunodeficiency. Stable gene transfer and expression of human ADA has now been obtained in hematopoietic stem cells of mice and, more recently, in large animals. The human ADA has also been introduced and expressed in the primitive human hematopoietic progenitor cells that initiate long-term bone marrow culture. Clinical trials of gene therapy for ADA deficiency have been initiated. The initial protocols were aimed at the correction of peripheral blood T lymphocytes, but recent strategies are attempting ADA gene transfer into peripheral blood or bone marrow stem cells. Other immunodeficiencies that may soon be amenable to somatic gene therapy include leukocyte adhesion deficiency and chronic granulomatous disease. Gene therapy may also be applied to the treatment of acquired disorders. In theory, the hematopoietic stem cells of a human immunodeficiency virus (HIV)-infected patient could be genetically modified and used to reconstitute an HIV-resistant hematopoietic system. Various strategies are currently being investigated to achieve this "intracellular immunization" against HIV. These include the transfer of genes encoding recombinant soluble CD4 molecules, suicide genes under the control of HIV-inducible promoter, and anti-HIV ribozymes. Gene transfer could also be used in the treatment of cancer to increase the immune response of the host, to activate prodrugs specifically in tumors, or to protect normal tissues against the toxicities of conventional treatment. Recent progress in all of these applications of gene therapy is reviewed here.

Gene transfer therapy for heritable disease: cell and expression targeting

Gene therapy is defined as the delivery of a functional gene for expression in somatic tissues with the intent to cure a disease. Different gene transfer strategies may be required to target different tissues. Adenosine deaminase (ADA) deficiency is a good gene therapy model for targeting a rare population of pluripotent hematopoietic stem cells capable of self-renewal. We present evidence for the highly efficient gene transfer and sustained expression of human ADA in human primitive hematopoietic progenitors using retroviral supernatant with a supportive stromal layer. A stem cell-enriched (CD34+) fraction was also successfully transduced. Duchenne muscular dystrophy (DMD) is also a good model for somatic gene therapy. Two of the challenges presented by this model are the large size of the gene and the large number of target cells. Germline gene transfer and correction of the phenotype has been demonstrated in transgenic mdx mice using both a full-length and a truncated form of the dystrophin cDNA. We present here a deletion mutagenesis strategy to truncate the dystrophin cDNA such that it can be accommodated by retroviral and adenoviral vectors useful for somatic gene therapy.

Long-term expression of retroviral-transduced adenosine deaminase in human primitive hematopoietic progenitors

Adenosine deaminase (ADA) deficiency, a rare autosomal recessive disorder, is an ideal candidate for gene replacement therapy. By means of co-cultivation with a retroviral vector-producing cell line, we have demonstrated efficient transfer and expression of the human ADA gene into human primitive hematopoietic progenitors. At 6 weeks post-transduction in myeloid long-term bone marrow culture, approximately 50% of the clonogenic progenitors were transduced by the provirus, with ADA expression detected in 30% of transduced colonies. The ADA activity increased by 3.7-fold in the nonadherent fraction of transduced bone marrow after 9 weeks. We have also achieved efficient transduction by retroviral supernatant of normal and ADA-deficient bone marrow cells that were allowed to establish a stromal layer in long-term culture, indicating the feasibility of proceeding with attempts to perform stem cell gene therapy on patients with ADA deficiency.

Failure in detecting mRNA transcripts from the mutated allele in myotonic dystrophy muscle

The expression of myotonin-protein kinase (MT-PK) gene was studied in myotonic dystrophy (DM) muscle and normal controls using a polymerase chain reaction protocol to analyse the 3' intragenic p(CTG) polymorphism. Unaffected individuals show bi-allelic expression, while the sole wild-type allele was transcribed in DM muscle. Our findings support a gene dosage effect in the pathogenesis of the disease.

Physical mapping of Xq24-25 around loci closely linked to the X-linked lymphoproliferative syndrome locus: an overlapping YAC map and linkage between DXS12, DXS42, and DXS37

We have localized several markers in the Xq24-25 region containing DXS12, DXS42 and DXS37 which are closely linked to the X-linked lymphoproliferative syndrome (XLP) locus. A 850-kb restriction map has been established by mapping overlapping YACs and showed that DXS12 and DXS42 are physically linked within about 50 kb. DXS37 is separated from these two loci at a maximum distance of 3,700 kb. Several new probes have been generated which will contribute to further physical mapping of this region.

The human genome project and clinical medicine

Genetic research has already begun to pay clinical dividends, as investigators have successfully isolated disease genes, including those responsible for Duchenne muscular dystrophy, cystic fibrosis, and the fragile X syndrome. This last disorder appears to be associated with the progressive amplification of a short, repeated DNA sequence, a mechanism that may also occur at other cytogenetically fragile sites and in other genetic disorders or neoplasias. This article reviews genetic mapping techniques being used by the Human Genome Project, methods for identifying disease genes, and clinical applications. It also includes discussions of mutation detection, diagnosis, and gene therapy.

Antisense and differentiation

The use of antisense technology in animals has great potential for studying individual genes and for generating animal models of human disorders. Further control can be obtained by the use of inducible promoters to regulate the expression of antisense constructs, so that the timing and degree of antisense inhibition can be manipulated. In addition, tissue-specific promoters and enhancers provide the potential for targeting antisense inhibition to specific organs. Transgene expression in mice directed by the Cyp1a-1 promoter and enhancer elements can be increased in the liver up to 10,000-fold by administration to the animals of the inducer, 3-methylcholanthrene. Transfected antisense constructs containing splice site regions of the hypoxanthine guanine phosphoribosyltransferase (HPRT) gene can reduce HPRT activity to less than 1% of levels in parental NIH-3T3, COS, or HeLa cells. Antisense constructs including splice site regions and driven by the inducible Cyp1a-1 promoter should prove to be powerful tools in generating mouse models of human disorders.

Anticipation in myotonic dystrophy. II. Complex relationships between clinical findings and structure of the GCT repeat

We studied the expansion of the GCT repeats within the myotonic dystrophy protein kinase gene in nine myotonic dystrophy (DM) kindreds. Southern blot and polymerase chain reaction analyses of the repeat region demonstrated the expansion in all 62 patients with the diagnosis of DM. Among 43 DM parent-child pairs, age of onset in the child was earlier than in the parent in 36 pairs, in the same decade as the parent in five, and undetermined in two. The clinical anticipation observed in the 36 pairs accompanied an increase in the fragment size in 32, a decrease in two, and no apparent change in two pairs. In the remaining pairs without documented clinical anticipation, the fragment size increased in four, decreased in two, and was apparently unchanged in one. Overall, the size of expansion showed an inverse correlation with the age of onset (p < 0.001). In all seven pairs in which the fragment did not increase in size, the affected parent was male. Two congenital DM children born to affected mothers had expanded DNA greater than 4.5 kb. The differences between parent and child in age of onset significantly correlated with the differences in the expansion size among father-child pairs (p < 0.001) but not mother-child pairs (p > 0.5). Our data suggest that the expansion of the GCT repeats plays an important role in anticipation although other factors, including the sex of the affected parent, may have significant effects on molecular mechanisms of anticipation.

Premature chain termination mutation causing Duchenne muscular dystrophy

We identified a premature chain termination mutation in two brothers with Duchenne muscular dystrophy and correlated the mutation in one of the brothers with immunologic detection of dystrophin in skeletal muscle. Southern and polymerase chain reaction (PCR) studies of genomic DNA from the affected boys showed no major gene rearrangements. However, the noted absence of a HindIII Southern fragment containing the proximal portion of exon 48 led to the identification of a point mutation that creates a new HindIII restriction site in that exon. Exon 48 was amplified by PCR from DNA of the patients and other family members and digested with HindIII to show the mutation in the two boys and also in their mother and maternal grandmother. Direct DNA sequencing demonstrated a cytosine-to-thymine transition at nucleotide 7163 of dystrophin that converts a glutamine codon (CAA) to an ochre chain termination codon (UAA). This mutation predicts a truncated dystrophin missing the distal spectrin-like repeat region, the cysteine-rich domain, and the carboxy terminal. Immunohistochemistry of skeletal muscle from one of the affected boys revealed membrane-localized dystrophin in the majority of fibers detected by anti-dystrophin antibodies against (1) the amino terminal and (2) part of the spectrin-like repeat region; both regions would be present in the truncated dystrophin predicted by the chain termination mutation. This suggests that the carboxy terminal may not be an absolute requirement for dystrophin membrane localization. Very few muscle fibers also showed peripheral immunostaining using anti-dystrophin antibodies against the carboxy terminal, suggesting gene reversion, suppression, or read-through in these rare fibers.

DNA methylation represses FMR-1 transcription in fragile X syndrome

Fragile X syndrome is the most frequent form of inherited mental retardation and segregates as an X-linked dominant with reduced penetrance. Recently, we have identified the FMR-1 gene at the fragile X locus. Two molecular differences of the FMR-1 gene have been found in fragile X patients: a size increase of an FMR-1 exon containing a CGG repeat and abnormal methylation of a CpG island 250 bp proximal to this repeat. Penetrant fragile X males who exhibit these changes typically show repression of FMR-1 transcription and the presumptive absence of FMR-1 protein is believed to contribute to the fragile X phenotype. It is unclear, however, if either or both molecular differences in FMR-1 gene is responsible for transcriptional silencing. We report here the prenatal diagnosis of a male fetus with fragile X syndrome by utilizing these molecular differences and show that while the expanded CGG-repeat mutation is observed in both the chorionic villi and fetus, the methylation of the CpG island is limited to the fetal DNA (as assessed by BssHII digestion). We further demonstrate that FMR-1 gene expression is repressed in the fetal tissue, as is characteristic of penetrant males, while the undermethylated chorionic villi expressed FMR-1. Since the genetic background of the tissues studied is identical, including the fragile X chromosome, these data indicate that the abnormal methylation of the FMR-1 CpG-island is responsible for the absence of FMR-1 transcription and suggests that the methylation may be acquired early in embryogenesis.

An intact cysteine-rich domain is required for dystrophin function

The carboxyl terminus of dystrophin is encoded by a highly conserved, alternatively spliced region of the gene. The few rare mutations reported in this region are of interest in unraveling the function of the dystrophin molecule. An unusual case of infantile onset Duchenne muscular dystrophy (DMD) with an internal 3' genomic deletion, and a membrane localized non-functional dystrophin protein, was used to explore the functional activity of this region. The patient's cDNA sequence showed an intragenic 1824-bp deletion precisely excising the cysteine rich and alternatively spliced COOH-terminal domains of dystrophin. The unaltered final 2.7 kb of the patients transcript was defined as a single exon localized to two genomic fragments, with the 5.9 kb HindIII fragment containing the stop codon. To understand the significance of deletions in this important region of the dystrophin gene, we mapped the order and cDNA coordinates for the 3' genomic HindIII fragments encoding the cysteine rich and alternative splicing domains. This 3' gene map was used to compare the clinical phenotype of the other reported COOH-terminal deletions in the literature. Our analysis concludes that the cysteine-rich domain confers an important function for the dystrophin protein.

PCR amplification and analysis of yeast artificial chromosomes

A strategy for the analysis of yeast artificial chromosome (YAC) clones that relies on polymerase chain reaction (PCR) amplification of small restriction fragments from isolated YACs following adapter ligation was developed. Using this method, termed YACadapt, we have amplified several YACs from a human Xq24-qter library and have used the PCR products for physical mapping by somatic cell hybrid deletion analysis and fluorescent in situ hybridization. One YAC, RS46, was mapped to band Xq27.3, near the fragile X mutation. The PCR product is an excellent renewable source of YAC DNA for analyses involving hybridization of YAC inserts to a variety of DNA/RNA sources.

Expression and localization of dystrophin in human cardiac Purkinje fibers

BACKGROUND

Mutations in the dystrophin gene produce clinical manifestations of disease in heart, brain, and skeletal muscle in patients with Duchenne and Beckers muscular dystrophy (DMD/BMD). Conduction disturbances and heart block contribute to cardiac decompensation in these patients, which suggests an important role for dystrophia in the cardiac conduction system. We therefore examined the messenger RNA (mRNA) expression and protein localization of dystrophin in normal human cardiac Purkinje fibers.

METHODS AND RESULTS

Polymerase chain reaction amplification of isolated Purkinje fiber complementary DNA identified several alternatively spliced mRNA transcripts encoding for carboxy-terminal isoforms of the dystrophin protein. The predominant mRNA transcript detected was a splice form previously detected in the brain. Antipeptide antibodies specific for a carboxy-terminal dystrophin sequence were used for Western blot analysis and immunocytochemical localization. These antisera detect approximately 400,000-d immunoreactive band or bands on Western blot in normal heart and Purkinje fibers but not in DMD heart. Immunocytochemical staining showed that dystrophin was localized to the membrane surface of the Purkinje fiber.

CONCLUSIONS

These results suggest that dystrophin may be an important molecule for membrane function in the Purkinje conduction system of the heart and support the hypothesis that defective dystrophin expression contributes to the cardiac conduction disturbances seen in DMD/BMD:

A transposon-like element in the deletion-prone region of the dystrophin gene

The central portion of the dystrophin gene locus is a preferential site for deletions causing progressive muscular dystrophy of the Duchenne type (DMD). The nucleotide sequence of a deletion junction fragment from a DMD patient was determined, revealing that the proximal breakpoint of the deletion in intron 43 fell within the sequence of a transposon-like element. This segment, belonging to the THE-1 family of human transposable elements, is normally present in a complete form in intron 43 of the dystrophin gene. The deletion mutation was maternally transmitted and eliminated two-thirds of the THE-1 element. Analysis of DNA from additional DMD patients revealed a second deletion with the proximal breakpoint mapping within the same THE-1 element.

Report of the MDA Gene Therapy Conference, Tucson, Arizona, September 27-28, 1991

C. Thomas Caskey, in summarizing the meeting, noted that phenotypic correction of DMD is likely to require restoration of the dystrophin protein; thus, this disease is a logical target for consideration of gene replacement therapy. A number of tools are available to the experimenter, including the dystrophin gene and cDNA, several viral vectors, and various animal models of the human disease. In addition, detailed knowledge is now becoming available about the mechanisms of muscle-specific gene expression. However, a number of uncertainties have yet to be resolved. The dystrophin gene has an extremely complex pattern of expression, with more than one promoter and a number of alternative splicing events; what are the reasons for this variety? The dystrophin-glycoprotein complex has been described but its function is unclear. The role of the satellite cell is uncertain. It is not yet clear whether viral delivery or direct injection of DNA will be the method of choice for gene transfer into muscle. If delivery methods do not target the appropriate tissues, then appropriate use of tissue-specific control elements will be required for selective gene expression. Which animal model system should be used? What role can myoblast transplantation (with or without gene transfer) play in the treatment of DMD and other inherited myopathies? It is hoped that in further meetings on this topic, some of these issues will have been resolved.

Diagnosis of Duchenne and Becker muscular dystrophies by polymerase chain reaction. A multicenter study

OBJECTIVE--To assess the efficiency, reliability, and ease of use of DNA diagnosis for Duchenne and Becker muscular dystrophies (DMD/BMD) using the polymerase chain reaction (PCR). DESIGN--DNA from the patients was screened for deletion mutations using multiplex PCR, and the results were compared with those obtained by Southern blot analysis. The PCR multiplex reaction detects nine specific "hot-spot" exons in the dystrophin gene while the Southern analysis detects 66 specific dystrophin gene restriction fragments. The multiplex reaction requires 50-fold less DNA than Southern analysis and thus is considerably more sensitive. SETTING--Fourteen university-affiliated and private genetic disease diagnostic laboratories. PATIENTS--Male patients with clinical signs of DMD/BMD. Cases were selected for analysis randomly, without knowledge of whether a deletion was present within the dystrophin gene. MAIN OUTCOME MEASURES--The percentage of cases that were detectable by multiplex PCR in comparison with Southern analysis, the frequency, extent, and location of the detected deletion mutations. In some cases, duplication mutations were monitored. RESULTS--The accuracy of a single PCR multiplex amplification (nine exons) was compared with Southern analysis with 10 cDNA probes that cover the full length of the gene. The multiplex PCR analytic method detected 82% of those deletions detected by Southern analysis methods. In one of 745 analyses, the multiplex method suggested a single exon deletion, which was not confirmed by Southern analysis, representing a false-positive rate of 0.013%. CONCLUSIONS--Multiplex PCR represents a sensitive and accurate method for deletion detection of 46% of all cases of DMD/BMD. The method requires 1 day for analysis, is easy to perform, and does not use radioactive tracers. As such, multiplex PCR represents an efficient and rapid method for prenatal or postnatal diagnosis of DMD/BMD.

Triplet repeat mutations in human disease

Triplet repeats are the sites of mutation in three human heritable disorders, spinal and bulbar muscular atrophy (SBMA), fragile X syndrome, and myotonic dystrophy (DM). These repeats are GC-rich and highly polymorphic in the normal population. Fragile X syndrome and DM are examples of diseases in which premutation alleles cause little or no disease in the individual, but give rise to significantly amplified repeats in affected progeny. This newly identified mechanism of mutation has, so far, been identified in two of the most common heritable disorders, fragile X syndrome and DM, and one rare disease, SBMA.

Point mutations and polymorphisms in the human dystrophin gene identified in genomic DNA sequences amplified by multiplex PCR

About one third of Duchenne muscular dystrophy (DMD) patients have no gross DNA rearrangements in the dystrophin gene detectable by Southern blot analysis or multiplex exon amplification. Presumably, in these cases, the deficiency is caused by minor structural lesions of the dystrophin gene. However, to date, only a single human DMD case has been described where a point mutation, producing a stop codon, accounts for the DMD phenotype. To screen for microheterogeneities in the dystrophin gene, we applied analysis by chemical mismatch cleavage to thirteen exons amplified in multiplex sets by the polymerase chain reaction. This analysis covers approximately 20% of the dystrophin-coding sequence. Sixty DMD patients without detectable deletions or duplications were investigated, leading to the identification of two point mutations and four polymorphisms with a frequency higher than 5%. Both point mutations are frameshift mutations in exons 12 and 48, respectively, and are closely followed by stop codons, thus explaining the functional deficiency of the dystrophin gene products in both patients.

Genetic marker technology

Advances in our understanding of polymorphisms found in eukaryotic genomes and improved methods for studying genetic markers should facilitate genetic linkage mapping and other applications. Progress within the past year includes characterization of the types, frequencies, and properties of tandemly repeated sequences, methods for obtaining the DNA sequence flanking genetic markers for use in the polymerase chain reaction, and new detection systems featuring automation and multiplexing.

Human and murine dystrophin mRNA transcripts are differentially expressed during skeletal muscle, heart, and brain development

Dystrophin transcripts were shown to be alternatively spliced in a pattern characteristic of both tissue type and developmental stage. Multiple novel spliced forms of dystrophin mRNA were identified in murine brain tissue, skeletal and cardiac muscle, diaphragm, and human cardiac Purkinje fibers. The transcript diversity was greatest in adult, non-skeletal muscle tissues. Sequence analysis revealed that four tandem exons of the murine gene are differentially spliced in at least 11 separate patterns to generate distinct isoforms. Two of these forms were observed in all tissues examined, while several others were uniquely observed in cardiac muscle and brain. Cardiac Purkinje fibers express an isoform primarily observed in brain tissue. Several spliced transcripts were observed only in postnatal development. Differential utilization of a fifth exon results in two mRNA splice forms that encode separate embryonic and adult C-termini of dystrophin. Comparison of murine with human dystrophin mRNAs showed that similar isoform expression patterns exist across species. These observations suggest that functionally distinct isoforms of the dystrophin protein are expressed in separate tissues and at different stages of development. These isoforms may be of significance in understanding the various tissue-specific effects produced by dystrophin gene mutations in Duchenne and Becker muscular dystrophy patients.

The sulfatase gene family: cross-species PCR cloning using the MOPAC technique

Several human sulfatase cDNAs have recently been cloned, revealing highly conserved domains of protein similarity. We have used this information for the isolation of sulfatase genes in different species using the polymerase chain reaction (PCR). Degenerate oligonucleotide primers corresponding to these regions of identity among human arylsulfatases A, B, and steroid sulfatase (ARSA, ARSB, and STS) were designed. The primers were used in the PCR amplification of reverse transcribed RNA (RT-PCR) from multiple tissues in human and mouse. Amplification products were obtained from mouse liver and from human liver, lymphoblasts, kidney, intestine, heart, muscle, and brain cDNA samples. Each of the PCR products was subcloned into a plasmid vector, and several subclones were characterized by colony hybridization and DNA sequencing. All the previously identified human ARSA, ARSB, and STS were found among our clones, indicating the power of the technique. Sequence analysis of two mouse clones showed high degrees of homology with the human ARSA and ARSB sequences, respectively, and likely represent the murine homologues of these enzymes. These are the first sulfatase genes isolated in the mouse. A murine equivalent for STS could not be identified, suggesting its strong diversity from the human homologue.

Retroviral-mediated gene transfer of human ornithine transcarbamylase into primary hepatocytes of spf and spf-ash mice

The sparse fur (spf) and the sparse fur/abnormal skin and hair (spf-ash) mice are two murine models of the human X-linked disorder ornithine transcarbamylase (OTC) deficiency. A defective recombinant retrovirus, delta N2OTC was used to transduce primary hepatocytes derived from these mutant animals. Transduction of the primary cultures was highly efficient, with an average proviral copy number of 0.5-2 per cell in the population of transduced hepatocytes. Northern analysis and slot blots of total RNA isolated from transduced cells showed levels of human OTC mRNA to be equivalent to that present in normal human liver. Enzymatic assays demonstrated that a partial biochemical correction of the defect was achieved. After retroviral transduction, the hepatocytes were trypsinized and replated for long-term culture. Viability after replating exceeded 90%, indicating that the transduced cells might be useful for transplantation. The successful in vitro correction of OTC deficiency by this vector suggests that it will also be useful in somatic gene therapy experiments.

Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups

Trimeric and tetrameric short tandem repeats (STRs) represent a rich source of highly polymorphic markers in the human genome that may be studied with the polymerase chain reaction (PCR). We report the analysis of a multilocus genotype survey of 97-380 chromosomes in U.S. Black, White, Mexican-American, and Asian populations at five STR loci located on chromosomes 1, 4, 11, and X. The heterozygote frequencies of the loci ranged from 0.36 to 0.91 and the number of alleles from 6 to 20 for the 20 population and locus combinations. Relative allele frequencies exhibited differences between populations and unimodal, bimodal, and complex distributions. Although deviations were noted at some locus-population test combinations, genotype data from the loci were consistent overall with Hardy-Weinberg equilibrium by three tests. Population subheterogeneity within each ethnic group was not detected by two additional tests. No mutations were detected in a total of 860 meioses for two loci studied in the CEPH kindreds and five loci studied in other families. An indirect estimate of the mutation rates gave values from 2.3 x 10(-5) to 15.9 x 10(-5) for the five loci. Higher mutation rates appear to be associated with greater numbers of tandem repeats in the core motif. The most frequent genotype for all five loci combined appears to have a frequency of 7.59 x 10(-4). Together, these results suggest that trimeric and tetrameric STR loci are useful markers for the study of new mutations and genetic linkage analysis and for application to personal identification in the medical and forensic sciences.